@article {pmid35750322,
year = {2022},
author = {Kelly, MS and Bunyavanich, S and Phipatanakul, W and Lai, PS},
title = {The Environmental Microbiome, Allergic Disease and Asthma.},
journal = {The journal of allergy and clinical immunology. In practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaip.2022.06.006},
pmid = {35750322},
issn = {2213-2201},
abstract = {The environmental microbiome represents the entirety of the microbes and their metabolites that we encounter in our environments. A growing body of evidence supports the role of the environmental microbiome in risk for and severity of allergic diseases and asthma. The environmental microbiome represents a ubiquitous, lifelong exposure to non-self antigens. During the critical window between birth and one year of life, interactions between our early immune system and the environmental microbiome have two consequences: our individual microbiome is populated by environmental microbes, and our immune system is trained regarding which antigens to tolerate. During this time, a diversity of exposures appears largely protective, dramatically decreasing the risk of developing allergic diseases and asthma. As we grow older, our interactions with the environmental microbiome change. While it continues to exert influence over the composition of the human microbiome, the environmental microbiome becomes increasingly a source for antigenic stimulation and infection. The same microbial exposure protective against disease development may exacerbate disease severity. While much has been learned about the importance of the environmental microbiome in allergic disease, much more remains to be understood about these complicated interactions between our environment, our microbiome, our immune system and disease.},
}
@article {pmid35750314,
year = {2022},
author = {Cuddihey, H and MacNaughton, WK and Sharkey, KA},
title = {The role of the endocannabinoid system in the regulation of intestinal homeostasis.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcmgh.2022.05.015},
pmid = {35750314},
issn = {2352-345X},
abstract = {The maintenance of intestinal homeostasis is fundamentally important to health. Intestinal barrier function and immune regulation are key determinants of intestinal homeostasis and are therefore tightly regulated by a variety of signaling mechanisms. The endocannabinoid system is a lipid mediator signaling system widely expressed in the gastrointestinal tract. Accumulating evidence suggests the endocannabinoid system is a critical nexus involved in the physiological processes that underlie the control of intestinal homeostasis. In this review we will illustrate how the endocannabinoid system is involved in regulation of intestinal permeability, fluid secretion and immune regulation. We will also demonstrate a reciprocal regulation between the endocannabinoid system and the gut microbiome. The role of the endocannabinoid system is complex and multifaceted, responding to both internal and external factors while also serving as an effector system for the maintenance of intestinal homeostasis.},
}
@article {pmid35750176,
year = {2022},
author = {Wang, G and Weng, L and Huang, Y and Ling, Y and Zhen, Z and Lin, Z and Hu, H and Li, C and Guo, J and Zhou, JL and Chen, S and Jia, Y and Ren, L},
title = {Microbiome-metabolome analysis directed isolation of rhizobacteria capable of enhancing salt tolerance of Sea Rice 86.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {156817},
doi = {10.1016/j.scitotenv.2022.156817},
pmid = {35750176},
issn = {1879-1026},
abstract = {Soil salinization has been recognized as one of the main factors causing the decrease of cultivated land area and global plant productivity. Application of salt tolerant plants and improvement of plant salt tolerance are recognized as the major routes for saline soil restoration and utilization. Sea rice 86 (SR86) is known as a rice cultivar capable of growing in saline soil. Genome sequencing and transcriptome analysis of SR86 have been conducted to explore its salt tolerance mechanisms while the contribution of rhizobacteria is underexplored. In the present study, we examined the rhizosphere bacterial diversity and soil metabolome of SR86 seedlings under different salinity to understand their contribution to plant salt tolerance. We found that salt stress could significantly change rhizobacterial diversity and rhizosphere metabolites. Keystone taxa were identified via co-occurrence analysis and the correlation analysis between keystone taxa and rhizosphere metabolites indicated lipids and their derivatives might play an important role in plant salt tolerance. Further, four plant growth promoting rhizobacteria (PGPR), capable of promoting the salt tolerance of SR86, were isolated and characterized. These findings might provide novel insights into the mechanisms of plant salt tolerance mediated by plant-microbe interaction, and promote the isolation and application of PGPR in the restoration and utilization of saline soil.},
}
@article {pmid35750053,
year = {2022},
author = {Pala, L and De Pas, T and Catania, C and Giaccone, G and Mantovani, A and Minucci, S and Viale, G and Gelber, RD and Conforti, F},
title = {Sex and cancer immunotherapy: Current understanding and challenges.},
journal = {Cancer cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ccell.2022.06.005},
pmid = {35750053},
issn = {1878-3686},
abstract = {Recent evidence highlights patients' sex relevance in antitumor immune response through a complex interaction-among hormones, genes, behaviors, and the microbiome-that affects both innate and adaptive immune functions, as well as immune evasion mechanisms. These complex interactions ultimately influence the efficacy and toxicity of immune checkpoint inhibitors in solid tumors.},
}
@article {pmid35750008,
year = {2022},
author = {Villamizar, A and Vemulapally, S and Guerra, T and Tocidlowski, ME and Forstner, MRJ and Hahn, D},
title = {Quantification of members of the Mycobacterium chelonae-abscessus complex in lesions of the endangered houston toad (Anaxyrus houstonensis).},
journal = {Systematic and applied microbiology},
volume = {45},
number = {4},
pages = {126342},
doi = {10.1016/j.syapm.2022.126342},
pmid = {35750008},
issn = {1618-0984},
abstract = {Illumina-based 16S rRNA V3 amplicon sequencing of total DNA obtained from soft tissue lesions (joint granulomas) of the endangered Houston toad (Anaxyrus houstonensis) demonstrated that many reads represented members of the actinobacterial Mycobacterium chelonae-abscessus complex. In order to quantify members of this complex in those lesions, we designed three complex-specific primer set/probe combinations (sets I, II and III) targeting variable regions on the 23S rRNA gene for SybrGreen- and Taqman-based quantitative polymerase chain reaction (qPCR). Both SybrGreen- and Taqman-based analyses specifically detected members of the M. chelonae-abscessus complex in lesion samples, with numbers between 104 and 107 cells per 100-mg sample. Values within individual samples were generally comparable between SybrGreen- and Taqman-based detection methods and between all primer set/probe combinations, except for SybrGreen-based analyses of a few samples analyzed with primer set I that used a less specific forward primer. The development of highly specific detection and quantification methods for members of the M. chelonae-abscessus complex in lesion samples can enable group specific tracking of these organisms, particularly in captive or stewardship settings where source and transmission monitoring are valuable tools to husbandry and species conservation.},
}
@article {pmid35749774,
year = {2022},
author = {},
title = {The Gastrointestinal Microbiome in Infant Colic: A Scoping Review.},
journal = {MCN. The American journal of maternal child nursing},
volume = {47},
number = {4},
pages = {E8},
doi = {10.1097/NMC.0000000000000853},
pmid = {35749774},
issn = {1539-0683},
}
@article {pmid35749750,
year = {2022},
author = {Hyoju, SK and Keskey, R and Castilo, G and Machhuta, K and Zaborin, A and Zaborina, O and Alverdy, JC},
title = {A Novel Non-Antibiotic Gut-Directed Strategy to Prevent Surgical Site Infections.},
journal = {Annals of surgery},
volume = {},
number = {},
pages = {},
doi = {10.1097/SLA.0000000000005547},
pmid = {35749750},
issn = {1528-1140},
abstract = {OBJECTIVE: Determine the efficacy of an orally delivered phosphate rich polymer, Pi-PEG, to prevent surgical site infection (SSI) in a mouse model of spontaneous wound infection involving gut-derived pathogens.<br><br>SUMMARY BACKGROUND DATA: Evidence suggests that pathogens originating from the gut microbiota can cause postoperative infection via a process by which they silently travel inside an immune cell and contaminate a remote operative site (Trojan Horse Hypothesis). Here we hypothesize that Pi-PEG can prevent SSIs in a novel model of postoperative SSIs in mice.<br><br>METHODS: Mice were fed either a standard Chow diet (high fiber/low fat, SD) or a western type diet (low fiber/high fat, WD), and exposed to antibiotics (p.o. clindamycin/ IP cefoxitin). Groups of mice had Pi-PEG added to their drinking water and SSI incidence determined. Gross clinical infections, wound cultures and amplicon sequence variant (ASV) analysis of the intestinal contents and wound were assessed to determine the incidence and source of the developing SSI.<br><br>RESULTS: In this model, consumption of a WD and exposure to antibiotics promoted the growth of SSI pathogens in gut and their subsequent presence in the wound. Mice subjected to this model drinking water spiked with Pi-PEG were protected against SSIs via mechanisms involving modulation of the gut-wound microbiome.<br><br>CONCLUSIONS: A non-antibiotic phosphate rich polymer, Pi-PEG, added to the drinking water of mice prevents SSIs and may represent a more sustainable approach in lieu of the current trend of greater sterility and the use of more powerful and broader antibiotic coverage.},
}
@article {pmid35749560,
year = {2022},
author = {Bellec, L and Du-Carré, JL and Almeras, F and Durand, L and Cambon-Bonavita, MA and Danion, M and Morin, T},
title = {Glyphosate-based herbicide exposure: effects on gill microbiota of rainbow trout (Oncorhynchus mykiss) and the aquatic bacterial ecosystem.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiac076},
pmid = {35749560},
issn = {1574-6941},
abstract = {The herbicide glyphosate has been widely used in the past 40 years, under the assumption that side effects were minimal. In recent years, its impact on microbial compositions and potential indirect effects on plant, animal and human health have been strongly suspected. Glyphosate and co-formulates have been detected in various water sources, but our understanding of their potential effects on aquatic animals is still in its infancy compared with mammals. In this study, we investigated the effect of chronic exposure to an environmentally relevant concentration of glyphosate on bacterial communities of rainbow trout (Oncorhynchus mykiss). Gills, gut contents and gut epithelia were then analyzed by metabarcoding targeting the 16S rRNA gene. Our results revealed that rainbow trout has its own bacterial communities that differ from their surrounding habitats and possesses microbiomes specific to these three compartments. The glyphosate-based herbicide treatment significantly affected the gill microbiome, with a decrease in diversity. Glyphosate treatments disrupted microbial taxonomic composition and some bacteria seem to be sensitive to this environmental pollutant. Lastly, co-occurrence networks showed that microbial interactions in gills tended to decrease with chemical exposure. These results demonstrate that glyphosate could affect microbiota associated with aquaculture fish.},
}
@article {pmid35749534,
year = {2022},
author = {Gaio, D and DeMaere, MZ and Anantanawat, K and Eamens, GJ and Falconer, L and Chapman, TA and Djordjevic, S and Darling, AE},
title = {Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig.},
journal = {PloS one},
volume = {17},
number = {6},
pages = {e0270372},
doi = {10.1371/journal.pone.0270372},
pmid = {35749534},
issn = {1932-6203},
abstract = {Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rd and 9th week of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors.},
}
@article {pmid35749527,
year = {2022},
author = {Apiwatsiri, P and Pupa, P and Sirichokchatchawan, W and Sawaswong, V and Nimsamer, P and Payungporn, S and Hampson, DJ and Prapasarakul, N},
title = {Metagenomic analysis of the gut microbiota in piglets either challenged or not with enterotoxigenic Escherichia coli reveals beneficial effects of probiotics on microbiome composition, resistome, digestive function and oxidative stress responses.},
journal = {PloS one},
volume = {17},
number = {6},
pages = {e0269959},
doi = {10.1371/journal.pone.0269959},
pmid = {35749527},
issn = {1932-6203},
abstract = {This study used metagenomic analysis to investigate the gut microbiota and resistome in piglets that were or were not challenged with enterotoxigenic Escherichia coli (ETEC) and had or had not received dietary supplementation with microencapsulated probiotics. The 72 piglets belonged to six groups that were either non-ETEC challenged (groups 1-3) or ETEC challenged (receiving 5ml of 109 CFU/ml pathogenic ETEC strain L3.2 one week following weaning at three weeks of age: groups 4-6). On five occasions at 2, 5, 8, 11, and 14 days of piglet age, groups 2 and 5 were supplemented with 109 CFU/ml of multi-strain probiotics (Lactiplantibacillus plantarum strains 22F and 25F, and Pediococcus acidilactici 72N) while group 4 received 109 CFU/ml of P. acidilactici 72N. Group 3 received 300mg/kg chlortetracycline in the weaner diet to mimic commercial conditions. Rectal faecal samples were obtained for metagenomic and resistome analysis at 2 days of age, and at 12 hours and 14 days after the timing of post-weaning challenge with ETEC. The piglets were all euthanized at 42 days of age. The piglets in groups 2 and 5 were enriched with several desirable microbial families, including Lactobacillaceae, Lachnospiraceae and Ruminococcaceae, while piglets in group 3 had increases in members of the Bacteroidaceae family and exhibited an increase in tetW and tetQ genes. Group 5 had less copper and multi-biocide resistance. Mobile genetic elements IncQ1 and IncX4 were the most prevalent replicons in antibiotic-fed piglets. Only groups 6 and 3 had the integrase gene (intl) class 2 and 3 detected, respectively. The insertion sequence (IS) 1380 was prevalent in group 3. IS3 and IS30, which are connected to dietary intake, were overrepresented in group 5. Furthermore, only group 5 showed genes associated with detoxification, with enrichment of genes associated with oxidative stress, glucose metabolism, and amino acid metabolism compared to the other groups. Overall, metagenomic analysis showed that employing a multi-strain probiotic could transform the gut microbiota, reduce the resistome, and boost genes associated with food metabolism.},
}
@article {pmid35749358,
year = {2022},
author = {Markowitz, RHG and LaBella, AL and Shi, M and Rokas, A and Capra, JA and Ferguson, JF and Mosley, JD and Bordenstein, SR},
title = {Microbiome-associated human genetic variants impact phenome-wide disease risk.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {26},
pages = {e2200551119},
doi = {10.1073/pnas.2200551119},
pmid = {35749358},
issn = {1091-6490},
support = {NLM T32LM012412//HHS | National Institutes of Health (NIH)/ ; P30CA068485//HHS | National Institutes of Health (NIH)/ ; R01 HL142856/HL/NHLBI NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; Vanderbilt Microbiome Innovation Center//Vanderbilt University (VU)/ ; ULTR000445//HHS | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; },
abstract = {Human genetic variation associates with the composition of the gut microbiome, yet its influence on clinical traits remains largely unknown. We analyzed the consequences of nearly a thousand gut microbiome-associated variants (MAVs) on phenotypes reported in electronic health records from tens of thousands of individuals. We discovered and replicated associations of MAVs with neurological, metabolic, digestive, and circulatory diseases. Five significant MAVs in these categories correlate with the relative abundance of microbes down to the strain level. We also demonstrate that these relationships are independently observed and concordant with microbe by disease associations reported in case-control studies. Moreover, a selective sweep and population differentiation impacted some disease-linked MAVs. Combined, these findings establish triad relationships among the human genome, microbiome, and disease. Consequently, human genetic influences may offer opportunities for precision diagnostics of microbiome-associated diseases but also highlight the relevance of genetic background for microbiome modulation and therapeutics.},
}
@article {pmid35749298,
year = {2022},
author = {Arjomand Fard, N and Armstrong, H and Perry, T and Wine, E},
title = {Appendix and Ulcerative Colitis: a Key to Explaining the Pathogenesis and Directing Novel Therapies?.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izac106},
pmid = {35749298},
issn = {1536-4844},
support = {/CAPMC/CIHR/Canada ; },
abstract = {The vermiform appendix is generally considered a redundant organ, but recent evidence suggests that the appendix could contribute to the pathogenesis of inflammatory bowel diseases, in particular ulcerative colitis (UC), and may even have a therapeutic role; however, mechanisms of the appendix involvement remain unclear. Here, we highlight current evidence on the link between the appendix and UC and consider plausible therapeutic implications. A literature search was conducted using PubMed and PubMed Central from inception to Nov 2021 using the terms "Appendix", "UC", "Appendix &amp; UC," "Appendectomy", and "Peri-appendicular patch," including only articles published in English. Reference lists from the selected studies were manually searched and reviewed to gather additional related reports. Inflammation around the appendix ("peri-appendicular patch") has been frequently observed in UC patients without other cecal involvement, and this inflammation can even precede the onset of UC. Epidemiologic studies propose that appendectomy reduces the risk of developing UC or even the risk of flare after UC is diagnosed, although this remains controversial. We reviewed studies showing altered host-microbe interactions in the appendix in UC, which suggest that the appendix could act as a priming site for disease via alterations in the immune response and changes in microbiota carried distally to the colon. In summary, recent literature suggests a possible role for microbes and immune cells within the appendix; however, the role of the appendix in the pathogenesis of UC remains unclear. Further research could clarify the therapeutic potential related to this organ.},
}
@article {pmid35748749,
year = {2022},
author = {Davar, D and Zarour, HM},
title = {Facts and Hopes for Gut Microbiota Interventions in Cancer Immunotherapy.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {},
number = {},
pages = {},
doi = {10.1158/1078-0432.CCR-21-1129},
pmid = {35748749},
issn = {1557-3265},
abstract = {Immune checkpoint inhibitors (ICI) targeting cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed death 1 (PD-1) proteins transformed the management of advanced cancers. Many tumor-intrinsic factors modulate immunological and clinical responses to such therapies, but ample evidence also implicates the gut microbiome in responses. The gut microbiome, comprising the bacteria, archaea, fungi, and viruses that live in the human digestive tract, is an established determinant of host immunity, but its impact on response to ICI therapy in mice and humans with cancer has only recently been appreciated. Therapeutic interventions to optimize microbiota composition to improve immunotherapy outcomes show promise in mice and humans with cancer. In this review, we discuss the rationale for gut microbiome-based cancer therapies, the results from early phase clinical trials, and possible future developments.},
}
@article {pmid35748742,
year = {2022},
author = {Prescott, SL and Logan, AC and Bristow, J and Rozzi, R and Moodie, R and Redvers, N and Haahtela, T and Warber, S and Poland, B and Hancock, T and Berman, B},
title = {Exiting the Anthropocene: Achieving Personal and Planetary Health in the 21st Century.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.15419},
pmid = {35748742},
issn = {1398-9995},
abstract = {Planetary health provides a perspective of ecological interdependence that connects the health and vitality of individuals, communities, and Earth's natural systems. It includes the social, political, and economic ecosystems that influence both individuals and whole societies. In an era of interconnected grand challenges threatening health of all systems at all scales, planetary health provides a framework for cross-sectoral collaboration and unified systems approaches to solutions. The field of allergy is at the forefront of these efforts. Allergic conditions are a sentinel measure of environmental impact on human health in early life-illuminating how ecological changes affect immune development and predispose to a wider range of inflammatory noncommunicable diseases (NCDs). This shows how adverse macroscale ecology in the Anthropocene penetrates to the molecular level of personal and microscale ecology, including the microbial systems at the foundations of all ecosystems. It provides the basis for more integrated efforts to address widespread environmental degradation and adverse effects of maladaptive urbanisation, food systems, lifestyle behaviours, and socioeconomic disadvantage. Nature-based solutions and efforts to improve nature-relatedness are crucial for restoring symbiosis, balance, and mutualism in every sense, recognizing that both personal lifestyle choices and collective structural actions are needed in tandem. Ultimately, meaningful ecological approaches will depend on placing greater emphasis on psychological and cultural dimensions such as mindfulness, values, and moral wisdom to ensure a sustainable and resilient future.},
}
@article {pmid35748637,
year = {2022},
author = {Poulin, R and Jorge, F and Salloum, PM},
title = {Inter-individual variation in parasite manipulation of host phenotype: a role for parasite microbiomes?.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.13764},
pmid = {35748637},
issn = {1365-2656},
abstract = {Alterations in host phenotype induced by metazoan parasites are widespread in nature, yet the underlying mechanisms and the sources of intraspecific variation in the extent of those alterations remain poorly understood. In light of the microbiome revolution sweeping through ecology and evolutionary biology, we hypothesise that the composition of symbiotic microbial communities living within individual parasites influences the nature and extent of their effect on host phenotype. The interests of both the parasite and its symbionts are aligned through the latter's vertical transmission, favouring joint contributions to the manipulation of host phenotype. Our hypothesis can explain the variation in the extent to which parasites alter host phenotype, as microbiome composition varies among individual parasites. We propose two non-exclusive approaches to test the hypothesis, furthering the integration of microbiomes into studies of host-parasite interactions.},
}
@article {pmid35748626,
year = {2022},
author = {Harshaw, C and Kojima, S and Wellman, CL and Demas, GE and Morrow, AL and Taft, DH and Kenkel, WM and Leffel, JK and Alberts, JR},
title = {Maternal antibiotics disrupt microbiome, behavior, and temperature regulation in unexposed infant mice.},
journal = {Developmental psychobiology},
volume = {64},
number = {6},
pages = {e22289},
doi = {10.1002/dev.22289},
pmid = {35748626},
issn = {1098-2302},
abstract = {Maternal antibiotic (ABx) exposure can significantly perturb the transfer of microbiota from mother to offspring, resulting in dysbiosis of potential relevance to neurodevelopmental disorders such as autism spectrum disorder (ASD). Studies in rodent models have found long-term neurobehavioral effects in offspring of ABx-treated dams, but ASD-relevant behavior during the early preweaning period has thus far been neglected. Here, we exposed C57BL/6J mouse dams to ABx (5 mg/ml neomycin, 1.25 μg/ml pimaricin, .075% v/v acetic acid) dissolved in drinking water from gestational day 12 through offspring postnatal day 14. A number of ASD-relevant behaviors were assayed in offspring, including ultrasonic vocalization (USV) production during maternal separation, group huddling in response to cold challenge, and olfactory-guided home orientation. In addition, we obtained measures of thermoregulatory competence in pups during and following behavioral testing. We found a number of behavioral differences in offspring of ABx-treated dams (e.g., modulation of USVs by pup weight, activity while huddling) and provide evidence that some of these behavioral effects can be related to thermoregulatory deficiencies, particularly at younger ages. Our results suggest not only that ABx can disrupt microbiomes, thermoregulation, and behavior, but that metabolic effects may confound the interpretation of behavioral differences observed after early-life ABx exposure.},
}
@article {pmid35748612,
year = {2022},
author = {Schneider, S and Biggerstaff, D and Barber, TM},
title = {Helpful or harmful? The impact of the ketogenic diet on eating disorder outcomes in type 1 diabetes mellitus.},
journal = {Expert review of endocrinology &amp; metabolism},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/17446651.2022.2089112},
pmid = {35748612},
issn = {1744-8417},
abstract = {INTRODUCTION: Eating disorders (EDs) are common complications in people with type 1 diabetes (PwT1D), given the rigid focus on food and insulin dose adjustment. Dietary recommendations for T1D match those for the general population, yet many fail to achieve target HbA1c. Evidence suggests that lower carbohydrate meals and thus reduced insulin requirements may decrease inconsistencies in insulin absorption, maintain euglycemia and weight. Dietary restriction is a recognized risk factor for ED development, and Ketogenic Diets (KD) involve restriction of common family-based foods, thus impacting social normality and microbiome diversity. We reviewed the current literature on PwT1D following a KD to understand effects on ED risks.<br><br>AREAS COVERED: Published data from MEDLINE, Embase, and PsycINFO were used. Search terms included: type 1 diabetes mellitus; or insulin dependent diabetes or T1D AND EDs or anorexia or bulimia or disordered eating AND low-carbohydrate diet or carbohydrate restricted diet or low carb diet or ketogenic diet.<br><br>EXPERT OPINION: Research into the effects of KDs on ED outcomes in PwT1D are limited, given the concerns over risks of diabetic ketoacidosis, hypoglycemia, and dyslipidemia. Longer term studies on the participants' experience and motivations of adhering or admonishing the diet are needed.},
}
@article {pmid35748271,
year = {2022},
author = {Araujo, R},
title = {Advances in Soil Engineering: Sustainable Strategies for Rhizosphere and Bulk Soil Microbiome Enrichment.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {27},
number = {6},
pages = {195},
doi = {10.31083/j.fbl2706195},
pmid = {35748271},
issn = {2768-6698},
abstract = {The preservation of natural ecosystems, as well as the correct management of human societies, largely depends on the maintenance of critical microbial functions associated with soils. Soils are biodiversity rich pools, and rhizosphere soils can be associated with increased plant functions in addition to the regulation of nutrient cycling, litter decomposition, soil fertility and food production by agriculture systems. The application of biocontrol agents or plant growth-promoting bacteria has been tested in order to colonize roots at initial stages and offer advantages by promoting healthier and higher-yielding crops. In this review we describe the efforts to develop more sustainable systems that seek to minimize environmental disruption while maintaining plant health. Particular emphasis is given in this review to soil improvement strategies and the taxonomic groups involved in plant growth and protection against biotic stresses. It is important to define the impacts of land management and crop production practices on the structure and composition of soil bacterial communities. By promoting, monitoring and controlling the plant microbiome, and understanding the role of certain biocontrol agents within the plant throughout the lifecycle of the plant, we may substantially improve nutritional and environmental standards and reduce the negative impact of some agrochemicals. The integration of biological alternatives with traditional strategies may be critical to improve the sustainability of agriculture systems.},
}
@article {pmid35748016,
year = {2022},
author = {Gosalbes, MJ and Jimenéz-Hernandéz, N and Moreno, E and Artacho, A and Pons, X and Ruíz-Pérez, S and Navia, B and Estrada, V and Manzano, M and Talavera-Rodriguez, A and Madrid, N and Vallejo, A and Luna, L and Pérez-Molina, JA and Moreno, S and Serrano-Villar, S},
title = {Interactions among the mycobiome, bacteriome, inflammation, and diet in people living with HIV.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2089002},
doi = {10.1080/19490976.2022.2089002},
pmid = {35748016},
issn = {1949-0984},
abstract = {While the intestinal microbiome seems a major driver of persistent immune defects in people with HIV (PWH), little is known about its fungal component, the mycobiome. We assessed the inter-kingdom mycobiome-bacteriome interactions, the impact of diet, and the association with the innate and adaptive immunity in PWH on antiretroviral therapy. We included 24 PWH individuals and 12 healthy controls. We sequenced the Internal Transcribed Spacer 2 amplicons, determined amplicon sequence variants, measured biomarkers of the innate and adaptive immunity in blood and relations with diet. Compared to healthy controls, PWH subjects exhibited a distinct and richer mycobiome and an enrichment for Debaryomyces hansenii, Candida albicans, and Candida parapsilosis. In PWH, Candida and Pichia species were strongly correlated with several bacterial genera, including Faecalibacterium genus. Regarding the links between the mycobiome and systemic immunology, we found a positive correlation between Candida species and the levels of proinflammatory cytokines (sTNF-R2 and IL-17), interleukin 22 (a cytokine implicated in the regulation of mucosal immunity), and CD8+ T cell counts. This suggests an important role of the yeasts in systemic innate and adaptive immune responses. Finally, we identified inter-kingdom interactions implicated in fiber degradation, short-chain fatty acid production, and lipid metabolism, and an effect of vegetable and fiber intake on the mycobiome. Therefore, despite the great differences in abundance and diversity between the bacterial and fungal communities of the gut, we defined the changes associated with HIV, determined several different inter-kingdom associations, and found links between the mycobiome, nutrient metabolism, and systemic immunity.},
}
@article {pmid35747534,
year = {2022},
author = {Ide, M and Karimova, M and Setterfield, J},
title = {Oral Health, Antimicrobials and Care for Patients With Chronic Oral Diseases - A Review of Knowledge and Treatment Strategies.},
journal = {Frontiers in oral health},
volume = {3},
number = {},
pages = {866695},
doi = {10.3389/froh.2022.866695},
pmid = {35747534},
issn = {2673-4842},
abstract = {Periodontal and chronic oral mucosal diseases are significant life impacting conditions which may co-exist and synergistically act to cause more severe and widespread oral pathology with enhanced challenges in effective management. Clinicians regularly observe these effects and struggle to effectively manage both problems in many patients. There is limited understanding of many basic and applied scientific elements underpinning potentially shared aetiopathological features and management. Recent developments in translational science provide an opportunity to greater improve knowledge and subsequently care for patients with these problems.},
}
@article {pmid35747138,
year = {2022},
author = {Yang, Y and Zhu, X and Huang, Y and Zhang, H and Liu, Y and Xu, N and Fu, G and Ai, X},
title = {RNA-Seq and 16S rRNA Analysis Revealed the Effect of Deltamethrin on Channel Catfish in the Early Stage of Acute Exposure.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {916100},
doi = {10.3389/fimmu.2022.916100},
pmid = {35747138},
issn = {1664-3224},
abstract = {Deltamethrin (Del) is a widely used pyrethroid insecticide and a dangerous material that has brought serious problems to the healthy breeding of aquatic animals. However, the toxicological mechanisms of Del on channel catfish remain unclear. In the present study, we exposed channel catfish to 0, 0.5, and 5 μg/L Del for 6 h, and analyzed the changes in histopathology, trunk kidney transcriptome, and intestinal microbiota composition. The pathological analyses showed that a high concentration of Del damaged the intestine and trunk kidney of channel catfish in the early stage. The transcriptome analysis detected 32 and 1837 differentially expressed genes (DEGs) in channel catfish trunk kidneys after exposure to 0.5 and 5 μg/L Del, respectively. Moreover, the KEGG pathway and GO enrichment analyses showed that the apoptosis signaling pathway was significantly enriched, and apoptosis-related DEGs, including cathepsin L, p53, Bax, and caspase-3, were also detected. These results suggested that apoptosis occurs in the trunk kidney of channel catfish in the early stage of acute exposure to Del. We also detected some DEGs and signaling pathways related to immunity and drug metabolism, indicating that early exposure to Del can lead to immunotoxicity and metabolic disorder of channel catfish, which increases the risk of pathogenic infections and energy metabolism disorders. Additionally, 16S rRNA gene sequencing showed that the composition of the intestinal microbiome significantly changed in channel catfish treated with Del. At the phylum level, the abundance of Firmicutes, Fusobacteria, and Actinobacteria significantly decreased in the early stage of Del exposure. At the genus level, the abundance of Romboutsia, Lactobacillus, and Cetobacterium decreased after Del exposure. Overall, early exposure to Del can lead to tissue damage, metabolic disorder, immunotoxicity, and apoptosis in channel catfish, and affect the composition of its intestinal microbiota. Herein, we clarified the toxic effects of Del on channel catfish in the early stage of exposure and explored why fish under Del stress are more vulnerable to microbial infections and slow growth.},
}
@article {pmid35747061,
year = {2022},
author = {Engelenburg, HJ and Lucassen, PJ and Sarafian, JT and Parker, W and Laman, JD},
title = {Multiple sclerosis and the microbiota: Progress in understanding the contribution of the gut microbiome to disease.},
journal = {Evolution, medicine, and public health},
volume = {10},
number = {1},
pages = {277-294},
doi = {10.1093/emph/eoac009},
pmid = {35747061},
issn = {2050-6201},
abstract = {Multiple sclerosis (MS), a neurological autoimmune disorder, has recently been linked to neuro-inflammatory influences from the gut. In this review, we address the idea that evolutionary mismatches could affect the pathogenesis of MS via the gut microbiota. The evolution of symbiosis as well as the recent introduction of evolutionary mismatches is considered, and evidence regarding the impact of diet on the MS-associated microbiota is evaluated. Distinctive microbial community compositions associated with the gut microbiota of MS patients are difficult to identify, and substantial study-to-study variation and even larger variations between individual profiles of MS patients are observed. Furthermore, although some dietary changes impact the progression of MS, MS-associated features of microbiota were found to be not necessarily associated with diet per se. In addition, immune function in MS patients potentially drives changes in microbial composition directly, in at least some individuals. Finally, assessment of evolutionary histories of animals with their gut symbionts suggests that the impact of evolutionary mismatch on the microbiota is less concerning than mismatches affecting helminths and protists. These observations suggest that the benefits of an anti-inflammatory diet for patients with MS may not be mediated by the microbiota per se. Furthermore, any alteration of the microbiota found in association with MS may be an effect rather than a cause. This conclusion is consistent with other studies indicating that a loss of complex eukaryotic symbionts, including helminths and protists, is a pivotal evolutionary mismatch that potentiates the increased prevalence of autoimmunity within a population.},
}
@article {pmid35746659,
year = {2022},
author = {Chen, TH and Hsu, MT and Lee, MY and Chou, CK},
title = {Gastrointestinal Involvement in SARS-CoV-2 Infection.},
journal = {Viruses},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/v14061188},
pmid = {35746659},
issn = {1999-4915},
abstract = {SARS-CoV-2 has evolved into a virus that primarily results in mild or asymptomatic disease, making its transmission more challenging to control. In addition to the respiratory tract, SARS-CoV-2 also infects the digestive tract. Some gastrointestinal symptoms occur with or before respiratory symptoms in patients with COVID-19. Respiratory infections are known to cause intestinal immune impairment and gastrointestinal symptoms. When the intestine is inflamed, cytokines affect the lung immune response and inflammation through blood circulation. The gastrointestinal microbiome may be a modifiable factor in determining the risk of SARS-CoV-2 infection and disease severity. The development of oral SARS-CoV-2 vaccine candidates and the maintenance of gut microbiota profiles may contribute to the early control of COVID-19 outbreaks. To this end, this review summarizes information on the gastrointestinal complications caused by SARS-CoV-2, SARS-CoV-2 infection, the gastrointestinal-lung axis immune response, potential control strategies for oral vaccine candidates and maintaining intestinal microbiota homeostasis.},
}
@article {pmid35746636,
year = {2022},
author = {Kaul, R and Liu, CM and Park, DE and Galiwango, RM and Tobian, AAR and Prodger, JL},
title = {The Penis, the Vagina and HIV Risk: Key Differences (Aside from the Obvious).},
journal = {Viruses},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/v14061164},
pmid = {35746636},
issn = {1999-4915},
support = {R01AI128779, R01AI123002 and R01DK131936-01/NH/NIH HHS/United States ; PJT-180629, PJT-156123, and TMI-138656/CAPMC/CIHR/Canada ; 950 - 233211//Canada Research Chairs/ ; },
abstract = {Globally, most Human Immunodeficiency Virus type 1 (HIV) transmission occurs through vaginal-penile sex (heterosexual transmission). The local immune environment at the site of HIV exposure is an important determinant of whether exposure during sex will lead to productive infection, and the vaginal and penile immune milieus are each critically shaped by the local microbiome. However, there are key differences in the microbial drivers of inflammation and immune quiescence at these tissue sites. In both, a high abundance of anaerobic taxa (e.g., Prevotella) is associated with an increased local density of HIV target cells and an increased risk of acquiring HIV through sex. However, the taxa that have been associated to date with increased risk in the vagina and penis are not identical. Just as importantly, the microbiota associated with comparatively less inflammation and HIV risk-i.e., the optimal microbiota-are very different at the two sites. In the vagina, Lactobacillus spp. are immunoregulatory and may protect against HIV acquisition, whereas on the penis, "skin type" flora such as Corynebacterium are associated with reduced inflammation. Compared to its vaginal counterpart, much less is known about the dynamics of the penile microbiome, the ability of clinical interventions to alter the penile microbiome, or the impact of natural/induced microbiome alterations on penile immunology and HIV risk.},
}
@article {pmid35745650,
year = {2022},
author = {Svanberg Frisinger, F and Pirolo, M and Ng, DYK and Mao, X and Nielsen, DS and Guardabassi, L},
title = {Impact of the Gram-Negative-Selective Inhibitor MAC13243 on In Vitro Simulated Gut Microbiota.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/ph15060731},
pmid = {35745650},
issn = {1424-8247},
support = {765147/MCCC_/Marie Curie/United Kingdom ; },
abstract = {New Gram-negative-selective antimicrobials are desirable to avoid perturbations in the gut microbiota leading to antibiotic-induced dysbiosis. We investigated the impact of a prototype drug (MAC13243) interfering with the Gram-negative outer membrane protein LolA on the faecal microbiota. Faecal suspensions from two healthy human donors were exposed to MAC13243 (16, 32, or 64 mg/L) using an in vitro gut model (CoMiniGut). Samples collected 0, 4, and 8 h after exposure were subjected to viable cell counts, 16S rRNA gene quantification and V3-V4 sequencing using the Illumina MiSeq platform. MAC13243 exhibited concentration-dependent killing of coliforms in both donors after 8 h. Concentrations of ≤32 mg/L reduced the growth of aerobic bacteria without influencing the microbiota composition and diversity. An expansion of Firmicutes at the expense of Bacteroidetes and Actinobacteria was observed in the faecal microbiota from one donor following exposure to 64 mg/L of MAC13242. At all concentrations tested, MAC13243 did not lead to the proliferation of Escherichia coli nor a reduced abundance of beneficial bacteria, which are typical changes observed in antibiotic-induced dysbiosis. These results support our hypothesis that a drug interfering with a specific target in Gram-negative bacteria has a low impact on the commensal gut microbiota and, therefore, a low risk of inducing dysbiosis.},
}
@article {pmid35745273,
year = {2022},
author = {Abdelhamid, M and Zhou, C and Jung, CG and Michikawa, M},
title = {Probiotic Bifidobacterium breve MCC1274 Mitigates Alzheimer's Disease-Related Pathologies in Wild-Type Mice.},
journal = {Nutrients},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/nu14122543},
pmid = {35745273},
issn = {2072-6643},
support = {15K15712//Grant-in-Aid for Challenging Exploratory Research/ ; 20K07762//Grant-in-Aid for Scientific Research C/ ; JP20dk0207050h001//AMED/ ; JP20de010702//AMED/ ; },
abstract = {Probiotics improve brain function, including memory and cognition, via the microbiome-gut-brain axis. Oral administration of Bifidobacterium breve MCC1274 (B. breve MCC1274) improves cognitive function in AppNL-G-F mice and mild cognitive impairment (MCI) subjects, and mitigates Alzheimer's disease (AD)-like pathologies. However, its effects on wild-type (WT) mice have not yet been explored. Thus, the effects of B. breve MCC1274 on AD-like pathologies in two-month-old WT mice were investigated, which were orally administered B. breve MCC1274 for four months. Aβ levels, amyloid precursor protein (APP), APP processing enzymes, phosphorylated tau, synaptic protein levels, glial activity, and cell proliferation in the subgranular zone of the dentate gyrus were evaluated. Data analysis was performed using Student's t-test, and normality was tested using the Shapiro-Wilk test. Oral administration of B. breve MCC1274 in WT mice decreased soluble hippocampal Aβ42 levels by reducing presenilin1 protein levels, and reduced phosphorylated tau levels. It also activated the protein kinase B (Akt)/glycogen synthase kinase-3β (GSK-3β) pathway, which may be responsible for the reduction in presenilin1 levels and inhibition of tau phosphorylation. B. breve MCC1274 supplementation attenuated microglial activation and elevated synaptic protein levels in the hippocampus. These findings suggest that B. breve MCC1274 may mitigate AD-like pathologies in WT mice by decreasing Aβ42 levels, inhibiting tau phosphorylation, attenuating neuroinflammation, and improving synaptic protein levels.},
}
@article {pmid35745235,
year = {2022},
author = {Yun, EJ and Imdad, S and Jang, J and Park, J and So, B and Kim, JH and Kang, C},
title = {Diet Is a Stronger Covariate than Exercise in Determining Gut Microbial Richness and Diversity.},
journal = {Nutrients},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/nu14122507},
pmid = {35745235},
issn = {2072-6643},
abstract = {Obesity is a common metabolic disorder caused by a sedentary lifestyle, and a high-fat and a high-glucose diet in the form of fast foods. High-fat diet-induced obesity is a major cause of diabetes and cardiovascular diseases, whereas exercise and physical activity can ameliorate these disorders. Moreover, exercise and the gut microbiota are known to be interconnected, since exercise can increase the gut microbial diversity and contribute to the beneficial health effects. In this context, we analyzed the effect of diet and exercise on the gut microbiota of mice, by next-generation sequencing of the bacterial V4 region of 16S rRNA. Briefly, mice were divided into four groups: chow-diet (CD), high-fat diet (HFD), high-fat diet + exercise (HFX), and exercise-only (EX). The mice underwent treadmill exercise and diet intervention for 8 weeks, followed by the collection of their feces and DNA extraction for sequencing. The data were analyzed using the QIIME 2 bioinformatics platform and R software to assess their gut microbial composition, richness, and diversity. The Bacteroidetes to Firmicutes ratio was found to be decreased manifold in the HFD and HFX groups compared to the CD and EX groups. The gut microbial richness was comparatively lower in the HFD and HFX groups and higher in the CD and EX groups (ACE, Chao1, and observed OTUs). However, the Shannon alpha diversity index was higher in the HFD and HFX groups than in the CD and EX groups. The beta diversity based on Jaccard, Bray-Curtis, and weighted UniFrac distance metrics was significant among the groups, as measured by PERMANOVA. Paraprevotella, Desulfovibrio, and Lactococcus were the differentially abundant/present genera based on the intervention groups and in addition to these three bacteria, Butyricimonas and Desulfovibrio C21c20 were differentially abundant/present based on diet. Hence, diet significantly contributed to the majority of the changes in the gut microbiota.},
}
@article {pmid35745233,
year = {2022},
author = {Stiefvatter, L and Neumann, U and Rings, A and Frick, K and Schmid-Staiger, U and Bischoff, SC},
title = {The Microalgae Phaeodactylum tricornutum Is Well Suited as a Food with Positive Effects on the Intestinal Microbiota and the Generation of SCFA: Results from a Pre-Clinical Study.},
journal = {Nutrients},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/nu14122504},
pmid = {35745233},
issn = {2072-6643},
support = {BÖBW2-105A, FKZ-7533-10-5-185B//Ministry for Science, Research and Art within the Bioeconomy research Program of Ba-den-Württemberg/ ; },
abstract = {Microalgae such as Phaeodactylum tricornutum (PT) are a sustainable source of nutrients, especially eicosapentaenoic acid (EPA), fucoxanthin (Fx), and chrysolaminarin (Chrl), the concentrations of which can vary depending on the culture conditions. We generated three types of diets containing either an EPA- and Fx-rich (EPA/Fx) or Chrl-rich microalgae (with 5, 15, or 25% added to the diet) or an isocaloric control diet (CD). These diets were evaluated over 14 days in young C57BL/6J mice for safety and bioavailability, short-chain fatty acid (SCFA) production, and microbiome analysis. Both microalgae diets increased body weight gain dose-dependently compared to the CD. Microalgae-derived EPA was well absorbed, resulting in increased liver and fat tissue levels and a decrease in the n-6:n-3 ratio in liver tissue. Both microalgae diets increased the production of selected SCFA and decreased the Firmicutes/Bacteriodota ratio, whereas the Chrl-rich diet led to an increase in Akkermansia. Doses of up to 4621 mg Chrl, 920 mg EPA, and 231 mg Fx per kg body weight daily were tolerated without adverse effects. This pre-clinical study shows that PT is suitable for mouse feed, with positive effects on microbiota composition and SCFA production, suggesting beneficial effects on gut health.},
}
@article {pmid35745227,
year = {2022},
author = {Winiarska-Mieczan, A and Tomaszewska, E and Donaldson, J and Jachimowicz, K},
title = {The Role of Nutritional Factors in the Modulation of the Composition of the Gut Microbiota in People with Autoimmune Diabetes.},
journal = {Nutrients},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/nu14122498},
pmid = {35745227},
issn = {2072-6643},
abstract = {Type 1 diabetes mellitus (T1DM) is a disease marked by oxidative stress, chronic inflammation, and the presence of autoantibodies. The gut microbiota has been shown to be involved in the alleviation of oxidative stress and inflammation as well as strengthening immunity, thus its' possible involvement in the pathogenesis of T1DM has been highlighted. The goal of the present study is to analyze information on the relationship between the structure of the intestinal microbiome and the occurrence of T1DM. The modification of the intestinal microbiota can increase the proportion of SCFA-producing bacteria, which could in turn be effective in the prevention and/or treatment of T1DM. The increased daily intake of soluble and non-soluble fibers, as well as the inclusion of pro-biotics, prebiotics, herbs, spices, and teas that are sources of phytobiotics, in the diet, could be important in improving the composition and activity of the microbiota and thus in the prevention of metabolic disorders. Understanding how the microbiota interacts with immune cells to create immune tolerance could enable the development of new therapeutic strategies for T1DM and improve the quality of life of people with T1DM.},
}
@article {pmid35745214,
year = {2022},
author = {Mo, SJ and Lee, K and Hong, HJ and Hong, DK and Jung, SH and Park, SD and Shim, JJ and Lee, JL},
title = {Effects of Lactobacillus curvatus HY7601 and Lactobacillus plantarum KY1032 on Overweight and the Gut Microbiota in Humans: Randomized, Double-Blinded, Placebo-Controlled Clinical Trial.},
journal = {Nutrients},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/nu14122484},
pmid = {35745214},
issn = {2072-6643},
abstract = {Obesity and overweight are closely related to diet, and the gut microbiota play an important role in body weight and human health. The aim of this study was to explore how Lactobacillus curvatus HY7601 and Lactobacillus plantarum KY1032 supplementation alleviate obesity by modulating the human gut microbiome. A randomized, double-blind, placebo-controlled study was conducted on 72 individuals with overweight. Over a 12-week period, probiotic groups consumed 1 × 1010 colony-forming units of HY7601 and KY1032, whereas the placebo group consumed the same product without probiotics. After treatment, the probiotic group displayed a reduction in body weight (p < 0.001), visceral fat mass (p < 0.025), and waist circumference (p < 0.007), and an increase in adiponectin (p < 0.046), compared with the placebo group. Additionally, HY7601 and KY1032 supplementation modulated bacterial gut microbiota characteristics and beta diversity by increasing Bifidobacteriaceae and Akkermansiaceae and decreasing Prevotellaceae and Selenomonadaceae. In summary, HY7601 and KY1032 probiotics exert anti-obesity effects by regulating the gut microbiota; hence, they have therapeutic potential for preventing or alleviating obesity and living with overweight.},
}
@article {pmid35745199,
year = {2022},
author = {Radziszewska, M and Smarkusz-Zarzecka, J and Ostrowska, L and Pogodziński, D},
title = {Nutrition and Supplementation in Ulcerative Colitis.},
journal = {Nutrients},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/nu14122469},
pmid = {35745199},
issn = {2072-6643},
abstract = {Ulcerative colitis (UC) belongs to the group of inflammatory bowel diseases (IBD). UC is an incurable, diffuse, and chronic inflammatory process of the colonic mucosa with alternating periods of exacerbation and remission. This review aimed to analyze the scientific research conducted to date to determine what impact different nutritional plans and dietary supplements may have on the course of UC. The latest 98 articles about nutrition and supplementation in ulcerative colitis were used to prepare the work. Certain components in food can greatly influence the course of UC, inducing changes in the composition and function of the gut microbiome. This activity may be an important part of therapy for people with IBD. The Mediterranean diet has shown the most promising results in the treatment of patients with UC due to its high content of biologically active foods. Patients with UC may benefit from the UC Exclusion Diet (UCED); however, it is a new nutritional plan that requires further research. Patents frequently resort to unconventional diets, which, because of their frequent elimination of nutrient-rich foods, can worsen the health and nutritional status of those who follow them. The benefits of omega-3 fatty acids and probiotics supplementation may have additional therapeutic effects; however, the evidence is not unequivocal.},
}
@article {pmid35745182,
year = {2022},
author = {Palmieri, O and Castellana, S and Bevilacqua, A and Latiano, A and Latiano, T and Panza, A and Fontana, R and Ippolito, AM and Biscaglia, G and Gentile, A and Gioffreda, D and Decina, I and Tricarico, M and Sinigaglia, M and Corbo, MR and Mazza, T and Perri, F and Lamacchia, C},
title = {Adherence to Gluten-Free Diet Restores Alpha Diversity in Celiac People but the Microbiome Composition Is Different to Healthy People.},
journal = {Nutrients},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/nu14122452},
pmid = {35745182},
issn = {2072-6643},
support = {Ricerca Corrente 2018-2021//This research was funded by the Italian Ministry of Health/ ; },
abstract = {Celiac disease (CD) is an autoimmune disease with the destruction of small intestinal villi, which occurs in genetically predisposed individuals. At the present moment, a gluten-free diet (GFD) is the only way to restore the functionality of gut mucosa. However, there is an open debate on the effects of long-term supplementation through a GFD, because some authors report an unbalance in microbial taxa composition.<br><br>METHODS: For microbiome analysis, fecal specimens were collected from 46 CD individuals in GFD for at least 2 years and 30 specimens from the healthy controls (HC). Data were analyzed using an ensemble of software packages: QIIME2, Coda-lasso, Clr-lasso, Selbal, PICRUSt2, ALDEx2, dissimilarity-overlap analysis, and dysbiosis detection tests.<br><br>RESULTS: The adherence to GFD restored the alpha biodiversity of the gut microbiota in celiac people but microbial composition at beta diversity resulted as different to HC. The microbial composition of the CD subjects was decreased in a number of taxa, namely Bifidobacterium longum and several belonging to Lachnospiraceae family, whereas Bacteroides genus was found to be more abundant. Predicted metabolic pathways among the CD bacterial communities revealed an important role in tetrapyrrole biosynthesis.<br><br>CONCLUSIONS: CD patients in GFD had a non-dysbiotic microbial composition for the crude alpha diversity metrics. We found significant differences in beta diversity, in certain taxon, and pathways between subjects with inactive CD in GFD and controls. Collectively, our data may suggest the development of new GFD products by modulating the gut microbiota through diet, supplements of vitamins, and the addition of specific prebiotics.},
}
@article {pmid35745156,
year = {2022},
author = {Santonocito, S and Giudice, A and Polizzi, A and Troiano, G and Merlo, EM and Sclafani, R and Grosso, G and Isola, G},
title = {A Cross-Talk between Diet and the Oral Microbiome: Balance of Nutrition on Inflammation and Immune System's Response during Periodontitis.},
journal = {Nutrients},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/nu14122426},
pmid = {35745156},
issn = {2072-6643},
support = {PIACERI 2020-2022//University of Catania/ ; },
abstract = {Over the last few decades, studies on the oral microbiome have increased awareness that the balance between the host and the microbial species that coexist in it is essential for oral health at all stages of life. However, this balance is extremely difficult to maintain, and many factors can disrupt it: general eating habits, sugar consumption, tobacco smoking, oral hygiene, and use of antibiotics and other antimicrobials. It is now known that alterations in the oral microbiota are responsible for developing and promoting many oral diseases, including periodontal disease. In this context, diet is an area for further investigation as it has been observed that the intake of particular foods, such as farmed animal meat, dairy products, refined vegetable oils, and processed cereals, affects the composition of the microbiota, leading to an increased representation of acid-producing and acid-tolerant organisms and periodontal pathogens. However, little is known about the influence of diet on the oral microbiome and the creation of a suitable microenvironment for the development of periodontal disease. The aim of the present study is to evaluate current knowledge on the role of diet in the oral dysbiosis underlying periodontal disease.},
}
@article {pmid35745141,
year = {2022},
author = {Frazer, LC and Yakah, W and Martin, CR},
title = {Decreased Acetic Acid in the Stool of Preterm Infants Is Associated with an Increased Risk of Bronchopulmonary Dysplasia.},
journal = {Nutrients},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/nu14122412},
pmid = {35745141},
issn = {2072-6643},
support = {N/A//The Charles H. and Judy Hood Family Infant Health Research Program/ ; T32HD098061//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; },
abstract = {BACKGROUND: Short-chain fatty acids (SCFAs), microbial metabolites, have been minimally studied in neonatal pathophysiology but have been associated with disease outcomes in adults. The objective of this manuscript was to determine if SCFA levels in maternal breastmilk (BM) and stool from preterm neonates impacted the risk of neonatal morbidities.<br><br>METHODS: SCFA levels were quantified by liquid chromatography with tandem mass spectrometry on maternal BM and neonatal stool for preterm infants < 28 weeks' gestation (N = 72) on postnatal days 14 and 28. SCFA levels in BM and stool of infants with and without bronchopulmonary disease (BPD) and retinopathy of prematurity (ROP) were compared. Logistic regression was applied to determine the association between stool acetic acid levels and disease.<br><br>RESULTS: Acetic, propionic, isobutyric, 2-methylbutyric, and isovaleric acid levels increased in BM and neonatal stool between days 14 and 28. Logistic regression demonstrated an inverse relationship between the quartile of fecal acetic acid level and the odds of BPD but not ROP on days 14 and 28. For each quartile increase in fecal acetic acid, the odds ratio (95% CI) of BPD was 0.41 (0.18, 0.83) for day 14 and 0.28 (0.09, 0.64) for day 28.<br><br>CONCLUSIONS: Low acetic acid levels in the stool of preterm infants are associated with increased odds of BPD. These findings support a relationship between intestinal and pulmonary health in preterm infants.},
}
@article {pmid35744874,
year = {2022},
author = {Bouchard, J and Malalgoda, M and Storsley, J and Malunga, L and Netticadan, T and Thandapilly, SJ},
title = {Health Benefits of Cereal Grain- and Pulse-Derived Proteins.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {12},
pages = {},
doi = {10.3390/molecules27123746},
pmid = {35744874},
issn = {1420-3049},
abstract = {Pulses and whole grains are considered staple foods that provide a significant amount of calories, fibre and protein, making them key food sources in a nutritionally balanced diet. Additionally, pulses and whole grains contain many bioactive compounds such as dietary fibre, resistant starch, phenolic compounds and mono- and polyunsaturated fatty acids that are known to combat chronic disease. Notably, recent research has demonstrated that protein derived from pulse and whole grain sources contains bioactive peptides that also possess disease-fighting properties. Mechanisms of action include inhibition or alteration of enzyme activities, vasodilatation, modulation of lipid metabolism and gut microbiome and oxidative stress reduction. Consumer demand for plant-based proteins has skyrocketed primarily based on the perceived health benefits and lower carbon footprint of consuming foods from plant sources versus animal. Therefore, more research should be invested in discovering the health-promoting effects that pulse and whole grain proteins have to offer.},
}
@article {pmid35744749,
year = {2022},
author = {Baltazar-Díaz, TA and González-Hernández, LA and Aldana-Ledesma, JM and Peña-Rodríguez, M and Vega-Magaña, AN and Zepeda-Morales, ASM and López-Roa, RI and Del Toro-Arreola, S and Martínez-López, E and Salazar-Montes, AM and Bueno-Topete, MR},
title = {Escherichia/Shigella, SCFAs, and Metabolic Pathways-The Triad That Orchestrates Intestinal Dysbiosis in Patients with Decompensated Alcoholic Cirrhosis from Western Mexico.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/microorganisms10061231},
pmid = {35744749},
issn = {2076-2607},
support = {P3E 260428//University of Guadalajara/ ; PIN 2021-II//University of Guadalajara/ ; },
abstract = {Gut microbiota undergoes profound alterations in alcohol cirrhosis. Microbiota-derived products, e.g., short chain fatty acids (SCFA), regulate the homeostasis of the gut-liver axis. The objective was to evaluate the composition and functions of the intestinal microbiota in patients with alcohol-decompensated cirrhosis. Fecal samples of 18 patients and 18 healthy controls (HC) were obtained. Microbial composition was characterized by 16S rRNA amplicon sequencing, SCFA quantification was performed by gas chromatography (GC), and metagenomic predictive profiles were analyzed by PICRUSt2. Gut microbiota in the cirrhosis group revealed a significant increase in the pathogenic/pathobionts genera Escherichia/Shigella and Prevotella, a decrease in beneficial bacteria, such as Blautia, Faecalibacterium, and a decreased α-diversity (p < 0.001) compared to HC. Fecal SCFA concentrations were significantly reduced in the cirrhosis group (p < 0.001). PICRUSt2 analysis indicated a decrease in acetyl-CoA fermentation to butyrate, as well as an increase in pathways related to antibiotics resistance, and aromatic amino acid biosynthesis. These metabolic pathways have been poorly described in the progression of alcohol-related decompensated cirrhosis. The gut microbiota of these patients possesses a pathogenic/inflammatory environment; therefore, future strategies to balance intestinal dysbiosis should be implemented. These findings are described for the first time in the population of western Mexico.},
}
@article {pmid35744721,
year = {2022},
author = {Kumar, U and Saqib, HSA and Islam, W and Prashant, P and Patel, N and Chen, W and Yang, F and You, M and He, W},
title = {Landscape Composition and Soil Physical-Chemical Properties Drive the Assemblages of Bacteria and Fungi in Conventional Vegetable Fields.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/microorganisms10061202},
pmid = {35744721},
issn = {2076-2607},
support = {32172503//National Natural Science Foundation of China/ ; 2019J01369//Natural Science Foundation of Fujian Province in China/ ; 2017YFD0200400//National Key R&amp;D Program of China/ ; KRA16001A//"111" program/ ; KJG18018A//Joint International Laboratory, China/ ; },
abstract = {The soil microbiome is crucial for improving the services and functioning of agroecosystems. Numerous studies have demonstrated the potential of soil physical-chemical properties in driving the belowground microbial assemblages in different agroecosystems. However, not much is known about the assemblage of bacteria and fungi in response to soil physical-chemical properties and the surrounding landscape composition in different vegetable fields of a highly intensive agricultural system. Here, we investigated the effects of soil physical-chemical properties and landscape composition on the community trends of bacteria and fungi in two different soil compartments (bulk and rhizospheric soils) of two different brassica crop types (Chinese cabbage and flower cabbage). The results revealed that bulk soil had a higher alpha diversity of both bacteria and fungi than rhizospheric soil. Each of the soil physical-chemical properties and landscape compositions contributed differently to driving the community structure of distinct bacterial and fungal taxa in both soil compartments and crop types. The higher proportions of forest, grassland, and cultivated land, along with the higher amount of soil calcium in flower cabbage fields, promote the assemblage of Gammaproteobacteria, Actinobacteria, Oxyophotobacteria, Agaricomycetes, and Eurotiomycetes. On the other hand, in Chinese cabbage fields, the increased amounts of iron, zinc, and manganese in the soil together with higher proportions of non-brassica crops in the surrounding landscape strongly support the assemblage of Deltaproteobacteria, Gemmatimonadetes, Bacilli, Clostridia, Alphaproteobacteria, an unknown bacterial species Subgroup-6, Mortierellomycetes, Rhizophlyctidomycetes, and Chytridiomycetes. The findings of this study provide the most comprehensive, comparative, and novel insights related to the bacterial and fungal responses in a highly intensive vegetable growing system for the improvement of the soil fertility and structure. These are important clues for the identification of key bacteria and fungi contributing to the plant-environment interactions and are of a practical significance for landscape-based ecological pest management.},
}
@article {pmid35744713,
year = {2022},
author = {Kumari V B, C and Huligere, SS and Shbeer, AM and Ageel, M and M K, J and S, JC and Ramu, R},
title = {Probiotic Potential Lacticaseibacillus casei and Limosilactobacillus fermentum Strains Isolated from Dosa Batter Inhibit α-Glucosidase and α-Amylase Enzymes.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/microorganisms10061195},
pmid = {35744713},
issn = {2076-2607},
abstract = {Fermented food plays a major role in gastrointestinal health, as well as possesses other health benefits, such as beneficiary effects in the management of diabetes. Probiotics are thought to be viable sources for enhancing the microbiome of the human gut. In the present study, using biochemical, physiological, and molecular approaches, the isolated Lactobacillus spp. from dosa batter were identified. The cell-free supernatant (CS), cell-free extract (CE), and intact cells (IC) were evaluated for their inhibitory potential against the carbohydrate hydrolyzing enzymes α-glucosidase and α-amylase. Then, 16S rDNA amplification and sequencing were used to identify the species. A homology search in NCBI database was performed that suggests the isolates are >95% similar to Limosilactobacillus fermentum and Lacticaseibacillus casei. Different standard parameters were used to evaluate the probiotic potential of strains RAMULAB07, RAMULAB08, RAMULAB09, RAMULAB10, RAMULAB11, and RAMULAB12. The strains expressed a significant tolerance to the gastric and intestinal juices with a higher survival rate (>98%). A high adhesion capability was observed by the isolates exhibited through hydrophobicity (>65%), aggregation assays (>75%), and adherence assay on HT-29 cells (>82%) and buccal epithelial cells. In addition, the isolates expressed antibacterial and antibiotic properties. Safety assessments (DNase and hemolytic assay) revealed that the isolates could be classified as safe. α-glucosidase and α-amylase inhibition of the isolates for CS, CE, and IC ranged from 7.50% to 65.01% and 20.21% to 56.91%, respectively. The results suggest that these species have exceptional antidiabetic potential, which may be explained by their use as foods that can have health-enhancing effects beyond basic nutrition.},
}
@article {pmid35744696,
year = {2022},
author = {Shapiro, D and Kapourchali, FR and Santilli, A and Han, Y and Cresci, GAM},
title = {Targeting the Gut Microbiota and Host Immunity with a Bacilli-Species Probiotic during Antibiotic Exposure in Mice.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/microorganisms10061178},
pmid = {35744696},
issn = {2076-2607},
support = {R01AA028043- 01A1/NH/NIH HHS/United States ; },
abstract = {Antibiotic therapy is necessary for the treatment of bacterial infections; however, it can also disrupt the balance and function of commensal gut microbes and negatively affect the host. Probiotics have been tested as a means to counteract the negative effects of antibiotic therapy, but many probiotics are also likely destroyed by antibiotics when taken together. Here we aimed to test the efficacy of a non-pathogenic spore-forming Bacillus-species containing a probiotic blend provided during antibiotic therapy on host immune defenses in mice. Mice were exposed to antibiotics and supplemented with or without the probiotic blend and compared to control mice. Fecal and cecal contents were analyzed for gut microbes, and intestinal tissue was tested for the expression of key enzymes involved in vitamin A metabolism, serum amyloid A, and inflammatory markers in the intestine. The probiotic blend protected against antibiotic-induced overgrowth of gram-negative bacteria and gammaproteobacteria in the cecum which correlated with host immune responses. Regional responses in mRNA expression of enzymes involved with vitamin A metabolism occurred between antibiotic groups, and intestinal inflammatory markers were mitigated with the probiotic blend. These data suggest prophylactic supplementation with a spore-forming Bacillus-containing probiotic may protect against antibiotic-induced dysregulation of host immune responses.},
}
@article {pmid35744684,
year = {2022},
author = {Tang, L and Gao, Y and Yan, L and Jia, H and Chu, H and Ma, X and He, L and Wang, X and Li, K and Hu, D and Zhang, D},
title = {Comparative Analysis of Microbiome Metagenomics in Reintroduced Wild Horses and Resident Asiatic Wild Asses in the Gobi Desert Steppe.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/microorganisms10061166},
pmid = {35744684},
issn = {2076-2607},
support = {2019JQ03018//Beijing Forestry University Outstanding Young Talent Cultivation Project/ ; 31872964//National Science Foundation of China/ ; },
abstract = {The gut microbiome offers important ecological benefits to the host; however, our understanding of the functional microbiome in relation to wildlife adaptation, especially for translocated endangered species, is lagging. In this study, we adopted a comparative metagenomics approach to test whether the microbiome diverges for translocated and resident species with different adaptive potentials. The composition and function of the microbiome of sympatric Przewalski's horses and Asiatic wild asses in desert steppe were compared for the first time using the metagenomic shotgun sequencing approach. We identified a significant difference in microbiome composition regarding the microbes present and their relative abundances, while the diversity of microbe species was similar. Furthermore, the functional profile seemed to converge between the two hosts, with genes related to core metabolism function tending to be more abundant in wild asses. Our results indicate that sympatric wild equids differ in their microbial composition while harboring a stable microbial functional core, which may enable them to survive in challenging habitats. A higher abundance of beneficial taxa, such as Akkermansia, and genes related to metabolism pathways and enzymes, such as lignin degradation, may contribute to more diverse diet choices and larger home ranges of wild asses.},
}
@article {pmid35744673,
year = {2022},
author = {Davis, EC and Wang, M and Donovan, SM},
title = {Microbial Interrelationships across Sites of Breastfeeding Mothers and Infants at 6 Weeks Postpartum.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/microorganisms10061155},
pmid = {35744673},
issn = {2076-2607},
support = {R01 DK107561/NH/NIH HHS/United States ; },
abstract = {Infancy is a critical life stage for the establishment of the gut microbiome. Human milk contains a unique microbial ecosystem that serves as a continuous source of commensal bacteria for the infant. However, the origin of the human milk microbiota, how it is influenced by breastfeeding exclusivity, and its role in infant gut microbiota assembly are not clear. To interrogate these questions, we examined the relationships among fecal, oral, breast skin, and human milk microbiota of 33 exclusively breastfeeding (EBF) and mixed-feeding (MF; human milk + infant formula) mother-infant pairs at 6 weeks postpartum. Here, we show that MF infants have a significantly more diverse oral microbiome comprised of lower relative abundances of Streptococcus and Gemella and higher abundances of Veillonella. Using both SourceTracker2 and FEAST, we demonstrate breast skin and infant saliva as the principal contributing sources to the human milk microbiota. Of the sampled sites, human milk and maternal stool were predicted to contribute the largest fraction to the infant fecal microbiome, but the majority of the community was estimated to arise from unknown sources. Lastly, we identified twenty-one significant co-occurrence relationships between bacteria in human milk and on other maternal and infant body sites. These results demonstrate several unique microbial interrelationships between breastfeeding dyads, providing insight into potential mechanisms of microbial assembly in early life.},
}
@article {pmid35744670,
year = {2022},
author = {Goodwin, PH},
title = {The Rhizosphere Microbiome of Ginseng.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/microorganisms10061152},
pmid = {35744670},
issn = {2076-2607},
abstract = {The rhizosphere of ginseng contains a wide range of microorganisms that can have beneficial or harmful effects on the plant. Root exudates of ginseng, particularly ginsenosides and phenolic acids, appear to select for particular microbial populations through their stimulatory and inhibitory activities, which may account for the similarities between the rhizosphere microbiomes of different cultivated species of Panax. Many practices of cultivation attempt to mimic the natural conditions of ginseng as an understory plant in hilly forested areas. However, these practices are often disruptive to soil, and thus the soil microbiome differs between wild and cultivated ginseng. Changes in the microbiome during cultivation can be harmful as they have been associated with negative changes of the soil physiochemistry as well as the promotion of plant diseases. However, isolation of a number of beneficial microbes from the ginseng rhizosphere indicates that many have the potential to improve ginseng production. The application of high-throughput sequencing to study the rhizosphere microbiome of ginseng grown under a variety of conditions continues to greatly expand our knowledge of the diversity and abundance of those organisms as well as their impacts of cultivation. While there is much more to be learnt, many aspects of the ginseng rhizosphere microbiome have already been revealed.},
}
@article {pmid35744659,
year = {2022},
author = {Tsakeng, CUB and Tanekou, TTM and Soffack, SF and Tirados, I and Noutchih, C and Njiokou, F and Bigoga, JD and Wondji, CS},
title = {Assessing the Tsetse Fly Microbiome Composition and the Potential Association of Some Bacteria Taxa with Trypanosome Establishment.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/microorganisms10061141},
pmid = {35744659},
issn = {2076-2607},
support = {MR/P027873/1/MRC_/Medical Research Council/United Kingdom ; 731060//Infravec2/ ; },
abstract = {The tsetse flies, biological vectors of African trypanosomes, harbour a variety of bacteria involved in their vector competence that may help in developing novel vector control tools. This study provides an inventory of tsetse bacterial communities in Cameroon and explores their possible associations with trypanosome establishment in Glossina palpalis palpalis. High throughput sequencing of the V3-V4 hypervariable region of the bacterial 16S rRNA gene, with subsequent metagenomic, multivariate, and association analyses, were used to investigate the levels and patterns of microbial diversity in four tsetse species. Overall, 31 bacterial genera and four phyla were identified. The primary symbiont Wigglesworthia dominated almost all the samples, with an overall relative abundance of 47.29%, and seemed to be replaced by Serratia or Burkholderia in some G. tachinoides flies. Globally, significant differences were observed in the microbiome diversity and composition among tsetse species and between teneral and non-teneral flies, or between flies displaying or not displaying mature trypanosome infections. In addition, differential abundance testing showed some OTUs, or some bacteria taxa, associated with trypanosome maturation in tsetse flies. These bacteria could be further investigated for an understanding of their mechanism of action and alternatively, transformed and used to block trypanosome development in tsetse flies.},
}
@article {pmid35744648,
year = {2022},
author = {Dinis, M and Traynor, W and Agnello, M and Sim, MS and He, X and Shi, W and Lux, R and Tran, NC},
title = {Tooth-Specific Streptococcus mutans Distribution and Associated Microbiome.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/microorganisms10061129},
pmid = {35744648},
issn = {2076-2607},
support = {N/A//UCLA Council on Research, Faculty Grant Program/ ; N/A//C3 Jian, Inc./ ; },
abstract = {Dental caries is multifactorial and polymicrobial in nature and remains one of the most common oral diseases. While caries research has focused on Streptococcus mutans as the main etiological pathogen, its impact at the tooth level is not fully understood. In this cross-sectional study, the levels and distribution of S. mutans in the posterior teeth at different dentition stages were investigated along with the corresponding tooth-specific microbiome. Occlusal plaque samples of 87 individual posterior teeth were collected from thirty children in three dentition stages (primary, mixed, and permanent). The S. mutans levels in the occlusal plaque of individual posterior teeth were quantified with qPCR, and those with preferential colonization were selected for tooth-specific microbiome analysis using 16S rRNA sequencing. Results: Quantification of S. mutans levels in the occlusal plaque confirmed the preferential colonization on the first primary and permanent molars. These teeth were selected for further tooth-specific microbiome sequencing, as they also displayed high caries experience. There were significant differences in the relative abundance of the four most abundant genera: Neisseria, Streptococcus, Rothia, and Veillonella. Furthermore, the tooth-level caries experience was correlated with a reduction in the microbiome diversity. Analyzing the different tooth-associated microbial communities, distinct tooth-specific core microbiomes were identified. Conclusions: Our findings suggest that caries susceptibility at the tooth level, depending on tooth type and dentition stage, is influenced by individual species as well as plaque community.},
}
@article {pmid35744646,
year = {2022},
author = {Lourenco, JM and Welch, CB and Krause, TR and Wieczorek, MA and Fluharty, FL and Rothrock, MJ and Pringle, TD and Callaway, TR},
title = {Fecal Microbiome Differences in Angus Steers with Differing Feed Efficiencies during the Feedlot-Finishing Phase.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/microorganisms10061128},
pmid = {35744646},
issn = {2076-2607},
abstract = {The gastrointestinal microbiota of cattle is important for feedstuff degradation and feed efficiency determination. This study evaluated the fecal microbiome of Angus steers with distinct feed efficiencies during the feedlot-finishing phase. Angus steers (n = 65), fed a feedlot-finishing diet for 82 days, had growth performance metrics evaluated. Steers were ranked based upon residual feed intake (RFI), and the 5 lowest RFI (most efficient) and 5 highest RFI (least efficient) steers were selected for evaluation. Fecal samples were collected on 0-d and 82-d of the finishing period and microbial DNA was extracted and evaluated by 16S rRNA gene sequencing. During the feedlot trial, inefficient steers had decreased (p = 0.02) Ruminococcaceae populations and increased (p = 0.01) Clostridiaceae populations. Conversely, efficient steers had increased Peptostreptococcaceae (p = 0.03) and Turicibacteraceae (p = 0.01), and a trend for decreased Proteobacteria abundance (p = 0.096). Efficient steers had increased microbial richness and diversity during the feedlot period, which likely resulted in increased fiber-degrading enzymes in their hindgut, allowing them to extract more energy from the feed. Results suggest that cattle with better feed efficiency have greater diversity of hindgut microorganisms, resulting in more enzymes available for digestion, and improving energy harvest in the gut of efficient cattle.},
}
@article {pmid35744642,
year = {2022},
author = {Gao, L and Huang, Y and Liu, Y and Mohamed, OAA and Fan, X and Wang, L and Li, L and Ma, J},
title = {Bacterial Community Structure and Potential Microbial Coexistence Mechanism Associated with Three Halophytes Adapting to the Extremely Hypersaline Environment.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/microorganisms10061124},
pmid = {35744642},
issn = {2076-2607},
abstract = {Halophytes play a crucial ecological role in drought and saline-alkali environments. However, there is limited knowledge about the structure of bacterial communities and the potential microbial coexistence mechanism associated with halophytes. This study investigated the diversity and community structure of endophytic and rhizospheric bacteria associated with three halophytes by applying high-throughput sequencing and geochemistry analyses on the studied soils. We collected 18 plant and 21 soil samples, and sequenced the V3 and V4 hypervariable regions of the 16S rRNA gene using next-generation sequencing (NGS). We also assessed geochemistry of the studied soils. The research suggested that rhizospheric bacterial richness and diversity associated with three halophytes were all significantly higher than for endophytic bacteria. The microbial community analysis indicated that Actinobacteria, Firmicutes, Bacteroidetes and Proteobacteria were the dominating bacterial phyla. Most unassigned operational taxonomic units (OTUs) implied that the microbes associated with halophytes contained abundant potential novel taxa, which are significant microbial resources. The high-abundance OTU phylogenetic tree supported the above views as well. Additionally, network analysis indicated that some conditional rare taxa (CRT) also might be keystone taxa during halophyte microbial community construction. The results of non-metric multidimensional scaling (NMDS) ordination analysis indicated significant dissimilarities in the microbial community among different sample groups. Sixty-two biomarkers were detected from seven different sample groups by linear discriminant analysis effect size (LEFSe) analysis. Microbial functions predicted based on phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) demonstrated that the abundances of nitrogen metabolism genes of endophytic bacteria were significantly higher than in rhizobacteria. Environmental factor analysis confirmed that different soil properties have different degrees of influence on the abundance and composition of the microbiota. To better adapt to the extreme hypersaline environment, halophytes could specifically recruit some plant beneficial bacterial taxa, such as nitrogen-fixing bacteria and extremely halophilic or halotolerant bacteria, to help them robustly grow and proliferate. All our preliminary results highlight microbial diversity and community related to halophytes grown on saline-alkali land of arid areas. Simultaneously, this work also advanced our further understanding of the halophyte microbiome associated with plants, and their role in plant adaptation to the extremely hypersaline environment.},
}
@article {pmid35744639,
year = {2022},
author = {Tsamakis, K and Galinaki, S and Alevyzakis, E and Hortis, I and Tsiptsios, D and Kollintza, E and Kympouropoulos, S and Triantafyllou, K and Smyrnis, N and Rizos, E},
title = {Gut Microbiome: A Brief Review on Its Role in Schizophrenia and First Episode of Psychosis.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/microorganisms10061121},
pmid = {35744639},
issn = {2076-2607},
abstract = {There is a growing body of evidence highlighting the role of gut microbiota as a biological basis of psychiatric disorders. The existing literature suggest that cognitive and emotional activities can be influenced by microbes through the microbiota-gut-brain axis and implies an association between alterations in the gut microbiome and several psychiatric conditions, such as autism, depression, bipolar disorder and psychosis. The aim of this review is to summarise recent findings and provide concise updates on the latest progress of the role of gut microbiota in the development and maintenance of psychiatric symptoms in schizophrenia and the first episode of psychosis. Despite the lack of consistent findings in regard to specific microbiome changes related to psychosis, the emerging literature reports significant differences in the gut microbiome of schizophrenic subjects compared to healthy controls and increasingly outlines the significance of an altered microbiome composition in the pathogenesis, development, symptom severity and prognosis of psychosis. Further human studies are, however, required, which should focus on identifying the drivers of microbiota changes in psychosis and establish the direction of causality between psychosis and microbiome alterations.},
}
@article {pmid35744625,
year = {2022},
author = {Cho, RM and Kogan, HV and Elikan, AB and Snow, JW},
title = {Paromomycin Reduces Vairimorpha (Nosema)ceranae Infection in Honey Bees but Perturbs Microbiome Levels and Midgut Cell Function.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/microorganisms10061107},
pmid = {35744625},
issn = {2076-2607},
abstract = {Paromomycin is a naturally occurring aminoglycoside antibiotic that has effects on both prokaryotic and eukaryotic microbes. However, previous reports have indicated that it has little effect on microsporidia, including Vairimorpha (Nosema) ceranae, in cell culture models. V. ceranae is one of a number of microsporidia species that cause disease in honey bees and substantial efforts to find new treatment strategies for bees that are infected with these pathogens are ongoing. When testing compounds for potential activity against V. ceranae in whole organisms, we found that paromomycin reduces the infection intensity of this parasite. Critically, the necessary doses of paromomycin have high activity against the bacteria of the honey bee microbiome and cause evident stress in bees. Microsporidia have been shown to lack an essential binding site on the ribosome that is known to allow for maximal inhibition by paromomycin. Thus, it is possible that paromomycin impacts parasite levels through non-cell autonomous effects on microsporidia infection levels via effects on the microbiome or midgut cellular function. As paromomycin treatment could cause widespread honey bee health issues in agricultural settings, it does not represent an appropriate anti-microsporidia agent for use in the field.},
}
@article {pmid35744617,
year = {2022},
author = {García-Mato, E and Martínez-Lamas, L and Álvarez-Fernández, M and Varela-Aneiros, I and Diniz-Freitas, M and Limeres-Posse, J and Diz-Dios, P},
title = {Molecular Detection of Streptococcus downii sp. nov. from Dental Plaque Samples from Patients with Down Syndrome and Non-Syndromic Individuals.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/microorganisms10061098},
pmid = {35744617},
issn = {2076-2607},
abstract = {A new bacterial species has recently been identified in the dental plaque of an adolescent with Down syndrome. The species is known as Streptococcus downii sp. nov. (abbreviated to S. downii), and it inhibits the growth of S. mutans and certain periodontal pathogens. The aim of this study was to determine the distribution of S. downii in the oral cavity of individuals with Down syndrome. Methods: A specific polymerase chain reaction for the operon of bacteriocin (class IIb lactobin A/cerein 7B family) was designed to detect S. downii in individuals with Down syndrome (n = 200) and in the general population (n = 100). We also compared the whole genome of S. downii and the regions related to its bacteriocins against 127 metagenomes of supragingival plaque of the "Human Microbiome Project". Results: We detected the specific gene of the S. downii bacteriocin in an individual with Down syndrome (Cq, 34.52; GE/μL, 13.0) and in an individual of the non-syndromic control group (Cq, 34.78 Cq; GE/μL, 4.93). The prevalence of S. downii was ≤1% both in Down syndrome and in the general population, which did not allow for clinical-microbiological correlations to be established. This result was confirmed by detecting only one metagenome with an ANIm with approximately 95% homology and with 100% homology with ORFs that code class IIb lactobiocin A/cerein 7B bacteriocins among the 127 metagenomes of the "Human Microbiome Project" tested. Conclusions: The detection rate of S. downii in the supragingival dental plaque was very low, both in the Down syndrome individuals and in the non-syndromic controls. A clinical-microbiological correlation could therefore not be established.},
}
@article {pmid35744594,
year = {2022},
author = {Dos Santos Guilherme, M and Valeri, F and Winter, J and Müller, MB and Schwiertz, A and Endres, K},
title = {Resilience and the Gut Microbiome: Insights from Chronically Socially Stressed Wild-Type Mice.},
journal = {Microorganisms},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/microorganisms10061077},
pmid = {35744594},
issn = {2076-2607},
support = {BIF04//Boehringer Ingelheim Fonds/ ; },
abstract = {The microbiome is an important player within physiological homeostasis of the body but also in pathophysiological derailments. Chronic social stress is a challenge to the organism, which results in psychological illnesses such as depression in some individuals and can be counterbalanced by others, namely resilient individuals. In this study, we wanted to elucidate the potential contribution of the microbiome to promote resilience. Male mice were subjected to the classical chronic social defeat paradigm. Defeated or undefeated mice were either controls (receiving normal drinking water) or pre-treated with antibiotics or probiotics. Following social defeat, resilient behavior was assessed by means of the social interaction test. Neither depletion nor probiotic-shifted alteration of the microbiome influenced stress-associated behavioral outcomes. Nevertheless, clear changes in microbiota composition due to the defeat stress were observed such as elevated Bacteroides spp. This stress-induced increase in Bacteroides in male mice could be confirmed in a related social stress paradigm (instable social hierarchy) in females. This indicates that while manipulation of the microbiome via the antibiotics- and probiotics-treatment regime used here has no direct impact on modulating individual stress susceptibility in rodents, it clearly affects the microbiome in the second line and in a sex-independent manner regarding Bacteroides.},
}
@article {pmid35743861,
year = {2022},
author = {Druzhinin, VG and Baranova, ED and Matskova, LV and Demenkov, PS and Volobaev, VP and Minina, VI and Larionov, AV and Paradnikova, SA},
title = {Sputum Microbiota in Coal Workers Diagnosed with Pneumoconiosis as Revealed by 16S rRNA Gene Sequencing.},
journal = {Life (Basel, Switzerland)},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/life12060830},
pmid = {35743861},
issn = {2075-1729},
support = {18-14-00022//Russian Science Foundation/ ; },
abstract = {Coal worker's pneumoconiosis (CWP) is an occupationally induced progressive fibrotic lung disease. This irreversible but preventable disease currently affects millions across the world, mainly in countries with developed coal mining industries. Here, we report a pilot study that explores the sputum microbiome as a potential non-invasive bacterial biomarker of CWP status. Sputum samples were collected from 35 former and active coal miners diagnosed with CWP and 35 healthy controls. Sequencing of bacterial 16S rRNA genes was used to study the taxonomic composition of the respiratory microbiome. There was no difference in alpha diversity between CWP and controls. The structure of bacterial communities in sputum samples (β diversity) differed significantly between cases and controls (pseudo-F = 3.61; p = 0.004). A significant increase in the abundance of Streptococcus (25.12 ± 11.37 vs. 16.85 ± 11.35%; p = 0.0003) was detected in samples from CWP subjects as compared to controls. The increased representation of Streptococcus in sputum from CWP patients was associated only with the presence of occupational pulmonary fibrosis, but did not depend on age, and did not differ between former and current miners. The study shows, for the first time, that the sputum microbiota of CWP subjects differs from that of controls. The results of our present exploratory study warrant further investigations on a larger cohort.},
}
@article {pmid35743789,
year = {2022},
author = {Graziani, C and Laterza, L and Talocco, C and Pizzoferrato, M and Di Simone, N and D'Ippolito, S and Ricci, C and Gervasoni, J and Persichilli, S and Del Chierico, F and Marzano, V and Mortera, SL and Primiano, A and Poscia, A and Ponziani, FR and Putignani, L and Urbani, A and Petito, V and Di Vincenzo, F and Masi, L and Lopetuso, LR and Cammarota, G and Romualdi, D and Lanzone, A and Gasbarrini, A and Scaldaferri, F},
title = {Intestinal Permeability and Dysbiosis in Female Patients with Recurrent Cystitis: A Pilot Study.},
journal = {Journal of personalized medicine},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/jpm12061005},
pmid = {35743789},
issn = {2075-4426},
abstract = {Recurrent cystitis (RC) is a common disease, especially in females. Anatomical, behavioral and genetic predisposing factors are associated with the ascending retrograde route, which often causes bladder infections. RC seems to be mainly caused by agents derived from the intestinal microbiota, and most frequently by Escherichia coli. Intestinal contiguity contributes to the etiopathogenesis of RC and an alteration in intestinal permeability could have a major role in RC. The aim of this pilot study is to assess gut microbiome dysbiosis and intestinal permeability in female patients with RC. Patients with RC (n = 16) were enrolled and compared with healthy female subjects (n = 15) and patients with chronic gastrointestinal (GI) disorders (n = 238). We calculated the Acute Cystitis Symptom Score/Urinary Tract Infection Symptom Assessment (ACSS/UTISA) and Gastrointestinal Symptom Rating Scale (GSRS) scores and evaluated intestinal permeability and the fecal microbiome in the first two cohorts. Patients with RC showed an increased prevalence of gastrointestinal symptoms compared with healthy controls. Of the patients with RC, 88% showed an increased intestinal permeability with reduced biodiversity of gut microbiota compared to healthy controls, and 68% of the RC patients had a final diagnosis of gastrointestinal disease. Similarly, GI patients reported a higher incidence of urinary symptoms with a diagnosis of RC in 20%. Gut barrier impairment seems to play a major role in the pathogenesis of RC. Further studies are necessary to elucidate the role of microbiota and intestinal permeability in urinary tract infections.},
}
@article {pmid35743678,
year = {2022},
author = {Maintz, L and Bieber, T and Simpson, HD and Demessant-Flavigny, AL},
title = {From Skin Barrier Dysfunction to Systemic Impact of Atopic Dermatitis: Implications for a Precision Approach in Dermocosmetics and Medicine.},
journal = {Journal of personalized medicine},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/jpm12060893},
pmid = {35743678},
issn = {2075-4426},
support = {N.A.//CK-CARE/ ; N.A.//La Roche-Posay International, 92300 Levallois-Perret, France/ ; },
abstract = {Atopic dermatitis (AD) affects up to 20% of children and is considered the starting point of the atopic march with the development of food allergy, asthma, and allergic rhinitis. The heterogeneous phenotype reflects distinct and/or overlapping pathogenetic mechanisms with varying degrees of epidermal barrier disruption, activation of different T cell subsets and dysbiosis of the skin microbiome. Here, we review current evidence suggesting a systemic impact of the cutaneous inflammation in AD together with a higher risk of asthma and other comorbidities, especially in severe and persistent AD. Thus, early therapy of AD to restore the impaired skin barrier, modified microbiome, and target type 2 inflammation, depending on the (endo)phenotype, in a tailored approach is crucial. We discuss what we can learn from the comorbidities and the implications for preventive and therapeutic interventions from precision dermocosmetics to precision medicine. The stratification of AD patients into biomarker-based endotypes for a precision medicine approach offers opportunities for better long-term control of AD with the potential to reduce the systemic impact of a chronic skin inflammation and even prevent or modify the course, not only of AD, but possibly also the comorbidities, depending on the patient's age and disease stage.},
}
@article {pmid35743626,
year = {2022},
author = {Agnoletti, D and Piani, F and Cicero, AFG and Borghi, C},
title = {The Gut Microbiota and Vascular Aging: A State-of-the-Art and Systematic Review of the Literature.},
journal = {Journal of clinical medicine},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/jcm11123557},
pmid = {35743626},
issn = {2077-0383},
abstract = {The gut microbiota is a critical regulator of human physiology, deleterious changes to its composition and function (dysbiosis) have been linked to the development and progression of cardiovascular diseases. Vascular ageing (VA) is a process of progressive stiffening of the arterial tree associated with arterial wall remodeling, which can precede hypertension and organ damage, and is associated with cardiovascular risk. Arterial stiffness has become the preferred marker of VA. In our systematic review, we found an association between gut microbiota composition and arterial stiffness, with two patterns, in most animal and human studies: a direct correlation between arterial stiffness and abundances of bacteria associated with altered gut permeability and inflammation; an inverse relationship between arterial stiffness, microbiota diversity, and abundances of bacteria associated with most fit microbiota composition. Interventional studies were able to show a stable link between microbiota modification and arterial stiffness only in animals. None of the human interventional trials was able to demonstrate this relationship, and very few adjusted the analyses for determinants of arterial stiffness. We observed a lack of large randomized interventional trials in humans that test the role of gut microbiota modifications on arterial stiffness, and take into account BP and hemodynamic alterations.},
}
@article {pmid35743414,
year = {2022},
author = {Bednarska-Czerwińska, A and Czerwiński, M and Morawiec, E and Łach, A and Ziaja, A and Kusaj, A and Strączyńska, P and Sagan, D and Boroń, D and Grabarek, BO},
title = {Marking the Profile of the Microflora of the Endometrium and Uterine Cervix in Women as a Potential Factor Determining the Effectiveness of In Vitro Fertilization.},
journal = {Journal of clinical medicine},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/jcm11123348},
pmid = {35743414},
issn = {2077-0383},
abstract = {One promising research trend involves evaluating the influence of microbiota in the reproductive system of women on becoming pregnant and maintaining pregnancy. The goal of this study was to define the microflora profile of the endometrium and uterine cervix in women qualified for an in vitro fertilization (IVF) procedure, which is expected to contribute to increasing the percentage of successful IVF implantations. Based on the conducted molecular analysis in the collected swabs, 22 bacterial strains were identified. Eleven strains (57%) that were isolated belong to the physiological microflora, the most common strain of which was Lactobacillus. Eight of the isolated strains (33%) were pathological microflora, among which the most common bacteria were from the Enterobacteriaceae family (which includes E. coli, Shigella, and Salmonella). Finally, three of the bacterial strains (10%) may be a component of both physiological or pathological microflora of the vagina: Bifidobacterium breve, Bifidobacterium longum group, and Alloscardovia omnicolens. The presence of Escherichia coli was detected in six women, Staphylococcus aureus also in six patients, Atopobium parvulum in three, Streptococcus salivarius group in three, Enterococcus faecalis in four, and Aerococcus christensenii in two patients. We found statistically significant relationships (p < 0.05) between Lactobacillus fermentum and Enterococcus faecalis, Lactobacillus delbrueckii and Escherichia coli groups, Lactobacillus FN667084_s and Staphylococcus aureus groups, as well as Lactobacillus fermentum and Streptococcus agalactiae. Based on the conducted study, it may be confirmed that the endometrium is, to a large extent, colonized by lactic acid bacilli. Apart from that, endometrial dysbiosis was not noted in patients qualified for the IVF procedure.},
}
@article {pmid35743317,
year = {2022},
author = {Gallego-Fabrega, C and Muiño, E and Cárcel-Márquez, J and Llucià-Carol, L and Lledós, M and Martín-Campos, JM and Cullell, N and Fernández-Cadenas, I},
title = {Genome-Wide Studies in Ischaemic Stroke: Are Genetics Only Useful for Finding Genes?.},
journal = {International journal of molecular sciences},
volume = {23},
number = {12},
pages = {},
doi = {10.3390/ijms23126840},
pmid = {35743317},
issn = {1422-0067},
support = {PI18/01338//Instituto de Salud Carlos III/ ; ERA NET NEURON IBIOSTROKE Fondos de recuperación FEDER//Instituto de Salud Carlos III/ ; },
abstract = {Ischaemic stroke is a complex disease with some degree of heritability. This means that heritability factors, such as genetics, could be risk factors for ischaemic stroke. The era of genome-wide studies has revealed some of these heritable risk factors, although the data generated by these studies may also be useful in other disciplines. Analysis of these data can be used to understand the biological mechanisms associated with stroke risk and stroke outcome, to determine the causality between stroke and other diseases without the need for expensive clinical trials, or to find potential drug targets with higher success rates than other strategies. In this review we will discuss several of the most relevant studies regarding the genetics of ischaemic stroke and the potential use of the data generated.},
}
@article {pmid35743280,
year = {2022},
author = {Ermolenko, E and Simanenkova, A and Voropaeva, L and Lavrenova, N and Kotyleva, M and Minasian, S and Chernikova, A and Timkina, N and Gladyshev, N and Dmitriev, A and Suvorov, A and Galagudza, M and Karonova, T},
title = {Metformin Influence on the Intestinal Microbiota and Organism of Rats with Metabolic Syndrome.},
journal = {International journal of molecular sciences},
volume = {23},
number = {12},
pages = {},
doi = {10.3390/ijms23126837},
pmid = {35743280},
issn = {1422-0067},
abstract = {Metformin is a first-line drug for DM2 treatment and prevention, but its complex effect on impaired glucose tolerance (IGT), including its influence on myocardial resistance to ischemia-reperfusion injury, is not completely studied. We aimed to evaluate the influence of metformin on the intestinal microbiota (IM), metabolism, and functional and morphological characteristics of myocardium in rats with IGT. IGT was modelled in SPF Wistar rats with a high-fat diet and streptozotocin and nicotinamide injection. Rats were divided into three groups: IGT (without treatment), IGT MET (metformin therapy), and CRL (without IGT induction and treatment). IGT group was characterized by: higher body weight, increased serum glucose and total cholesterol levels, atherogenic coefficient, impairment in the functional parameters of the isolated heart during perfusion, and larger myocardium infarction (MI) size in comparison with the CRL group. IM of IGT rats differed from that of CRL: an increase of Bacteroides, Acinetobacter, Akkermansia, Roseburia, and a decrease of Lactobacillus genera representation. Metformin therapy led to the diminishing of metabolic syndrome (MS) symptoms, which correlated with IM restoration, especially with the growth of Akkermansia spp. and decline of Roseburia populations and their influence on other members of IM. The obtained results allow us to consider from a new point of view the expediency of probiotic A. muciniphila use for MS treatment.},
}
@article {pmid35743202,
year = {2022},
author = {Hecking, I and Stegemann, LN and Theis, V and Vorgerd, M and Matschke, V and Stahlke, S and Theiss, C},
title = {Neuroprotective Effects of VEGF in the Enteric Nervous System.},
journal = {International journal of molecular sciences},
volume = {23},
number = {12},
pages = {},
doi = {10.3390/ijms23126756},
pmid = {35743202},
issn = {1422-0067},
abstract = {Although the enteric nervous system (ENS) functions largely autonomously as part of the peripheral nervous system (PNS), it is connected to the central nervous system (CNS) via the gut-brain axis. In many neurodegenerative diseases, pathological changes occur in addition to gastrointestinal symptoms, such as alpha-synuclein aggregates in Parkinson's disease, which are found early in the ENS. In both the CNS and PNS, vascular endothelial growth factor (VEGF) mediates neuroprotective and neuroregenerative effects. Since the ENS with its close connection to the microbiome and the immune system is discussed as the origin of neurodegenerative diseases, it is necessary to investigate the possibly positive effects of VEGF on enteric neurons. Using laser microdissection and subsequent quantitative RT-PCR as well as immunohistochemistry, for the first time we were able to detect and localize VEGF receptor expression in rat myenteric neurons of different ages. Furthermore, we demonstrate direct neuroprotective effects of VEGF in the ENS in cell cultures. Thus, our results suggest a promising approach regarding neuroprotection, as the use of VEGF (may) prevent neuronal damage in the ENS.},
}
@article {pmid35743087,
year = {2022},
author = {Lee, JE and Walton, D and O'Connor, CP and Wammes, M and Burton, JP and Osuch, EA},
title = {Drugs, Guts, Brains, but Not Rock and Roll: The Need to Consider the Role of Gut Microbiota in Contemporary Mental Health and Wellness of Emerging Adults.},
journal = {International journal of molecular sciences},
volume = {23},
number = {12},
pages = {},
doi = {10.3390/ijms23126643},
pmid = {35743087},
issn = {1422-0067},
abstract = {Emerging adulthood (ages 18-25) is a critical period for neurobiological development and the maturation of the hypothalamic-pituitary-adrenal axis. Recent findings also suggest that a natural perturbation of the gut microbiota (GM), combined with other factors, may create a unique vulnerability during this period of life. The GM of emerging adults is thought to be simpler, less diverse, and more unstable than either younger or older people. We postulate that this plasticity in the GM suggests a role in the rising mental health issues seen in westernized societies today via the gut-brain-microbiota axis. Studies have paid particular attention to the diversity of the microbiota, the specific function and abundance of bacteria, and the production of metabolites. In this narrative review, we focus specifically on diet, physical activity/exercise, substance use, and sleep in the context of the emerging adult. We propose that this is a crucial period for establishing a stable and more resilient microbiome for optimal health into adulthood. Recommendations will be made about future research into possible behavioral adjustments that may be beneficial to endorse during this critical period to reduce the probability of a "dysbiotic" GM and the emergence and severity of mental health concerns.},
}
@article {pmid35743072,
year = {2022},
author = {Pap, D and Veres-Székely, A and Szebeni, B and Vannay, Á},
title = {PARK7/DJ-1 as a Therapeutic Target in Gut-Brain Axis Diseases.},
journal = {International journal of molecular sciences},
volume = {23},
number = {12},
pages = {},
doi = {10.3390/ijms23126626},
pmid = {35743072},
issn = {1422-0067},
support = {TKP2020-NKA-09//Ministry for Innovation and Technology, Hungary/ ; TKP2020-NKA-13//Ministry for Innovation and Technology, Hungary/ ; K125470//National Research, Development and Innovation Office (NKFI), Hungary/ ; STIA-KFI-2020//Semmelweis Science and Innovation Fund, Hungary/ ; 20382-3/2018 FEKUTSTRAT//National Research, Development and Innovation Office, Hungary/ ; STIA-KFI-2021 (1492-15/IKP/2022)//Semmelweis Science and Innovation Fund, Hungary/ ; K124549//National Research, Development and Innovation Office (NKFI), Hungary/ ; },
abstract = {It is increasingly known that Parkinson's (PD) and Alzheimer's (AD) diseases occur more frequently in patients with inflammatory gastrointestinal diseases including inflammatory bowel (IBD) or celiac disease, indicating a pathological link between them. Although epidemiological observations suggest the existence of the gut-brain axis (GBA) involving systemic inflammatory and neural pathways, little is known about the exact molecular mechanisms. Parkinson's disease 7 (PARK7/DJ-1) is a multifunctional protein whose protective role has been widely demonstrated in neurodegenerative diseases, including PD, AD, or ischemic stroke. Recent studies also revealed the importance of PARK7/DJ-1 in the maintenance of the gut microbiome and also in the regulation of intestinal inflammation. All these findings suggest that PARK7/DJ-1 may be a link and also a potential therapeutic target in gut and brain diseases. In this review, therefore, we discuss our current knowledge about PARK7/DJ-1 in the context of GBA diseases.},
}
@article {pmid35743045,
year = {2022},
author = {Ahn, SY and Sung, DK and Chang, YS and Park, WS},
title = {Intratracheal Transplantation of Mesenchymal Stem Cells Attenuates Hyperoxia-Induced Microbial Dysbiosis in the Lungs, Brain, and Gut in Newborn Rats.},
journal = {International journal of molecular sciences},
volume = {23},
number = {12},
pages = {},
doi = {10.3390/ijms23126601},
pmid = {35743045},
issn = {1422-0067},
support = {SMX1210881//SMC-Ottogi Research Fund/ ; 2020R1A2C2010645//the National Research Foun-dation of Korea/ ; },
abstract = {We attempted to determine whether intratracheal (IT) transplantation of mesenchymal stem cells (MSCs) could simultaneously attenuate hyperoxia-induced lung injuries and microbial dysbiosis of the lungs, brain, and gut in newborn rats. Newborn rats were exposed to hyperoxia (90% oxygen) for 14 days. Human umbilical cord blood-derived MSCs (5 × 105) were transplanted via the IT route on postnatal day (P) five. At P14, the lungs were harvested for histological, biochemical, and microbiome analyses. Bacterial 16S ribosomal RNA genes from the lungs, brain, and large intestine were amplified, pyrosequenced, and analyzed. IT transplantation of MSCs simultaneously attenuated hyperoxia-induced lung inflammation and the ensuing injuries, as well as the dysbiosis of the lungs, brain, and gut. In correlation analyses, lung interleukin-6 (IL-6) levels were significantly positively correlated with the abundance of Proteobacteria in the lungs, brain, and gut, and it was significantly inversely correlated with the abundance of Firmicutes in the gut and lungs and that of Bacteroidetes in the lungs. In conclusion, microbial dysbiosis in the lungs, brain, and gut does not cause but is caused by hyperoxic lung inflammation and ensuing injuries, and IT transplantation of MSCs attenuates dysbiosis in the lungs, brain, and gut, primarily by their anti-oxidative and anti-inflammatory effects.},
}
@article {pmid35742974,
year = {2022},
author = {La Barbera, L and Macaluso, F and Fasano, S and Grasso, G and Ciccia, F and Guggino, G},
title = {Microbiome Changes in Connective Tissue Diseases and Vasculitis: Focus on Metabolism and Inflammation.},
journal = {International journal of molecular sciences},
volume = {23},
number = {12},
pages = {},
doi = {10.3390/ijms23126532},
pmid = {35742974},
issn = {1422-0067},
abstract = {The microbial community acts as an active player in maintaining homeostasis and immune functions through a continuous and changeable cross-talk with the host immune system. Emerging evidence suggests that altered microbial composition, known as dysbiosis, might perturb the delicate balance between the microbiota and the immune system, triggering inflammation and potentially contributing to the pathogenesis and development of chronic inflammatory diseases. This review will summarize the current evidence about the microbiome-immunity cross-talk, especially focusing on the microbiota alterations described in patients with rheumatic diseases and on the recent findings concerning the interaction between microbiota, metabolic function, and the immune system.},
}
@article {pmid35742895,
year = {2022},
author = {Kosecka-Strojek, M and Wolska-Gębarzewska, M and Podbielska-Kubera, A and Samet, A and Krawczyk, B and Międzobrodzki, J and Michalik, M},
title = {May Staphylococcus&amp;nbsp;lugdunensis Be an Etiological Factor of Chronic Maxillary Sinuses Infection?.},
journal = {International journal of molecular sciences},
volume = {23},
number = {12},
pages = {},
doi = {10.3390/ijms23126450},
pmid = {35742895},
issn = {1422-0067},
abstract = {Staphylococcus&amp;nbsp;lugdunensis is an opportunistic pathogen found in the healthy human skin microbiome bacterial community that is able to cause infections of diverse localization, manifestation, and course, including laryngological infections, such as necrotizing sinusitis. Chronic maxillary sinusitis is a disease present in up to one third of European and American populations, and its etiology is not fully described. Within this study, we aimed to characterize 18 S. lugdunensis strains recovered from maxillary sinuses and evaluate them as etiological agents of chronic disease. We performed MLST analysis, the complex analysis of both phenotypic and genetic virulence factors, antibiotic susceptibility profiles, and biofilm formation assay for the detection of biofilm-associated genes. Altogether, S. lugdunensis strains were clustered into eight different STs, and we demonstrated several virulence factors associated with the chronic disease. All tested strains were able to produce biofilm in vitro with numerous strains with a very strong ability, and overall, they were mostly susceptible to antibiotics, although we found resistance to fosfomycin, erythromycin, and clindamycin in several strains. We believe that further in-depth analysis of S. lugdunensis strains from different niches, including the nasal one, should be performed in the future in order to reduce infection rate and broaden the knowledge about this opportunistic pathogen that is gaining attention.},
}
@article {pmid35742758,
year = {2022},
author = {Alistar, CF and Nica, IC and Nita-Lazar, M and Vasile, GG and Gheorghe, S and Croitoru, AM and Dolete, G and Mihaiescu, DE and Ficai, A and Craciun, N and Gradisteanu Pircalabioru, G and Chifiriuc, MC and Stan, MS and Dinischiotu, A},
title = {Antioxidative Defense and Gut Microbial Changes under Pollution Stress in Carassius gibelio from Bucharest Lakes.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {12},
pages = {},
doi = {10.3390/ijerph19127510},
pmid = {35742758},
issn = {1660-4601},
support = {10PCCF/2018 RADAR (PN-III-P4-ID-PCCF-2016-0114)//Unitatea Executiva Pentru Finantarea Invatamantului Superior a Cercetarii Dezvoltarii si Inovarii/ ; },
abstract = {Fish are able to accumulate by ingestion various contaminants of aquatic environment, with negative consequences on their intestine, being continuously threatened worldwide by heavy metals, pesticides and antibiotics resulted from the human activities. Consequently, the health of other species can be affected by eating the contaminated fish meat. In this context, our study aimed to perform a comparison between the changes in intestine samples of Carassius gibelio individuals collected from different artificial lakes in Bucharest (Romania), used by people for leisure and fishing. The presence of various metals, pesticides and antibiotics in the gut of fish was assessed in order to correlate their accumulation with changes of antioxidative enzymes activities and microbiome. Our results showed that fish from Bucharest lakes designed for leisure (Chitila, Floreasca and Tei lakes) have an increased level of oxidative stress in intestine tissue, revealed by affected antioxidant enzymes activities and GSH levels, as well as the high degree of lipid peroxidation, compared to the fish from protected environment (Vacaresti Lake). Some heavy metals (Fe, Ni and Pb) and pesticides (aldrin and dieldrin) were in high amount in the gut of fish with modified antioxidative status. In conclusion, our study could improve the knowledge regarding the current state of urban aquatic pollution in order to impose several environmental health measures.},
}
@article {pmid35742743,
year = {2022},
author = {Wawrzyk, A and Rahnama, M and Sofińska-Chmiel, W and Wilczyński, S and Łobacz, M},
title = {The Use of the Diode Laser against the Microbiome on Composites Closing the Screw Access Hall (Sah) in the Reconstruction of Dental Implants: Ex Vivo Studies.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {12},
pages = {},
doi = {10.3390/ijerph19127494},
pmid = {35742743},
issn = {1660-4601},
abstract = {Patients undergoing implant treatment are at risk of peri-implant bone loss, which is most often caused by the adverse effects of microorganisms, but there are few proven procedures for their reduction. The aim of the research was to identify the microorganisms inhabiting the composites used to close the screw access hole (SAH), compare them numerically with those present on the surface of crowns and teeth, and optimize the doses of the diode laser, which will reduce microorganisms and will not deteriorate the roughness of polished composites. Patients were swabbed from the surface of SAH composites, from porcelain and zirconium restorations, and from teeth, and then the number of microorganisms was determined by using a culture technique. Microorganisms were identified by MALDI-TOF MS and NGS sequencing. The effectiveness of diode laser irradiation was achieved by using four variants of exposure. After polishing and laser irradiation, the surface roughness of the composites was studied by using optical profilometry. On the surface of SAH, 106 to 108 microorganisms were identified at 0.4 cm2, including many pathogenic species. Among the materials used for the reconstruction of dental implants, the greatest microbiological contamination was found on the composites used to close the SAH. The diode laser with a wavelength of 810 nm with an average power of 3.84 W, during 60 s and 2 × 30 s, has a biocidal effect and does not significantly change the surface roughness of composites. The best reduction of microorganisms was achieved on a composite polished with a polishing rubber and then with a Sof-Lex™ Pre-Polishing Spiral beige (3M ESPE, Ave. St. Paul., MN, USA). Studies have shown that using the optimal laser dose can help treat periimplantitis. These studies provide important information on the possibility of the effective elimination of microorganisms by using a diode laser in the treatment of peri-implant bone loss.},
}
@article {pmid35742735,
year = {2022},
author = {Di Spirito, F and Iandolo, A and Amato, A and Caggiano, M and Raimondo, A and Lembo, S and Martina, S},
title = {Prevalence, Features and Degree of Association of Oral Lesions in COVID-19: A Systematic Review of Systematic Reviews.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {12},
pages = {},
doi = {10.3390/ijerph19127486},
pmid = {35742735},
issn = {1660-4601},
abstract = {Regardless of rapidly emerging findings on oral lesions described in adult SARS-CoV-2-positive subjects, the evidence level remains quite low and rather contrasting; therefore, the present systematic review of systematic reviews primarily aims to point out the overall prevalence of diagnosed cases. Secondary aims are to estimate the degree of association between oral lesions and SARS-CoV-2 infection and to grade, based on the reported frequency, the primary oral lesions, with related clinical presentations and microscopic features, in relation to COVID-19 forms. A study protocol compliant with the PRISMA statement was developed. Twelve studies were included, reporting highly heterogeneous and incomplete findings, thus precluding a meta-analysis. Further studies should be conducted to assess the overall prevalence of cases diagnosed with oral lesions among adult SARS-CoV-2-positive subjects, especially considering novel viral variants, and to determine their degree of association with SARS-CoV-2 infection and COVID-19 forms. Moreover, the reported findings noticed the need to evaluate the putative role both of SARS-CoV-2 in oral lesions genesis and of periodontitis and periodontal microbiome in COVID-19 worsening and re-activations. Deeper insights into oral lesions in adult SARS-CoV-2-positive subjects could enhance the comprehension of illness pathogenesis, natural history and clinical presentation, thus improving the preparedness of health professionals in the inter-disciplinary management of COVID-19.},
}
@article {pmid35742022,
year = {2022},
author = {Trifkovič, KČ and Mičetić-Turk, D and Kmetec, S and Strauss, M and Dahlen, HG and Foster, JP and Fijan, S},
title = {Efficacy of Direct or Indirect Use of Probiotics for the Improvement of Maternal Depression during Pregnancy and in the Postnatal Period: A Systematic Review and Meta-Analysis.},
journal = {Healthcare (Basel, Switzerland)},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/healthcare10060970},
pmid = {35742022},
issn = {2227-9032},
abstract = {The mother and infant form a unique bond, with maternal mental health affecting the interactions with the infant and infant behaviours impacting maternal mental health. One of the possible mechanisms influencing maternal mental health is the manipulation of the gut-brain axis by consuming probiotic supplements. Probiotics can also have an indirect influence on maternal mental health via the modulation of the infant microbiome and consequently improving the infant's health and thus, indirectly leading to an improvement in maternal mood. This systematic review evaluated the efficacy of probiotics on maternal mental health by searching for randomised controlled trials via international databases: Cochrane Library, PubMed, Scopus, ScienceDirect, and Web of Science until January 2022. A meta-analysis was performed using the Cochrane Collaboration methodology where possible. We found seven clinical trials that included the word probiotics and addressed maternal depression and/or anxiety. Of these, five trials investigated the influence of maternal probiotic supplementation on the gut-brain axis. Two trials investigated the indirect influence of probiotics on maternal depression via supplementation of probiotics by infants and subsequent influence on the crying of colicky infants. Meta-analysis of two studies of pregnant and postnatal women and two studies of infants consuming probiotics on the outcome of the Edinburgh Postnatal Depression Scale for mothers showed no statistical difference. The findings indicate that maternal depression is very complex and is influenced by various bidirectional factors. One of the factors that can improve maternal mental health is probiotics, however, careful consideration must be given to correct strain selection as strain-specific effectiveness was observed. Further well-designed, robust clinical studies are warranted.},
}
@article {pmid35741992,
year = {2022},
author = {Lorenz, T and Iskandar, MM and Baeghbali, V and Ngadi, MO and Kubow, S},
title = {3D Food Printing Applications Related to Dysphagia: A Narrative Review.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/foods11121789},
pmid = {35741992},
issn = {2304-8158},
abstract = {Dysphagia is a condition in which the swallowing mechanism is impaired. It is most often a result of a stroke. Dysphagia has serious consequences, including choking and aspiration pneumonia, which can both be fatal. The population that is most affected by it is the elderly. Texture-modified diets are part of the treatment plan for dysphagia. This bland, restrictive diet often contributes to malnutrition in patients with dysphagia. Both energy and protein intake are of concern, which is especially worrying, as it affects the elderly. Making texture-modified diets more appealing is one method to increase food intake. As a recent technology, 3D food printing has great potential to increase the appeal of textured foods. With extrusion-based printing, both protein and vegetable products have already been 3D printed that fit into the texture categories provided by the International Dysphagia Diet Standardization Initiative. Another exciting advancement is 4D food printing which could make foods even more appealing by incorporating color change and aroma release following a stimulus. The ultra-processed nature of 3D-printed foods is of nutritional concern since this affects the digestion of the food and negatively affects the gut microbiome. There are mitigating strategies to this issue, including the addition of hydrocolloids that increase stomach content viscosity and the addition of probiotics. Therefore, 3D food printing is an improved method for the production of texture-modified diets that should be further explored.},
}
@article {pmid35741950,
year = {2022},
author = {Jiang, W and Chen, X and Guo, M and Yu, J and Yang, M and Pang, X},
title = {Analysis of Fungal Microbiomes in Edible Medicinal Morindae Officinalis Radix and Alpiniae Oxyphyllae Fructus Using DNA Metabarcoding.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/foods11121748},
pmid = {35741950},
issn = {2304-8158},
support = {2021-I2M-1-071//CAMS Innovation Fund for Medical Sciences (CIFMS)/ ; },
abstract = {Morindae Officinalis Radix (MOR) and Alpiniae Oxyphyllae Fructus (AOF) have been widely used as dietary supplements and traditional herbal medicines for centuries. Fungal and mycotoxin contamination in MOR and AOF has been reported recently. In this study, fungi in MOR and AOF are first investigated using DNA metabarcoding, and the differences in fungal microbiome between moldy and non-moldy samples are analyzed. The results show that Ascomycota is the most prevailing fungus at the phylum level in MOR and AOF with relative abundances of 49.53-94.32% and 14.81-81.85%, respectively. Penicillium (1.86-76.14%), Cladosporium (1.82-56.65%), and Trichoderma (0.12-19.71%) are the dominant genera in MOR. Penicillium (0.27-56.06%), Papiliotrema (0.04-51.71%), and Cladosporium (3.08-44.41%) are the dominant genera in AOF. Two potential toxigenic fungi were detected, namely, Trichoderma atroviride and Fusarium equiseti. Moreover, the differences in fungal communities between moldy and non-moldy samples were monitored. In conclusion, DNA metabarcoding can be used to assess the fungal microbiome in edible medicinal herbs, thereby providing a basis for ensuring food safety and drug efficacy.},
}
@article {pmid35741831,
year = {2022},
author = {Kumar, A and Gravdal, K and Segal, JP and Steed, H and Brookes, MJ and Al-Hassi, HO},
title = {Variability in the Pre-Analytical Stages Influences Microbiome Laboratory Analyses.},
journal = {Genes},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/genes13061069},
pmid = {35741831},
issn = {2073-4425},
support = {N/A//Bowel and Cancer Research/ ; N/A//Tillotts Pharma (Switzerland)/ ; },
abstract = {INTRODUCTION: There are numerous confounding variables in the pre-analytical steps in the analysis of gut microbial composition that affect data consistency and reproducibility. This study compared two DNA extraction methods from the same faecal samples to analyse differences in microbial composition.<br><br>METHODS: DNA was extracted from 20 faecal samples using either (A) chemical/enzymatic heat lysis (lysis buffer, proteinase K, 95 °C + 70 °C) or (B) mechanical and chemical/enzymatic heat lysis (bead-beating, lysis buffer, proteinase K, 65 °C). Gut microbiota was mapped through the 16S rRNA gene (V3-V9) using a set of pre-selected DNA probes targeting >300 bacteria on different taxonomic levels. Apart from the pre-analytical DNA extraction technique, all other parameters including microbial analysis remained the same. Bacterial abundance and deviations in the microbiome were compared between the two methods.<br><br>RESULTS: Significant variation in bacterial abundance was seen between the different DNA extraction techniques, with a higher yield of species noted in the combined mechanical and heat lysis technique (B). The five predominant bacteria seen in both (A) and (B) were Bacteroidota spp. and Prevotella spp. (p = NS), followed by Bacillota (p = 0.005), Lachhnospiraceae (p = 0.0001), Veillonella spp. (p < 0.0001) and Clostridioides (p < 0.0001).<br><br>CONCLUSION: As microbial testing becomes more easily and commercially accessible, a unified international consensus for optimal sampling and DNA isolation procedures must be implemented for robustness and reproducibility of the results.},
}
@article {pmid35741811,
year = {2022},
author = {Wu, Q and O'Malley, J and Datta, S and Gharaibeh, RZ and Jobin, C and Karagas, MR and Coker, MO and Hoen, AG and Christensen, BC and Madan, JC and Li, Z},
title = {MarZIC: A Marginal Mediation Model for Zero-Inflated Compositional Mediators with Applications to Microbiome Data.},
journal = {Genes},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/genes13061049},
pmid = {35741811},
issn = {2073-4425},
support = {RD83544201/EPA/EPA/United States ; R01GM123014, UH3OD023275, P01ES022832, P20GM104416, R01LM012723//National Institute of Health/ ; },
abstract = {BACKGROUND: The human microbiome can contribute to pathogeneses of many complex diseases by mediating disease-leading causal pathways. However, standard mediation analysis methods are not adequate to analyze the microbiome as a mediator due to the excessive number of zero-valued sequencing reads in the data and that the relative abundances have to sum to one. The two main challenges raised by the zero-inflated data structure are: (a) disentangling the mediation effect induced by the point mass at zero; and (b) identifying the observed zero-valued data points that are not zero (i.e., false zeros).<br><br>METHODS: We develop a novel marginal mediation analysis method under the potential-outcomes framework to address the issues. We also show that the marginal model can account for the compositional structure of microbiome data.<br><br>RESULTS: The mediation effect can be decomposed into two components that are inherent to the two-part nature of zero-inflated distributions. With probabilistic models to account for observing zeros, we also address the challenge with false zeros. A comprehensive simulation study and the application in a real microbiome study showcase our approach in comparison with existing approaches.<br><br>CONCLUSIONS: When analyzing the zero-inflated microbiome composition as the mediators, MarZIC approach has better performance than standard causal mediation analysis approaches and existing competing approach.},
}
@article {pmid35741702,
year = {2022},
author = {Yue, Y and Hu, YJ},
title = {Extension of PERMANOVA to Testing the Mediation Effect of the Microbiome.},
journal = {Genes},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/genes13060940},
pmid = {35741702},
issn = {2073-4425},
support = {R01GM116065/NH/NIH HHS/United States ; R01GM141074/NH/NIH HHS/United States ; },
abstract = {Recently, we have seen a growing volume of evidence linking the microbiome and human diseases or clinical outcomes, as well as evidence linking the microbiome and environmental exposures. Now comes the time to assess whether the microbiome mediates the effects of exposures on the outcomes, which will enable researchers to develop interventions to modulate outcomes by modifying microbiome compositions. Use of distance matrices is a popular approach to analyzing complex microbiome data that are high-dimensional, sparse, and compositional. However, the existing distance-based methods for mediation analysis of microbiome data, MedTest and MODIMA, only work well in limited scenarios. PERMANOVA is currently the most commonly used distance-based method for testing microbiome associations. Using the idea of inverse regression, here we extend PERMANOVA to test microbiome-mediation effects by including both the exposure and the outcome as covariates and basing the test on the product of their F statistics. This extension of PERMANOVA, which we call PERMANOVA-med, naturally inherits all the flexible features of PERMANOVA, e.g., allowing adjustment of confounders, accommodating continuous, binary, and multivariate exposure and outcome variables including survival outcomes, and providing an omnibus test that combines the results from analyzing multiple distance matrices. Our extensive simulations indicated that PERMANOVA-med always controlled the type I error and had compelling power over MedTest and MODIMA. Frequently, MedTest had diminished power and MODIMA had inflated type I error. Using real data on melanoma immunotherapy response, we demonstrated the wide applicability of PERMANOVA-med through 16 different mediation analyses, only 6 of which could be performed by MedTest and 4 by MODIMA.},
}
@article {pmid35741434,
year = {2022},
author = {Wolińska, A and Kruczyńska, A and Grządziel, J and Gałązka, A and Marzec-Grządziel, A and Szałaj, K and Kuźniar, A},
title = {Functional and Seasonal Changes in the Structure of Microbiome Inhabiting Bottom Sediments of a Pond Intended for Ecological King Carp Farming.},
journal = {Biology},
volume = {11},
number = {6},
pages = {},
doi = {10.3390/biology11060913},
pmid = {35741434},
issn = {2079-7737},
abstract = {The main goal of the study was to determine changes in the bacterial structure in bottom sediments occurring over the seasons of the year and to estimate microbial metabolic activity. Bottom sediments were collected four times in the year (spring, summer, autumn, and winter) from 10 different measurement points in Cardinal Pond (Ślesin, NW Poland). The Next-Generation Sequencing (MiSeq Illumina) and Community-Level Physiological Profiling techniques were used for identification of the bacterial diversity structure and bacterial metabolic and functional activities over the four seasons. It was evident that Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant phyla, while representatives of Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria predominated at the class level in the bottom sediments. An impact of the season on biodiversity and metabolic activity was revealed with the emphasis that the environmental conditions in summer modified the studied parameters most strongly. Carboxylic and acetic acids and carbohydrates were metabolized most frequently, whereas aerobic respiration I with the use of cytochrome C was the main pathway used by the microbiome of the studied bottom sediments.},
}
@article {pmid35741411,
year = {2022},
author = {Smirnova, M and Tafintseva, V and Kohler, A and Miamin, U and Shapaval, V},
title = {Temperature- and Nutrients-Induced Phenotypic Changes of Antarctic Green Snow Bacteria Probed by High-Throughput FTIR Spectroscopy.},
journal = {Biology},
volume = {11},
number = {6},
pages = {},
doi = {10.3390/biology11060890},
pmid = {35741411},
issn = {2079-7737},
support = {CPEA-LT-2016/10126, CPEA-STA-2019/10025.//Norwegian Agency for International Cooperation and Quality Enhancement in High Education/ ; },
abstract = {Temperature fluctuations and nutrient composition are the main parameters influencing green snow microbiome. In this study we investigated the influence of temperature and nutrient conditions on the growth and cellular chemical profile of bacteria isolated from green snow. Chemical profiling of the green snow bacteria was done by high-throughput FTIR spectroscopy combined with multivariate data analysis. We showed that temperature and nutrients fluctuations strongly affect growth ability and chemical profile of the green snow bacteria. The size of colonies for green snow bacteria grown at higher (25 °C) and lower (4 °C and 10 °C) than optimal temperature (18 °C) was smaller. All isolates grew on rich medium, and only 19 isolates were able to grow on synthetic minimal media. Lipid and mixed spectral regions showed to be phylogeny related. FTIR fingerprinting indicates that lipids are often affected by the temperature fluctuations. Growth on different media resulted in the change of the whole chemical profile, where lipids showed to be more affected than proteins and polysaccharides. Correlation analysis showed that nutrient composition is clearly strongly influencing chemical changes in the cells, followed by temperature.},
}
@article {pmid35741405,
year = {2022},
author = {Zhgun, AA and Potapov, MP and Avdanina, DA and Karpova, NV and Yaderets, VV and Dzhavakhiya, VV and Kardonsky, DA},
title = {Biotransformation of Androstenedione by Filamentous Fungi Isolated from Cultural Heritage Sites in the State Tretyakov Gallery.},
journal = {Biology},
volume = {11},
number = {6},
pages = {},
doi = {10.3390/biology11060883},
pmid = {35741405},
issn = {2079-7737},
abstract = {The transformation of steroids by microorganisms is widely used in medical biotechnology. A huge group of filamentous fungi is one of the most promising taxa for screening new biocatalytic reactions in order to obtain pharmaceutically significant steroids. In this work, we screened 10 filamentous fungi-destructors of egg tempera for the ability to biotransform androst-4-en-3,17-dione (AD) during cultivation in a liquid nutrient medium or in a buffer solution. These taxonomically unrelated strains, belonging to the classes Eurotiomycetes, Dothideomycetes and Sordariomycetes, are dominant representatives of the microbiome from halls where works of tempera painting are stored in the State Tretyakov Gallery (STG, Moscow, Russia). Since the binder of tempera paints, egg yolk, contains about 2% cholesterol, these degrading fungi appear to be a promising group for screening for steroid converting activity. It turned out that all the studied fungi-destructors are able to transform AD. Some strains showed transformation efficiency close to the industrial strain Curvularia lunata RNCIM F-981. In total, 33 steroids formed during the transformation of AD were characterized, for 19 of them the structure was established by gas chromatography/mass spectrometry analysis. In this work, we have shown for the first time that fungi-destructors of tempera paintings can efficiently transform steroids.},
}
@article {pmid35741032,
year = {2022},
author = {Islam, SMS and Ryu, HM and Sohn, S},
title = {Tetragenococcus halophilus Alleviates Intestinal Inflammation in Mice by Altering Gut Microbiota and Regulating Dendritic Cell Activation via CD83.},
journal = {Cells},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/cells11121903},
pmid = {35741032},
issn = {2073-4409},
support = {2017R1D1A1B03032168//National Research Foundation of Korea/ ; 2020R1A2C2012721//National Research Foundation of Korea/ ; 2019R1A6C1010003//Ministry of Education/ ; },
abstract = {Ulcerative colitis (UC) is one of the major subtypes of inflammatory bowel disease with unknown etiology. Probiotics have recently been introduced as a treatment for UC. Tetragenococcus halophilus (T. halophilus) is a lactic acid-producing bacterium that survives in environments with high salt concentrations, though little is known about its immunomodulatory function as a probiotic. The purpose of this study is to determine whether T. halophilus exerts an anti-inflammatory effect on intestinal inflammation in mice. Colitis was induced in C57BL/6J mice by feeding 4% DSS in drinking water for 7 days. T. halophilus was orally administered with DSS. Anti-inflammatory functions were subsequently evaluated by flow cytometry, qRT-PCT, and ELISA. Gut microbial composition was analyzed by 16S rRNA metagenomic analysis. DSS-induced colitis mice treated with T. halophilus showed less weight loss and significantly suppressed colonic shortening compared to DSS-induced colitis mice. T. halophilus significantly reduced the frequency of the dendritic cell activation molecule CD83 in peripheral blood leukocytes and intestinal epithelial lymphocytes. Frequencies of CD8+NK1.1+ cells decreased in mice with colitis after T. halophilus treatment and IL-1β levels were also reduced. Alteration of gut microbiota was observed in mice with colitis after administration of T. halophilus. These results suggest T. halophilus is effective in alleviating DSS-induced colitis in mice by altering immune regulation and gut microbiome compositions.},
}
@article {pmid35741028,
year = {2022},
author = {Amara, S and Yang, LV and Tiriveedhi, V and Muzaffar, M},
title = {Complex Role of Microbiome in Pancreatic Tumorigenesis: Potential Therapeutic Implications.},
journal = {Cells},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/cells11121900},
pmid = {35741028},
issn = {2073-4409},
abstract = {Pancreatic cancer (PC) is the fourth leading cause of cancer-related mortality with limited diagnostic and therapeutic options. Although immunotherapy has shown promise in the treatment of several cancers, its role in pancreatic cancer is rather limited. Several studies have focused on determining the role of the tumor microenvironment with cancer-cell-intrinsic events and tumor-infiltrating immune cellular properties. However, in the past decade, there has been emerging research aimed at delineating the role of the host microbiome, including the metabolites from microbes and host responses, on pancreatic tumorigenesis. Importantly, there is emerging evidence suggesting the beneficial role of a gut microbiome transplant to improve immunotherapeutic outcomes in cancer patients. In this review, we summarize the recent understanding of the role of the microbiome in pancreatic cancer progression, along with its clinical diagnostic and therapeutic implications.},
}
@article {pmid35741001,
year = {2022},
author = {Boubertakh, B and Silvestri, C and Di Marzo, V},
title = {Obesity: The Fat Tissue Disease Version of Cancer.},
journal = {Cells},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/cells11121872},
pmid = {35741001},
issn = {2073-4409},
support = {Not applicable//Canada Research Excellence Chair in the Microbiome-Endocannabinoidome Axis in Metabolic Health (CERC-MEND), which is funded by CIHR, NSERC, and SSHRC, to V.D./ ; },
abstract = {Obesity is a disease with high potential for fatality. It perfectly fits the disease definition, as cancer does. This is because it damages body structure and functions, both mechanically and biologically, and alters physical, mental, and social health. In addition, it shares many common morbid characteristics with the most feared disease, cancer. For example, it is influenced by a sophisticated interaction between a person's genetics, the environment, and an increasing number of other backgrounds. Furthermore, it displays abnormal cell growth and proliferation events, only limited to white fat, resulting in adipose tissue taking up an increasing amount of space within the body. This occurs through fat "metastases" and via altered signaling that further aggravates the pathology of obesity by inducing ubiquitous dishomeostasis. These metastases can be made graver by angiogenesis, which might boost diseased tissue growth. More common features with cancer include its progressive escalation through different levels of severity and its possibility of re-onset after recovery. Despite all these similarities with cancer, obesity is substantially less agitating for most people. Thus, the ideas proposed herein could have utility to sensitize the public opinion about the hard reality of obesity. This is increasingly needed, as the obesity pandemic has waged a fierce war against our bodies and society in general, while there is still doubt about whether it is a real disease or not. Hence, raising public consciousness to properly face health issues is crucial to improving our health instead of gaining weight unhealthily. It is obviously illogical to fight cancer extremely seriously on the one hand and to consider dying with obesity as self-inflicted on the other. In fact, obesity merits a top position among the most lethal diseases besides cancer.},
}
@article {pmid35740977,
year = {2022},
author = {Ngamsamer, C and Sirivarasai, J and Sutjarit, N},
title = {The Benefits of Anthocyanins against Obesity-Induced Inflammation.},
journal = {Biomolecules},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/biom12060852},
pmid = {35740977},
issn = {2218-273X},
abstract = {Obesity has become a serious public health epidemic because of its associations with chronic conditions such as type 2 diabetes mellitus, hypertension, cardiovascular disease, and cancer. Obesity triggers inflammation marked by the secretion of low-grade inflammatory cytokines including interleukin-6, C-reactive protein, and tumor necrosis factor-α, leading to a condition known as "meta-inflammation". Currently, there is great interest in studying the treatment of obesity with food-derived bioactive compounds, which have low toxicity and no severe adverse events compared with pharmacotherapeutic agents. Here, we reviewed the beneficial effects of the bioactive compounds known as anthocyanins on obesity-induced inflammation. Foods rich in anthocyanins include tart cherries, red raspberries, black soybeans, blueberries, sweet cherries, strawberries and Queen Garnet plums. These anthocyanin-rich foods have been evaluated in cell culture, animal, and clinical studies, and found to be beneficial for health, reportedly reducing inflammatory markers. One factor in the development of obesity-related inflammation may be dysbiosis of the gut microbiome. Therefore, we focused this review on the in vitro and in vivo effects of anthocyanins on inflammation and the gut microbiota in obesity.},
}
@article {pmid35740541,
year = {2022},
author = {Gamal, A and Elshaer, M and Alabdely, M and Kadry, A and McCormick, TS and Ghannoum, M},
title = {The Mycobiome: Cancer Pathogenesis, Diagnosis, and Therapy.},
journal = {Cancers},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/cancers14122875},
pmid = {35740541},
issn = {2072-6694},
support = {R01AI145289- 01A1/NH/NIH HHS/United States ; },
abstract = {Cancer is among the leading causes of death globally. Despite advances in cancer research, a full understanding of the exact cause has not been established. Recent data have shown that the microbiome has an important relationship with cancer on various levels, including cancer pathogenesis, diagnosis and prognosis, and treatment. Since most studies have focused only on the role of bacteria in this process, in this article we review the role of fungi-another important group of the microbiome, the totality of which is referred to as the "mycobiome"-in the development of cancer and how it can impact responses to anticancer medications. Furthermore, we provide recent evidence that shows how the different microbial communities interact and affect each other at gastrointestinal and non-gastrointestinal sites, including the skin, thereby emphasizing the importance of investigating the microbiome beyond bacteria.},
}
@article {pmid35740540,
year = {2022},
author = {Li, X and Wang, X and Huang, R and Stucky, A and Chen, X and Sun, L and Wen, Q and Zeng, Y and Fletcher, H and Wang, C and Xu, Y and Cao, H and Sun, F and Li, SC and Zhang, X and Zhong, JF},
title = {The Machine-Learning-Mediated Interface of Microbiome and Genetic Risk Stratification in Neuroblastoma Reveals Molecular Pathways Related to Patient Survival.},
journal = {Cancers},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/cancers14122874},
pmid = {35740540},
issn = {2072-6694},
support = {R01 CA251848/GF/NIH HHS/United States ; R01 CA197903/NH/NIH HHS/United States ; },
abstract = {Currently, most neuroblastoma patients are treated according to the Children's Oncology Group (COG) risk group assignment; however, neuroblastoma's heterogeneity renders only a few predictors for treatment response, resulting in excessive treatment. Here, we sought to couple COG risk classification with tumor intracellular microbiome, which is part of the molecular signature of a tumor. We determine that an intra-tumor microbial gene abundance score, namely M-score, separates the high COG-risk patients into two subpopulations (Mhigh and Mlow) with higher accuracy in risk stratification than the current COG risk assessment, thus sparing a subset of high COG-risk patients from being subjected to traditional high-risk therapies. Mechanistically, the classification power of M-scores implies the effect of CREB over-activation, which may influence the critical genes involved in cellular proliferation, anti-apoptosis, and angiogenesis, affecting tumor cell proliferation survival and metastasis. Thus, intracellular microbiota abundance in neuroblastoma regulates intracellular signals to affect patients' survival.},
}
@article {pmid35740457,
year = {2022},
author = {Zeber-Lubecka, N and Kulecka, M and Załęska-Oracka, K and Dąbrowska, M and Bałabas, A and Hennig, EE and Szymanek-Szwed, M and Mikula, M and Jurkiewicz, B and Ostrowski, J},
title = {Gene Expression-Based Functional Differences between the Bladder Body and Trigonal Urothelium in Adolescent Female Patients with Micturition Dysfunction.},
journal = {Biomedicines},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/biomedicines10061435},
pmid = {35740457},
issn = {2227-9059},
support = {501-1-068-31-20/MG3//Centre of Postgraduate Medical Education/ ; 501-1-009-12-20//Centre of Postgraduate Medical Education/ ; 2017/27/B/NZ5/01504//National Science Center/ ; },
abstract = {The aim of this study is to determine the molecular differences between the urothelial transcriptomes of the bladder body and trigone. The transcriptomes of the bladder body and trigonal epithelia were analyzed by massive sequencing of total epithelial RNA. The profiles of urothelial and urinal microbiomes were assessed by amplicon sequencing of bacterial 16S rRNA genes in 17 adolescent females with pain and micturition dysfunction and control female subjects. The RNA sequencing identified 10,261 differentially expressed genes (DEGs) in the urothelia of the bladder body and trigone, with the top 1000 DEGs at these locations annotated to 36 and 77 of the Reactome-related pathways in the bladder body and trigone, respectively. These pathways represented 11 categories enriched in the bladder body urothelium, including extracellular matrix organization, the neuronal system, and 15 categories enriched in the trigonal epithelium, including RHO GTPase effectors, cornified envelope formation, and neutrophil degranulation. Five bacterial taxa in urine differed significantly in patients and healthy adolescent controls. The evaluation of their transcriptomes indicated that the bladder body and trigonal urothelia were functionally different tissues. The molecular differences between the body and trigonal urothelia responsible for clinical symptoms in adolescents with bladder pain syndrome/interstitial cystitis remain unclear.},
}
@article {pmid35740320,
year = {2022},
author = {O-Sullivan, I and Natarajan Anbazhagan, A and Singh, G and Ma, K and Green, SJ and Singhal, M and Wang, J and Kumar, A and Dudeja, PK and Unterman, TG and Votta-Velis, G and Bruce, B and van Wijnen, AJ and Im, HJ},
title = {Lactobacillus acidophilus Mitigates Osteoarthritis-Associated Pain, Cartilage Disintegration and Gut Microbiota Dysbiosis in an Experimental Murine OA Model.},
journal = {Biomedicines},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/biomedicines10061298},
pmid = {35740320},
issn = {2227-9059},
support = {AR077890, DK54016, DK92441//National Institute of Health/ ; W81XWH-21-1-0549//United States Department of Defense/ ; I01BX002647, I01BX002011, I01BX001968//United States Department of Veterans Affairs/ ; IK6BX004477, IK6BX005242//United States Department of Veterans Affairs/ ; },
abstract = {To test probiotic therapy for osteoarthritis (OA), we administered Lactobacillus acidophilus (LA) by oral gavage (2×/week) after induction of OA by partial medial meniscectomy (PMM). Pain was assessed by von Frey filament and hot plate testing. Joint pathology and pain markers were comprehensively analyzed in knee joints, spinal cords, dorsal root ganglia and distal colon by Safranin O/fast green staining, immunofluorescence microscopy and RT-qPCR. LA acutely reduced inflammatory knee joint pain and prevented further OA progression. The therapeutic efficacy of LA was supported by a significant reduction of cartilage-degrading enzymes, pain markers and inflammatory factors in the tissues we examined. This finding suggests a likely clinical effect of LA on OA. The effect of LA treatment on the fecal microbiome was assessed by 16S rRNA gene amplicon sequencing analysis. LA significantly altered the fecal microbiota compared to vehicle-treated mice (PERMANOVA p < 0.009). Our pre-clinical OA animal model revealed significant OA disease modifying effects of LA as reflected by rapid joint pain reduction, cartilage protection, and reversal of dysbiosis. Our findings suggest that LA treatment has beneficial systemic effects that can potentially be developed as a safe OA disease-modifying drug (OADMD).},
}
@article {pmid35740264,
year = {2022},
author = {Yusuf, K and Saha, S and Umar, S},
title = {Health Benefits of Dietary Fiber for the Management of Inflammatory Bowel Disease.},
journal = {Biomedicines},
volume = {10},
number = {6},
pages = {},
doi = {10.3390/biomedicines10061242},
pmid = {35740264},
issn = {2227-9059},
support = {R01CA185322/CA/NCI NIH HHS/United States ; },
abstract = {Crohn's disease (CD) and ulcerative colitis (UC), two components of inflammatory bowel disease (IBD), are painful conditions that affect children and adults. Despite substantial research, there is no permanent cure for IBD, and patients face an increased risk of colon cancer. Dietary fiber's health advantages have been thoroughly investigated, and it is recommended for its enormous health benefits. This review article discusses the importance of appropriate fiber intake in managing IBD, emphasizing how optimal fiber consumption can significantly help IBD patients.},
}
@article {pmid35740186,
year = {2022},
author = {Melgarejo, T and Sharp, N and Krumbeck, JA and Wu, G and Kim, YJ and Linde, A},
title = {The Urinary Resistome of Clinically Healthy Companion Dogs: Potential One Health Implications.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {11},
number = {6},
pages = {},
doi = {10.3390/antibiotics11060780},
pmid = {35740186},
issn = {2079-6382},
abstract = {An interdisciplinary approach to antimicrobial resistance (AMR) is essential to effectively address what is projected to soon become a public health disaster. Veterinary medicine accounts for a majority of antimicrobial use, and mainly in support of industrial food animal production (IFAP), which has significant exposure implications for human and nonhuman animals. Companion dogs live in close proximity to humans and share environmental exposures, including food sources. This study aimed to elucidate the AMR-gene presence in microorganisms recovered from urine from clinically healthy dogs to highlight public health considerations in the context of a species-spanning framework. Urine was collected through cystocentesis from 50 companion dogs in Southern California, and microbial DNA was analyzed using next-generation sequencing. Thirteen AMR genes in urine from 48% of the dogs {n=24}
were detected. The most common AMR genes were aph(3')Ia, and ermB, which confer resistance to aminoglycosides and MLS (macrolides, lincosamides, streptogramins) antibiotics, respectively. Antibiotic-resistance profiles based on the AMR genes detected, and the intrinsic resistance profiles of bacterial species, were inferred in 24% of the samples {n=12}
for 57 species, with most belonging to Streptococcus, Staphylococcus, and Corynebacterium genera. The presence of AMR genes that confer resistance to medically important antibiotics suggests that dogs may serve as reservoirs of clinically relevant resistomes, which is likely rooted in excessive IFAP antimicrobial use.},
}
@article {pmid35740129,
year = {2022},
author = {Grada, A and Ghannoum, MA and Bunick, CG},
title = {Sarecycline Demonstrates Clinical Effectiveness against Staphylococcal Infections and Inflammatory Dermatoses: Evidence for Improving Antibiotic Stewardship in Dermatology.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {11},
number = {6},
pages = {},
doi = {10.3390/antibiotics11060722},
pmid = {35740129},
issn = {2079-6382},
abstract = {Tetracycline class antibiotics are widely used for multiple skin diseases, including acne vulgaris, acne rosacea, cutaneous infections, inflammatory dermatoses, and autoimmune blistering disorders. Concerns about antibiotic resistance and protecting the human/host microbiome beg the question whether broad-spectrum tetracyclines such as doxycycline and minocycline should be prescribed at such a high rate by dermatologists when a narrow-spectrum tetracycline derivative, sarecycline, exists. We evaluated the clinical effectiveness of oral sarecycline against cutaneous staphylococcal infections, eyelid stye, and mucous membrane pemphigoid to determine whether sarecycline is a viable option for clinicians to practice improved antibiotic stewardship. We observed significant improvement in staphylococcal infections and inflammatory dermatoses with courses of oral sarecycline as short as 9 days, with no reported adverse events. These clinical findings are consistent with in vitro microbiological data and anti-inflammatory properties of sarecycline. Our data provides a strong rationale for clinicians to use narrow-spectrum sarecycline rather than broad-spectrum tetracyclines as a first-line agent in treating staphylococcal skin infections and inflammatory skin diseases for which tetracyclines are currently commonly employed. Such advancement in the practice paradigm in dermatology will enhance antibiotic stewardship, reduce risk of antibiotic resistance, protect the human microbiome, and provide patients with precision medicine care.},
}
@article {pmid35739833,
year = {2022},
author = {Lucassen, A and Hankel, J and Finkler-Schade, C and Osbelt, L and Strowig, T and Visscher, C and Schuberth, HJ},
title = {Feeding a Saccharomyces cerevisiae Fermentation Product (Olimond BB) Does Not Alter the Fecal Microbiota of Thoroughbred Racehorses.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/ani12121496},
pmid = {35739833},
issn = {2076-2615},
abstract = {Feed supplements such as Saccharomyces cerevisiae fermentation products (SCFP) alter immune responses in horses. The purpose of this study was to analyze whether a prebiotic activity of the SCFP alters the gut microbiome in horses. Racehorses were fed either SCFP (Olimond BB, OLI, n = 6) or placebo pellets (PLA, n = 5) for 43 days. Fecal microbiota analysis was performed using 16S rRNA gene sequencing. The numbers and function of circulating immune cell subpopulations were analyzed by flow cytometry. SCFP supplementation resulted in non-consistent differences in fecal microbiota between the PLA and OLI during the feeding period. Rather, the individual animal had the highest impact on fecal microbiota composition. OLI and PLA horses displayed the same changes in numbers of blood leukocyte subpopulations over time. One day after a booster vaccination against equine influenza during the feeding period, the alpha diversity of fecal microbiota of PLA horses was significantly higher compared to OLI horses. This suggests that SCFP feeding altered the vaccination-induced spectrum of released mediators, potentially affecting gut microbiota. The overall non-consistent findings argue against a strong prebiotic effect of Olimond BB on the microbiota in racehorses. Fecal microbiota differences between the groups were also noticed outside the feeding period and, hence, are most likely not caused by the SCFP additive.},
}
@article {pmid35739814,
year = {2022},
author = {Kwasek, K and Patula, S and Wojno, M and Oliaro, F and Cabay, C and Pinnell, LJ},
title = {Does Exposure of Broodstock to Dietary Soybean Meal Affect Its Utilization in the Offspring of Zebrafish (Danio rerio)?.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/ani12121475},
pmid = {35739814},
issn = {2076-2615},
abstract = {Nutritional programming (NP) is a concept in which early nutritional events alter the physiology of an animal and its response to different dietary regimes later in life. The objective of this study was to determine if NP via broodstock with dietary plant protein (PP) has any effect on the gut microbiome of the progeny fish and whether this modified gut microbiome leads to better utilization of PP diet. The experiment consisted of four different treatments as follows: (1) progeny that received FM diet obtained from fishmeal (FM)-fed broodstock (FMBS-FM, +control); (2) progeny that received PP diet obtained from FM-fed parents (FMBS-PP); (3) progeny that received PP diet obtained from "nutritionally programmed" parents (PPBS-PP; -control); and (4) progeny that received FM diet obtained from "nutritionally programmed" parents (PPBS-FM). Zebrafish was used as a model species. This study found that parental programming seems to have some positive effect on dietary PP utilization in progeny. However, the influence of NP with PP through broodstock on gut microbiota of the offspring fish was not detected.},
}
@article {pmid35739812,
year = {2022},
author = {Zhang, X and Xu, H and Zhang, C and Bai, J and Song, J and Hao, B and Zhang, L and Xia, G},
title = {Effects of Vitamin A on Yanbian Yellow Cattle and Their Preadipocytes by Activating AKT/mTOR Signaling Pathway and Intestinal Microflora.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {12},
pages = {},
doi = {10.3390/ani12121477},
pmid = {35739812},
issn = {2076-2615},
support = {D20034//State Administration of Foreign Experts Affaris of the P.R.China/ ; 32160774//National Natural Science Foundation of China/ ; 20200402053NC//Jilin Science and Technology Development Plan/ ; Yanda Kehezi[2019] No.1//Yanbian University School-Enterprise Cooperation Project/ ; },
abstract = {In this study, the effects of vitamin A and its metabolite, all-trans retinoic acid (ATRA), on the proliferation and differentiation of preadipocytes and the intestinal microbiome in Yanbian yellow cattle were investigated. Preadipocytes collected from Yanbian yellow cattle treated with different concentrations of ATRA remained in the G1/G0 phase, as determined by flow cytometry. Quantitative reverse-transcription polymerase chain reaction and western blotting analyses showed that the mRNA and protein expression levels of key adipogenic factors, peroxisome proliferator- activated receptor gamma (PPARγ), CCAAT enhancer-binding protein α (C/EBPα), and extracellular signal-regulated kinase 2 (ERK2), decreased. ATRA was found to regulate the mTOR signaling pathway, which is involved in lipid metabolism, by inhibiting the expression of AKT2 and the adipogenic transcription factors SREBP1, ACC, and FAS; the protein and mRNA expression levels showed consistent trends. In addition, 16S rRNA sequencing results showed that a low concentration of vitamin A promoted the growth of intestinal microflora beneficial to lipid metabolism and maintained intestinal health. The results indicated that ATRA inhibited the adipogenic differentiation of preadipocytes from Yanbian yellow cattle through the AKT/mTOR signaling pathway, and that low concentrations of vitamin A may help maintain the intestinal microbes involved in lipid metabolism in cattle.},
}
@article {pmid35739571,
year = {2022},
author = {Münzker, J and Haase, N and Till, A and Sucher, R and Haange, SB and Nemetschke, L and Gnad, T and Jäger, E and Chen, J and Riede, SJ and Chakaroun, R and Massier, L and Kovacs, P and Ost, M and Rolle-Kampczyk, U and Jehmlich, N and Weiner, J and Heiker, JT and Klöting, N and Seeger, G and Morawski, M and Keitel, V and Pfeifer, A and von Bergen, M and Heeren, J and Krügel, U and Fenske, WK},
title = {Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {96},
pmid = {35739571},
issn = {2049-2618},
support = {IFB Adiposity Diseases//Bundesministerium für Bildung und Forschung/ ; 01EO1501//Bundesministerium für Bildung und Forschung/ ; TRR333/1, AOBJ: 450149205//Deutsche Forschungsgemeinschaft/ ; MO 2249/3-1//Deutsche Forschungsgemeinschaft/ ; TRR333/1, AOBJ: 450149205//Deutsche Forschungsgemeinschaft/ ; CRC1052//Deutsche Forschungsgemeinschaft/ ; SFB841-B6//Deutsche Forschungsgemeinschaft/ ; AOBJ: 624810//Deutsche Forschungsgemeinschaft/ ; TRR333/1, AOBJ: 450149205//Deutsche Forschungsgemeinschaft/ ; AFI #18072//Alzheimer Forschungsinitiative e.V./ ; FENSKE01//Else Kroener Fresenius Foundation/ ; },
abstract = {BACKGROUND: Bariatric surgery remains the most effective therapy for adiposity reduction and remission of type 2 diabetes. Although different bariatric procedures associate with pronounced shifts in the gut microbiota, their functional role in the regulation of energetic and metabolic benefits achieved with the surgery are not clear.<br><br>METHODS: To evaluate the causal as well as the inherent therapeutic character of the surgery-altered gut microbiome in improved energy and metabolic control in diet-induced obesity, an antibiotic cocktail was used to eliminate the gut microbiota in diet-induced obese rats after gastric bypass surgery, and gastric bypass-shaped gut microbiota was transplanted into obese littermates. Thorough metabolic profiling was combined with omics technologies on samples collected from cecum and plasma to identify adaptions in gut microbiota-host signaling, which control improved energy balance and metabolic profile after surgery.<br><br>RESULTS: In this study, we first demonstrate that depletion of the gut microbiota largely reversed the beneficial effects of gastric bypass surgery on negative energy balance and improved glucolipid metabolism. Further, we show that the gastric bypass-shaped gut microbiota reduces adiposity in diet-induced obese recipients by re-activating energy expenditure from metabolic active brown adipose tissue. These beneficial effects were linked to improved glucose homeostasis, lipid control, and improved fatty liver disease. Mechanistically, these effects were triggered by modulation of taurine metabolism by the gastric bypass gut microbiota, fostering an increased abundance of intestinal and circulating taurine-conjugated bile acid species. In turn, these bile acids activated gut-restricted FXR and systemic TGR5 signaling to stimulate adaptive thermogenesis.<br><br>CONCLUSION: Our results establish the role of the gut microbiome in the weight loss and metabolic success of gastric bypass surgery. We here identify a signaling cascade that entails altered bile acid receptor signaling resulting from a collective, hitherto undescribed change in the metabolic activity of a cluster of bacteria, thereby readjusting energy imbalance and metabolic disease in the obese host. These findings strengthen the rationale for microbiota-targeted strategies to improve and refine current therapies of obesity and metabolic syndrome. Video Abstract Bariatric Surgery (i.e. RYGB) or the repeated fecal microbiota transfer (FMT) from RYGB donors into DIO (diet-induced obesity) animals induces shifts in the intestinal microbiome, an effect that can be impaired by oral application of antibiotics (ABx). Our current study shows that RYGB-dependent alterations in the intestinal microbiome result in an increase in the luminal and systemic pool of Taurine-conjugated Bile acids (TCBAs) by various cellular mechanisms acting in the intestine and the liver. TCBAs induce signaling via two different receptors, farnesoid X receptor (FXR, specifically in the intestines) and the G-protein-coupled bile acid receptor TGR5 (systemically), finally resulting in metabolic improvement and advanced weight management. BSH, bile salt hydrolase; BAT brown adipose tissue.},
}
@article {pmid35739482,
year = {2022},
author = {Costa, D and Tavares, RM and Baptista, P and Lino-Neto, T},
title = {The influence of bioclimate on soil microbial communities of cork oak.},
journal = {BMC microbiology},
volume = {22},
number = {1},
pages = {163},
pmid = {35739482},
issn = {1471-2180},
support = {POCI-01-0145-FEDER-028635//FEDER funds through COMPETE (Programa Operacional Factores de Competitividade) and by national funds by FCT/ ; POCI-01-0145-FEDER-028635//FEDER funds through COMPETE (Programa Operacional Factores de Competitividade) and by national funds by FCT/ ; POCI-01-0145-FEDER-028635//FEDER funds through COMPETE (Programa Operacional Factores de Competitividade) and by national funds by FCT/ ; POCI-01-0145-FEDER-028635//FEDER funds through COMPETE (Programa Operacional Factores de Competitividade) and by national funds by FCT/ ; UIDB/04046/2020//Fundação para a Ciência e a Tecnologia/ ; UIDB/04046/2020//Fundação para a Ciência e a Tecnologia/ ; UID/AGR/00690/2020//Fundação para a Ciência e a Tecnologia/ ; UIDB/04046/2020//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {BACKGROUND: Soil microbiomes are important to maintain soil processes in forests and confer protection to plants against abiotic and biotic stresses. These microbiomes can be affected by environmental changes. In this work, soil microbial communities from different cork oak Portuguese forests under different edaphoclimatic conditions were described by using a metabarcoding strategy targeting ITS2 and 16S barcodes.<br><br>RESULTS: A total of 11,974 fungal and 12,010 bacterial amplicon sequence variants (ASVs) were obtained, revealing rich and diverse microbial communities associated with different cork oak forests. Bioclimate was described as the major factor influencing variability in these communities (or bioclimates/cork oak forest for fungal community), followed by boron and granulometry. Also, pH explained variation of fungal communities, while C:N ratio contributed to bacterial variation. Fungal and bacterial biomarker genera for specific bioclimates were described. Their co-occurrence network revealed the existence of a complex and delicate balance among microbial communities.<br><br>CONCLUSIONS: The findings revealed that bacterial communities are more likely to be affected by different edaphoclimatic conditions than fungal communities, also predicting a higher impact of climate change on bacterial communities. The integration of cork oak fungal and bacterial microbiota under different bioclimates could be further explored to provide information about useful interactions for increasing cork oak forest sustainability in a world subject to climate changes.},
}
@article {pmid35739345,
year = {2022},
author = {Sumithra, TG and Sharma, SRK and Gayathri, S and Ebeneezar, S and Reshma, KJ and Anikuttan, KK and Narasimapallavan, GI and Rameshkumar, P and Sakthivel, M and Prabu, DL and Tamilmani, G and Vijayagopal, P and Gopalakrishnan, A},
title = {Comparative evaluation of fish larval preservation methods on microbiome profiles to aid in metagenomics research.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {35739345},
issn = {1432-0614},
support = {BT/AAQ/3/SP29267/2018 dated 11/05/2020.//Department of Biotechnology, Ministry of Science and Technology, Government of India/ ; },
abstract = {Applications of microbiome research through metagenomics promise to generate microbiome manipulation strategies for improved larval survival in aquaculture. However, existing lacunae on the effects of sample preservation methods in metagenome profiles hinder the successful application of this technique. In this context, four preservation methods were scrutinized to identify reliable methods for fish larval microbiome research. The results showed that a total of ten metagenomics metrics, including DNA yield, taxonomic and functional microbiome profiles, and diversity measures, were significantly (P < 0.05) influenced by the preservation method. Activity ranking based on the performance and reproducibility showed that three methods, namely immediate direct freezing, room temperature preservation in absolute ethanol, and preservation at - 20 °C in lysis, storage, and transportation buffer, could be recommended for larval microbiome research. Furthermore, as there was an apparent deviation of the microbiome profiles of ethanol preserved samples at room temperature, the other methods are preferred. Detailed analysis showed that this deviation was due to the bias towards Vibrionales and Rhodobacterales. The microbial taxa responsible for the dissimilarity across different methods were identified. Altogether, the paper sheds light on the preservation protocols of fish larval microbiome research for the first time. The results can help in cross-comparison of future and past larval microbiome studies. Furthermore, this is the first report on the activity ranking of preservation methods based on metagenomics metrics. Apart from methodological perspectives, the paper provides for the first time certain insights into larval microbial profiles of Rachycentron canadum, a potential marine aquaculture species. KEY POINTS: • First report on effects of preservation methods on fish larval microbiome profiles. • First report on activity ranking of preservation methods based on metagenomics metrics. • Storage methods influenced DNA yield, taxonomic and functional microbiome profiles.},
}
@article {pmid35739325,
year = {2022},
author = {Legeay, J and Hijri, M},
title = {A Comprehensive Insight of Current and Future Challenges in Large-Scale Soil Microbiome Analyses.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {35739325},
issn = {1432-184X},
abstract = {In the last decade, various large-scale projects describing soil microbial diversity across large geographical gradients have been undertaken. However, many questions remain unanswered about the best ways to conduct these studies. In this review, we present an overview of the experience gathered during these projects, and of the challenges that future projects will face, such as standardization of protocols and results, considering the temporal variation of microbiomes, and the legal constraints limiting such studies. We also present the arguments for and against the exhaustive description of soil microbiomes. Finally, we look at future developments of soil microbiome studies, notably emphasizing the important role of cultivation techniques.},
}
@article {pmid35739218,
year = {2022},
author = {Broccanello, C and Ravi, S and Deb, S and Bolton, M and Secor, G and Richards, C and Maretto, L and Lucia, MCD and Bertoldo, G and Orsini, E and Ronquillo-López, MG and Concheri, G and Campagna, G and Squartini, A and Stevanato, P},
title = {Bacterial endophytes as indicators of susceptibility to Cercospora Leaf Spot (CLS) disease in Beta vulgaris L.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10719},
pmid = {35739218},
issn = {2045-2322},
abstract = {The fungus Cercospora beticola causes Cercospora Leaf Spot (CLS) of sugar beet (Beta vulgaris L.). Despite the global importance of this disease, durable resistance to CLS has still not been obtained. Therefore, the breeding of tolerant hybrids is a major goal for the sugar beet sector. Although recent studies have suggested that the leaf microbiome composition can offer useful predictors to assist plant breeders, this is an untapped resource in sugar beet breeding efforts. Using Ion GeneStudio S5 technology to sequence amplicons from seven 16S rRNA hypervariable regions, the most recurring endophytes discriminating CLS-symptomatic and symptomless sea beets (Beta vulgaris L.ssp. maritima) were identified. This allowed the design of taxon-specific primer pairs to quantify the abundance of the most representative endophytic species in large naturally occurring populations of sea beet and subsequently in sugar beet breeding genotypes under either CLS symptomless or infection stages using qPCR. Among the screened bacterial genera, Methylobacterium and Mucilaginibacter were found to be significantly (p < 0.05) more abundant in symptomatic sea beets with respect to symptomless. In cultivated sugar beet material under CLS infection, the comparison between resistant and susceptible genotypes confirmed that the susceptible genotypes hosted higher contents of the above-mentioned bacterial genera. These results suggest that the abundance of these species can be correlated with increased sensitivity to CLS disease. This evidence can further prompt novel protocols to assist plant breeding of sugar beet in the pursuit of improved pathogen resistance.},
}
@article {pmid35739206,
year = {2022},
author = {Anderson, KE and Maes, P},
title = {Social microbiota and social gland gene expression of worker honey bees by age and climate.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10690},
pmid = {35739206},
issn = {2045-2322},
support = {2022-21000-021-00D//Agricultural Research Service/ ; },
abstract = {Winter forage dearth is a major contributor to honey bee colony loss and can influence disease susceptibility. Honey bees possess a secretory head gland that interfaces with the social environment on many levels. During winter or forage dearth, colonies produce a long-lived (diutinus) worker phenotype that survives until environmental conditions improve. We used a known-age worker cohort to investigate microbiome integrity and social gene expression of workers in early and late winter. We provide additional context by contrasting host-microbial interactions from warm outdoor and cold indoor environments. Our results provide novel evidence that social immune gene expression is associated with worker longevity, and highlight the midgut as a target of opportunistic disease during winter. Host microbial interactions suggest opportunistic disease progression and resistance in long-lived workers, but susceptibility to opportunistic disease in younger workers that emerged during the winter, including increases in Enterobacteriaceae, fungal load and non-core bacterial abundance. The results are consistent with increased social immunity, including host associations with the social microbiota, and a social immune response by long-lived workers to combat microbial opportunism. The cost/benefit ratio associated with limited expression of the diutinus phenotype may be a strong determinant of colony survival during winter forage dearth.},
}
@article {pmid35739175,
year = {2022},
author = {Wong, OWH and Lam, AMW and Or, BPN and Mo, FYM and Shea, CKS and Lai, KYC and Ma, SL and Hung, SF and Chan, S and Kwong, TNY and Wong, S and Leung, PWL},
title = {Disentangling the relationship of gut microbiota, functional gastrointestinal disorders and autism: a case-control study on prepubertal Chinese boys.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10659},
pmid = {35739175},
issn = {2045-2322},
abstract = {Emerging evidence of an altered gut microbiome in autism spectrum disorder (ASD) suggests a pathomechanism through the gut-brain axis despite the inconsistent microbiome profile reported across studies. One of the knowledge gaps in the existing ASD microbiota studies is the lack of systematic exploration of the role of comorbid functional gastrointestinal disorder (FGID) in the association of ASD and altered gut microbiome. Consequently, 92 ASD and 112 age-matched typically developing (TD) boys were profiled on general psychopathology, FGID status by Rome IV classification, and gut microbiota using 16S ribosomal RNA amplicon sequencing at the V4 hypervariable region. Compared to TD, a significant decrease in the within-sample abundance of taxa was observed in ASD, regardless of FGID status. The microbiota of ASD FGID+ and ASD FGID- clustered apart from the TD groups. The microbiota of ASD FGID+ also showed qualitative differences from that of ASD FGID- and had the highest-level Firmicutes: Bacteroidetes ratio, which was paralleled by elevated levels of anxiety and overall psychopathology. The altered gastrointestinal microbiota composition in ASD appeared to be independent of comorbid FGID. Further studies should address how FGID may mediate neuropsychiatric symptoms in ASD through inflammation along the microbiota-gut-brain axis.},
}
@article {pmid35739018,
year = {2022},
author = {Carneiro, PV and Montenegro, NA and Lana, A and Amato, AA and Santos, GM},
title = {Lipids from gut microbiota: pursuing a personalized treatment.},
journal = {Trends in molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molmed.2022.06.001},
pmid = {35739018},
issn = {1471-499X},
abstract = {The discovery of microbiome metabolites has enlivened the field of fecal transplantation for therapeutic purposes. However, the transfer of pathogenic living organisms was recently observed to limit its therapeutic potential by increasing the risk of infection. Lipids produced by gut microbiota enter the circulation and control many phenotypic changes associated with microbiota composition. Fecal lipids significantly impact the regulation of several cell signaling pathways, including inflammation. Focusing on these molecules, we review how bioactive gut microbiota-associated lipids affect cellular functioning and clinical outcome. Here, we interrogate whether the gut microbiota can be considered a cutting-edge biotechnological tool for rapid metabolic engineering of meaningful lipids to offer a novel personalized therapy.},
}
@article {pmid35738801,
year = {2022},
author = {Lee, PC and Wu, CJ and Hung, YW and Lee, CJ and Chi, CT and Lee, IC and Yu-Lun, K and Chou, SH and Luo, JC and Hou, MC and Huang, YH},
title = {Gut microbiota and metabolites associate with outcomes of immune checkpoint inhibitor-treated unresectable hepatocellular carcinoma.},
journal = {Journal for immunotherapy of cancer},
volume = {10},
number = {6},
pages = {},
doi = {10.1136/jitc-2022-004779},
pmid = {35738801},
issn = {2051-1426},
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) are promising agents for unresectable hepatocellular carcinoma (uHCC), but lack effective biomarker to predict outcomes. The gut microbiome can modulate tumor response to immunotherapy, but its effect on HCC remains unclear.<br><br>METHODS: From May 2018 to February 2020, patients receiving ICI treatment for uHCC were prospectively enrolled; their fecal samples were collected before treatment. The fecal microbiota and metabolites were analyzed from 20 patients with radiology-proven objective responses (OR) and 21 randomly selected patients with progressive disease (PD). After March 2020, 33 consecutive Child-Pugh-A patients were recruited as a validation cohort. Additionally, feces from 17 healthy volunteers were collected for comparison of background microbes.<br><br>RESULTS: A significant dissimilarity was observed in fecal bacteria between patients with OR and patients with PD before immunotherapy. Prevotella 9 was enriched in patients with PD, whereas Lachnoclostridium, Lachnospiraceae, and Veillonella were predominant in patients with OR. Ursodeoxycholic acid and ursocholic acid were significantly enriched in the feces of patients with OR and strongly correlated with the abundance of Lachnoclostridium. The coexistence of Lachnoclostridium enrichment and Prevotella 9 depletion significantly predicted better overall survival (OS). In the validation cohort, better progression-free survival (PFS) and OS were noted in patients who had a preferable microbial signature in comparison with counter-group (PFS: 8.8 months vs 1.8 months; OS: not reached vs 6.5 months, both p<0.001).<br><br>CONCLUSIONS: Fecal microbiota and bile acids were associated with outcomes of immunotherapy for uHCC. These findings highlight the potential role of gut microbiota and metabolites as biomarkers to predict outcomes of ICI-treated HCC.},
}
@article {pmid35738342,
year = {2022},
author = {Xu, A and Zhao, Y and Shi, Y and Zuo, X and Yang, Y and Wang, Y and Xu, P},
title = {Effects of oxidation-based tea processing on the characteristics of the derived polysaccharide conjugates and their regulation of intestinal homeostasis in DSS-induced colitis mice.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijbiomac.2022.06.115},
pmid = {35738342},
issn = {1879-0003},
abstract = {Different cultivars and processing technologies involved in producing tea result in the high heterogeneity of derived polysaccharide conjugates, which limits the understanding of their composition and structure, and biological activity. Here, raw tea leaves from the same cultivar were used to produce dried fresh tea leaves, green tea, and black tea, and three polysaccharide conjugates derived from dried fresh tea leaves (FTPS), green tea (GTPS), and black tea (BTPS) were prepared accordingly. Their physiochemical characteristics and bioactivities were investigated. The results showed that the oxidation during tea processing increased the phenolics and proteins while decreasing the GalA in the derived TPS conjugates; meanwhile, it reduced the molecular weight and particle size of BTPS but enhanced their antioxidant activity in vitro. Furthermore, all three TPS conjugates improved intestinal homeostasis by reducing TJ protein loss and inflammation and alleviated DSS-induced colitis symptoms in mice. In addition, the three TPS conjugates showed differential regulation of the intestinal microbiome and altered the produced SCFAs, which contributed to the prevention of colitis. Our findings suggest that TPS conjugates could be applied in colitis prevention in association with the regulation of gut microbiota, and their efficacy could be optimized by employing suitable tea processing technologies.},
}
@article {pmid35738203,
year = {2022},
author = {Wang, Q and Huang, J and Liu, S and Wang, C and Jin, Y and Lai, H and Tu, W},
title = {Aberrant hepatic lipid metabolism associated with gut microbiota dysbiosis triggers hepatotoxicity of novel PFOS alternatives in adult zebrafish.},
journal = {Environment international},
volume = {166},
number = {},
pages = {107351},
doi = {10.1016/j.envint.2022.107351},
pmid = {35738203},
issn = {1873-6750},
abstract = {Perfluorooctane sulfonate (PFOS) has been reported to induce hepatotoxicity in wildlife and humans. Novel PFOS alternatives have been widely used following restrictions on PFOS, but little is known about their potential toxicity. Here, the first comprehensive investigation on the chronic hepatotoxicity and underlying molecular mechanisms of PFOS, 6:2Cl-PFESA (F-53B), and sodium p-perfluorous nonenoxybenzene sulfonate (OBS) was carried out on adult zebrafish through a histopathological examination, biochemical measurement, and multi-omics analysis. PFOS and its alternatives caused changes in liver histopathology and liver function indices in the order of F-53B > PFOS > OBS, which was consistent with their concentration in the liver. In silico modeling and transcriptional profiles suggested that the aberrant hepatic lipid metabolism induced by F-53B and PFOS was initiated by the action on peroxisome proliferator-activated receptor γ (PPARγ), which triggered changes in downstream genes transcription and led to an imbalance between lipid synthesis and expenditure. Gut microbiome analysis provided another novel mechanistic perspective that changes in the abundance of Legionella, Ralstonia, Brevundimonas, Alphaproteobacteria, Plesiomonas, and Hyphomicrobium might link to alterations in the PPAR pathway based on their significant correlation. This study provides insight into the molecular mechanisms of hepatotoxicity induced by PFOS and its novel alternatives and highlights the need for concern about their environmental exposure risks.},
}
@article {pmid35738062,
year = {2022},
author = {Feng, LA and Liang, B and Zeng, X and Shi, C and Yin, H and Feng, Y and Chen, Y and Yu, Q},
title = {Engineered bacterium-binding protein promotes root recruitment of functional bacteria for enhanced cadmium removal from wastewater by phytoremediation.},
journal = {Water research},
volume = {221},
number = {},
pages = {118746},
doi = {10.1016/j.watres.2022.118746},
pmid = {35738062},
issn = {1879-2448},
abstract = {Functional bacteria promote the efficiency of phytoremediation by enhancing plant growth and participating in decontamination. However, their activity is frequently compromised by the weakness of their interaction with plant roots. In this study, we designed the artificial protein LcGC composed of a bacterium-binding domain, a GFP fluorescence reporter, and a carbohydrate-binding domain to function as a physical contact between functional bacteria and plant roots. This protein was then expressed in an engineered yeast cell factory and extracted to assess its effect on rhizosphere microbiome composition, plant growth, and cadmium removal in a simulated phytoremediation system containing the remediation plant Lemna minor and the functional heavy metal-capturing bacteria Cupriavidus taiwanensis and Pseudomonas putida. LcGC efficiently bound bacterial cell wall components and glucan, endowing it high efficiency to bind both functional bacteria and plant roots. Scanning microscopy and microbiome analysis revealed that LcGC enhanced root recruitment and colonization of functional bacteria on the root surfaces. Furthermore, LcGC with the aid of single C. taiwanensis or of C. taiwanensis and P. putida in combination promoted plant growth, enhanced tolerance to cadmium-induced oxidative stress, and consequently improved cadmium-removing capacity of the plants, with the percent of cadmium removal reaching up to 91% for LcGC plus C. taiwanensis, and to 96% for LcGC plus C. taiwanensis and P. putida on day 7. This study provided a physical contact-based strategy to enhance the interaction between functional microbes and plant roots for efficient phytoremediation.},
}
@article {pmid35737975,
year = {2022},
author = {Singh, D and Agusti, A and Martinez, FJ and Papi, A and Pavord, ID and Wedzicha, JA and Vogelmeier, CF and Halpin, DMG},
title = {Blood Eosinophils and Chronic Obstructive Pulmonary Disease: A GOLD Science Committee 2022 Review.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.202201-0209PP},
pmid = {35737975},
issn = {1535-4970},
abstract = {COPD is a heterogeneous condition. Some patients benefit from treatment with inhaled corticosteroids (ICS) but this requires a precision medicine approach, based on clinical characteristics (phenotyping) and biological information (endotyping) in order to select patients most likely to benefit. The GOLD 2019 report recommended using exacerbation history combined with blood eosinophil counts (BEC) to identify such patients. Importantly, the relationship between BEC and ICS effects is continuous; no / small effects are observed at lower BEC, with increasing effects at higher BEC. The GOLD 2022 report has added additional evidence and recommendations concerning the use of BEC in COPD in clinical practice. Notably, associations have been demonstrated in COPD patients between higher BEC and increased levels of type-2 inflammation in the lungs. These differences in type-2 inflammation can explain the differential ICS response according to BEC. Additionally, lower BEC are associated with greater presence of proteobacteria, notably haemophilus, and increased bacterial infections and pneumonia risk. These observations support management strategies that use BEC to help identify subgroups with increased ICS response (higher BEC) or increased risk of bacterial infection (lower BEC). Recent studies in younger individuals without COPD have also shown that higher BEC are associated with increased risk of FEV1 decline and the development of COPD. Here we discuss and summarise the GOLD 2022 recommendations concerning the use of BEC as a biomarker that can facilitate a personalised management approach in COPD.},
}
@article {pmid35737931,
year = {2022},
author = {Zarei, M and Lee, G and Lee, SG and Cho, K},
title = {Advances in Biodegradable Electronic Skin: Material Progress and Recent Applications in Sensing, Robotics, and Human-Machine Interfaces.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e2203193},
doi = {10.1002/adma.202203193},
pmid = {35737931},
issn = {1521-4095},
abstract = {The rapid growth of the electronics industry and proliferation of electronic materials and telecommunications technologies has led to the release of a massive amount of untreated electronic waste (e-waste) into the environment. Consequently, catastrophic environmental damage at the microbiome level and serious human health diseases threaten the natural fate of our planet. Currently, the demand for wearable and flexible electronics for applications in personalized medicine, electronic skins (e-skin), and health monitoring platforms is substantial and growing. Therefore, "green" characteristics such as biodegradability, self-healing behavior, and biocompatibility ensure the future application of wearable electronics and e-skins in biomedical engineering and bioanalytical sciences. Leveraging the biodegradability, sustainability, and biocompatibility of natural materials will dramatically influence the fabrication of environmentally friendly e-skins and wearable electronics. Here, the molecular and structural characteristics of biological skins and artificial e-skins are discussed. The focus then turns to the biodegradable materials, including natural and synthetic polymer-based materials, and their most recent applications in the development of biodegradable e-skin in wearable sensors, robotics, and human-machine interfaces (HMIs). Finally, the main challenges and outlook regarding the preparation and application of biodegradable e-skins are critically discussed in a near-future scenario, which is expected to lead to the next generation of biodegradable e-skins and electronics. This article is protected by copyright. All rights reserved.},
}
@article {pmid35737929,
year = {2022},
author = {Moreira, L and Guimarães, NM and Pereira, S and Santos, RS and Loureiro, JA and Pereira, MC and Azevedo, NF},
title = {Liposome Delivery of Nucleic Acids in Bacteria: Toward In Vivo Labeling of Human Microbiota.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.1c00601},
pmid = {35737929},
issn = {2373-8227},
abstract = {Development of specific probes to study the in vivo spatial distribution of microorganisms is essential to understand the ecology of human microbiota. Herein, we assess the possibility of using liposomes loaded with fluorescently labeled nucleic acid mimics (LipoNAMs) to image Gram-negative and Gram-positive bacteria. We proved that liposome fusion efficiencies were similar in both Gram-negative and Gram-positive bacteria but that the efficiency was highly dependent on the lipid concentration. Notably, LipoNAMs were significantly more effective for the internalization of oligonucleotides in bacteria than the fixation/permeabilization methods commonly used in vitro. Furthermore, a structural and morphological assessment of the changes on bacteria allowed us to observe that liposomes increased the permeability of the cell envelope especially in Gram-negative bacteria. Considering the delivery efficiency and permeabilization effect, lipid concentrations of approximately 5 mM should be selected to maximize the detection of bacteria without compromising the bacterial cellular structure.},
}
@article {pmid35737868,
year = {2022},
author = {Rungjang, A and Meephansan, J and Payungporn, S and Sawaswong, V and Chanchaem, P and Pureesrisak, P and Wongpiyabovorn, J and Thio, HB},
title = {Alteration of gut microbiota during narrowband ultraviolet B therapy: A preliminary study.},
journal = {Experimental dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/exd.14631},
pmid = {35737868},
issn = {1600-0625},
abstract = {BACKGROUND: Gut microbiome dysbiosis is associated with psoriasis development. A relationship between gut microbiota and psoriasis treatment response has been reported. No study has reported the effect of narrowband ultraviolet B (NBUVB) therapy, a standard treatment of psoriasis, on gut microbiota.<br><br>QUESTION ADDRESSED: This study aimed to evaluate gut microbiota change during NBUVB therapy.<br><br>EXPERIMENTAL DESIGN: Stool samples from 22 participants, including 13 patients with chronic plaque psoriasis and nine healthy controls, were recruited. Fecal microbiota composition was analyzed using 16S rRNA sequencing before and after NBUVB therapy. Serum 25-OH Vitamin D of patients with psoriasis was evaluated simultaneously.<br><br>RESULTS: The most abundant phyla of gut microbiota in patients with psoriasis were Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria in all participants. Bilophila, Paraprevotella, Alistipes, Sutterella, Romboutsia, Clostridium sensu stricto, and Agathobacter are significantly more enriched in healthy controls. Lactobacillales and Ruminococus torques appeared more enriched after NBUVB treatment in responders but not non-responders. Serum Vitamin D levels significantly increased after NBUVB treatment.<br><br>CONCLUSIONS&amp;PERSPECTIVE: The present study revealed that gut microbiota altered after NBUVB treatment. The change might be treatment-specific and influence the treatment response.},
}
@article {pmid35737518,
year = {2022},
author = {Fiege, JK and Langlois, RA},
title = {Embracing the heterogeneity of natural viruses in mouse studies.},
journal = {The Journal of general virology},
volume = {103},
number = {6},
pages = {},
doi = {10.1099/jgv.0.001758},
pmid = {35737518},
issn = {1465-2099},
abstract = {Animal models are a critical tool in modern biology. To increase reproducibility and to reduce confounding variables modern animal models exclude many microbes, including key natural commensals and pathogens. Here we discuss recent strategies to incorporate a natural microbiota to laboratory mouse models and the impacts the microbiota has on immune responses, with a focus on viruses.},
}
@article {pmid35736871,
year = {2022},
author = {Lee, HS and Jo, HH and Kim, KW and Shin, BS and Kang, HG},
title = {Atypical Cognitive Impairment and Recovery in Two Colorectal Cancer Patients.},
journal = {Tomography (Ann Arbor, Mich.)},
volume = {8},
number = {3},
pages = {1503-1508},
doi = {10.3390/tomography8030123},
pmid = {35736871},
issn = {2379-139X},
support = {2022//Jeonbuk National University/ ; },
abstract = {Cognitive impairment in cancer patients can be caused by various factors; in approximately 30% of cancer patients, the symptoms appear before starting treatment. Paraneoplastic limbic encephalitis (PLE) is a rare disease associated with an autoimmune response, and is characterized by memory loss, depression, and personality changes; it is one of the potential causes of cognitive dysfunction in cancer patients. Two patients were previously diagnosed with mild cognitive impairment and maintained clinical stability; after suffering a rapid change in personality and sudden cognitive decline, colorectal cancer was diagnosed within a few months. The patients did not meet the diagnostic criteria for PLE in several tests. The symptoms improved after the underlying cancer was treated, and the patients returned to their previous stable state. Sudden cognitive impairment may appear as an early cancer symptom, and PLE is considered an atypical cause for these symptoms. However, in patients with unexplained PLE-like symptoms who do not meet the diagnostic criteria for PLE, probable etiologies to be considered are the gut-brain connection, CD8+ T-cell-mediated limbic encephalitis, and somatic mutations in dementia-related genes. Currently, few studies have investigated these symptoms, and further research will offer significant therapeutic strategies for cognitive impairment in cancer patients.},
}
@article {pmid35736648,
year = {2022},
author = {Vojdani, A and Vojdani, E and Rosenberg, AZ and Shoenfeld, Y},
title = {The Role of Exposomes in the Pathophysiology of Autoimmune Diseases II: Pathogens.},
journal = {Pathophysiology : the official journal of the International Society for Pathophysiology},
volume = {29},
number = {2},
pages = {243-280},
doi = {10.3390/pathophysiology29020020},
pmid = {35736648},
issn = {1873-149X},
abstract = {In our continuing examination of the role of exposomes in autoimmune disease, we use this review to focus on pathogens. Infections are major contributors to the pathophysiology of autoimmune diseases through various mechanisms, foremost being molecular mimicry, when the structural similarity between the pathogen and a human tissue antigen leads to autoimmune reactivity and even autoimmune disease. The three best examples of this are oral pathogens, SARS-CoV-2, and the herpesviruses. Oral pathogens reach the gut, disturb the microbiota, increase gut permeability, cause local inflammation, and generate autoantigens, leading to systemic inflammation, multiple autoimmune reactivities, and systemic autoimmunity. The COVID-19 pandemic put the spotlight on SARS-CoV-2, which has been called "the autoimmune virus." We explore in detail the evidence supporting this. We also describe how viruses, in particular herpesviruses, have a role in the induction of many different autoimmune diseases, detailing the various mechanisms involved. Lastly, we discuss the microbiome and the beneficial microbiota that populate it. We look at the role of the gut microbiome in autoimmune disorders, because of its role in regulating the immune system. Dysbiosis of the microbiota in the gut microbiome can lead to multiple autoimmune disorders. We conclude that understanding the precise roles and relationships shared by all these factors that comprise the exposome and identifying early events and root causes of these disorders can help us to develop more targeted therapeutic protocols for the management of this worldwide epidemic of autoimmunity.},
}
@article {pmid35736613,
year = {2022},
author = {Baranwal, M and Clark, RL and Thompson, J and Sun, Z and Hero, AO and Venturelli, OS},
title = {Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
doi = {10.7554/eLife.73870},
pmid = {35736613},
issn = {2050-084X},
support = {R35GM124774/NH/NIH HHS/United States ; W911NF1910269//Army Research Office/ ; R01 EB030340/EB/NIBIB NIH HHS/United States ; },
abstract = {Predicting the dynamics and functions of microbiomes constructed from the bottom-up is a key challenge in exploiting them to our benefit. Current models based on ecological theory fail to capture complex community behaviors due to higher order interactions, do not scale well with increasing complexity and in considering multiple functions. We develop and apply a long short-term memory (LSTM) framework to advance our understanding of community assembly and health-relevant metabolite production using a synthetic human gut community. A mainstay of recurrent neural networks, the LSTM learns a high dimensional data-driven non-linear dynamical system model. We show that the LSTM model can outperform the widely used generalized Lotka-Volterra model based on ecological theory. We build methods to decipher microbe-microbe and microbe-metabolite interactions from an otherwise black-box model. These methods highlight that Actinobacteria, Firmicutes and Proteobacteria are significant drivers of metabolite production whereas Bacteroides shape community dynamics. We use the LSTM model to navigate a large multidimensional functional landscape to design communities with unique health-relevant metabolite profiles and temporal behaviors. In sum, the accuracy of the LSTM model can be exploited for experimental planning and to guide the design of synthetic microbiomes with target dynamic functions.},
}
@article {pmid35736471,
year = {2022},
author = {Kar, SK and Te Pas, MFW and Kruijt, L and Vervoort, JJM and Jansman, AJM and Schokker, D},
title = {Sanitary Conditions on the Farm Alters Fecal Metabolite Profile in Growing Pigs.},
journal = {Metabolites},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/metabo12060538},
pmid = {35736471},
issn = {2218-1989},
support = {"Breed&amp;Feed4Food" (TKI-AF-14215)//TKI Agri &amp; Food/ ; "Feed4Foodure" (TKI-AF-16123)//TKI Agri &amp; Food/ ; },
abstract = {The aim of this study was to use fecal metabolite profiling to evaluate the effects of contrasting sanitary conditions and the associated subclinical health status of pigs. We analyzed fecal metabolite profiles by nuclear magnetic resonance (1H NMR) from pigs aged 14 and 22 weeks. Pigs kept under low and high sanitary conditions differed in fecal metabolites related to the degradation of dietary starch, metabolism of the gut microbiome, and degradation of components of animal (host) origin. The metabolites that differed significantly (FDR < 0.1) were from metabolic processes involved in either maintaining nutrient digestive capacity, including purine metabolism, energy metabolism, bile acid breakdown and recycling, or immune system metabolism. The results show that the fecal metabolite profiles reflect the sanitary conditions under which the pigs are kept. The fecal metabolite profiles closely resembled the profiles of metabolites found in the colon of pigs. Fecal valerate and kynurenic acid could potentially be used as "non-invasive" biomarkers of immune or inflammatory status that could form the basis for monitoring subclinical health status in pigs.},
}
@article {pmid35736470,
year = {2022},
author = {Deutsch, L and Debevec, T and Millet, GP and Osredkar, D and Opara, S and Šket, R and Murovec, B and Mramor, M and Plavec, J and Stres, B},
title = {Urine and Fecal 1H-NMR Metabolomes Differ Significantly between Pre-Term and Full-Term Born Physically Fit Healthy Adult Males.},
journal = {Metabolites},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/metabo12060536},
pmid = {35736470},
issn = {2218-1989},
support = {research project J3-7536//Slovenian Research Agency/ ; grant no. P1-0242//Slovenian Research Agency/ ; Grant No-TP20140088//Ljubljana University Medical Centre/ ; MR+ (SRA R#51867)//Slovenian Research Agency/ ; grant no. P2-0095//Slovenian Research Agency/ ; },
abstract = {Preterm birth (before 37 weeks gestation) accounts for ~10% of births worldwide and remains one of the leading causes of death in children under 5 years of age. Preterm born adults have been consistently shown to be at an increased risk for chronic disorders including cardiovascular, endocrine/metabolic, respiratory, renal, neurologic, and psychiatric disorders that result in increased death risk. Oxidative stress was shown to be an important risk factor for hypertension, metabolic syndrome and lung disease (reduced pulmonary function, long-term obstructive pulmonary disease, respiratory infections, and sleep disturbances). The aim of this study was to explore the differences between preterm and full-term male participants' levels of urine and fecal proton nuclear magnetic resonance (1H-NMR) metabolomes, during rest and exercise in normoxia and hypoxia and to assess general differences in human gut-microbiomes through metagenomics at the level of taxonomy, diversity, functional genes, enzymatic reactions, metabolic pathways and predicted gut metabolites. Significant differences existed between the two groups based on the analysis of 1H-NMR urine and fecal metabolomes and their respective metabolic pathways, enabling the elucidation of a complex set of microbiome related metabolic biomarkers, supporting the idea of distinct host-microbiome interactions between the two groups and enabling the efficient classification of samples; however, this could not be directed to specific taxonomic characteristics.},
}
@article {pmid35736458,
year = {2022},
author = {Kim, KS and Lee, Y and Chae, W and Cho, JY},
title = {An Improved Method to Quantify Short-Chain Fatty Acids in Biological Samples Using Gas Chromatography-Mass Spectrometry.},
journal = {Metabolites},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/metabo12060525},
pmid = {35736458},
issn = {2218-1989},
support = {NRF-2016M3A9B6902851//Bio &amp; Medical Technology Development Program of the National Research Foundation/ ; 20013712//Ministry of Science &amp; ICT and the Technology Innovation Program/ ; },
abstract = {Gut microbial metabolites, short-chain fatty acids (SCFAs), are found at multiple locations in the host body and are identified as important metabolites in gut microbiome-associated diseases. Quantifying SCFAs in diverse biological samples is important to understand their roles in host health. This study developed an accurate SCFA quantification method by performing gas chromatography-mass spectrometry (GC/MS) in human plasma, serum, feces, and mouse cecum tissue. The samples were acidified with hydrochloric acid, and the SCFAs were extracted using methyl tert-butyl ether. In this method, distilled water was selected as a surrogate matrix for the quantification of SCFAs in target biological samples. The method was validated in terms of linearity, parallelism, precision, recovery, and matrix effect. The developed method was further applied in target biological samples. In conclusion, this optimized method can be used as a simultaneous SCFA quantification method in diverse biological samples.},
}
@article {pmid35736447,
year = {2022},
author = {Teunis, C and Nieuwdorp, M and Hanssen, N},
title = {Interactions between Tryptophan Metabolism, the Gut Microbiome and the Immune System as Potential Drivers of Non-Alcoholic Fatty Liver Disease (NAFLD) and Metabolic Diseases.},
journal = {Metabolites},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/metabo12060514},
pmid = {35736447},
issn = {2218-1989},
support = {2021T055//Hartstichting/ ; },
abstract = {The prevalence of non-alcoholic fatty liver disease (NAFLD) is increasing and therefore is its burden of disease as NALFD is a risk factor for cirrhosis and is associated with other metabolic conditions such as type II diabetes, obesity, dyslipidaemia and atherosclerosis. Linking these cardiometabolic diseases is a state of low-grade inflammation, with higher cytokines and c-reactive protein levels found in individuals with NAFLD, obesity and type II diabetes. A possible therapeutic target to decrease this state of low-grade inflammation is the metabolism of the essential amino-acid tryptophan. Its three main metabolic pathways (kynurenine pathway, indole pathway and serotonin/melatonin pathway) result in metabolites such as kynurenic acid, xanturenic acid, indole-3-propionic acid and serotonin/melatonin. The kynurenine pathway is regulated by indoleamine 2,3-dioxygenase (IDO), an enzyme that is upregulated by pro-inflammatory molecules such as INF, IL-6 and LPS. Higher activity of IDO is associated with increased inflammation and fibrosis in NAFLD, as well with increased glucose levels, obesity and atherosclerosis. On the other hand, increased concentrations of the indole pathway metabolites, regulated by the gut microbiome, seem to result in more favorable outcomes. This narrative review summarizes the interactions between tryptophan metabolism, the gut microbiome and the immune system as potential drivers of cardiometabolic diseases in NAFLD.},
}
@article {pmid35736422,
year = {2022},
author = {Adolf, LA and Heilbronner, S},
title = {Nutritional Interactions between Bacterial Species Colonising the Human Nasal Cavity: Current Knowledge and Future Prospects.},
journal = {Metabolites},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/metabo12060489},
pmid = {35736422},
issn = {2218-1989},
support = {TTU 08.708//German Center for Infection Research/ ; EXC 2124//Deutsche Forschungsgemeinschaft/ ; },
abstract = {The human nasal microbiome can be a reservoir for several pathogens, including Staphylococcus aureus. However, certain harmless nasal commensals can interfere with pathogen colonisation, an ability that could be exploited to prevent infection. Although attractive as a prophylactic strategy, manipulation of nasal microbiomes to prevent pathogen colonisation requires a better understanding of the molecular mechanisms of interaction that occur between nasal commensals as well as between commensals and pathogens. Our knowledge concerning the mechanisms of pathogen exclusion and how stable community structures are established is patchy and incomplete. Nutrients are scarce in nasal cavities, which makes competitive or mutualistic traits in nutrient acquisition very likely. In this review, we focus on nutritional interactions that have been shown to or might occur between nasal microbiome members. We summarise concepts of nutrient release from complex host molecules and host cells as well as of intracommunity exchange of energy-rich fermentation products and siderophores. Finally, we discuss the potential of genome-based metabolic models to predict complex nutritional interactions between members of the nasal microbiome.},
}
@article {pmid35736405,
year = {2022},
author = {Setyabrata, D and Vierck, K and Sheets, TR and Legako, JF and Cooper, BR and Johnson, TA and Kim, YHB},
title = {Characterizing the Flavor Precursors and Liberation Mechanisms of Various Dry-Aging Methods in Cull Beef Loins Using Metabolomics and Microbiome Approaches.},
journal = {Metabolites},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/metabo12060472},
pmid = {35736405},
issn = {2218-1989},
support = {2017-67017-26475//United States Department of Agriculture/ ; },
abstract = {The objective of this study was to characterize and compare the dry-aging flavor precursors and their liberation mechanisms in beef aged with different methods. Thirteen paired loins were collected at 5 days postmortem, divided into four sections, and randomly assigned into four aging methods (wet-aging (WA), conventional dry-aging (DA), dry-aging in a water-permeable bag (DWA), and UV-light dry-aging (UDA)). All sections were aged for 28 days at 2 °C, 65% RH, and a 0.8 m/s airflow before trimming and sample collection for chemical, metabolomics, and microbiome analyses. Higher concentrations of free amino acids and reducing sugars were observed in all dry-aging samples (p < 0.05). Similarly, metabolomics revealed greater short-chain peptides in the dry-aged beef (p < 0.05). The DWA samples had an increase in polyunsaturated free fatty acids (C18:2trans, C18:3n3, C20:2, and C20:5; p < 0.05) along with higher volatile compound concentrations compared to other aging methods (aldehyde, nonanal, octanal, octanol, and carbon disulfide; p < 0.05). Microbiome profiling identified a clear separation in beta diversity between dry and wet aging methods. The Pseudomonas spp. are the most prominent bacterial species in dry-aged meat, potentially contributing to the greater accumulation of flavor precursor concentrations in addition to the dehydration process during the dry-aging. Minor microbial species involvement, such as Bacillus spp., could potentially liberate unique and potent flavor precursors.},
}
@article {pmid35736237,
year = {2022},
author = {Deng, L and Chen, S and Meng, W and Zhou, Z and Liu, H and Zhong, Z and Fu, H and Shen, L and Cao, S and Tan, KSW and Peng, G},
title = {Changes in Gut Microbiota Composition Associated with the Presence of Enteric Protist Blastocystis in Captive Forest Musk Deer (Moschus Berezovskii).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0226921},
doi = {10.1128/spectrum.02269-21},
pmid = {35736237},
issn = {2165-0497},
abstract = {Blastocystis is a common protistan parasite inhabiting the gastrointestinal tract of a wide range of hosts including humans and domestic and wild animals. Many studies have revealed the associations between Blastocystis and gut microbiome in humans. However, only a few studies have focused on the associations between Blastocystis and gut microbiome of animals, especially in forest musk deer (Moschus berezovskii). We investigated the effects of the Blastocystis colonization on the intestinal bacterial community compositions using amplicon sequencing targeting the V4 variable region of the 16S rRNA. Two subtypes of Blastocystis (ST5 and ST10) and Blastocystis-free (control) were included in this study. We found that compared with the forest musk deer without Blastocystis, ST10-colonized forest musk deer had higher bacterial richness and diversity, while ST5-colonized forest musk deer showed a comparable bacterial diversity. Likewise, beta diversity revealed significant differences in bacterial community structure between ST10-colonized and Blastocystis-free forest musk deer. The proportion of Bacteroidetes were significantly enriched in ST10-colonized forest musk deer. Bacterial community structure between ST5-colonized and Blastocystis-free forest musk deer did not differ significantly. The present study explored the associations between Blastocystis and gut microbial community of forest musk deer for the first time, and revealed ST10 colonization, instead of ST5, is associated with higher bacterial diversity and shifted microbial structure. Our data provides valuable insights into the associations between gut microbiomes and parasites. IMPORTANCE Forest musk deer is listed as an endangered species by International Union for Conservation of Nature Red List, and the Chinese government has introduced captivity breeding measures to curb the rapid decline of the musk deer population since the 1950s. It has been suggested that Blastocystis colonization can modulate the composition of the host's intestinal microbiota, thereby affecting the host health. The present study investigated the effects of the Blastocystis colonization on the gut microbiota in the feces of forest musk deer in Sichuan Province, China. Two subtypes (ST5 and ST10) have differential effects on the bacterial diversity and community composition, suggesting that the study of Blastocystis should be distinguished at the subtype level. Because the pathogenicity of Blastocystis is controversial, pathogenic, or commensal, continuous monitoring of the impact of Blastocystis colonization on the intestinal microbiota is of great significance to assess its health effects on forest musk deer.},
}
@article {pmid35736193,
year = {2022},
author = {Rumph, JT and Stephens, VR and Ameli, S and Gaines, PN and Osteen, KG and Bruner-Tran, KL and Nde, PN},
title = {A Paternal Fish Oil Diet Preconception Modulates the Gut Microbiome and Attenuates Necrotizing Enterocolitis in Neonatal Mice.},
journal = {Marine drugs},
volume = {20},
number = {6},
pages = {},
doi = {10.3390/md20060390},
pmid = {35736193},
issn = {1660-3397},
support = {TOX T32 ES007028/ES/NIEHS NIH HHS/United States ; T32GM007628/GM/NIGMS NIH HHS/United States ; 1SC1AI127352/NH/NIH HHS/United States ; 5R25GM059994/NH/NIH HHS/United States ; 1F31AI67579/NH/NIH HHS/United States ; Microbiome Initiative Fund//Vanderbilt University/ ; U54MD007586/MD/NIMHD NIH HHS/United States ; I01BX002583//Veteran's Administration/ ; },
abstract = {Epidemiology and animal studies suggest that a paternal history of toxicant exposure contributes to the developmental origins of health and disease. Using a mouse model, our laboratory previously reported that a paternal history of in utero exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) increased his offspring's risk of developing necrotizing enterocolitis (NEC). Additionally, our group and others have found that formula supplementation also increases the risk of NEC in both humans and mice. Our murine studies revealed that intervening with a paternal fish oil diet preconception eliminated the TCDD-associated outcomes that are risk factors for NEC (e.g., intrauterine growth restriction, delayed postnatal growth, and preterm birth). However, the efficacy of a paternal fish oil diet in eliminating the risk of disease development in his offspring was not investigated. Herein, reproductive-age male mice exposed to TCDD in utero were weaned to a standard or fish oil diet for one full cycle of spermatogenesis, then mated to age-matched unexposed females. Their offspring were randomized to a strict maternal milk diet or a supplemental formula diet from postnatal days 7-10. Offspring colon contents and intestines were collected to determine the onset of gut dysbiosis and NEC. We found that a paternal fish oil diet preconception reduced his offspring's risk of toxicant-driven NEC, which was associated with a decrease in the relative abundance of the Firmicutes phylum, but an increase in the relative abundance of the Negativicutes class.},
}
@article {pmid35736108,
year = {2022},
author = {Chavarria-Pizarro, T and Resl, P and Kuhl-Nagel, T and Janjic, A and Fernandez Mendoza, F and Werth, S},
title = {Antibiotic-Induced Treatments Reveal Stress-Responsive Gene Expression in the Endangered Lichen Lobaria&amp;nbsp;pulmonaria.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {6},
pages = {},
doi = {10.3390/jof8060625},
pmid = {35736108},
issn = {2309-608X},
abstract = {Antibiotics are primarily found in the environment due to human activity, which has been reported to influence the structure of biotic communities and the ecological functions of soil and water ecosystems. Nonetheless, their effects in other terrestrial ecosystems have not been well studied. As a result of oxidative stress in organisms exposed to high levels of antibiotics, genotoxicity can lead to DNA damage and, potentially, cell death. In addition, in symbiotic organisms, removal of the associated microbiome by antibiotic treatment has been observed to have a big impact on the host, e.g., corals. The lung lichen Lobaria pulmonaria has more than 800 associated bacterial species, a microbiome which has been hypothesized to increase the lichen's fitness. We artificially exposed samples of L. pulmonaria to antibiotics and a stepwise temperature increase to determine the relative effects of antibiotic treatments vs. temperature on the mycobiont and photobiont gene expression and the viability and on the community structure of the lichen-associated bacteria. We found that the mycobiont and photobiont highly reacted to different antibiotics, independently of temperature exposure. We did not find major differences in bacterial community composition or alpha diversity between antibiotic treatments and controls. For these reasons, the upregulation of stress-related genes in antibiotic-treated samples could be caused by genotoxicity in L. pulmonaria and its photobiont caused by exposure to antibiotics, and the observed stress responses are reactions of the symbiotic partners to reduce damage to their cells. Our study is of great interest for the community of researchers studying symbiotic organisms as it represents one of the first steps to understanding gene expression in an endangered lichen in response to exposure to toxic environments, along with dynamics in its associated bacterial communities.},
}
@article {pmid35735985,
year = {2022},
author = {Zuo, YW and He, P and Zhang, JH and Li, WQ and Ning, DH and Zeng, YL and Yang, Y and Xia, CY and Zhang, H and Deng, HP},
title = {Contrasting Responses of Multispatial Soil Fungal Communities of Thuja sutchuenensis Franch., an Extremely Endangered Conifer in Southwestern China.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0026022},
doi = {10.1128/spectrum.00260-22},
pmid = {35735985},
issn = {2165-0497},
abstract = {Thuja sutchuenensis Franch. is an endangered species in southwest China, distributed sporadically in mountainous areas. Soil property and soil fungal community play a crucial role in plant growth and survival. Nevertheless, understanding soil properties and the soil fungal community in the areas where T. sutchuenensis is distributed is extremely limited. Hence, this study collected a total of 180 soil samples from five altitudinal distribution areas (altitudinal gradients) and three vertical depths throughout four horizontal distances from the base of each tree. The results found that altitudinal gradients and vertical depths altered soil properties, including pH, organic matter content, water content, total nitrogen, phosphorus, and potassium, and available nitrogen, phosphorus, and potassium. The fungal alpha diversity indexes (Chao1 and Shannon) and beta diversity were dramatically decreased with elevation. In addition, high altitudes (2,119 m) harbored the highest relative abundance of ectomycorrhizal fungi (27.57%) and the lowest relative abundance of plant-pathogenic fungi (1.81%). Meanwhile, we identified a series of fungal communities, such as Tomentella, Piloderma, Cortinarius, Sebacina, and Boletaceae, that play an essential role in the survival of T. sutchuenensis. The correlation analysis and random forest model identified that water content and total phosphorus showed strong relationships with fungal characteristics and were the primary variables for Zygomycota and Rozellomycota. Collectively, the findings of this integrated analysis provide profound insights into understanding the contrasting responses of T. sutchuenensis soil fungal communities and provide a theoretical basis for T. sutchuenensis habitat restoration and species conservation from multispatial perspectives. IMPORTANCE The present study highlights the importance of fungal communities in an endangered plant, T. sutchuenensis. Comparative analysis of soil samples in nearly all extant T. sutchuenensis populations identified that soil properties, especially soil nutrients, might play critical roles in the survival of T. sutchuenensis. Our findings prove that a series of fungal communities (e.g., Tomentella, Piloderma, and Cortinarius) could be key indicators for T. sutchuenensis survival. In addition, this is the first time that large-scale soil property and fungal community investigations have been carried out in southwest China, offering important values for exploring the distribution pattern of regional soil microorganisms. Collectively, our findings display a holistic picture of soil microbiome and environmental factors associated with T. sutchuenensis.},
}
@article {pmid35735411,
year = {2022},
author = {Dandekar, MP and Palepu, MSK and Satti, S and Jaiswal, Y and Singh, AA and Dash, SP and Gajula, SNR and Sonti, R},
title = {Multi-strain Probiotic Formulation Reverses Maternal Separation and Chronic Unpredictable Mild Stress-Generated Anxiety- and Depression-like Phenotypes by Modulating Gut Microbiome-Brain Activity in Rats.},
journal = {ACS chemical neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschemneuro.2c00143},
pmid = {35735411},
issn = {1948-7193},
abstract = {Depression is a debilitating mental disorder that affects >322 million people worldwide. Despite the availability of several antidepressant agents, many patients remain treatment refractory. A growing literature study has indicated the role of gut microbiota in neuropsychiatric disorders. Herein, we examined the psychobiotic-like activity of multi-strain probiotic formulation in maternal separation (MS) and chronic unpredictable mild stress (CUMS) models of anxiety- and depression-like phenotypes in Sprague-Dawley rats. Early- and late-life stress was employed in both male and female rats by exposing them to MS and CUMS. The multi-strain probiotic formulation (Cognisol) containing Bacillus coagulans Unique IS-2, Lactobacillus plantarum UBLP-40, Lactobacillus rhamnosus UBLR-58, Bifidobacterium lactis UBBLa-70, Bifidobacterium breve UBBr-01, and Bifidobacterium infantis UBBI-01 at a total strength of 10 billion cfu along with l-glutamine was administered for 6 weeks via drinking water. Neurobehavioral assessment was done using the forced swim test (FST), sucrose preference test (SPT), elevated plus maze (EPM), and open field test (OFT). Animals were sacrificed after behavioral assessment, and blood, brain, and intestine samples were collected to analyze the levels of cytokines, metabolites, and neurotransmitters and histology. Animals exposed to stress showed increased passivity, consumed less sucrose solution, and minimally explored the open arms in the FST, SPT, and EPM, respectively. Administration of multi-strain probiotics along with l-glutamine for 6 weeks ameliorated the behavioral abnormalities. The locomotor activity of animals in the OFT and their body weight remained unchanged across the groups. Cognisol treatment reversed the decreased BDNF and serotonin levels and increased CRP, TNF-α, and dopamine levels in the hippocampus and/or frontal cortex. Administration of Cognisol also restored the plasma levels of l-tryptophan, l-kynurenine, kynurenic-acid, and 3-hydroxyanthranilic acid; the Firmicutes-to-Bacteroides ratio; the levels of acetate, propionate, and butyrate in fecal samples; the villi/crypt ratio; and the goblet cell count, which manifested in the restoration of intestinal functions. We suggest that the multi-strain probiotic and glutamine formulation (Cognisol) ameliorated the MS + UCMS-generated anxiety- and depression-like phenotypes by reshaping the gut microbiome-brain activity in both sexes.},
}
@article {pmid35735103,
year = {2022},
author = {Qian, X and Zhang, HY and Li, QL and Ma, GJ and Chen, Z and Ji, XM and Li, CY and Zhang, AQ},
title = {Integrated microbiome, metabolome, and proteome analysis identifies a novel interplay among commensal bacteria, metabolites and candidate targets in non-small cell lung cancer.},
journal = {Clinical and translational medicine},
volume = {12},
number = {6},
pages = {e947},
doi = {10.1002/ctm2.947},
pmid = {35735103},
issn = {2001-1326},
support = {81973771//National Natural Science Foundation of China/ ; 2019ZZ002//Key Research Projects of Traditional Chinese Medicine of Zhejiang Province/ ; },
abstract = {BACKGROUND: Accumulation of evidence suggests that the gut microbiome, its specific metabolites, and differentially expressed proteins (DEPs) are related to non-small cell lung cancer (NSCLC) pathogenesis. We now report the influences of the gut microbiota, metabolites, and DEPs on the mediation of NSCLC's chronic inflammation and immune dysregulation.<br><br>METHODS: We conducted 16S ribosomal RNA sequencing for the gut microbiome in healthy volunteers and NSCLC patients. Liquid chromatography-mass spectrometry (LC-MS) analysis was employed to explore differences between metabolites and DEPs in serum samples. Additionally, LC-MS-based metabolomic analysis was conducted in 40 NSCLC tissues and 40 adjacent tissues. The omics data were separately analysed and integrated by using Spearman's correlation coefficient. Then, faecal microbiota transplantation (FMT) assay was used to assess the effects of the gut microbiome and specific metabolites in mice.<br><br>RESULTS: Faecal microbiome analysis revealed gut microflora dysbiosis in NSCLC patients with Prevotella, Gemmiger, and Roseburia significantly upregulated at the genus level. Then, we identified that nervonic acid/all-trans-retinoic acid level was negatively related to Prevotella. Additionally, a total of core 8 DEPs were selected in the proteome analysis, which mainly participated in the production of IL-8 and NF-κB pathways. CRP, LBP, and CD14 were identified as potential biomarkers for NSCLC. Transplantation of faecal microbiota from patients with NSCLC or Prevotella copri-colonized recipient in mice resulted in inflammation and immune dysregulation. In turn, nervonic acid/all-trans-retinoic acid treatment improved the phenotype of C57BL/6 mice bearing P. copri-treated Lewis lung cancer (LLC).<br><br>CONCLUSIONS: Overall, these results pointed out that P. copri-nervonic acid/all-trans-retinoic acid axis may contribute to the pathogenesis of NSCLC.},
}
@article {pmid35734856,
year = {2022},
author = {Shen, X and Zhang, B and Hu, X and Li, J and Wu, M and Yan, C and Yang, Y and Li, Y},
title = {Neisseria sicca and Corynebacterium matruchotii inhibited oral squamous cell carcinomas by regulating genome stability.},
journal = {Bioengineered},
volume = {13},
number = {6},
pages = {14094-14106},
doi = {10.1080/21655979.2022.2078556},
pmid = {35734856},
issn = {2165-5987},
abstract = {Periodontitis is a risk factor for the development of oral squamous cell carcinomas (OSCC). Both DNA damage response (DDR) and activation of inflammasomes induced by the microbiome might play important roles in the development of tumors, in relation to genome stability of tumor cells. Herein, we explored whether periodontitis negative-associated bacteria (Neisseria sicca and Corynebacterium matruchotii, namely called 'PNB'), which were highly abundant in healthy populations, could inhibit OSCC by promoting genome stability. Firstly, a murine SCC-7 tumor-bearing model that colonized with PNB was designed and used in this study. Then, cyclin D1 was detected by immunohistochemistry. Levels of DDR, NLRP3 inflammasomes and pro-inflammatory cytokines in tumors were detected by RT-qPCR or Western blot. Immune cells in spleens were detected by immunohistochemistry or immunofluorescence. Finally, the anti-cancer activity of PNB was assessed in vitro using CCK-8 assays and flow cystometry. Compared with the control, PNB decreased tumor weights from 0.77 ± 0.26 g to 0.42 ± 0.15 g and downregulated the expression of Cyclin D1. PNB activated the DDR by up-regulating γ-H2AX, p-ATR, and p-CHK1. PNB activated NLRP3 inflammasome-mediated pyroptosis via increases of NLRP3, gasdermin D, and mRNA levels of apoptosis-associated speck-like protein, Caspase-1. PNB suppressed the inflammatory response by down-regulating mRNA levels of NF-κΒ and IL-6 in tumors as well as the populations of CD4+ T cells and CD206+ immune cells in spleens. PNB inhibited proliferation and promoted cell death of HSC-3 cells. In conclusion, Neisseria sicca and Corynebacterium matruchotii showed a 'probiotic bacterial' potential to inhibit OSCC by regulating genome stability.},
}
@article {pmid35734426,
year = {2022},
author = {Mallick, H and An, L and Chen, M and Wang, P and Zhao, N},
title = {Editorial: Methods for Single-Cell and Microbiome Sequencing Data.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {920191},
doi = {10.3389/fgene.2022.920191},
pmid = {35734426},
issn = {1664-8021},
}
@article {pmid35734371,
year = {2022},
author = {Tu, P and Chi, L and Bian, X and Gao, B and Ru, H and Lu, K},
title = {A Black Raspberry-Rich Diet Protects From Dextran Sulfate Sodium-Induced Intestinal Inflammation and Host Metabolic Perturbation in Association With Increased Aryl Hydrocarbon Receptor Ligands in the Gut Microbiota of Mice.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {842298},
doi = {10.3389/fnut.2022.842298},
pmid = {35734371},
issn = {2296-861X},
abstract = {Dietary modulation of the gut microbiota recently received considerable attention, and ligand activation of aryl hydrocarbon receptor (AHR) plays a pivotal role in intestinal immunity. Importantly, black raspberry (BRB, Rubus occidentalis) is associated with a variety of beneficial health effects. We aim to investigate effects of a BRB-rich diet on dextran sulfate sodium (DSS)-induced intestinal inflammation and to determine whether its consequent anti-inflammatory effects are relevant to modulation of the gut microbiota, especially its production of AHR ligands. A mouse model of DSS-induced intestinal inflammation was used in the present study. C57BL/6J mice were fed either AIN-76A or BRB diet. Composition and functions of the gut microbiota were assessed by 16S rRNA sequencing and comparative metagenome analysis. Metabolic profiles of host and the gut microbiome were assessed by serum and fecal metabolomic profiling and identification. BRB diet was found to ameliorate DSS-induced intestinal inflammation and host metabolic perturbation. BRB diet also protected from DSS-induced perturbation in diversity and composition in the gut microbiota. BRB diet promoted AHR ligand production by the gut microbiota, as revealed by increased levels of fecal AHR activity in addition to increased levels of two known AHR ligands, hemin and biliverdin. Accordingly, enrichment of bacterial genes and pathways responsible for production of hemin and biliverdin were found, specific gut bacteria that are highly correlated with abundances of hemin and biliverdin were also identified. BRB dietary intervention ameliorated intestinal inflammation in mice in association with promotion of AHR ligand production by the gut microbiota.},
}
@article {pmid35734258,
year = {2022},
author = {Bittleston, LS and Benson, EL and Bernardin, JR and Pierce, NE},
title = {Characterization and Comparison of Convergence Among Cephalotus follicularis Pitcher Plant-Associated Communities With Those of Nepenthes and Sarracenia Found Worldwide.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {887635},
doi = {10.3389/fpls.2022.887635},
pmid = {35734258},
issn = {1664-462X},
abstract = {The Albany pitcher plant, Cephalotus follicularis, has evolved cup-shaped leaves and a carnivorous habit completely independently from other lineages of pitcher plants. It is the only species in the family Cephalotaceae and is restricted to a small region of Western Australia. Here, we used metabarcoding to characterize the bacterial and eukaryotic communities living in C. follicularis pitchers at two different sites. Bacterial and eukaryotic communities were correlated in both richness and composition; however, the factors associated with richness were not the same across bacteria and eukaryotes, with bacterial richness differing with fluid color, and eukaryotic richness differing with the concentration of DNA extracted from the fluid, a measure roughly related to biomass. For turnover in composition, the variation in both bacterial and eukaryotic communities primarily differed with fluid acidity, fluid color, and sampling site. We compared C. follicularis-associated community diversity with that of Australian Nepenthes mirabilis, as well as a global comparison of Southeast Asian Nepenthes and North American Sarracenia. Our results showed similarity in richness with communities from other pitcher plants, and specific bacterial taxa shared among all three independent lineages of pitcher plants. Overall, we saw convergence in richness and particular clades colonizing pitcher plants around the world, suggesting that these highly specialized habitats select for certain numbers and types of inhabitants.},
}
@article {pmid35733987,
year = {2022},
author = {Ishimwe, JA and Breier, N and Saleem, M and Kastner, PD and Kirabo, A and Shibao, CA},
title = {The Gut Microbiota and Short-Chain Fatty Acids Profile in Postural Orthostatic Tachycardia Syndrome.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {879012},
doi = {10.3389/fphys.2022.879012},
pmid = {35733987},
issn = {1664-042X},
abstract = {Postural orthostatic tachycardia syndrome (POTS) is a devastating chronic form of orthostatic intolerance associated with excessive heart rate increase without hypotension during upright posture. POTS patients exhibit increased circulating norepinephrine levels with exaggerated sympathetic nervous system response upon standing. Emerging evidence suggests a role for the gut microbiome in cardiovascular disorders. However, the etiology of POTS and whether the gut microbiome plays a role are not fully elucidated. We assessed whether the gut microbiome and fecal short-chain fatty acids were different in POTS patients (N = 25) compared to healthy control (N = 23) women. Patients underwent hemodynamic measurements while supine and upon standing. Fecal samples were collected and analyzed using shotgun sequencing and Liquid Chromatography-High Resolution Mass Spectrometry and dietary habits were measured with a fitness application. We found that POTS patients in the standing position had higher circulating norepinephrine and epinephrine levels and increased heart rate. There were no differences in diet composition between groups. Of note dietary salt intake was also similar despite the fact that these patients are advised to consume a high salt diet. Alpha and beta diversity were similar between groups. We observed no differences in bacteria at the phylum levels or Firmicutes to Bacteroidetes ratio. We found no significant differences at the genus level, but observed trends in certain bacteria. Lachnoclostridium genus were higher in POTS when compared to the control group. On the other hand, Coprococcus and Coprobacter, were lower in POTS patients compared to controls. Although our KEGG metabolic pathways indicated differences related to short-chain fatty acids (SCFAs), we found that both POTS patients and healthy controls had similar levels of SCFAs. These results suggest POTs per se may have limited effects on gut microbiota composition and derived SCFAs. Further studies are needed to assess the role of the alterations observed at the genus level.},
}
@article {pmid35733965,
year = {2022},
author = {Zhang, J and Liang, Z and Ding Kao, R and Han, J and Du, M and Ahmad, AA and Wang, S and Salekdeh, GH and Long, R and Yan, P and Ding, X},
title = {Maternal Fecal Microbes Contribute to Shaping the Early Life Assembly of the Intestinal Microbiota of Co-inhabiting Yak and Cattle Calves.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {916735},
doi = {10.3389/fmicb.2022.916735},
pmid = {35733965},
issn = {1664-302X},
abstract = {The Qinghai-Tibetan Plateau offers one of the most extreme environments for yaks (Bos grunniens). Although the genetic adaptability of yak and rumen metagenomes is increasingly understood, the relative contribution of host genetics and maternal symbiotic microbes throughout early intestinal microbial successions in yaks remains elusive. In this study, we assessed the intestinal microbiota succession of co-inhabiting yak and cattle (Bos taurus) calves at different weeks after birth as well as the modes of transmission of maternal symbiotic microbes (i.e., rumen fluid, feces, oral cavity, and breast skin) to their calves' intestinal microbiota colonization. We found that the fecal microbiota of yak and cattle calves after birth was dominated by members of the families Ruminococcaceae, Bacteroidaceae, and Lachnospiraceae. The Source Tracker model revealed that maternal fecal microbes played an important role (the average contribution was about 80%) in the intestinal microbial colonization of yak and cattle calves at different weeks after birth. Unlike cattle calves, there was no significant difference in the fecal microbiota composition of yak calves between 5 and 9 weeks after birth (Wilcoxon test, P > 0.05), indicating that yak may adapt to its natural extreme environment to stabilize its intestinal microbiota composition. Additionally, our results also find that the intestinal microbial composition of yak and cattle calves, with age, gradually tend to become similar, and the differences between species gradually decrease. The findings of this study are vital for developing strategies to manipulate the intestinal microbiota in grazing yaks and cattle for better growth and performance on the Qinghai-Tibetan Plateau.},
}
@article {pmid35733964,
year = {2022},
author = {Xiao, C and Xu, C and Zhang, J and Jiang, W and Zhang, X and Yang, C and Xu, J and Zhang, Y and Zhou, T},
title = {Soil Microbial Communities Affect the Growth and Secondary Metabolite Accumulation in Bletilla striata (Thunb.) Rchb. f.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {916418},
doi = {10.3389/fmicb.2022.916418},
pmid = {35733964},
issn = {1664-302X},
abstract = {Bletilla striata (Thunb.) Rchb.f. is a perennial herb belonging to the Orchidaceae family. Its tubers are used in traditional Chinese medicine to treat gastric ulcers, inflammation, silicosis tuberculosis, and pneumogastric hemorrhage. It has been reported that different soil types can affect the growth of B. striata and the accumulation of secondary metabolites in its tubers, but the biological mechanisms underlying these effects remain unclear. In this study, we compared agronomic traits and the accumulation of secondary metabolites (extractum, polysaccharide, total phenol, militarine) in B. striata grown in sandy loam or sandy clay soil. In addition, we compared physicochemical properties and microbial communities between the two soil types. In pot experiments, we tested how irradiating soil or transplanting microbiota from clay or loam into soil affected B. striata growth and accumulation of secondary metabolites. The results showed that sandy loam and sandy clay soils differed significantly in their physicochemical properties as well as in the structure and composition of their microbial communities. Sandy loam soil had higher pH, SOM, SOC, T-Ca, T-N, T-Mg, T-Mn, T-Zn, A-Ca, A-Mn, and A-Cu than sandy clay soil, but significantly lower T-P, T-K, T-Fe, and A-P content. Sandy loam soil showed 7.32% less bacterial diversity based on the Shannon index, 19.59% less based on the Ace index, and 24.55% less based on the Chao index. The first two components of the PCoA explained 74.43% of the variation in the bacterial community (PC1 = 64.92%, PC2 = 9.51%). Similarly, the first two components of the PCoA explained 58.48% of the variation in the fungal community (PC1 = 43.67%, PC2 = 14.81%). The microbiome associated with sandy clay soil can promote the accumulation of militarine in B. striata tubers, but it inhibits the growth of B. striata. The accumulation of secondary metabolites such as militarine in B. striata was significantly higher in sandy clay than in sandy loam soil. Conversely, B. striata grew better in sandy loam soil. The microbiome associated with sandy loam soil can promote the growth of B. striata, but it reduces the accumulation of militarine in B. striata tubers. Pot experiment results further confirmed that the accumulation of secondary metabolites such as militarine was higher in soil transplanted with loam microbiota than in soil transplanted with clay microbiota. These results may help guide efforts to improve B. striata yield and its accumulation of specific secondary metabolites.},
}
@article {pmid35733963,
year = {2022},
author = {Bathia, J and Schröder, K and Fraune, S and Lachnit, T and Rosenstiel, P and Bosch, TCG},
title = {Symbiotic Algae of Hydra viridissima Play a Key Role in Maintaining Homeostatic Bacterial Colonization.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {869666},
doi = {10.3389/fmicb.2022.869666},
pmid = {35733963},
issn = {1664-302X},
abstract = {The freshwater polyp Hydra viridissima (H. viridissima) harbors endosymbiotic Chlorella algae in addition to a species-specific microbiome. The molecular basis of the symbiosis between Hydra and Chlorella has been characterized to be metabolic in nature. Here, we studied the interaction between the extracellularly located microbiota and the algal photobiont, which resides in Hydra's endodermal epithelium, with main focus on Legionella bacterium. We aimed at evaluating the influence of the symbiotic algae on microbial colonization and in shaping the host microbiome. We report that the microbiome composition of symbiotic and aposymbiotic (algae free) H. viridissima is significantly different and dominated by Legionella spp. Hvir in aposymbiotic animals. Co-cultivation of these animals resulted in horizontal transmission of Legionella spp. Hvir bacteria from aposymbiotic to symbiotic animals. Acquisition of this bacterium increased the release of algae into ambient water. From there, algae could subsequently be taken up again by the aposymbiotic animals. The presence of algal symbionts had negative impact on Legionella spp. Hvir and resulted in a decrease of the relative abundance of this bacterium. Prolonged co-cultivation ultimately resulted in the disappearance of the Legionella spp. Hvir bacterium from the Hydra tissue. Our observations suggest an important role of the photobiont in controlling an invasive species in a metacommunity and, thereby, shaping the microbiome.},
}
@article {pmid35733962,
year = {2022},
author = {Sultana, MF and Suzuki, M and Yamasaki, F and Kubota, W and Takahashi, K and Abo, H and Kawashima, H},
title = {Identification of Crucial Amino Acid Residues for Antimicrobial Activity of Angiogenin 4 and Its Modulation of Gut Microbiota in Mice.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {900948},
doi = {10.3389/fmicb.2022.900948},
pmid = {35733962},
issn = {1664-302X},
abstract = {Angiogenin 4 bearing ribonuclease activity is an endogenous antimicrobial protein expressed in small and large intestine. However, the crucial amino acid residues responsible for the antibacterial activity of Ang4 and its impact on gut microbiota remain unknown. Here, we report the contribution of critical amino acid residues in the functional regions of Ang4 to its activity against Salmonella typhimurium LT2 and the effect of Ang4 on gut microbiota in mice. We found that Ang4 binds S. typhimurium LT2 through two consecutive basic amino acid residues, K58 and K59, in the cell-binding segment and disrupts the bacterial membrane integrity at the N-terminal α-helix containing residues K7 and K30, as evidenced by the specific mutations of cationic residues of Ang4. We also found that the RNase activity of Ang4 was not involved in its bactericidal activity, as shown by the H12 mutant, which lacks RNase activity. In vivo administration of Ang4 through the mouse rectum and subsequent bacterial 16S rRNA gene sequencing analyses demonstrated that administration of Ang4 not only increased beneficial bacteria such as Lactobacillus, Akkermansia, Dubosiella, Coriobacteriaceae UCG-002, and Adlercreutzia, but also decreased certain pathogenic bacteria, including Alistipes and Enterohabdus, indicating that Ang4 regulates the shape of gut microbiota composition. We conclude that Ang4 kills bacteria by disrupting bacterial membrane integrity through critical basic amino acid residues with different functionalities rather than overall electrostatic interactions and potentially maintains gut microflora in vivo under physiological and pathophysiological conditions.},
}
@article {pmid35733959,
year = {2022},
author = {Li, R and Yi, X and Yang, J and Zhu, Z and Wang, Y and Liu, X and Huang, X and Wan, Y and Fu, X and Shu, W and Zhang, W and Wang, Z},
title = {Gut Microbiome Signatures in the Progression of Hepatitis B Virus-Induced Liver Disease.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {916061},
doi = {10.3389/fmicb.2022.916061},
pmid = {35733959},
issn = {1664-302X},
abstract = {The gut microbiome is associated with hepatitis B virus (HBV)-induced liver disease, which progresses from chronic hepatitis B, to liver cirrhosis, and eventually to hepatocellular carcinoma. Studies have analyzed the gut microbiome at each stage of HBV-induced liver diseases, but a consensus has not been reached on the microbial signatures across these stages. Here, we conducted by a systematic meta-analysis of 486 fecal samples from publicly available 16S rRNA gene datasets across all disease stages, and validated the results by a gut microbiome characterization on an independent cohort of 15 controls, 23 chronic hepatitis B, 20 liver cirrhosis, and 22 hepatocellular carcinoma patients. The integrative analyses revealed 13 genera consistently altered at each of the disease stages both in public and validation datasets, suggesting highly robust microbiome signatures. Specifically, Colidextribacter and Monoglobus were enriched in healthy controls. An unclassified Lachnospiraceae genus was specifically elevated in chronic hepatitis B, whereas Bilophia was depleted. Prevotella and Oscillibacter were depleted in liver cirrhosis. And Coprococcus and Faecalibacterium were depleted in hepatocellular carcinoma. Classifiers established using these 13 genera showed diagnostic power across all disease stages in a cross-validation between public and validation datasets (AUC = 0.65-0.832). The identified microbial taxonomy serves as non-invasive biomarkers for monitoring the progression of HBV-induced liver disease, and may contribute to microbiome-based therapies.},
}
@article {pmid35733791,
year = {2022},
author = {Liu, W and Li, C and Li, B and Shang, Q and Han, Z and Zhang, Y and Liu, X and Fan, H and Zhang, J and Chen, Y and Zhang, H},
title = {Lactiplantibacillus plantarum P9 improved gut microbial metabolites and alleviated inflammatory response in pesticide exposure cohorts.},
journal = {iScience},
volume = {25},
number = {7},
pages = {104472},
doi = {10.1016/j.isci.2022.104472},
pmid = {35733791},
issn = {2589-0042},
abstract = {Multiple pesticide residue accumulations increase the probability of chronic metabolic diseases in humans. Thus, we applied multi-omics techniques to reveal how the gut microbiome responded to pesticide exposure. Then, we explored how probiotic Lactiplantibacillus plantarum P9 (P9) consumption impacted the gut microbiota and immune factors after high pesticide exposure. Multi-omics results indicated frequent exposure to pesticides did not alter the composition of the intestinal microbiota, but it did increase the abundance of Lipopolysaccharide in the gut, which might contribute to chronic inflammation. Supplementation with P9 maintained the homeostasis of the gut microbiota and reduced the abundance of pathogens in the high pesticide-exposed subjects. By detecting metabolites, we observed uridine and 5-oxoproline concentrations increased significantly after P9 consumption. Furthermore, P9 alleviated immune factors disorder and promoted pesticide residue excretion. Our findings provide new insights into the application of probiotics for pesticide detoxification, and suggest probiotics as daily supplements for pesticide exposure prevention.},
}
@article {pmid35733625,
year = {2022},
author = {Liu, W and Lu, NH and Zhou, X and Li, Y and Xie, Y and Zheng, L and Zhu, W and Xiao, Q and Yang, N and Zuo, K and Wu, Q and Xu, T and Zhang, H},
title = {Effects of Lactobacillus plantarum P9 Probiotics on Defecation and Quality of Life of Individuals with Chronic Constipation: Protocol for a Randomized, Double-Blind, Placebo-Controlled Clinical Trial.},
journal = {Evidence-based complementary and alternative medicine : eCAM},
volume = {2022},
number = {},
pages = {4144321},
doi = {10.1155/2022/4144321},
pmid = {35733625},
issn = {1741-427X},
abstract = {Background: Although probiotics have been shown to improve constipation-related symptoms, a clear consensus on the use of probiotics as a constipation-relieving agent has not been reached, which is attributed to the limited available evidence and inconsistent protocols used in existing studies.<br><br>Method: A randomized, double-blind, placebo-controlled clinical trial is designed to study the efficiency and possible mechanism of action of probiotics for chronic constipation, in which 200 eligible volunteers with chronic constipation will be randomly assigned to a probiotic group (oral Lactobacillus plantarum P9 probiotic powder, 100 billion colony-forming units (CFUs)/day) or a placebo group. Volunteers, treatment distributors, data collectors, and data analysts will be blinded. The primary outcome is the weekly mean frequency of complete spontaneous bowel movements (CSBMs), and secondary outcomes include weekly mean frequency of CSBMs ≥3, weekly mean frequency of spontaneous bowel movements (SBMs), weekly mean stool appearance score, weekly mean difficulty of passing stool score, weekly percentage of volunteers who use auxiliary measures to assist with defecation (WPUAMA), quality-of-life (QOL) score, emotional status score, gut microbiome, and faecal metabolome. Each outcome measure will be assessed at the time points of preadministration (day 0), administration (day 14 and/or 28), and postadministration (day 42) to identify inter- and intragroup differences. Adverse events will be recorded to evaluate the safety of L. plantarum P9. Discussion. The protocol will provide methodological guidance for other similar studies, avoiding methodological bias and ultimately facilitating the formulation of consensus on the use of probiotics as a constipation-relieving agent. In addition, the results are more comprehensive than those of existing studies and may objectively and scientifically reflect the effectiveness of L. plantarum P9 on constipation. If the expected study findings are obtained, L. plantarum P9, taken as a probiotic, may become a complementary choice for chronically constipated patients. This trial is registered with Chinese Clinical Trial Registry (ChiCTR) (no. ChiCTR2000038396) registered on November 22, 2020, https://www.chictr.org.cn/showproj.aspx?proj=54024.},
}
@article {pmid35732882,
year = {2022},
author = {Nalluri-Butz, H and Bobel, MC and Nugent, J and Boatman, S and Emanuelson, R and Melton-Meaux, G and Madoff, RD and Jahansouz, C and Staley, C and Gaertner, WB},
title = {A pilot study demonstrating the impact of surgical bowel preparation on intestinal microbiota composition following colon and rectal surgery.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10559},
pmid = {35732882},
issn = {2045-2322},
support = {21692 - University of Minnesota//Hubbard Family private fund for advancing treatment practices to improve patient outcomes in colorectal surgery/ ; 21692 - University of Minnesota//Hubbard Family private fund for advancing treatment practices to improve patient outcomes in colorectal surgery/ ; 21692 - University of Minnesota//Hubbard Family private fund for advancing treatment practices to improve patient outcomes in colorectal surgery/ ; 21692 - University of Minnesota//Hubbard Family private fund for advancing treatment practices to improve patient outcomes in colorectal surgery/ ; },
abstract = {The intestinal microbiota has been implicated in the pathogenesis of complications following colorectal surgery, yet perioperative changes in gut microbiome composition are poorly understood. The objective of this study was to characterize the perioperative gut microbiome in patients undergoing colonoscopy and colorectal surgery and determine factors influencing its composition. Using Illumina amplicon sequencing coupled with targeted metabolomics, we characterized the fecal microbiota in: (A) patients (n = 15) undergoing colonoscopy who received mechanical bowel preparation, and (B) patients (n = 15) undergoing colorectal surgery who received surgical bowel preparation, composed of mechanical bowel preparation with oral antibiotics, and perioperative intravenous antibiotics. Microbiome composition was characterized before and up to six months following each intervention. Colonoscopy patients had minor shifts in bacterial community composition that recovered to baseline at a mean of 3 (1-13) days. Surgery patients demonstrated substantial shifts in bacterial composition with greater abundances of Enterococcus, Lactobacillus, and Streptococcus. Compositional changes persisted in the early postoperative period with recovery to baseline beginning at a mean of 31 (16-43) days. Our results support surgical bowel preparation as a factor significantly influencing gut microbial composition following colorectal surgery, while mechanical bowel preparation has little impact.},
}
@article {pmid35732881,
year = {2022},
author = {Imai, Y and Lee, SW and Sakaguchi, S and Kato-Kogoe, N and Taniguchi, K and Omori, M and Tanaka, R and Honda, K and Osumi, W and Nakano, T and Ueno, T and Uchiyama, K},
title = {Comparison of the gastric microbiome in Billroth I and Roux-en-Y reconstructions after distal gastrectomy.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10594},
pmid = {35732881},
issn = {2045-2322},
support = {20K09932//Japan Society for the Promotion of Science KAKENHI/ ; 20K18521//Japan Society for the Promotion of Science KAKENHI/ ; 20K17633//Japan Society for the Promotion of Science KAKENHI/ ; },
abstract = {The changes in gastric microbiota following reconstruction after gastrectomy have not been reported. This study aimed to compare the gastric microbiota following Billroth I and Roux-en-Y reconstructions after distal gastrectomy. We enrolled 71 gastrectomized patients with gastric cancer; 31 and 40 underwent Billroth I and Roux-en-Y reconstructions, respectively. During upper gastrointestinal endoscopy, gastric fluid was collected immediately before and 6 months after distal gastrectomy. Deoxyribonucleic acid isolated from each sample was evaluated using 16S ribosomal ribonucleic acid metagenomic analysis. Analysis revealed that the gastric microbiota's species richness (expressed as the alpha diversity) was significantly lower after than before distal gastrectomy (operational taxonomic units, p = 0.001; Shannon index, p = 0.03). The interindividual diversity (beta diversity) was significantly different before and after distal gastrectomy (unweighted UniFrac distances, p = 0.04; weighted UniFrac distances, p = 0.001; Bray-Curtis, p = 0.001). Alpha and beta diversity were not significantly different between Billroth I and Roux-en-Y reconstructions (observed operational taxonomic units, p = 0.58; Shannon index, p = 0.95; unweighted UniFrac distances, p = 0.65; weighted UniFrac distances, p = 0.67; Bray-Curtis, p = 0.63). Our study demonstrated significant differences in gastric microbiota diversity, composition, and community before and after distal gastrectomy but no difference between Billroth I and Roux-en-Y reconstruction after distal gastrectomy.},
}
@article {pmid35732819,
year = {2022},
author = {Loke, P and Lee, SC and Oyesola, OO},
title = {Effects of helminths on the human immune response and the microbiome.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
pmid = {35732819},
issn = {1935-3456},
abstract = {Helminths have evolved sophisticated immune regulating mechanisms to prevent rejection by their mammalian host. Our understanding of how the human immune system responds to these parasites remains poor compared to mouse models of infection and this limits our ability to develop vaccines as well as harness their unique properties as therapeutic strategies against inflammatory disorders. Here, we review how recent studies on human challenge infections, self-infected individuals, travelers, and endemic populations have improved our understanding of human type 2 immunity and its effects on the microbiome. The heterogeneity of responses between individuals and the limited access to tissue samples beyond the peripheral blood are challenges that limit human studies on helminths, but also provide opportunities to transform our understanding of human immunology. Organoids and single-cell sequencing are exciting new tools for immunological analysis that may aid this pursuit. Learning about the genetic and immunological basis of resistance, tolerance, and pathogenesis to helminth infections may thus uncover mechanisms that can be utilized for therapeutic purposes.},
}
@article {pmid35732737,
year = {2022},
author = {Serger, E and Luengo-Gutierrez, L and Chadwick, JS and Kong, G and Zhou, L and Crawford, G and Danzi, MC and Myridakis, A and Brandis, A and Bello, AT and Müller, F and Sanchez-Vassopoulos, A and De Virgiliis, F and Liddell, P and Dumas, ME and Strid, J and Mani, S and Dodd, D and Di Giovanni, S},
title = {The gut metabolite indole-3 propionate promotes nerve regeneration and repair.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {35732737},
issn = {1476-4687},
abstract = {The regenerative potential of mammalian peripheral nervous system neurons after injury is critically limited by their slow axonal regenerative rate1. Regenerative ability is influenced by both injury-dependent and injury-independent mechanisms2. Among the latter, environmental factors such as exercise and environmental enrichment have been shown to affect signalling pathways that promote axonal regeneration3. Several of these pathways, including modifications in gene transcription and protein synthesis, mitochondrial metabolism and the release of neurotrophins, can be activated by intermittent fasting (IF)4,5. However, whether IF influences the axonal regenerative ability remains to be investigated. Here we show that IF promotes axonal regeneration after sciatic nerve crush in mice through an unexpected mechanism that relies on the gram-positive gut microbiome and an increase in the gut bacteria-derived metabolite indole-3-propionic acid (IPA) in the serum. IPA production by Clostridium sporogenes is required for efficient axonal regeneration, and delivery of IPA after sciatic injury significantly enhances axonal regeneration, accelerating the recovery of sensory function. Mechanistically, RNA sequencing analysis from sciatic dorsal root ganglia suggested a role for neutrophil chemotaxis in the IPA-dependent regenerative phenotype, which was confirmed by inhibition of neutrophil chemotaxis. Our results demonstrate the ability of a microbiome-derived metabolite, such as IPA, to facilitate regeneration and functional recovery of sensory axons through an immune-mediated mechanism.},
}
@article {pmid35732736,
year = {2022},
author = {Paoli, L and Ruscheweyh, HJ and Forneris, CC and Hubrich, F and Kautsar, S and Bhushan, A and Lotti, A and Clayssen, Q and Salazar, G and Milanese, A and Carlström, CI and Papadopoulou, C and Gehrig, D and Karasikov, M and Mustafa, H and Larralde, M and Carroll, LM and Sánchez, P and Zayed, AA and Cronin, DR and Acinas, SG and Bork, P and Bowler, C and Delmont, TO and Gasol, JM and Gossert, AD and Kahles, A and Sullivan, MB and Wincker, P and Zeller, G and Robinson, SL and Piel, J and Sunagawa, S},
title = {Biosynthetic potential of the global ocean microbiome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {35732736},
issn = {1476-4687},
abstract = {Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups1, this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds2,3. However, studying this diversity to identify genomic pathways for the synthesis of such compounds4 and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters ('Candidatus Eudoremicrobiaceae') that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments.},
}
@article {pmid35732716,
year = {2022},
author = {},
title = {A wealth of new biosynthetic pathways from the global ocean microbiome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {35732716},
issn = {1476-4687},
}
@article {pmid35732671,
year = {2022},
author = {Jafari, M and Juanson Arabit, JG and Courville, R and Kiani, D and Chaston, JM and Nguyen, CD and Jena, N and Liu, ZY and Tata, P and Van Etten, RA},
title = {The impact of Rhodiola rosea on biomarkers of diabetes, inflammation, and microbiota in a leptin receptor-knockout mouse model.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10581},
pmid = {35732671},
issn = {2045-2322},
abstract = {Type 2 diabetes is the most prevalent endocrine disease in the world, and recently the gut microbiota have become a potential target for its management. Recent studies have illustrated that this disease may predispose individuals to certain microbiome compositions, and treatments like metformin have been shown to change gut microbiota and their associated metabolic pathways. However, given the limitations and side effects associated with pharmaceuticals currently being used for therapy of diabetes, there is a significant need for alternative treatments. In this study, we investigated the effects of a root extract from Rhodiola rosea in a Leptin receptor knockout (db/db) mouse model of type 2 diabetes. Our previous work showed that Rhodiola rosea had anti-inflammatory and gut microbiome-modulating properties, while extending lifespan in several animal models. In this study, treatment with Rhodiola rosea improved fasting blood glucose levels, altered the response to exogenous insulin, and decreased circulating lipopolysaccharide and hepatic C-reactive protein transcript levels. We hypothesize that these changes may in part reflect the modulation of the microbiota, resulting in improved gut barrier integrity and decreasing the translocation of inflammatory biomolecules into the bloodstream. These findings indicate that Rhodiola rosea is an attractive candidate for further research in the management of type 2 diabetes.},
}
@article {pmid35732630,
year = {2022},
author = {Sharp, C and Foster, KR},
title = {Host control and the evolution of cooperation in host microbiomes.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3567},
pmid = {35732630},
issn = {2041-1723},
support = {209397/Z/17/Z//Wellcome Trust (Wellcome)/ ; },
abstract = {Humans, and many other species, are host to diverse symbionts. It is often suggested that the mutual benefits of host-microbe relationships can alone explain cooperative evolution. Here, we evaluate this hypothesis with evolutionary modelling. Our model predicts that mutual benefits are insufficient to drive cooperation in systems like the human microbiome, because of competition between symbionts. However, cooperation can emerge if hosts can exert control over symbionts, so long as there are constraints that limit symbiont counter evolution. We test our model with genomic data of two bacterial traits monitored by animal immune systems. In both cases, bacteria have evolved as predicted under host control, tending to lose flagella and maintain butyrate production when host-associated. Moreover, an analysis of bacteria that retain flagella supports the evolution of host control, via toll-like receptor 5, which limits symbiont counter evolution. Our work puts host control mechanisms, including the immune system, at the centre of microbiome evolution.},
}
@article {pmid35732113,
year = {2022},
author = {Fremin, BJ and Bhatt, AS and Kyrpides, NC and , },
title = {Thousands of small, novel genes predicted in global phage genomes.},
journal = {Cell reports},
volume = {39},
number = {12},
pages = {110984},
doi = {10.1016/j.celrep.2022.110984},
pmid = {35732113},
issn = {2211-1247},
abstract = {Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.},
}
@article {pmid35731859,
year = {2022},
author = {Borody, TJ and Dolai, S and Gunaratne, AW and Clancy, RL},
title = {Targeting the microbiome in Crohn's disease.},
journal = {Expert review of clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1080/1744666X.2022.2093186},
pmid = {35731859},
issn = {1744-8409},
}
@article {pmid35731208,
year = {2022},
author = {Lin, D and Hu, Q and Yang, L and Zeng, X and Xiao, Y and Wang, D and Dai, W and Lu, H and Fang, J and Tang, Z and Wang, Z},
title = {The niche-specialist and age-related oral microbial ecosystem: crosstalk with host immune cells in homeostasis.},
journal = {Microbial genomics},
volume = {8},
number = {6},
pages = {},
doi = {10.1099/mgen.0.000811},
pmid = {35731208},
issn = {2057-5858},
abstract = {Although characterization of the baseline oral microbiota has been discussed, the current literature seems insufficient to draw a definitive conclusion on the interactions between the microbes themselves or with the host. This study focuses on the spatial and temporal characteristics of the oral microbial ecosystem in a mouse model and its crosstalk with host immune cells in homeostasis. The V3V4 regions of the 16S rRNA gene of 20 samples from four niches (tongue, buccal mucosa, keratinized gingiva and hard palate) and 10 samples from two life stages (adult and old) were analysed. Flow cytometry (FCM) was used to investigate the resident immune cells. The niche-specialist and age-related communities, characterized based on the microbiota structure, interspecies communications, microbial functions and interactions with immune cells, were addressed. The phylum Firmicutes was the major component in the oral community. The microbial community profiles at the genus level showed that the relative abundances of the genera Bacteroides, Lactobacillus and Porphyromonas were enriched in the gingiva. The abundance of the genera Streptococcus, Faecalibaculum and Veillonella was increased in palatal samples, while the abundance of Neisseria and Bradyrhizobium was enriched in buccal samples. The genera Corynebacterium, Stenotrophomonas, Streptococcus and Fusobacterium were proportionally enriched in old samples, while Prevotella and Lacobacillus were enriched in adult samples. Network analysis showed that the genus Lactobacillus performed as a central node in the buccal module, while in the gingiva module, the central nodes were Nesterenkonia and Hydrogenophilus. FCM showed that the proportion of Th1 cells in the tongue samples (38.18 % [27.03-49.34 %]) (mean [range]) was the highest. The proportion of γδT cells in the buccal mucosa (25.82 % [22.1-29.54 %]) and gingiva (20.42 % [18.31-22.53 %]) samples was higher (P<0.01) than those in the palate (14.18 % [11.69-16.67 %]) and tongue (9.38 % [5.38-13.37 %] samples. The proportion of Th2 (31.3 % [16.16-46.44 %]), Th17 (27.06 % [15.76-38.36 %]) and Treg (29.74 % [15.71-43.77 %]) cells in the old samples was higher than that in the adult samples (P<0.01). Further analysis of the interplays between the microbiomes and immune cells indicated that Th1 cells in the adult group, nd Th2, Th17 and Treg cells in the old group were the main immune factors strongly associated with the oral microbiota. For example, Th2, Th17 and Treg cells showed a significantly positive correlation with age-related microorganisms such as Sphingomonas, Streptococcus and Acinetobacter, while Th1 cells showed a negative correlation. Another positive correlation occurred between Th1 cells and several commensal microbiomes such as Lactobacillus, Jeotgalicoccus and Sporosarcina. Th2, Th17 and Treg cells showed the opposite trend. Together, our findings identify the niche-specialist and age-related characteristics of the oral microbial ecosystem and the potential associations between the microbiomes and the mucosal immune cells, providing critical insights into mucosal microbiology.},
}
@article {pmid35730958,
year = {2022},
author = {Saini, A and Dalal, P and Sharma, D},
title = {Deciphering the Interdependent Labyrinth between Gut Microbiota and the Immune System.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/lam.13775},
pmid = {35730958},
issn = {1472-765X},
abstract = {The human gut microbiome interacts with each other and the host, which has significant effects on health and disease development. Intestinal homeostasis and inflammation are maintained by the dynamic interactions between gut microbiota and the innate and adaptive immune systems. Numerous metabolic products produced by the gut microbiota play a role in mediating cross-talk between gut epithelial and immune cells. In the event of an imbalance between the immune system and microbiota, the body becomes susceptible to infections, and homeostasis is compromised. This review mainly focuses on the interplay between microbes and the immune system, such as, T-cell and B-cell mediated adaptive responses to microbiota and signaling pathways for effective communication between the two. We have also highlighted the role of microbes in the activation of the immune response, the development of memory cells, and how the immune system determines the diversity of human gut microbiota. The review also explains the relationship of commensal microbiota and their relation in the production of immunoglobulins.},
}
@article {pmid35730950,
year = {2022},
author = {Song, H and Yi, S and Kim, WH and Guk, JH and Ha, M and Kwak, I and Han, J and Yeon, SC and Cho, S},
title = {Environmental Perturbations during the Rehabilitation of Wild Migratory Birds Induce Gut Microbiome Alteration and Antibiotic Resistance Acquisition.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0116322},
doi = {10.1128/spectrum.01163-22},
pmid = {35730950},
issn = {2165-0497},
abstract = {Wild migratory birds are essential for sustaining healthy ecosystems, but the effects of a rehabilitation period on their gut microbiomes are still unclear. Here, we performed longitudinal sampling, 16S rRNA sequencing, and antibiotic resistance monitoring of the gut microbiome of six species of wild migratory birds protected as natural monuments in South Korea that are subject to short- or long-term rehabilitation periods. Overall, gut microbiome diversity was significantly decreased in the early stages of rehabilitation, and it did not recover to a level comparable to that of wild birds. Moreover, while the abundance of short-chain fatty acid-producing bacteria decreased, that of zoonotic pathogens increased, indicating rehabilitation-induced dysbiosis. The metabolic pathways involved in the degradation of aromatic pollutants were significantly downregulated, suggesting the depletion of pollutant-degrading microorganisms. Antibiotic resistance of Escherichia coli significantly increased during rehabilitation, particularly ciprofloxacin and tetracycline resistance, and seven of the rehabilitated wild birds acquired multidrug resistance. The diet and habitat changes experienced by wild migratory birds during rehabilitation may have induced the observed gut microbiome dysbiosis and acquisition of antibiotic resistance. These rehabilitation-induced alterations might affect the adaptability of wild birds to their natural environments and contribute to the spread of antibiotic resistance after their release. IMPORTANCE Wild migratory birds are key for ecosystem health but highly sensitive to anthropogenic activities. Therefore, wild migratory birds often undergo rehabilitation to prevent species extinction or biodiversity monitoring. However, the impact of rehabilitation on the gut microbiome of wild migratory birds, which is closely associated with host fitness, remains unclear. For the migratory bird species considered natural monuments in South Korea evaluated here, such impacts could include rehabilitation-induced gut microbiome dysbiosis and acquisition of antibiotic resistance, with possible repercussions on the adaptability of wild birds and spread of antibiotic resistance in the environment after their release. Therefore, the dynamics of the gut microbiome and antibiotic resistance should be considered for implementing sustainable rehabilitation strategies.},
}
@article {pmid35730938,
year = {2022},
author = {O'Connell, LM and Blouin, T and Soule, A and Burne, RA and Nascimento, MM and Richards, VP},
title = {Optimization and Evaluation of the 30S-S11 rRNA Gene for Taxonomic Profiling of Oral Streptococci.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0045322},
doi = {10.1128/aem.00453-22},
pmid = {35730938},
issn = {1098-5336},
abstract = {Dental caries is a multifactorial disease driven by interactions between the highly complex microbial biofilm community and host factors like diet, oral hygiene habits, and age. The oral streptococci are one of the most dominant members of the plaque biofilm and are implicated in disease but also in maintaining oral health. Current methods used for studying the supragingival plaque community commonly sequence portions of the16S rRNA gene, which often cannot taxonomically resolve members of the streptococcal community past the genus level due to their sequence similarity. The goal of this study was to design and evaluate a more reliable and cost-effective method to identify oral streptococci at the species level by applying a new locus, the 30S-S11 rRNA gene, for high-throughput amplicon sequencing. The study results demonstrate that the newly developed single-copy 30S-S11 gene locus resolved multiple amplicon sequence variants (ASVs) within numerous species, providing much improved taxonomic resolution over 16S rRNA V4. Moreover, the results reveal that different ASVs within a species were found to change in abundance at different stages of caries progression. These findings suggest that strains of a single species may perform distinct roles along a biochemical spectrum associated with health and disease. The improved identification of oral streptococcal species will provide a better understanding of the different ecological roles of oral streptococci and inform the design of novel oral probiotic formulations for prevention and treatment of dental caries. IMPORTANCE The microbiota associated with the initiation and progression of dental caries has yet to be fully characterized. Although much insight has been gained from 16S rRNA hypervariable region DNA sequencing, this approach has several limitations, including poor taxonomic resolution at the species level. This is particularly relevant for oral streptococci, which are abundant members of oral biofilm communities and major players in health and caries disease. Here, we develop a new method for taxonomic profiling of oral streptococci based on the 30S-S11 rRNA gene, which provides much improved resolution over 16S rRNA V4 (resolving 10 as opposed to 2 species). Importantly, 30S-S11 can resolve multiple amplicon sequence variants (ASVs) within species, providing an unprecedented insight into the ecological progression of caries. For example, our findings reveal multiple incidences of different ASVs within a species with contrasting associations with health or disease, a finding that has high relevance toward the informed design of prebiotic and probiotic therapy.},
}
@article {pmid35730934,
year = {2022},
author = {Morris, MM and Kimbrel, JA and Geng, H and Tran-Gyamfi, MB and Yu, ET and Sale, KL and Lane, TW and Mayali, X},
title = {Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0023122},
doi = {10.1128/msphere.00231-22},
pmid = {35730934},
issn = {2379-5042},
abstract = {Outdoor cultivation of microalgae has promising potential for renewable bioenergy, but there is a knowledge gap on the structure and function of the algal microbiome that coinhabits these ecosystems. Here, we describe the assembly mechanisms, taxonomic structure, and metabolic potential of bacteria associated with Microchloropsis salina cultivated outdoors. Open mesocosms were inoculated with algal cultures that were either free of bacteria or coincubated with one of two different strains of alga-associated bacteria and were sampled across five time points taken over multiple harvesting rounds of a 40-day experiment. Using quantitative analyses of metagenome-assembled genomes (MAGs), we tracked bacterial community compositional abundance and taxon-specific functional capacity involved in algal-bacterial interactions. One of the inoculated bacteria (Alteromonas sp.) persisted and dispersed across mesocosms, whereas the other inoculated strain (Phaeobacter gallaeciensis) disappeared by day 17 while a taxonomically similar but functionally distinct Phaeobacter strain became established. The inoculated strains were less abundant than 6 numerically dominant newly recruited taxa with functional capacities for mutualistic or saprophytic lifestyles, suggesting a generalist approach to persistence. This includes a highly abundant unclassified Rhodobacteraceae species that fluctuated between 25% and 77% of the total community. Overall, we did not find evidence for priority effects exerted by the distinct inoculum conditions; all mesocosms converged with similar microbial community compositions by the end of the experiment. Instead, we infer that the 15 total populations were retained due to host selection, as they showed high metabolic potential for algal-bacterial interactions such as recycling alga-produced carbon and nitrogen and production of vitamins and secondary metabolites associated with algal growth and senescence, including B vitamins, tropodithietic acid, and roseobacticides. IMPORTANCE Bacteria proliferate in nutrient-rich aquatic environments, including engineered algal biofuel systems, where they remineralize photosynthates, exchange secondary metabolites with algae, and can influence system output of biomass or oil. Despite this, knowledge on the microbial ecology of algal cultivation systems is lacking, and the subject is worthy of investigation. Here, we used metagenomics to characterize the metabolic capacities of the predominant bacteria associated with the biofuel-relevant microalga Microchloropsis salina and to predict testable metabolic interactions between algae and manipulated communities of bacteria. We identified a previously undescribed and uncultivated organism that dominated the community. Collectively, the microbial community may interact with the alga in cultivation via exchange of secondary metabolites which could affect algal success, which we demonstrate as a possible outcome from controlled experiments with metabolically analogous isolates. These findings address the scalability of lab-based algal-bacterial interactions through to cultivation systems and more broadly provide a framework for empirical testing of genome-based metabolic predictions.},
}
@article {pmid35730344,
year = {2022},
author = {Angerami Almeida, K and de Queiroz Andrade, E and Burns, G and Hoedt, EC and Mattes, J and Keely, S and Collison, A},
title = {The Microbiota in Eosinophilic esophagitis: a systematic review.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.15921},
pmid = {35730344},
issn = {1440-1746},
abstract = {BACKGROUND: Eosinophilic esophagitis (EoE) is an atopic disease of the esophagus that has shown a significant increase in incidence and prevalence in the last 20 years. The etiology of EoE is unclear, and few studies explore the esophageal microbiota in EoE. The local microbiome has been implicated in the pathogenesis of several allergic and inflammatory diseases, such as asthma and eczema. In this study, we performed a systematic review to evaluate differences in the microbiota profile of patients with EoE compared to controls.<br><br>METHODS: MEDLINE, Embase, Cochrane Library, Scopus, and CINAHL (Cumulative Index to Nursing and Allied Health Literature) databases were searched to identify studies investigating the microbiota composition in EoE. Three reviewers screened the articles for eligibility and quality. Seven articles underwent full-text review, and a narrative synthesis was undertaken.<br><br>RESULTS: The microbiota of the mouth and esophagus are correlated. Patients with active EoE present increased esophageal microbial load and increased abundance in particular species, such as Haemophilus and Aggregatibacter. On the other hand, EoE patients present a decrease in Firmicutes.<br><br>CONCLUSION: High microbial load and abundance of Haemophilus are observed in EoE patients, but little evidence exists to demonstrate their influence on inflammation and disease.<br><br>TRANSLATIONAL IMPACT: Understanding microbial signatures in EoE might contribute to the development of novel therapeutic strategies.},
}
@article {pmid35730325,
year = {2022},
author = {Muhammad, JS and Siddiqui, R and Khan, NA},
title = {Is there a role of epigenetics in gut microbiome and neurological disorders?.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {},
number = {},
pages = {},
doi = {10.1111/apm.13257},
pmid = {35730325},
issn = {1600-0463},
abstract = {Cross-talk between gut microbiota and the nervous system in the pathophysiology of neurological diseases has become a recent focus of interest. The underlying mechanisms are complex, and we suggest that they might involve gut bacterial metabolite-induced epigenetic modulations of neurodegenerative disorders. Advances in epigenetic techniques could provide the key to understanding the epigenetics of the gut-brain axis.},
}
@article {pmid35729906,
year = {2022},
author = {Williams, SD and Klinges, JG and Zinman, S and Clark, AS and Bartels, E and Villoch Diaz Maurino, M and Muller, EM},
title = {Geographically driven differences in microbiomes of Acropora cervicornis originating from different regions of Florida's Coral Reef.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13574},
doi = {10.7717/peerj.13574},
pmid = {35729906},
issn = {2167-8359},
abstract = {Effective coral restoration must include comprehensive investigations of the targeted coral community that consider all aspects of the coral holobiont-the coral host, symbiotic algae, and microbiome. For example, the richness and composition of microorganisms associated with corals may be indicative of the corals' health status and thus help guide restoration activities. Potential differences in microbiomes of restoration corals due to differences in host genetics, environmental condition, or geographic location, may then influence outplant success. The objective of the present study was to characterize and compare the microbiomes of apparently healthy Acropora cervicornis genotypes that were originally collected from environmentally distinct regions of Florida's Coral Reef and sampled after residing within Mote Marine Laboratory's in situ nursery near Looe Key, FL (USA) for multiple years. By using 16S rRNA high-throughput sequencing, we described the microbial communities of 74 A. cervicornis genotypes originating from the Lower Florida Keys (n = 40 genotypes), the Middle Florida Keys (n = 15 genotypes), and the Upper Florida Keys (n = 19 genotypes). Our findings demonstrated that the bacterial communities of A. cervicornis originating from the Lower Keys were significantly different from the bacterial communities of those originating from the Upper and Middle Keys even after these corals were held within the same common garden nursery for an average of 3.4 years. However, the bacterial communities of corals originating in the Upper Keys were not significantly different from those in the Middle Keys. The majority of the genotypes, regardless of collection region, were dominated by Alphaproteobacteria, namely an obligate intracellular parasite of the genus Ca. Aquarickettsia. Genotypes from the Upper and Middle Keys also had high relative abundances of Spirochaeta bacteria. Several genotypes originating from both the Lower and Upper Keys had lower abundances of Aquarickettsia, resulting in significantly higher species richness and diversity. Low abundance of Aquarickettsia has been previously identified as a signature of disease resistance. While the low-Aquarickettsia corals from both the Upper and Lower Keys had high abundances of an unclassified Proteobacteria, the genotypes in the Upper Keys were also dominated by Spirochaeta. The results of this study suggest that the abundance of Aquarickettsia and Spirochaeta may play an important role in distinguishing bacterial communities among A. cervicornis populations and compositional differences of these bacterial communities may be driven by regional processes that are influenced by both the environmental history and genetic relatedness of the host. Additionally, the high microbial diversity of low-Aquarickettsia genotypes may provide resilience to their hosts, and these genotypes may be a potential resource for restoration practices and management.},
}
@article {pmid35729770,
year = {2022},
author = {Rastall, RA and Diez-Municio, M and Forssten, SD and Hamaker, B and Meynier, A and Moreno, FJ and Respondek, F and Stah, B and Venema, K and Wiese, M},
title = {Structure and function of non-digestible carbohydrates in the gut microbiome.},
journal = {Beneficial microbes},
volume = {13},
number = {2},
pages = {95-168},
doi = {10.3920/BM2021.0090},
pmid = {35729770},
issn = {1876-2891},
abstract = {Together with proteins and fats, carbohydrates are one of the macronutrients in the human diet. Digestible carbohydrates, such as starch, starch-based products, sucrose, lactose, glucose and some sugar alcohols and unusual (and fairly rare) α-linked glucans, directly provide us with energy while other carbohydrates including high molecular weight polysaccharides, mainly from plant cell walls, provide us with dietary fibre. Carbohydrates which are efficiently digested in the small intestine are not available in appreciable quantities to act as substrates for gut bacteria. Some oligo- and polysaccharides, many of which are also dietary fibres, are resistant to digestion in the small intestines and enter the colon where they provide substrates for the complex bacterial ecosystem that resides there. This review will focus on these non-digestible carbohydrates (NDC) and examine their impact on the gut microbiota and their physiological impact. Of particular focus will be the potential of non-digestible carbohydrates to act as prebiotics, but the review will also evaluate direct effects of NDC on human cells and systems.},
}
@article {pmid35729748,
year = {2022},
author = {Sylvain, FÉ and Normandeau, E and Holland, A and Luis Val, A and Derome, N},
title = {Genomics of Serrasalmidae teleosts through the lens of microbiome fingerprinting.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16574},
pmid = {35729748},
issn = {1365-294X},
abstract = {Associations between host genotype and host-associated microbiomes have been shown in a variety of animal clades, but studies on teleosts mostly show weak associations. Our study aimed to explore these relationships in four sympatric Serrasalmidae (i.e. piranha) teleosts from an Amazonian lake, using datasets from the hosts genomes (SNPs from GBS), skin and gut microbiomes (16S rRNA gene metataxonomics), and diets (COI metabarcoding) from the same fish individuals. Firstly, we investigated whether there were significant covariations of microbiome and fish genotypes at the inter and intraspecific levels. We also assessed the extent of co-variation between Serrasalmidae diet and microbiome, to isolate genotypic from dietary effects on community structure. We observed a significant covariation of skin microbiomes and host genotypes at interspecific (R2 =24.4%) and intraspecific (R2 =6.2%) levels, whereas gut microbiomes correlated poorly with host genotypes. Serrasalmidae diet composition was significantly correlated to fish genotype only at the interspecific level (R2 =5.4%), but did not covary with gut microbiome composition (mantel R=-0.04). Secondly, we investigated whether the study of interspecific differentiation could benefit from considering host associated microbial communities in addition to host genotypes. By using a NMDS ordination-based approach, we observed that ordinations from skin and gut species-specific bacterial biomarkers identified through a random forest algorithm, could significantly increase the average interspecific differentiation detected through host genotype data alone. Although future studies encompassing additional species and environments are needed, our results suggest Serrasalmidae microbiomes could constitute an insightful trait to be considered when studying the interspecific differences between members of this clade.},
}
@article {pmid35729677,
year = {2022},
author = {Weinert-Nelson, JR and Biddle, AS and Williams, CA},
title = {Fecal microbiome of horses transitioning between warm-season and cool-season grass pasture within integrated rotational grazing systems.},
journal = {Animal microbiome},
volume = {4},
number = {1},
pages = {41},
pmid = {35729677},
issn = {2524-4671},
support = {gne17-162//Northeast SARE/ ; gne17-162//Northeast SARE/ ; 1003557//National Institute of Food and Agriculture/ ; NJ06170//New Jersey Agricultural Experiment Station/ ; },
abstract = {BACKGROUND: Diet is a key driver of equine hindgut microbial community structure and composition. The aim of this study was to characterize shifts in the fecal microbiota of grazing horses during transitions between forage types within integrated warm- (WSG) and cool-season grass (CSG) rotational grazing systems (IRS). Eight mares were randomly assigned to two IRS containing mixed cool-season grass and one of two warm-season grasses: bermudagrass [Cynodon dactylon (L.) Pers.] or crabgrass [Digitaria sanguinalis (L.) Scop.]. Fecal samples were collected during transitions from CSG to WSG pasture sections (C-W) and WSG to CSG (W-C) on days 0, 2, 4, and 6 following pasture rotation and compared using 16S rRNA gene sequencing.<br><br>RESULTS: Regardless of IRS or transition (C-W vs. W-C), species richness was greater on day 4 and 6 in comparison to day 0 (P < 0.05). Evenness, however, did not differ by day. Weighted UniFrac also did not differ by day, and the most influential factor impacting β-diversity was the individual horse (R2 ≥ 0.24; P = 0.0001). Random forest modeling was unable to accurately predict days within C-W and W-C, but could predict the individual horse based on microbial composition (accuracy: 0.92 ± 0.05). Only three differentially abundant bacterial co-abundance groups (BCG) were identified across days within all C-W and W-C for both IRS (W ≥ 126). The BCG differing by day for all transitions included amplicon sequence variants (ASV) assigned to bacterial groups with known fibrolytic and butyrate-producing functions including members of Lachnospiraceae, Clostridium sensu stricto 1, Anaerovorax the NK4A214 group of Oscillospiraceae, and Sarcina maxima. In comparison, 38 BCG were identified as differentially abundant by horse (W ≥ 704). The ASV in these groups were most commonly assigned to genera associated with degradation of structural carbohydrates included Rikenellaceae RC9 gut group, Treponema, Christensenellaceae R-7 group, and the NK4A214 group of Oscillospiraceae. Fecal pH also did not differ by day.<br><br>CONCLUSIONS: Overall, these results demonstrated a strong influence of individual horse on the fecal microbial community, particularly on the specific composition of fiber-degraders. The equine fecal microbiota were largely stable across transitions between forages within IRS suggesting that the equine gut microbiota adjusted at the individual level to the subtle dietary changes imposed by these transitions. This adaptive capacity indicates that horses can be managed in IRS without inducing gastrointestinal dysfunction.},
}
@article {pmid35729658,
year = {2022},
author = {Xu, X and Ocansey, DKW and Hang, S and Wang, B and Amoah, S and Yi, C and Zhang, X and Liu, L and Mao, F},
title = {The gut metagenomics and metabolomics signature in patients with inflammatory bowel disease.},
journal = {Gut pathogens},
volume = {14},
number = {1},
pages = {26},
pmid = {35729658},
issn = {1757-4749},
support = {SH2019025//The project of Zhenjiang key research and development plan (social development)/ ; SH2020066//The project of Zhenjiang key research and development plan (social development)/ ; SH2019025//The project of Zhenjiang key research and development plan (social development)/ ; },
abstract = {Inflammatory bowel disease (IBD), a chronic gut immune dysregulation and dysbiosis condition is rapidly increasing in global incidence. Regardless, there is a lack of ideal diagnostic markers, while conventional treatment provides scarce desired results, thus, the exploration for better options. Changes in the gut microbial composition and metabolites either lead to or are caused by the immune dysregulation that characterizes IBD. This study examined the fecal metagenomics and metabolomic changes in IBD patients. A total of 30 fecal samples were collected from 15 IBD patients and 15 healthy controls for 16S rDNA gene sequencing and UHPLC/Q-TOF-MS detection of metabolomics. Results showed that there was a severe perturbation of gut bacteria community composition, diversity, metabolites, and associated functions and metabolic pathways in IBD. This included a significantly decreased abundance of Bacteroidetes and Firmicutes, increased disease-associated phyla such as Proteobacteria and Actinobacteria, and increased Escherichia coli and Klebsiella pneumoniae in IBD. A total of 3146 metabolites were detected out of which 135 were differentially expressed between IBD and controls. Metabolites with high sensitivity and specificity in differentiating IBD from healthy individuals included 6,7,4'-trihydroxyisoflavone and thyroxine 4'-o-.beta.-d-glucuronide (AUC = 0.92), normorphine and salvinorin a (AUC = 0.90), and trichostachine (AUC = 0.91). Moreover, the IBD group had significantly affected pathways including primary bile acid biosynthesis, vitamin digestion and absorption, and carbohydrate metabolism. This study reveals that the combined evaluation of metabolites and fecal microbiome can be useful to discriminate between healthy subjects and IBD patients and consequently serve as therapeutic and diagnostic targets.},
}
@article {pmid35729638,
year = {2022},
author = {Zhang, R and Zhang, Q and Chen, Y and Zhao, Q and Zhang, B and Wang, L and Zhou, C and Zhang, Q and Chen, K and Zhang, Y and Hou, X and Chen, H and Liu, X and Ni, M and Jiang, B},
title = {Combined treatment with Rg1 and adipose-derived stem cells alleviates DSS-induced colitis in a mouse model.},
journal = {Stem cell research &amp; therapy},
volume = {13},
number = {1},
pages = {272},
pmid = {35729638},
issn = {1757-6512},
support = {81803926//innovative research group project of the national natural science foundation of china/ ; ZKX17034//science and technology development project of nanjing of china/ ; ZDB2020002//key scientific research projects of jiangsu commission of health/ ; },
abstract = {BACKGROUND: Inflammatory bowel diseases, consisting of Crohn's disease and ulcerative colitis constitute chronic inflammatory conditions that may compromise the whole gastrointestinal tract as well as the colonic mucosa. Currently, there are no curative interventions for IBD, and all available treatments have side effects that limit their use. Adipose-derived stem cell (ADSC) treatment is a prospective treatment option for IBD. Previous findings indicated that ginsenoside (Rg1) dampened inflammatory diseases like colitis by inhibiting the binding of LPS to TLR4 on macrophages and restoring the Th17/Treg ratio. The purpose of this work was to investigate whether Rg1 can increase the influence of ADSC in a mouse model of colitis triggered by dextran sulfate sodium (DSS).<br><br>METHODS: ADSC was intravenously inoculated into mice with DSS-triggered colitis, while Rg1 was delivered via oral gavage. Colon inflammation was assessed via body weight, colon length along with H&amp;E staining. Serum cytokine levels were measured using ELISA. Besides, flow cytometry was adopted to determine the percentage, as well as FMI of immune cells in the spleen. The effects of simultaneous Rg1 and ADSC treatment on TLR4-MyD88 signaling were assessed via immunofluorescence.<br><br>RESULTS: Rg1 and ADSC effectively alleviated the impacts of colon inflammation, weight loss, and colon length reduction along with histological score. Treatment with Rg1 and ADSC reduced serum levels of the proinflammatory cytokines, IL-1β, TNF-α, IL-6, IL-4, and IL-17A and upregulated the level of immunosuppressive cytokine, IL-10. Compared with ADSC or Rg1 alone, combined treatment with Rg1 and ADSC significantly improved the structure of microbial community. Additionally, treatment with Rg1 plus ADSC selectively elevated the level of splenic regulatory T (Treg) cells and downregulated the proportion of T helper type 17 (Th17) cells, indicating restoration of intestinal homeostasis. Besides, we established that the combination of ADSC + Rg1 restored immunological balance more effectively than either ADSC or Rg1 alone, illustrating that Rg1's modulatory function on the gut microbiota may boost the impact of ADSCs in restoration of the immune balance. ADSC combined with Rg1 might downregulate the expression of TLR4 and MyD88, thereby suppressing TLR4-MyD8 signaling. The immunofluorescence results also suggested that co-therapy with Rg-1 and ADSC may optimize treatment strategies of IBD.<br><br>CONCLUSIONS: Here, we find that the combination of Rg1 and ADSC alleviates DSS-induced colitis in a mouse model more efficiently than ADSC alone, indicating that Rg1 enhances the effect of ADSC against colitis.},
}
@article {pmid35729615,
year = {2022},
author = {Al-Ashhab, A and Alexander-Shani, R and Avrahami, Y and Ehrlich, R and Strem, RI and Meshner, S and Shental, N and Sharon, G},
title = {Sparus aurata and Lates calcarifer skin microbiota under healthy and diseased conditions in UV and non-UV treated water.},
journal = {Animal microbiome},
volume = {4},
number = {1},
pages = {42},
pmid = {35729615},
issn = {2524-4671},
support = {709 and 793//ICA Foundation; JCA charitable association/ ; 709 and 793//ICA Foundation; JCA charitable association/ ; 709 and 793//ICA Foundation; JCA charitable association/ ; 709 and 793//ICA Foundation; JCA charitable association/ ; 709 and 793//ICA Foundation; JCA charitable association/ ; 709 and 793//ICA Foundation; JCA charitable association/ ; 709 and 793//ICA Foundation; JCA charitable association/ ; 709 and 793//ICA Foundation; JCA charitable association/ ; },
abstract = {BACKGROUND: The welfare of farmed fish is influenced by numerous environmental and management factors. Fish skin is an important site for immunity and a major route by which infections are acquired. The objective of this study was to characterize bacterial composition variability on skin of healthy, diseased, and recovered Gilthead Seabream (Sparus aurata) and Barramundi (Lates calcarifer). S. aurata, which are highly sensitive to gram-negative bacteria, were challenged with Vibrio harveyi. In addition, and to provide a wider range of infections, both fish species (S. aurata and L. calcarifer) were infected with gram-positive Streptococcus iniae, to compare the response of the highly sensitive L. calcarifer to that of the more resistant S. aurata. All experiments also compared microbial communities found on skin of fish reared in UV (a general practice used in aquaculture) and non-UV treated water tanks.<br><br>RESULTS: Skin swab samples were taken from different areas of the fish (lateral lines, abdomen and gills) prior to controlled infection, and 24, 48 and 72 h, 5 days, one week and one-month post-infection. Fish skin microbial communities were determined using Illumina iSeq100 16S rDNA for bacterial sequencing. The results showed that naturally present bacterial composition is similar on all sampled fish skin sites prior to infection, but the controlled infections (T1 24 h post infection) altered the bacterial communities found on fish skin. Moreover, when the naturally occurring skin microbiota did not quickly recover, fish mortality was common following T1 (24 h post infection). We further confirmed the differences in bacterial communities found on skin and in the water of fish reared in non-UV and UV treated water under healthy and diseased conditions.<br><br>CONCLUSIONS: Our experimental findings shed light on the fish skin microbiota in relation to fish survival (in diseased and healthy conditions). The results can be harnessed to provide management tools for commercial fish farmers; predicting and preventing fish diseases can increase fish health, welfare, and enhance commercial fish yields.},
}
@article {pmid35729515,
year = {2022},
author = {Dai, W and Li, C and Li, T and Hu, J and Zhang, H},
title = {Super-taxon in human microbiome are identified to be associated with colorectal cancer.},
journal = {BMC bioinformatics},
volume = {23},
number = {1},
pages = {243},
pmid = {35729515},
issn = {1471-2105},
support = {R01MH116527 and R01HG010171/NH/NIH HHS/United States ; R01MH116527 and R01HG010171/NH/NIH HHS/United States ; R01MH116527 and R01HG010171/NH/NIH HHS/United States ; R01MH116527 and R01HG010171/NH/NIH HHS/United States ; DMS-2112711//National Science Foundation, United States/ ; },
abstract = {BACKGROUND: Microbial communities in the human body, also known as human microbiota, impact human health, such as colorectal cancer (CRC). However, the different roles that microbial communities play in healthy and disease hosts remain largely unknown. The microbial communities are typically recorded through the taxa counts of operational taxonomic units (OTUs). The sparsity and high correlations among OTUs pose major challenges for understanding the microbiota-disease relation. Furthermore, the taxa data are structured in the sense that OTUs are related evolutionarily by a hierarchical structure.<br><br>RESULTS: In this study, we borrow the idea of super-variant from statistical genetics, and propose a new concept called super-taxon to exploit hierarchical structure of taxa for microbiome studies, which is essentially a combination of taxonomic units. Specifically, we model a genus which consists of a set of OTUs at low hierarchy and is designed to reflect both marginal and joint effects of OTUs associated with the risk of CRC to address these issues. We first demonstrate the power of super-taxon in detecting highly correlated OTUs. Then, we identify CRC-associated OTUs in two publicly available datasets via a discovery-validation procedure. Specifically, four species of two genera are found to be associated with CRC: Parvimonas micra, Parvimonas sp., Peptostreptococcus stomatis, and Peptostreptococcus anaerobius. More importantly, for the first time, we report the joint effect of Parvimonas micra and Parvimonas sp. (p = 0.0084) as well as that of Peptostrepto-coccus stomatis and Peptostreptococcus anaerobius (p = 8.21e-06) on CRC. The proposed approach provides a novel and useful tool for identifying disease-related microbes by taking the hierarchical structure of taxa into account and further sheds new lights on their potential joint effects as a community in disease development.<br><br>CONCLUSIONS: Our work shows that proposed approaches are effective to study the microbiota-disease relation taking into account for the sparsity, hierarchical and correlated structure among microbes.},
}
@article {pmid35729301,
year = {2022},
author = {Shaha, CM and Dar, MA and Pandit, RS},
title = {Mining the diversity and functional profile of bacterial symbionts from the larvae of Chironomus circumdatus (bloodworms).},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {35729301},
issn = {1874-9356},
abstract = {Chironomids are the most abundant aquatic insects in freshwater habitats that can survive in extreme conditions. In this study, as the microbiome provides extended genotype to the host to perform various functions, we explored the microbiota of the Chironomus circumdatus larvae to find out the putative role played by the symbiotic bacteria for the host. The metabarcoding analyses of the larvae revealed that the insect harbors 1771 phylotypes. Out of the various microbial communities found, the majority corresponded to the phyla Proteobacteria (52.59%) and Actinobacteria (20.56%), respectively. The midges also harbored Klebsiella (2.57%), Enterobacter (1.32%), Bacillus (2.29%), and Acinetobacter (2.13%) genera that are involved in detoxification of xenobiotics present in the water. The presence of radiation-resistant genera like Deinococcus, including bacterial species like radiodurans, a highly radiation-resistant bacterium, indicates its potential to support the host's ability to sustain in adverse environments. The functional profiling of the bacteria showed the relative abundance of many enzyme groups, such as transferases (40.62%), oxidoreductases (23.49%), and hydrolases (3.77%). The results indicate that the larvae harbor a considerable variety of bacteria that help the host adapt and survive in the polluted waters. The present study provides thorough insights into the microbiome of the C. circumdatus larvae that can be exploited for the bioremediation of certain pollutants through biomimetic strategies. It also gives us a wake-up call to take a good look at the guts of these disease-carrying insects' inabilities to spread deadly human diseases.},
}
@article {pmid35729225,
year = {2022},
author = {Mayneris-Perxachs, J and Arnoriaga-Rodríguez, M and Garre-Olmo, J and Puig, J and Ramos, R and Trelis, M and Burokas, A and Coll, C and Zapata-Tona, C and Pedraza, S and Pérez-Brocal, V and Ramió, L and Ricart, W and Moya, A and Jové, M and Sol, J and Portero-Otin, M and Pamplona, R and Maldonado, R and Fernández-Real, JM},
title = {Presence of Blastocystis in gut microbiota is associated with cognitive traits and decreased executive function.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {35729225},
issn = {1751-7370},
support = {PI15/01934//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI20/01090//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; CP18/00009//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; CM19/00190//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; },
abstract = {Growing evidence implicates the gut microbiome in cognition. Blastocystis is a common gut single-cell eukaryote parasite frequently detected in humans but its potential involvement in human pathophysiology has been poorly characterized. Here we describe how the presence of Blastocystis in the gut microbiome was associated with deficits in executive function and altered gut bacterial composition in a discovery (n = 114) and replication cohorts (n = 942). We also found that Blastocystis was linked to bacterial functions related to aromatic amino acids metabolism and folate-mediated pyrimidine and one-carbon metabolism. Blastocystis-associated shifts in bacterial functionality translated into the circulating metabolome. Finally, we evaluated the effects of microbiota transplantation. Donor's Blastocystis subtypes led to altered recipient's mice cognitive function and prefrontal cortex gene expression. In summary, Blastocystis warrant further consideration as a novel actor in the gut microbiome-brain axis.},
}
@article {pmid35729185,
year = {2022},
author = {Beterams, A and Calatayud Arroyo, M and De Paepe, K and De Craemer, AS and Elewaut, D and Venken, K and Van de Wiele, T},
title = {In vitro triple coculture with gut microbiota from spondyloarthritis patients is characterized by inter-individual differences in inflammatory responses.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10475},
pmid = {35729185},
issn = {2045-2322},
support = {G062519N//Fonds Wetenschappelijk Onderzoek/ ; G062519N//Fonds Wetenschappelijk Onderzoek/ ; G062519N//Fonds Wetenschappelijk Onderzoek/ ; G062519N//Fonds Wetenschappelijk Onderzoek/ ; BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; BOF17/GOA/032//Bijzonder Onderzoeksfonds UGent/ ; },
abstract = {Spondyloarthritis is a group of chronic inflammatory diseases that primarily affects axial or peripheral joints and is frequently associated with inflammation at non-articular sites. The disease is multifactorial, involving genetics, immunity and environmental factors, including the gut microbiota. In vivo, microbiome contributions are difficult to assess due to the multifactorial disease complexity. In a proof-of-concept approach, we therefore used a triple coculture model of immune-like, goblet and epithelial cells to investigate whether we could detect a differential impact from spondyloarthritis- vs. healthy-derived gut microbiota on host cell response. Despite their phylogenetic resemblance, flow cytometry-based phenotypic clustering revealed human-derived gut microbiota from healthy origin to cluster together and apart from spondyloarthritis donors. At host level, mucus production was higher upon exposure to healthy microbiota. Pro-inflammatory cytokine responses displayed more inter-individual variability in spondyloarthritis than in healthy donors. Interestingly, the high dominance in the initial sample of one patient of Prevotella, a genus previously linked to spondyloarthritis, resulted in the most differential host response upon 16 h host-microbe coincubation. While future research should further focus on inter-individual variability by using gut microbiota from a large cohort of patients, this study underscores the importance of the gut microbiota during the SpA disease course.},
}
@article {pmid35729169,
year = {2022},
author = {Kean, IRL and Wagner, J and Wijeyesekera, A and De Goffau, M and Thurston, S and Clark, JA and White, DK and Ridout, J and Agrawal, S and Kayani, R and O'Donnell, R and Ramnarayan, P and Peters, MJ and Klein, N and Holmes, E and Parkhill, J and Baker, S and Pathan, N},
title = {Profiling gut microbiota and bile acid metabolism in critically ill children.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10432},
pmid = {35729169},
issn = {2045-2322},
support = {215515/WT_/Wellcome Trust/United Kingdom ; GN2751//Action Medical Research/ ; },
abstract = {Broad-spectrum antimicrobial use during the treatment of critical illness influences gastrointestinal fermentation endpoints, host immune response and metabolic activity including the conversion of primary to secondary bile acids. We previously observed reduced fermentation capacity in the faecal microbiota of critically ill children upon hospital admission. Here, we further explore the timecourse of the relationship between the microbiome and bile acid profile in faecal samples collected from critically ill children. The microbiome was assayed by sequencing of the 16S rRNA gene, and faecal water bile acids were measured by liquid chromatography mass spectrometry. In comparison to admission faecal samples, members of the Lachnospiraceae recovered during the late-acute phase (days 8-10) of hospitalisation. Patients with infections had a lower proportion of Lachnospiraceae in their gut microbiota than controls and patients with primary admitting diagnoses. Keystone species linked to ecological recovery were observed to decline with the length of PICU admission. These species were further suppressed in patients with systemic infection, respiratory failure, and undergoing surgery. Bile acid composition recovers quickly after intervention for critical illness which may be aided by the compositional shift in Lachnospiraceae. Our findings suggest gut microbiota recovery can be readily assessed via measurement of faecal bile acids.},
}
@article {pmid35729161,
year = {2022},
author = {Zhang, L and Jonscher, KR and Zhang, Z and Xiong, Y and Mueller, RS and Friedman, JE and Pan, C},
title = {Islet autoantibody seroconversion in type-1 diabetes is associated with metagenome-assembled genomes in infant gut microbiomes.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3551},
pmid = {35729161},
issn = {2041-1723},
support = {R01AT011618//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT011618//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {The immune system of some genetically susceptible children can be triggered by certain environmental factors to produce islet autoantibodies (IA) against pancreatic β cells, which greatly increases their risk for Type-1 diabetes. An environmental factor under active investigation is the gut microbiome due to its important role in immune system education. Here, we study gut metagenomes that are de-novo-assembled in 887 at-risk children in the Environmental Determinants of Diabetes in the Young (TEDDY) project. Our results reveal a small set of core protein families, present in >50% of the subjects, which account for 64% of the sequencing reads. Time-series binning generates 21,536 high-quality metagenome-assembled genomes (MAGs) from 883 species, including 176 species that hitherto have no MAG representation in previous comprehensive human microbiome surveys. IA seroconversion is positively associated with 2373 MAGs and negatively with 1549 MAGs. Comparative genomics analysis identifies lipopolysaccharides biosynthesis in Bacteroides MAGs and sulfate reduction in Anaerostipes MAGs as functional signatures of MAGs with positive IA-association. The functional signatures in the MAGs with negative IA-association include carbohydrate degradation in lactic acid bacteria MAGs and nitrate reduction in Escherichia MAGs. Overall, our results show a distinct set of gut microorganisms associated with IA seroconversion and uncovered the functional genomics signatures of these IA-associated microorganisms.},
}
@article {pmid35728960,
year = {2022},
author = {Nováková, B},
title = {Metabolic dysfunction-associated fatty liver disease (MAFLD) as a more accurate name for NAFLD - common aspects of pathogenesis.},
journal = {Casopis lekaru ceskych},
volume = {161},
number = {2},
pages = {65-71},
pmid = {35728960},
issn = {0008-7335},
abstract = {Non-alcoholic fatty liver disease is considered a common hepatic manifestation of metabolic syndrome. With respect to the pathogenesis of liver steatosis and non-alcoholic steatohepatitis, recently a consensus of international experts proposed a change in the name of the disease to metabolic dysfunction-associated fatty liver disease (MAFLD). The new name should not only better reflect the pathogenesis, but also better stratify risks of the patients treatment and eliminate stigmatization originating from the presence of the term "alcohol" in the name of the disease. This work also emphasizes the common pathophysiological mechanisms involved in both metabolic syndrome and liver steatosis, such as dyslipidemia, insulin resistance, gut dysbiosis, oxidative stress, genetic, epigenetic and hormonal factors.},
}
@article {pmid35728619,
year = {2022},
author = {Alvarenga, DO and Rousk, K},
title = {Unraveling host-microbe interactions and ecosystem functions in moss-bacteria symbioses.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erac091},
pmid = {35728619},
issn = {1460-2431},
abstract = {Mosses are non-vascular plants usually found in moist and shaded areas with ecological importance in several ecosystems. This is especially true in northern latitudes, where mosses are responsible for up to 100 % of primary production in some ecosystems. Mosses establish symbiotic associations with unique bacteria that play key roles in the carbon and nitrogen cycles. For instance, in boreal environments, up to more than 35 % of the nitrogen fixed by diazotrophic symbionts in peatlands is transferred to mosses, directly affecting carbon fixation by the hosts, while moss-associated methanotrophic bacteria contribute with 10-30 % of moss carbon. Further, half of ecosystem N input may derive from moss-cyanobacteria associations in pristine ecosystems. Moss-bacteria interactions have consequences on a global scale since northern environments sequester 20 % of all the carbon generated by forests in the world and stock at least 32 % of global terrestrial carbon. Different moss hosts influence bacteria in distinct ways, which suggests that threats to mosses also threaten unique microbial communities with important ecological and biogeochemical consequences. Mosses have interacted with bacteria since their origin at ~500Ma BP, making these associations ideal models for understanding the evolution of plant-microbe associations and their contribution to biogeochemical cycles.},
}
@article {pmid35728316,
year = {2022},
author = {Liu, J and Wang, P and Wang, Y and Zhang, Y and Xu, T and Zhang, Y and Xi, J and Hou, L and Li, L and Zhang, Z and Lin, Y},
title = {Negative effects of poly(butylene adipate-co-terephthalate) microplastics on Arabidopsis and its root-associated microbiome.},
journal = {Journal of hazardous materials},
volume = {437},
number = {},
pages = {129294},
doi = {10.1016/j.jhazmat.2022.129294},
pmid = {35728316},
issn = {1873-3336},
abstract = {The degradable plastic poly(butylene adipate-co-terephthalate) (PBAT) is considered a potential replacement for low-density polyethylene (LDPE) as the main component of mulch film. However, it is not clear whether PBAT is harmful to the plant-soil system. Thus, we determined the effects of LDPE microplastics (LDPE-MPs) and PBAT microplastics (PBAT-MPs) on the growth of Arabidopsis. The inhibitory effect of PBAT-MPs was greater than that of LDPE-MPs on the growth of Arabidopsis. Transcriptome analysis showed that PBAT-MPs severely disrupted the photosynthetic system of Arabidopsis and increased the expression levels of genes in drug transport-related pathways. PBAT-MPs increased the relative abundances of Bradyrhizobium, Hydrogenophaga, and Arthrobacter in the bulk soil and rhizosphere soil. The abundances of Variovorax, Flavobacterium, and Microbacterium increased in the plant root zone only under PBAT-MPs. Functional prediction analysis suggested that microorganisms in the soil and plant root zone could degrade xenobiotics. Furthermore, the degradation products from PBAT comprising adipic acid, terephthalic acid, and butanediol were more toxic than PBAT-MPs. Our findings demonstrate that PBAT-MPs may be degraded by microorganisms to produce chemicals that are highly toxic to plants. Thus, biodegradable plastics may pose a great risk to the environment.},
}
@article {pmid35728042,
year = {2022},
author = {So, D and Loughman, A and Staudacher, HM},
title = {Effects of a low FODMAP diet on the colonic microbiome in irritable bowel syndrome: a systematic review with meta-analysis.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajcn/nqac176},
pmid = {35728042},
issn = {1938-3207},
abstract = {BACKGROUND: A low FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) diet is increasingly used to manage symptoms in irritable bowel syndrome (IBS). While this approach may alter the colonic microbiome, the nature of these changes has not been comprehensively synthesized.<br><br>OBJECTIVES: The aim of this study was to conduct a systematic review with meta-analysis of randomized controlled trials (RCTs) examining the impact of a low FODMAP diet on the composition and function of the microbiome in patients with IBS.<br><br>DESIGN: A systematic search was conducted for using MEDLINE, EMBASE, CENTRAL and Web of Science from inception to April 2022. Outcomes included diversity of the microbiome, specific bacterial abundances, fecal short-chain fatty acid (SCFA) concentration and fecal pH. For fecal SCFA concentrations and pH, meta-analyses were performed via random-effects model.<br><br>RESULTS: Nine trials involving 403 patients were included. There were no clear effects of the low FODMAP diet on diversity of the microbiome. For Bifidobacteria, a low FODMAP diet consistently led to lower abundance of Bifidobacteria, but there were no clear effects on diversity of the microbiome or abundances of other specific taxa. There were no differences in total fecal SCFA concentration between the low FODMAP diet and control diets [Standardized Mean Difference -0.24 (95% CI: -0.62, 0.13), P = 0.21], nor were there differences for fecal concentrations of specific SCFA or fecal pH.<br><br>CONCLUSIONS: In patients with IBS, the effects of a low FODMAP diet on the colonic microbiome appear to be specific to Bifidobacteria with no consistent impacts on other microbiome metrics, including diversity, fecal SCFA concentrations and fecal pH. Further, adequately powered trials are needed to confirm these findings. Trial registration: CRD42020192243.},
}
@article {pmid35727976,
year = {2022},
author = {Ge, X and Pereira, FC and Mitteregger, M and Berry, D and Zhang, M and Hausmann, B and Zhang, J and Schintlmeister, A and Wagner, M and Cheng, JX},
title = {SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {26},
pages = {e2203519119},
doi = {10.1073/pnas.2203519119},
pmid = {35727976},
issn = {1091-6490},
support = {R35GM136223//HHS | National Institutes of Health (NIH)/ ; R01AI141439//HHS | National Institutes of Health (NIH)/ ; Z383-B//Austrian Science Fund (FWF)/ ; ZK-57//Austrian Science Fund (FWF)/ ; },
abstract = {One of the biggest challenges in microbiome research in environmental and medical samples is to better understand functional properties of microbial community members at a single-cell level. Single-cell isotope probing has become a key tool for this purpose, but the current detection methods for determination of isotope incorporation into single cells do not allow high-throughput analyses. Here, we report on the development of an imaging-based approach termed stimulated Raman scattering-two-photon fluorescence in situ hybridization (SRS-FISH) for high-throughput metabolism and identity analyses of microbial communities with single-cell resolution. SRS-FISH offers an imaging speed of 10 to 100 ms per cell, which is two to three orders of magnitude faster than achievable by state-of-the-art methods. Using this technique, we delineated metabolic responses of 30,000 individual cells to various mucosal sugars in the human gut microbiome via incorporation of deuterium from heavy water as an activity marker. Application of SRS-FISH to investigate the utilization of host-derived nutrients by two major human gut microbiome taxa revealed that response to mucosal sugars tends to be dominated by Bacteroidales, with an unexpected finding that Clostridia can outperform Bacteroidales at foraging fucose. With high sensitivity and speed, SRS-FISH will enable researchers to probe the fine-scale temporal, spatial, and individual activity patterns of microbial cells in complex communities with unprecedented detail.},
}
@article {pmid35727787,
year = {2022},
author = {Baltsavias, S and Van Treuren, W and Sawaby, A and Baker, SW and Sonnenburg, JL and Arbabian, A},
title = {Gut Microbiome Redox Sensors With Ultrasonic Wake-Up and Galvanic Coupling Wireless Links.},
journal = {IEEE transactions on bio-medical engineering},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TBME.2022.3184972},
pmid = {35727787},
issn = {1558-2531},
abstract = {Tools to measure in vivo redox activity of the gut microbiome and its influence on host health are lacking. In this paper, we present the design of new in vivo gut oxidation-reduction potential (ORP) sensors for rodents, to study host-microbe and microbe-environment interactions throughout the gut. These are the first in vivo sensors to combine ultrasonic wake-up and galvanic coupling telemetry, allowing for sensor miniaturization, experiment flexibility, and robust wireless measurements in live rodents. A novel study of in situ ORP along the intestine reveals biogeographical redox features that the ORP sensors can uniquely access in future gut microbiome studies.},
}
@article {pmid35727619,
year = {2022},
author = {Maki, KA and Alkhatib, J and Butera, G and Wallen, GR},
title = {Examining the Relationships Between Sleep Physiology and the Gut Microbiome in Preclinical and Translational Research: Protocol for a Scoping Review.},
journal = {JMIR research protocols},
volume = {11},
number = {6},
pages = {e38605},
doi = {10.2196/38605},
pmid = {35727619},
issn = {1929-0748},
abstract = {BACKGROUND: Sleep is an instrumental behavioral state with evidence supporting its active role in brain function, metabolism, immune function, and cardiovascular systems. Research supports that there are pathways underlying the bidirectional communication between the brain and gastrointestinal system, also known as the "gut-brain axis." Primary research examining sleep and gut microbiome relationships continues to increase. Although current data include both preclinical and clinical research, gut microbiome results are reported through a wide range of metrics (alpha diversity, beta diversity, and bacterial compositional changes), which makes cross-study comparison challenging. Therefore, a synthesis of the research examining sleep and gut microbiome relationships is necessary to understand the state of the science and address gaps in the literature for future research.<br><br>OBJECTIVE: In this paper, we outline a scoping review protocol to evaluate and synthesize preclinical and clinical primary research focused on the associations between sleep and the gut microbiome.<br><br>METHODS: The search strategy was facilitated through a medical research librarian and involved electronic databases including PubMed/MEDLINE, Embase, Scopus, Web of Science, CENTRAL trials database, BIOSIS Citation Index, and the Zoological Record. Gray literature sources including medRxiv and bioRxiv preprint servers were also searched. Studies were screened according to the aims and exclusion and inclusion criteria of the protocol. After screening, data will be extracted and synthesized from the included studies according to predefined sleep and microbiome methodology metrics.<br><br>RESULTS: The search strategy yielded 4622 references that were imported for study screening, and source screening was completed in May 2022 by 2 independent investigators, resulting in a total of 93 sources for data extraction and synthesis. The data synthesis table is expected to be completed by August 2022, and the results will be disseminated through paper submission by December 2022 and presented at conferences related to neuroscience, sleep physiology, bioinformatics, and the microbiome.<br><br>CONCLUSIONS: A scoping review of preclinical and clinical research is needed to synthesize the growing data focused on the relationships between sleep and the gut microbiome. We expect the results of this synthesis will identify gaps in the literature and highlight pathways linking the gut-brain axis and sleep physiology to stimulate future research questions.<br><br>TRIAL REGISTRATION: Open Science Framework 69TBR; https://osf.io/69tbr.<br><br>PRR1-10.2196/38605.},
}
@article {pmid35727522,
year = {2022},
author = {Kon, V and Shelton, EL and Pitzer, A and Yang, HC and Kirabo, A},
title = {Inflammation, Lymphatics, and Cardiovascular Disease: Amplification by Chronic Kidney Disease.},
journal = {Current hypertension reports},
volume = {},
number = {},
pages = {},
pmid = {35727522},
issn = {1534-3111},
support = {1P01HL116263/HL/NHLBI NIH HHS/United States ; K01HL13049/HL/NHLBI NIH HHS/United States ; R03HL155041/HL/NHLBI NIH HHS/United States ; R01HL144941/HL/NHLBI NIH HHS/United States ; R01HD099777//U.S. Department of Health and Human Services/ ; },
abstract = {PURPOSE OF REVIEW: Kidney disease is a strong modulator of the composition and metabolism of the intestinal microbiome that produces toxins and inflammatory factors. The primary pathways for these harmful factors are blood vessels and nerves. Although lymphatic vessels are responsible for clearance of interstitial fluids, macromolecules, and cells, little is known about whether and how kidney injury impacts the intestinal lymphatic network.<br><br>RECENT FINDINGS: Kidney injury stimulates intestinal lymphangiogenesis, activates lymphatic endothelial cells, and increases mesenteric lymph flow. The mesenteric lymph of kidney-injured animals contains increased levels of cytokines, immune cells, isolevuglandin (IsoLG), a highly reactive dicarbonyl, and of apolipoprotein AI (apoAI). IsoLG is increased in the ileum of kidney injured animals, and intestinal epithelial cells exposed to myeloperoxidase produce more IsoLG. IsoLG-modified apoAI directly increases lymphatic vessel contractions and activates lymphatic endothelial cells. Inhibition of IsoLG by carbonyl scavenger treatment reduces intestinal lymphangiogenesis in kidney-injured animals. Research from our group and others suggests a novel mediator (IsoLG-modified apoAI) and a new pathway (intestinal lymphatic network) in the cross talk between kidneys and intestines and heart. Kidney injury activates intestinal lymphangiogenesis and increases lymphatic flow via mechanisms involving intestinally generated IsoLG. The data identify a new pathway in the kidney gut-heart axis and present a new target for kidney disease-induced intestinal disruptions that may lessen the major adverse consequence of kidney impairment, namely cardiovascular disease.},
}
@article {pmid35727505,
year = {2022},
author = {Lee, E and Ahn, H and Park, S and Kim, G and Kim, H and Noh, MG and Kim, Y and Yeon, JS and Park, H},
title = {Staphylococcus epidermidis WF2R11 Suppresses PM2.5-Mediated Activation of the Aryl Hydrocarbon Receptor in HaCaT Keratinocytes.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {35727505},
issn = {1867-1314},
support = {GK12640//Gwangju Institute of Science and Technology/ ; },
abstract = {The skin supports a diverse microbiome whose imbalance is related to skin inflammation and diseases. Exposure to fine particulate matter (PM2.5), a major air pollutant, can adversely affect the skin microbiota equilibrium. In this study, the effect and mechanism of PM2.5 exposure in HaCaT keratinocytes were investigated. PM2.5 stimulated the aryl hydrocarbon receptor (AhR) to produce reactive oxygen species (ROS) in HaCaT cells, leading to mitochondrial dysfunction and intrinsic mitochondrial apoptosis. We observed that the culture medium derived from a particular skin microbe, Staphylococcus epidermidis WF2R11, remarkably reduced oxidative stress in HaCaT cells caused by PM2.5-mediated activation of the AhR pathway. Staphylococcus epidermidis WF2R11 also exhibited inhibition of ROS-induced inflammatory cytokine secretion. Herein, we demonstrated that S. epidermidis WF2R11 could act as a suppressor of AhRs, affect cell proliferation, and inhibit apoptosis. Our results highlight the importance of the clinical application of skin microbiome interventions in the treatment of inflammatory skin diseases.},
}
@article {pmid35727391,
year = {2022},
author = {Yuan, D and Tao, Y and Wang, H and Wang, J and Cao, Y and Cao, W and Pan, S and Yu, Z},
title = {A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer.},
journal = {Investigational new drugs},
volume = {},
number = {},
pages = {},
pmid = {35727391},
issn = {1573-0646},
abstract = {Studies of both, microbiota and target therapy associated with gene mutations in colorectal cancer, (CRC) have attracted increasing attention. However, only a few of them analyzed the combined effects on CRC. we analyzed differences in intestinal microbiota of 44 colorectal cancer patients and 20 healthy controls (HC) using 16S rRNA gene sequencing of fecal samples. For 39 of the CRC patients, targeted Next Generation Sequencing (NGS) was carried out at formalin fixed paraffin embedded (FFPE) samples to identify somatic mutation profiles. Compared to the HC group, the microbial diversity of CRC patients was significantly lower. In the CRC group, we found a microbiome that was significantly enriched for strains of Bifidobacterium, Bacteroides, and Megasphaera whereas in the HC group the abundance of Collinsella, Faecalibacterium, and Agathobacter strains was higher. Among the mutations detected in the CRC group, the APC gene had the highest mutation rate (77%, 30/39). We found that the KRAS mutant type was closely associated with Faecalibacterium, Roseburia, Megamonas, Lachnoclostridium, and Harryflintia. Notably, Spearman correlation analysis showed that KRAS mutations were negatively correlated with the existence of Bifidobacterium and positively correlated with Faecalibacterium. By employing 16S rRNA gene sequencing, we identified more unique features of microbiota profiles in CRC patients. For the first time, our study showed that gene mutations could directly be linked to the microbiota composition of CRC patients. We hypothesize that the effect of a targeted colorectal cancer therapy is also closely related to the colorectal flora, however, this requires further investigation.},
}
@article {pmid35727055,
year = {2022},
author = {LaMartina, EL and Schmoldt, AL and Newton, RJ},
title = {Full-Length 16S rRNA Gene Sequences from Raw Sewage Samples Spanning Geographic and Seasonal Gradients in Conveyance Systems across the United States.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0031922},
doi = {10.1128/mra.00319-22},
pmid = {35727055},
issn = {2576-098X},
abstract = {Wastewater microbiome research often relies on sequencing of hypervariable regions of 16S rRNA genes, which are difficult to classify at refined taxonomic levels. Here, we introduce a data set of near-full-length 16S rRNA genes from samples designed to capture known geographic and seasonal variations in municipal wastewater microbial communities.},
}
@article {pmid35727021,
year = {2022},
author = {Saville, CR and Metris, A and Humphreys, GJ and O'Neill, C and Barrett, P and Fernandez-Piquer, J and McBain, AJ},
title = {Transitory Shifts in Skin Microbiota Composition and Reductions in Bacterial Load and Psoriasin following Ethanol Perturbation.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0017122},
doi = {10.1128/msphere.00171-22},
pmid = {35727021},
issn = {2379-5042},
abstract = {Personal care and hygiene regimens may substantially alter the composition of the skin microbiota through direct and indirect mechanisms. An understanding of the timescales of commensal skin microbiota reestablishment following perturbation is required to inform consumer safety risk assessment, and support product development. In the current investigation, the microbiota of the volar and dorsal forearm of 10 volunteers was sampled immediately before and after wiping with 70% ethanol and at up to 24 h afterwards. Quantitative PCR and amplicon sequencing were used to measure microbial load and composition, and concentrations of the antimicrobial peptide psoriasin were measured using an enzyme-linked immunosorbent assay (ELISA). Ethanol wiping significantly reduced the total bacterial abundance at 2 h post-wipe. Recovery was observed after 6 h for total bacterial populations and for Staphylococcus epidermidis depending on the site tested. Microbiome diversity recovered by 6 h after wiping. Psoriasin concentrations were highly variable between volunteers, ranging from 42 to 1,569 ng/mL, and dorsal concentrations were significantly higher than volar concentrations (P < 0.05). For most of the volunteers, the application of ethanol decreased psoriasin concentrations, particularly for the dorsal samples, but the overall effect was not significant. This work extends observations of skin microbiome stability and demonstrates resilience in a key antimicrobial peptide. IMPORTANCE An understanding of the timescales of commensal skin microbiota reestablishment following perturbation is required to inform consumer safety risk assessment and support product development. Following ethanol exposure, total bacterial populations and microbiome diversity recovered after 6 h. For most of the volunteers, the application of ethanol decreased psoriasin concentrations, but the overall effect was not significant. This work extends observations of skin microbiome stability and demonstrates resilience in a key antimicrobial peptide.},
}
@article {pmid35726918,
year = {2022},
author = {Brumfield, KD and Leddy, M and Usmani, M and Cotruvo, JA and Tien, CT and Dorsey, S and Graubics, K and Fanelli, B and Zhou, I and Registe, N and Dadlani, M and Wimalarante, M and Jinasena, D and Abayagunawardena, R and Withanachchi, C and Huq, A and Jutla, A and Colwell, RR},
title = {Microbiome Analysis for Wastewater Surveillance during COVID-19.},
journal = {mBio},
volume = {},
number = {},
pages = {e0059122},
doi = {10.1128/mbio.00591-22},
pmid = {35726918},
issn = {2150-7511},
abstract = {Wastewater surveillance (WS), when coupled with advanced molecular techniques, offers near real-time monitoring of community-wide transmission of SARS-CoV-2 and allows assessing and mitigating COVID-19 outbreaks, by evaluating the total microbial assemblage in a community. Composite wastewater samples (24 h) were collected weekly from a manhole between December 2020 and November 2021 in Maryland, USA. RT-qPCR results showed concentrations of SARS-CoV-2 RNA recovered from wastewater samples reflected incidence of COVID-19 cases. When a drastic increase in COVID-19 was detected in February 2021, samples were selected for microbiome analysis (DNA metagenomics, RNA metatranscriptomics, and targeted SARS-CoV-2 sequencing). Targeted SARS-CoV-2 sequencing allowed for detection of important genetic mutations, such as spike: K417N, D614G, P681H, T716I, S982A, and D1118H, commonly associated with increased cell entry and reinfection. Microbiome analysis (DNA and RNA) provided important insight with respect to human health-related factors, including detection of pathogens and their virulence/antibiotic resistance genes. Specific microbial species comprising the wastewater microbiome correlated with incidence of SARS-CoV-2 RNA, suggesting potential association with SARS-CoV-2 infection. Climatic conditions, namely, temperature, were related to incidence of COVID-19 and detection of SARS-CoV-2 in wastewater, having been monitored as part of an environmental risk score assessment carried out in this study. In summary, the wastewater microbiome provides useful public health information, and hence, a valuable tool to proactively detect and characterize pathogenic agents circulating in a community. In effect, metagenomics of wastewater can serve as an early warning system for communicable diseases, by providing a larger source of information for health departments and public officials. IMPORTANCE Traditionally, testing for COVID-19 is done by detecting SARS-CoV-2 in samples collected from nasal swabs and/or saliva. However, SARS-CoV-2 can also be detected in feces of infected individuals. Therefore, wastewater samples can be used to test all individuals of a community contributing to the sewage collection system, i.e., the infrastructure, such as gravity pipes, manholes, tanks, lift stations, control structures, and force mains, that collects used water from residential and commercial sources and conveys the flow to a wastewater treatment plant. Here, we profile community wastewater collected from a manhole, detect presence of SARS-CoV-2, identify genetic mutations of SARS-CoV-2, and perform COVID-19 risk score assessment of the study area. Using metagenomics analysis, we also detect other microorganisms (bacteria, fungi, protists, and viruses) present in the samples. Results show that by analyzing all microorganisms present in wastewater, pathogens circulating in a community can provide an early warning for contagious diseases.},
}
@article {pmid35726797,
year = {2022},
author = {Zhong, M and Yan, Y and Yuan, H and A, R and Xu, G and Cai, F and Yang, Y and Wang, Y and Zhang, W},
title = {Astragalus mongholicus polysaccharides ameliorate hepatic lipid accumulation and inflammation as well as modulate gut microbiota in NAFLD rats.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d2fo01009g},
pmid = {35726797},
issn = {2042-650X},
abstract = {Hepatic lipid accumulation, inflammation and gut microbiota dysbiosis are hallmarks of non-alcoholic fatty liver disease (NAFLD), which is the leading cause of chronic liver disease with no therapeutic consensus. The aim of the present study was to elucidate the mechanism of the effects of Astragalus mongholicus polysaccharides (mAPS) on lipid metabolism, inflammation and gut microbiota in a rat model of NAFLD induced by a high-fat diet (HFD). Our results showed that mAPS and Berberine supplementation reduced HFD-induced increases in body weight, alanine aminotransferase (ALT), aspartate aminotransferase (AST) and homeostasis model assessment of insulin resistance (HOMA-IR), and these changes were accompanied by improved histological changes in the liver. Moreover, administration of mAPS and Berberine resulted in lower levels of serum triglycerides, total cholesterol and low-density lipoprotein cholesterol (LDL-c) but higher levels of high-density lipoprotein cholesterol (HDL-c) in HFD-fed rats. mAPS and Berberine treatment markedly reduced HFD-induced hepatic lipid accumulation, which was associated with increased expression of phosphorylated- adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK) and peroxisome proliferator-activated receptor-α (PPAR-α) but decreased expression of sterol-regulatory element binding proteins (SREBP-1). Pretreatment with mAPS or Berberine reduced HFD-induced expression of proinflammatory cytokines, such as tumor necrosis factor-α (TNF-α). In addition, mAPS downregulated the expression of colonic and hepatic Toll-like receptor 4 (TLR4) as well as phosphorylated- nuclear factor-κB (NF-κB) and nucleotide-binding domain, leucine-rich repeat-containing receptor, pyrin domain-containing-3 (NLRP3) but upregulated the expression of zonula occludens-1 (ZO-1) and occludin in HFD-fed rats. Notably, mAPS treatment reshaped the intestinal microbiome by lowering the Firmicutes to Bacteroidetes (F/B) ratio and increasing the abundance of Proteobacteria and Epsilonbacteria. mAPS supplementation had little effect on the profile of fecal short-chain fatty acids (SCFAs), but it significantly decreased the expression of colonic and hepatic G-protein coupled receptor (GPR) 41 and 43. Therefore, mAPS supplementation ameliorates hepatic inflammation and lipid accumulation in NAFLD by modulating the gut microbiota and SCFA-GPR signaling pathways. The present study provides new evidence for mAPS as a natural active substance in the treatment of NAFLD.},
}
@article {pmid35726110,
year = {2022},
author = {Anderson, KM and Ferranti, EP and Alagha, EC and Mykityshyn, E and French, CE and Reilly, CM},
title = {The heart and gut relationship: a systematic review of the evaluation of the microbiome and trimethylamine-N-oxide (TMAO) in heart failure.},
journal = {Heart failure reviews},
volume = {},
number = {},
pages = {},
pmid = {35726110},
issn = {1573-7322},
abstract = {There is an expanding body of research on the bidirectional relationship of the human gut microbiome and cardiovascular disease, including heart failure (HF). Researchers are examining the microbiome and gut metabolites, primarily trimethylamine-N-oxide (TMAO), to understand clinically observed outcomes. This systematic review explored the current state of the science on the evaluation and testing of the gut biome in persons with HF. Using electronic search methods of Medline, Embase, CINAHL, and Web of Science, until December 2021, we identified 511 HF biome investigations between 2014 and 2021. Of the 30 studies included in the review, six were 16S rRNA and nineteen TMAO, and three both TMAO and 16S rRNA, and two bacterial cultures. A limited range of study designs were represented, the majority involving single cohorts (n = 10) and comparing individuals with HF to controls (n = 15). Patients with HF had less biodiversity in fecal samples compared to controls. TMAO is associated with age, BNP, eGFR, HF severity, and poor outcomes including hospitalizations and mortality. Inconsistent across studies was the ability of TMAO to predict HF development, the independent prognostic value of TMAO when controlling for renal indices, and the relationship of TMAO to LVEF and CRP. Gut microbiome dysbiosis is associated with HF diagnosis, disease severity, and prognostication related to hospitalizations and mortality. Gut microbiome research in patients with HF is developing. Further longitudinal and multi-centered studies are required to inform interventions to promote clinical decision-making and improved patient outcomes.},
}
@article {pmid35726098,
year = {2022},
author = {Heydari, S and Malekzadeh, R and Jazayeri, MH and Sarrafnejad, A and Siavoshi, F},
title = {Detection of peptidoglycan in yeast as a marker for the presence or abundance of intracellular Helicobacter pylori and Staphylococcus.},
journal = {Archives of microbiology},
volume = {204},
number = {7},
pages = {407},
pmid = {35726098},
issn = {1432-072X},
mesh = {DNA, Ribosomal ; Fluorescein-5-isothiocyanate ; *Helicobacter pylori/genetics ; Peptidoglycan ; Staphylococcus/genetics ; Yeasts/genetics ; },
abstract = {Peptidoglycan (PG) was targeted as the marker for bacterial occurrence inside yeast. Detection of only few bacteria in old and new generations of yeast raised the question of how yeast controls the abundance of its intracellular bacteria. One gastric C. tropicalis that showed concurrence of H. pylori and Staphylococcus 16S rDNA was stained for assessing the viability of intracellular bacteria. Fluorescein isothiocyanate (FITC)-labeled anti-PG monoclonal antibody (APGMAb) was used for detection of PG inside yeast by direct immunofluorescence. APGMAb-coated magnetic beads were used for separation of bacteria from disrupted yeasts. Bead-bound bacteria were separated, fixed, stained, and examined by scanning electron microscope (SEM). Bead-bound bacteria were cultured and identified by amplification and sequencing of 16S rDNA. Fluorescence microscopy demonstrated occurrence of few live bacteria inside yeast cells. FITC- APGMAb interacted with PG of intracellular bacteria, appearing as few green spots in mother and daughter yeast cells. Interestingly, PG fragments were also detected in the exterior of yeast cells. SEM observations showed separated bead-bound bacilli and cocci. Culture of Staphylococcus was positive. Sequencing results confirmed identity of separated bacteria as H. pylori and Staphylococcus. PG detected inside yeast may have belonged to H. pylori, Staphylococcus or any other intracellular bacteria that coexisted in yeast as its microbiome. Detection of only few intracellular bacteria in old and new generations of yeast as well as PG fragments in their exterior suggested that yeast controls the abundance of its intracellular bacteria at low rate by hydrolysis and exporting of PG.},
}
@article {pmid35715833,
year = {2022},
author = {Cui, GY and Rao, BC and Zeng, ZH and Wang, XM and Ren, T and Wang, HY and Luo, H and Ren, HY and Liu, C and Ding, SY and Tan, JJ and Liu, ZG and Zou, YW and Ren, ZG and Yu, ZJ},
title = {Characterization of oral and gut microbiome and plasma metabolomics in COVID-19 patients after 1-year follow-up.},
journal = {Military Medical Research},
volume = {9},
number = {1},
pages = {32},
pmid = {35715833},
issn = {2054-9369},
support = {2018YFC2000501//National Key Research and Development Program of China/ ; U2004121//National Natural Science Foundation of China/ ; 82070643//National Natural Science Foundation of China/ ; U1904164//National Natural Science Foundation of China/ ; },
mesh = {*COVID-19 ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Humans ; Metabolomics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Due to the outbreak and rapid spread of coronavirus disease 2019 (COVID-19), more than 160 million patients have become convalescents worldwide to date. Significant alterations have occurred in the gut and oral microbiome and metabonomics of patients with COVID-19. However, it is unknown whether their characteristics return to normal after the 1-year recovery.<br><br>METHODS: We recruited 35 confirmed patients to provide specimens at discharge and one year later, as well as 160 healthy controls. A total of 497 samples were prospectively collected, including 219 tongue-coating, 129 stool and 149 plasma samples. Tongue-coating and stool samples were subjected to 16S rRNA sequencing, and plasma samples were subjected to untargeted metabolomics testing.<br><br>RESULTS: The oral and gut microbiome and metabolomics characteristics of the 1-year convalescents were restored to a large extent but did not completely return to normal. In the recovery process, the microbial diversity gradually increased. Butyric acid-producing microbes and Bifidobacterium gradually increased, whereas lipopolysaccharide-producing microbes gradually decreased. In addition, sphingosine-1-phosphate, which is closely related to the inflammatory factor storm of COVID-19, increased significantly during the recovery process. Moreover, the predictive models established based on the microbiome and metabolites of patients at the time of discharge reached high efficacy in predicting their neutralizing antibody levels one year later.<br><br>CONCLUSIONS: This study is the first to characterize the oral and gut microbiome and metabonomics in 1-year convalescents of COVID-19. The key microbiome and metabolites in the process of recovery were identified, and provided new treatment ideas for accelerating recovery. And the predictive models based on the microbiome and metabolomics afford new insights for predicting the recovery situation which benefited affected individuals and healthcare.},
}
@article {pmid35715821,
year = {2022},
author = {Connell, E and Le Gall, G and Pontifex, MG and Sami, S and Cryan, JF and Clarke, G and Müller, M and Vauzour, D},
title = {Microbial-derived metabolites as a risk factor of age-related cognitive decline and dementia.},
journal = {Molecular neurodegeneration},
volume = {17},
number = {1},
pages = {43},
pmid = {35715821},
issn = {1750-1326},
mesh = {Aging ; *Cognitive Dysfunction ; *Dementia ; *Gastrointestinal Microbiome/physiology ; Humans ; Risk Factors ; },
abstract = {A consequence of our progressively ageing global population is the increasing prevalence of worldwide age-related cognitive decline and dementia. In the absence of effective therapeutic interventions, identifying risk factors associated with cognitive decline becomes increasingly vital. Novel perspectives suggest that a dynamic bidirectional communication system between the gut, its microbiome, and the central nervous system, commonly referred to as the microbiota-gut-brain axis, may be a contributing factor for cognitive health and disease. However, the exact mechanisms remain undefined. Microbial-derived metabolites produced in the gut can cross the intestinal epithelial barrier, enter systemic circulation and trigger physiological responses both directly and indirectly affecting the central nervous system and its functions. Dysregulation of this system (i.e., dysbiosis) can modulate cytotoxic metabolite production, promote neuroinflammation and negatively impact cognition. In this review, we explore critical connections between microbial-derived metabolites (secondary bile acids, trimethylamine-N-oxide (TMAO), tryptophan derivatives and others) and their influence upon cognitive function and neurodegenerative disorders, with a particular interest in their less-explored role as risk factors of cognitive decline.},
}
@article {pmid35715810,
year = {2022},
author = {Becker, MF and Hellmann, M and Knief, C},
title = {Spatio-temporal variation in the root-associated microbiota of orchard-grown apple trees.},
journal = {Environmental microbiome},
volume = {17},
number = {1},
pages = {31},
pmid = {35715810},
issn = {2524-6372},
abstract = {BACKGROUND: The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Studies about spatio-temporal variation of the root-associated microbiome focused so far primarily on community-compositional changes of annual plants, while little is known about their perennial counterparts. The aim of this work was to get deep insight into the spatial patterns and temporal dynamics of the root associated microbiota of apple trees.<br><br>RESULTS: The bacterial community structure in rhizospheric soil and endospheric root material from orchard-grown apple trees was characterized based on 16S rRNA gene amplicon sequencing. At the small scale, the rhizosphere and endosphere bacterial communities shifted gradually with increasing root size diameter (PERMANOVA R2-values up to 0.359). At the larger scale, bulk soil heterogeneity introduced variation between tree individuals, especially in the rhizosphere microbiota, while the presence of a root pathogen was contributing to tree-to-tree variation in the endosphere microbiota. Moreover, the communities of both compartments underwent seasonal changes and displayed year-to-year variation (PERMANOVA R2-values of 0.454 and 0.371, respectively).<br><br>CONCLUSIONS: The apple tree root-associated microbiota can be spatially heterogeneous at field scale due to soil heterogeneities, which particularly influence the microbiota in the rhizosphere soil, resulting in tree-to-tree variation. The presence of pathogens can contribute to this variation, though primarily in the endosphere microbiota. Smaller-scale spatial heterogeneity is observed in the rhizosphere and endosphere microbiota related to root diameter, likely influenced by root traits and processes such as rhizodeposition. The microbiota is also subject to temporal variation, including seasonal effects and annual variation. As a consequence, responses of the tree root microbiota to further environmental cues should be considered in the context of this spatio-temporal variation.},
}
@article {pmid35715496,
year = {2022},
author = {Shell, WA and Rehan, SM},
title = {Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {603},
pmid = {35715496},
issn = {2399-3642},
support = {9659-15//National Geographic Society/ ; },
mesh = {Agriculture ; Animals ; Bees ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Plants ; },
abstract = {The holobiont approach proposes that species are most fully understood within the context of their associated microbiomes, and that both host and microbial community are locked in a mutual circuit of co-evolutionary selection. Bees are an ideal group for this approach, as they comprise a critical group of pollinators that contribute to both ecological and agricultural health worldwide. Metagenomic analyses offer comprehensive insights into an organism's microbiome, diet, and viral load, but remain largely unapplied to wild bees. Here, we present metagenomic data from three species of carpenter bees sampled from around the globe, representative of the first ever carpenter bee core microbiome. Machine learning, co-occurrence, and network analyses reveal that wild bee metagenomes are unique to host species. Further, we find that microbiomes are likely strongly affected by features of their local environment, and feature evidence of plant pathogens previously known only in honey bees. Performing the most comprehensive comparative analysis of bee microbiomes to date we discover that microbiome diversity is inversely proportional to host species social complexity. Our study helps to establish some of the first wild bee hologenomic data while offering powerful empirical insights into the biology and health of vital pollinators.},
}
@article {pmid35715467,
year = {2022},
author = {Korgan, AC and Foxx, CL and Hashmi, H and Sago, SA and Stamper, CE and Heinze, JD and O'Leary, E and King, JL and Perrot, TS and Lowry, CA and Weaver, ICG},
title = {Effects of paternal high-fat diet and maternal rearing environment on the gut microbiota and behavior.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10179},
pmid = {35715467},
issn = {2045-2322},
support = {MED-SS-2014-9644//Nova Scotia Health Research Foundation/ ; RGPIN-2014-04348//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2013-436204//Natural Sciences and Engineering Research Council of Canada/ ; 1R21MH116263/MH/NIMH NIH HHS/United States ; CTGG1-2020-3064//Colorado Office of Economic Development and International Trade Advanced Industries Accelerator Program/ ; },
mesh = {Animals ; Diet, High-Fat/adverse effects ; Fathers ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; RNA, Ribosomal, 16S/genetics ; Rats ; },
abstract = {Exposing a male rat to an obesogenic high-fat diet (HFD) influences attractiveness to potential female mates, the subsequent interaction of female mates with infant offspring, and the development of stress-related behavioral and neural responses in offspring. To examine the stomach and fecal microbiome's potential roles, fecal samples from 44 offspring and stomach samples from offspring and their fathers were collected and bacterial community composition was studied by 16 small subunit ribosomal RNA (16S rRNA) gene sequencing. Paternal diet (control, high-fat), maternal housing conditions (standard or semi-naturalistic housing), and maternal care (quality of nursing and other maternal behaviors) affected the within-subjects alpha-diversity of the offspring stomach and fecal microbiomes. We provide evidence from beta-diversity analyses that paternal diet and maternal behavior induced community-wide shifts to the adult offspring gut microbiome. Additionally, we show that paternal HFD significantly altered the adult offspring Firmicutes to Bacteroidetes ratio, an indicator of obesogenic potential in the gut microbiome. Additional machine-learning analyses indicated that microbial species driving these differences converged on Bifidobacterium pseudolongum. These results suggest that differences in early-life care induced by paternal diet and maternal care significantly influence the microbiota composition of offspring through the microbiota-gut-brain axis, having implications for adult stress reactivity.},
}
@article {pmid35715396,
year = {2022},
author = {Kim, CS and Shin, GE and Cheong, Y and Shin, JH and Shin, DM and Chun, WY},
title = {Experiencing social exclusion changes gut microbiota composition.},
journal = {Translational psychiatry},
volume = {12},
number = {1},
pages = {254},
pmid = {35715396},
issn = {2158-3188},
mesh = {Adult ; Anxiety ; *Gastrointestinal Microbiome/physiology ; Humans ; *Microbiota ; Pain ; Social Isolation ; },
abstract = {Gut microbiota is suggested to regulate the host's mental health via the gut-brain axis. In this study, we investigated the relationship between the microbiome and psychological pain due to social exclusion. Adult individuals with (n = 14) and without (n = 25) social exclusion experience were assessed for the psychological status using self-reported questionnaires: Beck Anxiety Inventory (BAI), Beck Depression Inventory, and the UCLA Loneliness Scale. The gut microbiota was analyzed by 16 S rRNA gene sequencing and bioinformatics. The exclusion group had a 1.70-fold higher total BAI score and 2.16-fold higher levels of anxiety-related physical symptoms (p < 0.05). The gut microbial profiles also differed between the two groups. The exclusion group showed higher probability of having Prevotella-enriched microbiome (odds ratio, 2.29; 95% confidence interval, 1.65-2.75; p < 0.05), a significantly reduced Firmicutes/Bacteroidetes ratio, and decreased abundance of Faecalibacterium spp. (p < 0.05) which was associated with the duration and intensity of social exclusion (p < 0.05). Our results indicate that the psychological pain due to social exclusion is correlated with the gut microbiota composition, suggesting that targeting social exclusion-related microorganisms can be a new approach to solving psychological problems and related social issues.},
}
@article {pmid35715385,
year = {2022},
author = {Gronniger, JL and Wang, Z and Brandt, GR and Ward, CS and Tsementzi, D and Mu, H and Gu, J and Johnson, ZI and Konstantinidis, KT and Hunt, DE},
title = {Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16086},
pmid = {35715385},
issn = {1462-2920},
support = {ICER 2033934//National Science Foundation/ ; OCE 1416665//National Science Foundation/ ; OCE 1416673//National Science Foundation/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; },
abstract = {Disturbances, here defined as events that directly alter microbial community composition, are commonly studied in host-associated and engineered systems. In spite of global change both altering environmental averages and increasing extreme events, there has been relatively little research into the causes, persistence and population-level impacts of disturbance in the dynamic coastal ocean. Here, we utilize 3 years of observations from a coastal time series to identify disturbances based on the largest week-over-week changes in the microbiome (i.e. identifying disturbance as events that alter the community composition). In general, these microbiome disturbances were not clearly linked to specific environmental factors and responsive taxa largely differed, aside from SAR11, which generally declined. However, several disturbance metagenomes identified increased phage-associated genes, suggesting that unexplained community shifts might be caused by increased mortality. Furthermore, a category 1 hurricane, the only event that would likely be classified a priori as an environmental disturbance, was not an outlier in microbiome composition, but did enhance a bloom in seasonally abundant phytoplankton. Thus, as extreme environmental changes intensify, assumptions of what constitutes a disturbance should be re-examined in the context of ecological history and microbiome responses.},
}
@article {pmid35725732,
year = {2022},
author = {Odrzywolek, K and Karwowska, Z and Majta, J and Byrski, A and Milanowska-Zabel, K and Kosciolek, T},
title = {Deep embeddings to comprehend and visualize microbiome protein space.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10332},
pmid = {35725732},
issn = {2045-2322},
support = {POIR.01.01.01-00-0347/17//European Regional Development Fund/ ; 2019/35/D/NZ2/04353//Narodowe Centrum Nauki/ ; 2019/35/D/NZ2/04353//Narodowe Centrum Nauki/ ; PPN/PPO/2018/1/00014//Narodowa Agencja Wymiany Akademickiej/ ; },
mesh = {Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Proteins/genetics ; },
abstract = {Understanding the function of microbial proteins is essential to reveal the clinical potential of the microbiome. The application of high-throughput sequencing technologies allows for fast and increasingly cheaper acquisition of data from microbial communities. However, many of the inferred protein sequences are novel and not catalogued, hence the possibility of predicting their function through conventional homology-based approaches is limited, which indicates the need for further research on alignment-free methods. Here, we leverage a deep-learning-based representation of proteins to assess its utility in alignment-free analysis of microbial proteins. We trained a language model on the Unified Human Gastrointestinal Protein catalogue and validated the resulting protein representation on the bacterial part of the SwissProt database. Finally, we present a use case on proteins involved in SCFA metabolism. Results indicate that the deep learning model manages to accurately represent features related to protein structure and function, allowing for alignment-free protein analyses. Technologies that contextualize metagenomic data are a promising direction to deeply understand the microbiome.},
}
@article {pmid35725658,
year = {2022},
author = {Liu, H and Qu, X and Yin, X and Li, J and Cao, Y and Wang, Y and Chen, L and Zhang, Z and Han, F and Wang, C and Zhang, Z},
title = {Intestinal microbiome and metabolome changes induced by sevoflurane, propofol, and sevoflurane-propofol anaesthesia in patients undergoing nephrectomy.},
journal = {British journal of anaesthesia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bja.2022.04.028},
pmid = {35725658},
issn = {1471-6771},
}
@article {pmid35724951,
year = {2022},
author = {Huang, YJ and Porsche, C and Kozik, AJ and Lynch, SV},
title = {Microbiome-Immune Interactions in Allergy and Asthma.},
journal = {The journal of allergy and clinical immunology. In practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaip.2022.05.038},
pmid = {35724951},
issn = {2213-2201},
abstract = {The human microbiota has been established as a key regulator of host health, in large part due to its constant interaction with, and impact on, host immunity. A range of environmental exposures, spanning from the prenatal period through adulthood are now known to impact the composition and molecular productivity of microbiomes across mucosal and dermal tissues with short- and long-term consequences for host immune function. Here we review the more recent findings in the field that provide insights into how microbial-immune interactions promote and sustain immune dysfunction associated with allergy and asthma. We consider both early life microbiome perturbation and the molecular underpinnings of immune dysfunction associated with subsequent allergy and asthma development in childhood, as well as microbiome features that relate to phenotypic attributes of allergy and asthma in older patients with established disease.},
}
@article {pmid35724813,
year = {2022},
author = {Hsu, CN and Yu, HR and Lin, IC and Tiao, MM and Huang, LT and Hou, CY and Chang-Chien, GP and Lin, S and Tain, YL},
title = {Sodium Butyrate Modulates Blood Pressure and Gut Microbiota in Maternal Tryptophan-Free Diet-induced Hypertension Rat Offspring.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {109090},
doi = {10.1016/j.jnutbio.2022.109090},
pmid = {35724813},
issn = {1873-4847},
abstract = {Maternal nutrition, gut microbiome composition, and metabolites derived from gut microbiota are closely related to the development of hypertension in offspring. A plethora of metabolites generated from diverse tryptophan metabolic pathways show both beneficial and harmful effects. Butyrate, one of the short-chain fatty acids (SCFAs), has shown vasodilation effects. We examined whether sodium butyrate administration in pregnancy and lactation can prevent hypertension induced by a maternal tryptophan-free diet in adult progeny and explored the protective mechanisms. Pregnant Sprague-Dawley rats received normal chow (CN), tryptophan-free diet (TF), sodium butyrate 400 mg/kg/day in drinking water (CNSB), or TF diet plus sodium butyrate (TFSB) in pregnancy and lactation. Male offspring were sacrificed at the age of 16 weeks (n = 8 per group). Compared with normal chow, offspring exposed to the maternal tryptophan-free diet had markedly increased blood pressure, associated with activation of the renin-angiotensin system (RAS). Treatment with sodium butyrate rescued maternal TF-exposed offspring from hypertension. The protective effect of sodium butyrate is related to alterations to microbiome composition, increased renal expression of SCFA receptor G protein-coupled receptor 41 (GPR41) and GPR109A, and restoration of RAS balance. In summary, these results suggest that sodium butyrate protects against maternal TF-induced offspring hypertension, likely by modulating gut microbiota, its derived metabolites, and the RAS.},
}
@article {pmid35724791,
year = {2022},
author = {Leroy-Freitas, D and Machado, EC and Torres-Franco, AF and Dias, MF and Leal, CD and Araújo, JC},
title = {Exploring the microbiome, antibiotic resistance genes, mobile genetic element, and potential resistant pathogens in municipal wastewater treatment plants in Brazil.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {156773},
doi = {10.1016/j.scitotenv.2022.156773},
pmid = {35724791},
issn = {1879-1026},
abstract = {Wastewater treatment plants (WWTPs) have been widely investigated in Europe, Asia and North America regarding the occurrence and fate of antibiotic resistance (AR) elements, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and antibiotic resistant bacteria and pathogens. However, monitoring data about AR elements in municipal WWTPs in Brazil are scarce. This study investigated the abundance of intI1, five ARGs (sul1, tetA, blaTEM, ermB and qnrB) and 16S rRNA in raw and treated wastewater of three WWTPs, using different sewage treatments named CAS (Conventional activated sludge), UASB/BTF (UASB followed by biological trickling filter) and MAS/UV (modified activated sludge with UV disinfection stage). Bacterial diversity and the presence of potentially pathogenic groups were also evaluated, and associations between genetic markers and the bacterial populations were presented. All WWTPs decreased the loads of genetic markers finally discharged to receiving water bodies and showed no evidence of being hotspots for antimicrobial resistance amplification in wastewater, since the abundances of intI1 and ARGs within the bacterial population were not increased in the treated effluents. UASB/BTF showed a similar performance to that of the CAS and MAS/UV, reinforcing the sanitary and environmental advantages of this biological treatment, widely applied for wastewater treatment in warm climate regions. Bacterial diversity and richness increased after treatments, and bacterial communities in wastewater samples differed due to catchment areas and treatment typologies. Potential pathogenic population underwent considerable decrease after the treatments; however, strong significant correlations with intI1 and ARGs revealed potential multidrug-resistant pathogenic bacteria (Aeromonas, Arcobacter, Enterobacter, Escherichia-Shigella, Stenotrophomonas and Streptococcus) in the treated effluents, although in reduced relative abundances. These are contributive results for understanding the fate of ARGs, MGEs and potential pathogenic bacteria after wastewater treatments, which might support actions to mitigate their release into Brazilian aquatic environments in the near future.},
}
@article {pmid35724776,
year = {2022},
author = {Chang, J and van Veen, JA and Tian, C and Kuramae, EE},
title = {A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {156706},
doi = {10.1016/j.scitotenv.2022.156706},
pmid = {35724776},
issn = {1879-1026},
abstract = {The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment-plant-rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.},
}
@article {pmid35724732,
year = {2022},
author = {Glass, SE and Coffey, RJ},
title = {Recent Advances in the Study of Extracellular Vesicles in Colorectal Cancer.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2022.06.039},
pmid = {35724732},
issn = {1528-0012},
abstract = {There has been significant progress in the study of extracellular vesicles (EVs) since the 2017 American Gastroenterological Association-sponsored Freston conference Extracellular Vesicles: Biology, Translation and Clinical Application in GI Disorders. The burgeoning interest in this field stems from the increasing recognition that EVs represent an understudied form of cell-to-cell communication and contain cargo replete with biomarkers and therapeutic targets. This short review will highlight recent advances in the field with an emphasis on colorectal cancer (CRC). Following a short introduction to secreted particles, we will describe how our lab became interested in EVs, which led to refined methods of isolation and identification of two secreted nanoparticles. We will then summarize the cargo found in small (s)EVs released from CRC cells and other cells in the tumor microenvironment (TME), as well as those found in the circulation of CRC patients. Finally, we will consider the continuing challenges and future opportunities in this rapidly evolving field.},
}
@article {pmid35724506,
year = {2022},
author = {Wu, YX and Yang, XY and Han, BS and Hu, YY and An, T and Lv, BH and Lian, J and Wang, TY and Bao, XL and Gao, L and Jiang, GJ},
title = {Naringenin regulates gut microbiota and SIRT1/ PGC-1ɑ signaling pathway in rats with letrozole-induced polycystic ovary syndrome.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {153},
number = {},
pages = {113286},
doi = {10.1016/j.biopha.2022.113286},
pmid = {35724506},
issn = {1950-6007},
abstract = {PURPOSE: To evaluate the effect of naringenin on improving PCOS and explore the mechanism.<br><br>METHODS: Firstly, we carried out differential gene expression analysis from transcriptome sequencing data of human oocyte to screen the KEGG pathway, then the PCOS-like rat model was induced by letrozole. They were randomly divided into four groups: Normal group (N), PCOS group (P), Diane-35 group (D), and Naringenin group (Nar). The changes of estrus cycle, body weight, ovarian function, serum hormone levels, glucose metabolism, along with the expression of SIRT1, PGC-1ɑ, claudin-1 and occludin of the ovary and colon were investigated. Furthermore, the composition of the gut microbiome of fecal was tested.<br><br>RESULTS: By searching the KEGG pathway in target genes, we found that at least 15 KEGG pathways are significantly enriched in the ovarian function, such as AMPK signaling pathway, insulin secretion, and ovarian steroidogenesis. Interestingly, naringenin supplementation significantly reduced body weight, ameliorated hormone levels, improved insulin resistance, and mitigated pathological changes in ovarian tissue, up-regulated the expression of PGC-1ɑ, SIRT1, occludin and claudin-1 in colon. In addition, we also found that the abundance of Prevotella and Gemella was down-regulated, while the abundance of Butyricimonas, Lachnospira, Parabacteroides, Butyricicoccus, Streptococcus, Coprococcus was up-regulated.<br><br>CONCLUSION: Our data suggest that naringenin exerts a treatment PCOS effect, which may be related to the modulation of the gut microbiota and SIRT1/PGC-1ɑ signaling pathway. Our research may provide a new perspective for the treatment of PCOS and related diseases.},
}
@article {pmid35724423,
year = {2022},
author = {Smith, G and Manzano Marín, A and Reyes-Prieto, M and Ribeiro Antunes, CS and Ashworth, V and Goselle, ON and Jan, AAA and Moya, A and Latorre, A and Perotti, MA and Braig, HR},
title = {Human follicular mites: Ectoparasites becoming symbionts.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msac125},
pmid = {35724423},
issn = {1537-1719},
abstract = {Most humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites are the only metazoans tha continuously live on humans. We propose that Demodex folliculorum (Acari) represents a transitional stage from a host-injuring obligate parasite to an obligate symbiont. Here, we describe the profound impact of this transition on the genome and physiology of the mite. Genome sequencing revealed that the permanent host association of D. folliculorum led to an extensive genome reduction through relaxed selection and genetic drift, resulting in the smallest number of protein-coding genes yet identified among panarthropods. Confocal microscopy revealed that this gene loss coincided with an extreme reduction in the number of cells. Single uninucleate muscle cells are sufficient to operate each of the three segments that form each walking leg. While it has been assumed that the reduction of the cell number in parasites starts early in development, we identified a greater total number of cells in the last developmental stage (nymph) than in the terminal adult stage, suggesting that reduction starts at the adult or ultimate stage of development. This is the first evolutionary step in an arthropod species adopting a reductive, parasitic or endosymbiotic lifestyle. Somatic nuclei show underreplication at the diploid stage. Novel eye structures or photoreceptors as well as a unique human host melatonin-guided day/night rhythm are proposed for the first time. The loss of DNA repair genes coupled with extreme endogamy might have set this mite species on an evolutionary dead-end trajectory.},
}
@article {pmid35724325,
year = {2022},
author = {},
title = {Retraction: Human microbiome and homeostasis: Insights into the key role of prebiotics, probiotics, and symbiotics.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-2},
doi = {10.1080/10408398.2022.2078104},
pmid = {35724325},
issn = {1549-7852},
}
@article {pmid35723568,
year = {2022},
author = {Hu, YJ and Satten, GA},
title = {A rarefaction-without-resampling extension of PERMANOVA for testing presence-absence associations in the microbiome.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btac399},
pmid = {35723568},
issn = {1367-4811},
abstract = {MOTIVATION: PERMANOVA (McArdle and Anderson, 2001) is currently the most commonly used method for testing community-level hypotheses about microbiome associations with covariates of interest. PERMANOVA can test for associations that result from changes in which taxa are present or absent by using the Jaccard or unweighted UniFrac distance. However, such presence-absence analyses face a unique challenge: confounding by library size (total sample read count), which occurs when library size is associated with covariates in the analysis. It is known that rarefaction (subsampling to a common library size) controls this bias, but at the potential costs of information loss and the introduction of a stochastic component into the analysis.<br><br>RESULTS: Here we develop a non-stochastic approach to PERMANOVA presence-absence analyses that aggregates information over all potential rarefaction replicates without actual resampling, when the Jaccard or unweighted UniFrac distance is used. We compare this new approach to three possible ways of aggregating PERMANOVA over multiple rarefactions obtained from resampling: averaging the distance matrix, averaging the (element-wise) squared distance matrix, and averaging the F-statistic. Our simulations indicate that our non-stochastic approach is robust to confounding by library size and outperforms each of the stochastic resampling approaches. We also show that, when overdispersion is low, averaging the (element-wise) squared distance outperforms averaging the unsquared distance, currently implemented in the R package vegan. We illustrate our methods using an analysis of data on inflammatory bowel disease (IBD) in which samples from case participants have systematically smaller library sizes than samples from control participants.<br><br>We have implemented all the approaches described above, including the function for calculating the analytical average of the squared or unsquared distance matrix, in our R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid35723531,
year = {2022},
author = {Xie, A and Ensink, E and Li, P and Gordevičius, J and Marshall, LL and George, S and Pospisilik, JA and Aho, VTE and Houser, MC and Pereira, PAB and Rudi, K and Paulin, L and Tansey, MG and Auvinen, P and Brundin, P and Brundin, L and Labrie, V and Scheperjans, F},
title = {Bacterial Butyrate in Parkinson's Disease Is Linked to Epigenetic Changes and Depressive Symptoms.},
journal = {Movement disorders : official journal of the Movement Disorder Society},
volume = {},
number = {},
pages = {},
doi = {10.1002/mds.29128},
pmid = {35723531},
issn = {1531-8257},
support = {//Farmer Family Foundation/ ; //Finnish Parkinson Foundation/ ; //Gibby &amp; Friends vs. Parky/ ; UAK1014004//Hospital District of Helsinki and Uusimaa/ ; UAK1014005//Hospital District of Helsinki and Uusimaa/ ; TYH2018224//Hospital District of Helsinki and Uusimaa/ ; //Finnish Medical Foundation/ ; 295724//Academy of Finland/ ; 310835//Academy of Finland/ ; //Michael J. Fox Foundation for Parkinson's Research/ ; },
abstract = {BACKGROUND: The gut microbiome and its metabolites can impact brain health and are altered in Parkinson's disease (PD) patients. It has been recently demonstrated that PD patients have reduced fecal levels of the potent epigenetic modulator butyrate and its bacterial producers.<br><br>OBJECTIVES: Here, we investigate whether the changes in the gut microbiome and associated metabolites are related to PD symptoms and epigenetic markers in leucocytes and neurons.<br><br>METHODS: Stool, whole blood samples, and clinical data were collected from 55 PD patients and 55 controls. We performed DNA methylation analysis on whole blood samples and analyzed the results in relation to fecal short-chain fatty acid concentrations and microbiota composition. In another cohort, prefrontal cortex neurons were isolated from control and PD brains. We identified genome-wide DNA methylation by targeted bisulfite sequencing.<br><br>RESULTS: We show that lower fecal butyrate and reduced counts of genera Roseburia, Romboutsia, and Prevotella are related to depressive symptoms in PD patients. Genes containing butyrate-associated methylation sites include PD risk genes and significantly overlap with sites epigenetically altered in PD blood leucocytes, predominantly neutrophils, and in brain neurons, relative to controls. Moreover, butyrate-associated methylated-DNA regions in PD overlap with those altered in gastrointestinal (GI), autoimmune, and psychiatric diseases.<br><br>CONCLUSIONS: Decreased levels of bacterially produced butyrate are related to epigenetic changes in leucocytes and neurons from PD patients and to the severity of their depressive symptoms. PD shares common butyrate-dependent epigenetic changes with certain GI and psychiatric disorders, which could be relevant for their epidemiological relation. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.},
}
@article {pmid35723471,
year = {2022},
author = {Liou, CW and Yao, TH and Wu, WL},
title = {Intracerebroventricular Delivery of Gut-derived Microbial Metabolites in Freely Moving Mice.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {184},
pages = {},
doi = {10.3791/63972},
pmid = {35723471},
issn = {1940-087X},
mesh = {Animals ; Bacteria/metabolism ; Brain/metabolism ; *Fatty Acids, Volatile/metabolism ; Fermentation ; *Gastrointestinal Microbiome/physiology ; Mice ; },
abstract = {The impact of gut microbiota and their metabolites on host physiology and behavior has been extensively investigated in this decade. Numerous studies have revealed that gut microbiota-derived metabolites modulate brain-mediated physiological functions through intricate gut-brain pathways in the host. Short-chain fatty acids (SCFAs) are the major bacteria-derived metabolites produced during dietary fiber fermentation by the gut microbiome. Secreted SCFAs from the gut can act at multiple sites in the periphery, affecting the immune, endocrine, and neural responses due to the vast distribution of SCFAs receptors. Therefore, it is challenging to differentiate the central and peripheral effects of SCFAs through oral and intraperitoneal administration of SCFAs. This paper presents a video-based method to interrogate the functional role of SCFAs in the brain via a guide cannula in freely moving mice. The amount and type of SCFAs in the brain can be adjusted by controlling the infusion volume and rate. This method can provide scientists with a way to appreciate the role of gut-derived metabolites in the brain.},
}
@article {pmid35723361,
year = {2022},
author = {Molinero, N and Taladrid, D and Zorraquín-Peña, I and de Celis, M and Belda, I and Mira, A and Bartolomé, B and Moreno-Arribas, MV},
title = {Ulcerative Colitis Seems to Imply Oral Microbiome Dysbiosis.},
journal = {Current issues in molecular biology},
volume = {44},
number = {4},
pages = {1513-1527},
doi = {10.3390/cimb44040103},
pmid = {35723361},
issn = {1467-3045},
abstract = {Ulcerative colitis (UC) is a recurrent pathology of complex etiology that has been occasionally associated with oral lesions, but the overall composition of the oral microbiome in UC patients and its role in the pathogenesis of the disease are still poorly understood. In this study, the oral microbiome of UC patients and healthy individuals was compared to ascertain the possible changes in the oral microbial communities associated with UC. For this, the salivary microbiota of 10 patients diagnosed with an active phase of UC and 11 healthy controls was analyzed by 16S rRNA gene sequencing (trial ref. ISRCTN39987). Metataxonomic analysis revealed a decrease in the alpha diversity and an imbalance in the relative proportions of some key members of the oral core microbiome in UC patients. Additionally, Staphylococcus members and four differential species or phylotypes were only present in UC patients, not being detected in healthy subjects. This study provides a global snapshot of the existence of oral dysbiosis associated with UC, and the possible presence of potential oral biomarkers.},
}
@article {pmid35723354,
year = {2022},
author = {Tette, FM and Kwofie, SK and Wilson, MD},
title = {Therapeutic Anti-Depressant Potential of Microbial GABA Produced by Lactobacillus rhamnosus Strains for GABAergic Signaling Restoration and Inhibition of Addiction-Induced HPA Axis Hyperactivity.},
journal = {Current issues in molecular biology},
volume = {44},
number = {4},
pages = {1434-1451},
doi = {10.3390/cimb44040096},
pmid = {35723354},
issn = {1467-3045},
abstract = {The role of the microbiota-gut-brain (MGB) axis in mood regulation and depression treatment has gained attention in recent years, as evidenced by the growing number of animal and human studies that have reported the anti-depressive and associated gamma-aminobutyric acid-ergic (GABAergic) effects of probiotics developed from Lactobacillus rhamnosus bacterial strains in the gut microbiome. The depressive states attenuated by these probiotics in patients suffering from clinical depression also characterize the severe and relapse-inducing withdrawal phase of the addiction cycle, which has been found to arise from the intoxication-enabled hyperregulation of the hypothalamic-pituitary-adrenal (HPA) axis, the body's major stress response system, and a corresponding attenuation of its main inhibitory system, the gamma-aminobutyric acid (GABA) signaling system. Therefore, the use of probiotics in the treatment of general cases of depression provides hope for a novel therapeutic approach to withdrawal depression remediation. This review discusses potential therapeutic avenues by which probiotic application of Lactobacillus rhamnosus strains can be used to restore the central GABAergic activity responsible for attenuating the depression-inducing HPA axis hyperactivity in addiction withdrawal. Also, information is provided on brain GABAergic signaling from other known GABA-producing strains of gut microbiota.},
}
@article {pmid35723116,
year = {2022},
author = {Shannon, KM},
title = {Infections and Changes in Commensal Bacteria and the Pathogenesis of Parkinson's Disease.},
journal = {Journal of Parkinson's disease},
volume = {},
number = {},
pages = {},
doi = {10.3233/JPD-223271},
pmid = {35723116},
issn = {1877-718X},
abstract = {The cause of Parkinson's disease (PD) is unknown, but environmental factors are purported to influence risk. Interest in PD as a sequel of infection dates back to reports of parkinsonism arising from encephalitis lethargica. The objective of this paper is to review the literature as it relates to infections and changes in microbiome and the genesis of PD. There is evidence to support prior infection with Helicobacter pylori, hepatitis C virus, Malassezia, and Strep pneumonia in association with PD. A large number of studies support an association between changes in commensal bacteria, especially gut bacteria, and PD. Extant literature supports a role for some infections and changes in commensal bacteria in the genesis of PD. Studies support an inflammatory mechanism for this association, but additional research is required for translation of these findings to therapeutic options.},
}
@article {pmid35722720,
year = {2022},
author = {Ernakovich, JG and Barbato, RA and Rich, VI and Schädel, C and Hewitt, RE and Doherty, SJ and Whalen, ED and Abbott, BW and Barta, J and Biasi, C and Chabot, CL and Hultman, J and Knoblauch, C and Vetter, MCYL and Leewis, MC and Liebner, S and Mackelprang, R and Onstott, TC and Richter, A and Schütte, UME and Siljanen, HMP and Taş, N and Timling, I and Vishnivetskaya, TA and Waldrop, MP and Winkel, M},
title = {Microbiome assembly in thawing permafrost and its feedbacks to climate.},
journal = {Global change biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/gcb.16231},
pmid = {35722720},
issn = {1365-2486},
support = {290315//Academy of Finland/ ; 313114//Academy of Finland/ ; 314630//Academy of Finland/ ; 773421//EU Horizon 2020/ ; EXC 2037 'Climate, Climatic Change, and Society'//Germany's Excellence Strategy/ ; 20-21259J//Grantová Agentura České Republiky/ ; NNH15AB58I/NASA/NASA/United States ; NNX15AM12G/NASA/NASA/United States ; //New Hampshire Agriculture Experiment Station/ ; //U.S. Army Basic and Applied Research Program/ ; DE-SC0020369//U.S. Department of Energy/ ; Early Career Research program//U.S. Department of Energy/ ; Climate and Land Use Research Development Program//U.S. Geological Survey/ ; DE-SC0016440//United States Department of Energy Office of Biological and Environmental Research/ ; 1331083//United States National Science Foundation/ ; 1916565//United States National Science Foundation/ ; 1931333//United States National Science Foundation/ ; 2022070//United States National Science Foundation/ ; DEB-1442262//United States National Science Foundation/ ; 2144961//National Science Foundation/ ; },
abstract = {The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost-climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post-thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw-mediated microbiome changes and the implications for community function and climate feedbacks. This framework posits that the prevalence of deterministic or stochastic processes indicates whether the community is well-suited to thrive in changing environmental conditions. We predict that on a short timescale and following high-disturbance thaw (e.g., thermokarst), stochasticity dominates post-thaw microbiome assembly, suggesting that functional predictions will be aided by detailed information about the microbiome. At a longer timescale and lower-intensity disturbance (e.g., active layer deepening), deterministic processes likely dominate, making environmental parameters sufficient for predicting function. We propose that the contribution of stochastic and deterministic processes to post-thaw microbiome assembly depends on the characteristics of the thaw disturbance, as well as characteristics of the microbial community, such as the ecological and phylogenetic breadth of functional guilds, their functional redundancy, and biotic interactions. These propagate across space and time, potentially providing a means for predicting the microbial forcing of greenhouse gas feedbacks to global climate change.},
}
@article {pmid35722401,
year = {2022},
author = {Tan, W and Chen, R and Song, J and He, D and Wu, J and Chen, X and Yang, X and Ye, L},
title = {Microbiota analysis with next-generation 16S rDNA gene sequencing in recurrent common bile duct stones.},
journal = {Annals of translational medicine},
volume = {10},
number = {10},
pages = {576},
doi = {10.21037/atm-22-2247},
pmid = {35722401},
issn = {2305-5839},
abstract = {Background: Endoscopic retrograde cholangiopancreatography (ERCP) is the main remedy for gallstones, but the postoperative recurrence rate is high. Recent research has indicated that the biliary microbiome takes part in the pathogenesis of cholelithiasis. However, it is not yet known whether biliary microbiome dysbiosis is relevant to recurrent cholelithiasis.<br><br>Methods: Thus, we investigated the bacterial communities of the biliary microbiomes of patients with recurrent common bile duct (CBD) stones and analyzed the relationship between recurrent CBD stones and biliary microbiota. The bile specimens of 5 patients with recurrent CBD stones (FF) and 45 patients with primary CBD stones (YF) were collected during the ERCP process. The microbiota was analyzed using 16S ribosomal DNA (rDNA) high-throughput sequencing. We also identified the link between recurrent CBD stones and biliary microbiota.<br><br>Results: Our results showed that at the phylum level, proteobacteria and firmicutes were the main two genera groups, and proteobacteria was high in FF patients. Additionally, synergistetes were high, but Bacteroidetes and actinobacteria were low in FF patients. The microbiomes in the bile of the YF patients were more evenly distributed than those in the bile of the FF patients. We also discovered that FF patients had decreased microbial bile diversity. At the genus level, klebsiella dominated in the FF patients, while Escherichia-shigella dominated in the YF patients. Additionally, klebsiella was higher in the FF patients than the YF patients.<br><br>Conclusions: The observed differences in the genera between the recurrent CBD stone FF patients and the YF patients provide novel insights into the link between biliary microbiota changes and recurrent CBD stones.},
}
@article {pmid35722392,
year = {2022},
author = {Peng, YC and Xu, JX and Zeng, CF and Zhao, XH and Li, LQ and Qi, LN},
title = {Gut microbiome dysbiosis in patients with hepatitis B virus-related hepatocellular carcinoma after extended hepatectomy liver failure.},
journal = {Annals of translational medicine},
volume = {10},
number = {10},
pages = {549},
doi = {10.21037/atm-22-1958},
pmid = {35722392},
issn = {2305-5839},
abstract = {Background: Hepatitis B virus-related hepatocellular carcinoma (B-HCC) negatively affects the gut microbiome. This study aimed to investigate the gut microbiome profiles and functions post-hepatectomy liver failure (PHLF) after extended hepatectomy (e-PHLF) to obtain valuable insights, identify potential diagnostic biomarkers, and assist in the treatment of this disease.<br><br>Methods: B-HCC patients who underwent extended hepatectomy were consecutively recruited and divided into Group A (n=15) and Group B (n=15) based on the presence and absence of e-PHLF, respectively. The relationships between gut microbiota and extended hepatectomy liver failure were explored using 16S ribosomal RNA (16S rRNA) gene sequencing data.<br><br>Results: Following extended hepatectomy, the α-diversity of Group A was significantly higher than that of Group B (Shannon P=0.034 or Simpson P=0.031), and the β-diversity differed significantly between Groups A and B (P=0.004, R=0.100). At the genus level, 10 bacterial genera (Bacteroides, Pantoea, Methylobacterium-Methylorubrum, Inquilinus, Mycobacterium, Allisonella, Helicobacter, GCA-900066575, IS-44, and Faecalibacterium) were significantly enriched in Group A, whereas five genera (Papillibacter, Scardovia, Turicibacter, Catabacter, and Senegalimassilia) were significantly enriched in Group B. The highly abundant genera Bacteroides, Pantoea, Faecalibacterium, and Turicibacter participated in multiple amino acid metabolism pathways, organic acid metabolism pathways, pyrimidine metabolism pathways, palmitate biosynthesis, and stearate biosynthesis. Redundancy analysis showed that four environmental factors (total bilirubin, international normalized ratio, prealbumin, and albumin) were significantly correlated with intestinal microorganisms. The formation of interaction networks between different gut microbiomes revealed important correlations between the gut microbiome, and there was a significant correlation between the highly abundant gut microbiome and main functions.<br><br>Conclusions: The gut microbiota characteristics in B-HCC patients after extended hepatectomy liver failure might allow for the use of non-invasive biomarkers for disease diagnosis and treatment.},
}
@article {pmid35722352,
year = {2022},
author = {Paddock, KJ and Finke, DL and Kim, KS and Sappington, TW and Hibbard, BE},
title = {Patterns of Microbiome Composition Vary Across Spatial Scales in a Specialist Insect.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {898744},
doi = {10.3389/fmicb.2022.898744},
pmid = {35722352},
issn = {1664-302X},
abstract = {Microbial communities associated with animals vary based on both intrinsic and extrinsic factors. Of many possible determinants affecting microbiome composition, host phylogeny, host diet, and local environment are the most important. How these factors interact across spatial scales is not well understood. Here, we seek to identify the main influences on microbiome composition in a specialist insect, the western corn rootworm (WCR; Diabrotica virgifera virgifera), by analyzing the bacterial communities of adults collected from their obligate host plant, corn (Zea mays), across several geographic locations and comparing the patterns in communities to its congeneric species, the northern corn rootworm (NCR; Diabrotica barberi). We found that bacterial communities of WCR and NCR shared a portion of their bacterial communities even when collected from disparate locations. However, within each species, the location of collection significantly influenced the composition of their microbiome. Correlations of geographic distance between sites with WCR bacterial community composition revealed different patterns at different spatial scales. Community similarity decreased with increased geographic distance at smaller spatial scales (~25 km between the nearest sites). At broad spatial scales (>200 km), community composition was not correlated with distances between sites, but instead reflected the historical invasion path of WCR across the United States. These results suggest bacterial communities are structured directly by dispersal dynamics at small, regional spatial scales, while landscape-level genetic or environmental differences may drive community composition across broad spatial scales in this specialist insect.},
}
@article {pmid35722334,
year = {2022},
author = {Isenring, J and Stevens, MJA and Jans, C and Lacroix, C and Geirnaert, A},
title = {Identification of Valerate as Carrying Capacity Modulator by Analyzing Lactiplantibacillus plantarum Colonization of Colonic Microbiota in vitro.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {910609},
doi = {10.3389/fmicb.2022.910609},
pmid = {35722334},
issn = {1664-302X},
abstract = {Humans ingest many microorganisms, which may colonize and interact with the resident gut microbiota. However, extensive knowledge about host-independent microbe-microbe interactions is lacking. Here, we investigated such colonization process using a derivative of the model probiotic Lactiplantibacillus plantarum WCFS1 into continuously cultivated gut microbiota in the intestinal PolyFermS fermentation model inoculated with five independently immobilized human adult fecal microbiota. L. plantarum successfully colonized and organized itself spatially in the planktonic, that is, the reactor effluent, and sessile, that is, reactor biofilm, fractions of distinct human adult microbiota. The microbiota carrying capacity for L. plantarum was independent of L. plantarum introduction dose and second supplementation. Adult microbiota (n = 3) dominated by Prevotella and Ruminoccocus exhibited a higher carrying capacity than microbiota (n = 2) dominated by Bacteroides with 105 and 103 CFU/ml of L. plantarum, respectively. Cultivation of human adult microbiota over 3 months resulted in decreased carrying capacity and correlated positively with richness and evenness, suggesting enhanced resistance toward colonizers. Our analyses ultimately allowed us to identify the fermentation metabolite valerate as a modulator to increase the carrying capacity in a microbiota-independent manner. In conclusion, by uncoupling microbe-microbe interactions from host factors, we showed that L. plantarum colonizes the in vitro colonic community in a microbiota-dependent manner. We were further able to demonstrate that L. plantarum colonization levels were not susceptible to the introduction parameters dose and repeated administration but to microbiota features. Such knowledge is relevant in gaining a deeper ecological understanding of colonizer-microbiota interactions and developing robust probiotic strategies.},
}
@article {pmid35722333,
year = {2022},
author = {Song, C and Wen, H and Liu, G and Ma, X and Lv, G and Wu, N and Chen, J and Xue, M and Li, H and Xu, P},
title = {Gut Microbes Reveal Pseudomonas Medicates Ingestion Preference via Protein Utilization and Cellular Homeostasis Under Feed Domestication in Freshwater Drum, Aplodinotus grunniens.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {861705},
doi = {10.3389/fmicb.2022.861705},
pmid = {35722333},
issn = {1664-302X},
abstract = {With strong demand for aquatic products, as well as a rapid decrease in global fishery resources and capture fisheries, domesticating animals to provide more high-quality proteins is meaningful for humans. Freshwater drum (Aplodinotus grunniens) is widely distributed in the wild habitats of North America. However, the research on A. grunniens and the feed domestication with diets composed of artificial compounds remains unclear. In this study, a 4-month feeding domestication experiment was conducted with A. grunniens larvae to evaluate the underlying mechanism and molecular targets responsible for alternations in the ingestion performance. The results indicated that a significant increase in the final body weight was exhibited by the feed domesticated group (DOM, 114.8 g) when compared to the group that did not ingest the feed (WT, 5.3 g) as the latest version we raised From the result, the final body weight exhibited significant increase between unfavorable with the feed (WT, 5.3 g) and feed domesticated group (DOM, 114.8 g). In addition, the enzyme activity of digestive enzymes like amylase, lipase, and trypsin was increased in DOM. Genes related to appetite and perception, such as NPY4R, PYY, and LEPR, were activated in DOM. 16s rRNA gene sequencing analysis revealed that Pseudomonas sp. increased from 58.74% to 89.77% in DOM, which accounts for the dominant upregulated microbial community at the genus level, followed by Plesiomonas. Analogously, Mycobacterium, Methylocystis, and Romboutsia also accounted for the down-regulated microbes in the diversity. Transcriptome and RT-PCR analysis revealed that feed domestication significantly improved protein digestion and absorption, inhibited apoptosis by AGE-RAGE signaling, and activated extracellular matrix remodeling by relaxin signaling. Integrated analysis of the microbiome and host transcriptome revealed that Pseudomonas-mediated ingestion capacity, protein utilization, and cellular homeostasis might be the underlying mechanism under feed domestication. These results indicate Pseudomonas and its key genes relating to food ingestion and digestion could serve as the molecular targets for feed domestication and sustainable development in A. grunniens.},
}
@article {pmid35722300,
year = {2022},
author = {León, ED and Francino, MP},
title = {Roles of Secretory Immunoglobulin A in Host-Microbiota Interactions in the Gut Ecosystem.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {880484},
doi = {10.3389/fmicb.2022.880484},
pmid = {35722300},
issn = {1664-302X},
abstract = {In the gastrointestinal tract (GIT), the immune system interacts with a variety of microorganisms, including pathogens as well as beneficial symbionts that perform important physiological functions for the host and are crucial to sustain intestinal homeostasis. In normal conditions, secretory immunoglobulin A (SIgA) is the principal antibody produced by B cells in the GIT mucosa. Polyreactivity provides certain SIgA molecules with the ability of binding different antigens in the bacterial surface, such as O-antigens and teichoic acids, while cross-species reactivity allows them to recognize and interact with different types of bacteria. These functions may be crucial in allowing SIgA to modulate the complex gut microbiota in an efficient manner. Several studies suggest that SIgA can help with the retention and proliferation of helpful members of the gut microbiota. Gut microbiota alterations in people with IgA deficiency include the lack of some species that are known to be normally coated by SIgA. Here, we discuss the different ways in which SIgA behaves in relation to pathogens and beneficial bacteria of the gut microbiota and how the immune system might protect and facilitate the establishment and maintenance of certain gut symbionts.},
}
@article {pmid35722294,
year = {2022},
author = {Guo, X and Tang, P and Hou, C and Chong, L and Zhang, X and Liu, P and Chen, L and Liu, Y and Zhang, L and Li, R},
title = {Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to Blautia Genus: Evidence From Feces, Blood, and Brain.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {875101},
doi = {10.3389/fmicb.2022.875101},
pmid = {35722294},
issn = {1664-302X},
abstract = {A link between the gut microbiome and Parkinson's disease (PD) has been intensively studied, and more than 100 differential genera were identified across the studies. However, the predominant genera contributing to PD remain poorly understood. Inspired by recent advances showing microbiota distribution in the blood and brain, we, here, comprehensively investigated currently available fecal microbiome data (1,914 samples) to identify significantly altered genera, which were further validated by comparison to the results from microbiome analysis of blood (85 samples) and brain (268 samples). Our data showed that the composition of fecal microbiota was different from that of blood and brain. We found that Blautia was the unique genus consistently depleted across feces, blood, and brain samples of PD patients (P < 0.05), despite using rigorous criteria to remove contaminants. Moreover, enrichment analyses revealed that host genes correlated with Blautia genus abundance were mainly involved in mitochondrial function and energy metabolism, and mapped to neurodegenerative diseases (NDDs) and metabolic diseases. A random forest classifier constructed with fecal microbiota data demonstrated that Blautia genus was an important feature contributing to discriminating PD patients from controls [receiver operating characteristic (ROC)-area under curve (AUC) = 0.704, precision-recall curve (PRC)-AUC = 0.787]. Through the integration of microbiome and transcriptome, our study depicted microbial profiles in the feces, blood, and brain of PD patients, and identified Blautia genus as a potential genus linked to PD. Further studies are greatly encouraged to determine the role of Blautia genus in the pathogenesis of PD.},
}
@article {pmid35722279,
year = {2022},
author = {Egenriether, S and Sanford, R and Yang, WH and Kent, AD},
title = {Nitrogen Cycling Microbial Diversity and Operational Taxonomic Unit Clustering: When to Prioritize Accuracy Over Speed.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {730340},
doi = {10.3389/fmicb.2022.730340},
pmid = {35722279},
issn = {1664-302X},
abstract = {Background: Assessments of the soil microbiome provide valuable insight to ecosystem function due to the integral role microorganisms play in biogeochemical cycling of carbon and nutrients. For example, treatment effects on nitrogen cycling functional groups are often presented alongside one another to demonstrate how agricultural management practices affect various nitrogen cycling processes. However, the functional groups commonly evaluated in nitrogen cycling microbiome studies range from phylogenetically narrow (e.g., N-fixation, nitrification) to broad [e.g., denitrification, dissimilatory nitrate reduction to ammonium (DNRA)]. The bioinformatics methods used in such studies were developed for 16S rRNA gene sequence data, and how these tools perform across functional genes of different phylogenetic diversity has not been established. For example, an OTU clustering method that can accurately characterize sequences harboring comparatively little diversity may not accurately resolve the diversity within a gene comprised of a large number of clades. This study uses two nitrogen cycling genes, nifH, a gene which segregates into only three distinct clades, and nrfA, a gene which is comprised of at least eighteen clades, to investigate differences which may arise when using heuristic OTU clustering (abundance-based greedy clustering, AGC) vs. true hierarchical OTU clustering (Matthews Correlation Coefficient optimizing algorithm, Opti-MCC). Detection of treatment differences for each gene were evaluated to demonstrate how conclusions drawn from a given dataset may differ depending on clustering method used.<br><br>Results: The heuristic and hierarchical methods performed comparably for the more conserved gene, nifH. The hierarchical method outperformed the heuristic method for the more diverse gene, nrfA; this included both the ability to detect treatment differences using PERMANOVA, as well as higher resolution in taxonomic classification. The difference in performance between the two methods may be traced to the AGC method's preferential assignment of sequences to the most abundant OTUs: when analysis was limited to only the largest 100 OTUs, results from the AGC-assembled OTU table more closely resembled those of the Opti-MCC OTU table. Additionally, both AGC and Opti-MCC OTU tables detected comparable treatment differences using the rank-based ANOSIM test. This demonstrates that treatment differences were preserved using both clustering methods but were structured differently within the OTU tables produced using each method.<br><br>Conclusion: For questions which can be answered using tests agnostic to clustering method (e.g., ANOSIM), or for genes of relatively low phylogenetic diversity (e.g., nifH), most upstream processing methods should lead to similar conclusions from downstream analyses. For studies involving more diverse genes, however, care should be exercised to choose methods that ensure accurate clustering for all genes. This will mitigate the risk of introducing Type II errors by allowing for detection of comparable treatment differences for all genes assessed, rather than disproportionately detecting treatment differences in only low-diversity genes.},
}
@article {pmid35722272,
year = {2022},
author = {Yang, B and Liu, C and Huang, Y and Wu, Q and Xiong, Y and Yang, X and Hu, S and Jiang, Z and Wang, L and Yi, H},
title = {The Responses of Lactobacillus reuteri LR1 or Antibiotic on Intestinal Barrier Function and Microbiota in the Cecum of Pigs.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {877297},
doi = {10.3389/fmicb.2022.877297},
pmid = {35722272},
issn = {1664-302X},
abstract = {This study aimed to investigate responses of the Lactobacillus reuteri or an antibiotic on cecal microbiota and intestinal barrier function in different stages of pigs. A total of 144 weaned pigs (Duroc × Landrace × Yorkshire, 21 days of age) were randomly assigned to the control group (CON, fed with a basal diet), the antibiotic group (AO, fed with basal diet plus 100 mg/kg olaquindox and 75 mg/kg aureomycin), and the L. reuteri group (LR, fed with the basal diet + 5 × 1010 CFU/kg L. reuteri LR1) throughout the 164-d experiment. A total of 45 cecal content samples (5 samples per group) from different periods (14th, 42th, and 164th days) were collected for 16S rRNA gene amplification. The results revealed that although LR and AO did not change the diversity of cecal microbiota in pigs, the abundance of some bacteria at the genus level was changed with age. The proportion of Lactobacillus was increased by LR in early life, whereas it was decreased by AO compared with the control group. The relative abundance of Ruminococcaceae was increased along with age. In addition, the gas chromatography results showed that age, not AO or LR, has significant effects on the concentrations of SCFAs in the cecum of pigs (P < 0.05). However, the mRNA expression of tight junction proteins zonula occluden-1 (ZO-1) and occludin were increased by AO in the cecum of pigs on day 14, while LR increased the mRNA expression of intestinal barrier-related proteins ZO-1, occludin, mucin-1, mucin-2, PG1-5, and pBD2 in the cecum of pigs on days 14 and 164 (P < 0.05). In conclusion, LR and AO have different effects on the intestinal barrier function of the cecum, and neither LR nor AO damaged the intestinal barrier function of pig cecum. In addition, LR and AO have little effects on cecal microflora in different stages of the pigs. The microflora and their metabolite SCFAs were significantly changed along with age. These findings provide important information to understand the homeostasis of the cecum of pigs after antibiotic or probiotic treatment.},
}
@article {pmid35721889,
year = {2022},
author = {Kang, YB and Cai, Y},
title = {Future prospect of "Gut microbiome composition can predict the response to nivolumab in advanced hepatocellular carcinoma patients".},
journal = {World journal of gastroenterology},
volume = {28},
number = {20},
pages = {2248-2250},
doi = {10.3748/wjg.v28.i20.2248},
pmid = {35721889},
issn = {2219-2840},
mesh = {*Carcinoma, Hepatocellular/pathology ; *Gastrointestinal Microbiome ; Humans ; Immunotherapy/methods ; *Liver Neoplasms/pathology ; Nivolumab/therapeutic use ; },
abstract = {Recently, we read the article "Gut microbiome composition can predict the response to nivolumab in advanced hepatocellular carcinoma patients" with interest, and it is preliminary suggested that gut microbiota is closely related to therapeutic effect of nivolumab. Based on the meaningful results of this article, several valuable research directions are proposed to enhance the therapeutic effect of immune checkpoint inhibitors on advanced hepatocellular carcinoma.},
}
@article {pmid35721806,
year = {2022},
author = {Kim, HY and Park, ES and Choi, YS and Park, SJ and Kim, JH and Chang, HK and Park, KY},
title = {Kimchi improves irritable bowel syndrome: results of a randomized, double-blind placebo-controlled study.},
journal = {Food &amp; nutrition research},
volume = {66},
number = {},
pages = {},
doi = {10.29219/fnr.v66.8268},
pmid = {35721806},
issn = {1654-661X},
abstract = {Background: Irritable bowel syndrome (IBS) can be caused by abnormal bowel movements, altered brain-gut axis, gut microbiota change, and low levels of inflammation or immune activation. The intake of food containing much fiber and lactic acid bacteria (LABs) can alleviate IBS.<br><br>Objective: This study was undertaken to confirm the alleviative effect of kimchi on symptoms of IBS.<br><br>Design: Three types of kimchi (standard kimchi, SK; dead nano-sized Lactobacillus plantarum nF1 (nLp) added to standard kimchi, nLpSK; or functional kimchi, FK) were given to 30 individuals in each of three groups, that is, the SK group (n = 30), the nLpSK group (n = 30), or the FK group (n = 30) at 210 g a day for 12 weeks. Food intake records, serum levels of inflammatory factors, fecal levels of harmful enzymes, and microbiome changes were investigated over the 12-week study period.<br><br>Results: After intervention, dietary fiber intake was increased in all groups. Typical IBS symptoms (abdominal pain or inconvenience, desperation, incomplete evacuation, and bloating), defecation time, and stool type were also improved. In serum, all groups showed reductions in tumor necrosis factor (TNF)-α (P < 0.001) levels. In addition, serum IL-4 (P < 0.001), IL-10 (P < 0.001), and IL-12 (P < 0.01) were significantly reduced in the nLpSK and FK groups, and serum monocyte chemotactic protein (MCP)-1 (P < 0.05) was significantly reduced in the nLpSK group. Furthermore, activities of fecal β-glucosidase and β-glucuronidase were significantly decreased in all three groups, and these reductions were greatest in the nLpSK group. Gut microbiome analysis showed that kimchi consumption increased Firmicutes populations at the expense of Bacteroidetes and Tenericutes populations. In addition, the Bifidobacterium adolescentis population increased significantly in the FK group (P = 0.026).<br><br>Conclusion: Kimchi intake helps alleviate IBS by increasing dietary fiber intake and reducing serum inflammatory cytokine levels and harmful fecal enzyme activities. Notably, nLp improved the immune system, and several functional ingredients in FK promoted the growth of Bifidobacterium adolescentis in gut.},
}
@article {pmid35721748,
year = {2022},
author = {Lu, G and Yu, X and Jiang, W and Luo, Q and Tong, J and Fan, S and Chai, L and Gao, D and Qiao, T and Wang, R and Deng, C and Lv, Z and Li, D},
title = {Alterations of Gut Microbiome and Metabolite Profiles Associated With Anabatic Lipid Dysmetabolism in Thyroid Cancer.},
journal = {Frontiers in endocrinology},
volume = {13},
number = {},
pages = {893164},
doi = {10.3389/fendo.2022.893164},
pmid = {35721748},
issn = {1664-2392},
mesh = {Cholesterol ; *Gastrointestinal Microbiome ; Humans ; Lipids ; RNA, Ribosomal, 16S/genetics ; *Thyroid Neoplasms ; },
abstract = {Background: Currently, the high morbidity of individuals with thyroid cancer (TC) is an increasing health care burden worldwide. The aim of our study was to investigate the relationship among the gut microbiota community, metabolites, and the development of differentiated thyroid cancer.<br><br>Methods: 16S rRNA gene sequencing and an integrated LC-MS-based metabolomics approach were performed to obtain the components and characteristics of fecal microbiota and metabolites from 50 patients with TC and 58 healthy controls (HCs).<br><br>Results: The diversity and richness of the gut microbiota in the TC patients were markedly decreased. The composition of the gut microbiota was significantly altered, and the Bacteroides enterotype was the dominant enterotype in TC patients. Additionally, the diagnostic validity of the combined model (three genera and eight metabolites) and the metabolite model (six metabolites) were markedly higher than that of the microbial model (seven genera) for distinguishing TC patients from HCs. LEfSe analysis demonstrated that genera (g_Christensenellaceae_R-7_group, g_Eubacterium_coprostanoligenes_group) and metabolites [27-hydroxycholesterol (27HC), cholesterol] closely related to lipid metabolism were greatly reduced in the TC group. In addition, a clinical serum indicator (total cholesterol) and metabolites (27HC and cholesterol) had the strongest influence on the sample distribution. Furthermore, functional pathways related to steroid biosynthesis and lipid digestion were inhibited in the TC group. In the microbiota-metabolite network, 27HC was significantly related to metabolism-related microorganisms (g_Christensenellaceae_R-7_group).<br><br>Conclusions: Our research explored the characteristics of the gut microecology of patients with TC. The findings of this study will help to discover risk factors that affect the occurrence and development of TC in the intestinal microecology.},
}
@article {pmid35721506,
year = {2022},
author = {Li, Y and Cao, H and Fei, B and Gao, Q and Yi, W and Han, W and Bao, C and Xu, J and Zhao, W and Zhang, F},
title = {Gut Microbiota Signatures in Tumor, Para-Cancerous, Normal Mucosa, and Feces in Colorectal Cancer Patients.},
journal = {Frontiers in cell and developmental biology},
volume = {10},
number = {},
pages = {916961},
doi = {10.3389/fcell.2022.916961},
pmid = {35721506},
issn = {2296-634X},
abstract = {Background: Association studies have linked microbiome alterations with colorectal cancer (CRC). However, differences in tumor, para-cancerous, normal mucosal, and fecal microbiota remain to be strengthened. Methods: We performed a study on the ecologically rich and taxonomically diverse of gut microbiota using three types of colorectal mucosa (tumor mucosa, para-cancerous mucosa, normal mucosa) and feces from 98 CRC patients. Additionally, we profiled the microbiota in the fecal occult blood test (FOBT) positive and negative groups at different sampling sites. Results: We found striking variations between tumor mucosal microbiota and normal mucosal microbiota. However, there was no significant difference between tumor and para-cancerous mucosal microbiota, as well as between para-cancerous and normal mucosal microbiota, revealing that the para-cancerous mucosal microbiota was a transitional state between the tumor and normal mucosal microbiota. And the substantial shifts in the fecal microbiota compared to mucosal microbiota indicated the risk of using fecal microbiota to define mucosal microbiota. A strong correlation between FOBT positive and Fusobacterium was discovered, indicating this adherent-invasive genus was closely related to intestinal bleeding. Furthermore, we identified six key genera, including Fusobacterium, Gemella, Campylobacter, Peptostreptococcus, Alloprevotella, and Parvimonas, which appear to be consistently over-represented in tumor mucosa compared to normal mucosa and/or in mucosa compared to feces. Conclusion: Compositional alterations in the microbiota existed in three types of colorectal mucosa and feces in CRC patients. Six key genera may contribute to the topographic variances in the microbiota of tumor-bearing colorectum.},
}
@article {pmid35721206,
year = {2022},
author = {Fasina, OB and Wang, J and Mo, J and Osada, H and Ohno, H and Pan, W and Xiang, L and Qi, J},
title = {Gastrodin From Gastrodia elata Enhances Cognitive Function and Neuroprotection of AD Mice via the Regulation of Gut Microbiota Composition and Inhibition of Neuron Inflammation.},
journal = {Frontiers in pharmacology},
volume = {13},
number = {},
pages = {814271},
doi = {10.3389/fphar.2022.814271},
pmid = {35721206},
issn = {1663-9812},
abstract = {Gastrodin (Gas) is known to exhibit neuroprotective effects in Alzheimer's disease (AD). However, the detailed mechanism of action is still unclear. In the present study, we focused on the microbiome-gut-brain axis to investigate the mechanism of action of Gas using a D-galactose (Dgal)-induced AD model. Gas reversed the memory dysfunction of Dgal-administered mice. Neurons in the cerebral cortex and hippocampus were reduced in the Dgal-administered group, and the decrease of neurons was suppressed in 90 and 210 mg/kg Gas treatment groups. 16S rRNA sequence analysis was carried out to explore the composition of gut microbiota in fecal samples of mice. Gas treatment had a positive correlation with Firmicutes and had a negative correlation with Cyanobacteria, Proteobacteria, and Deferribaceters. Importantly, the LPS and proinflammatory cytokines in the brain increased in Dgal-administered mice, but these parameters recovered to normal levels after oral administration of Gas. To determine whether the microbiota-gut-brain axis is involved in the neuroprotective effect of Gas, the mice were given antibiotic cocktail before and during the trial period to decrease the gut microbiota of mice. The antibiotic cocktail partially eliminated the neuroprotective effect of Gas by changing the gut microbiome composition. These results indicated that Gas improves the memory of the AD mouse model via partly targeting the microbiota-gut-brain axis and mitigating neuron inflammation.},
}
@article {pmid35721102,
year = {2022},
author = {Zhang, J and Guo, Y and Duan, L},
title = {Features of Gut Microbiome Associated With Responses to Fecal Microbiota Transplantation for Inflammatory Bowel Disease: A Systematic Review.},
journal = {Frontiers in medicine},
volume = {9},
number = {},
pages = {773105},
doi = {10.3389/fmed.2022.773105},
pmid = {35721102},
issn = {2296-858X},
abstract = {Fecal microbiota transplantation (FMT) has been seen as a novel treatment for inflammatory bowel disease (IBD). The results on microbial alterations and their relationship to treatment efficacy are varied among studies. We performed a systematic review to explore the association between microbial features and therapy outcomes. We searched PubMed, Web of Science, Embase, and Cochrane Library databases from inception to November 2020. Studies that investigated the efficacy of FMT and baseline microbial features or dynamic alteration of the microbiome during FMT were included. The methodological quality of the included cohort studies and randomized controlled trials (RCTs) was assessed using the Newcastle-Ottawa Scale (NOS) and the Cochrane risk of bias tool, respectively. A total of 30 studies were included in the analysis. Compared to non-responders, the microbial structure of patients who responded to FMT had a higher similarity to that of their donors after FMT. Donors of responders (R-d) and non-responders (NR-d) had different microbial taxa, but the results were inconsistent. After FMT, several beneficial short-chain fatty acids- (SCFA-) producing taxa, such as Faecalibacterium, Eubacterium, Roseburia, and species belonging to them, were enriched in responders, while pathogenic bacteria (Escherichia coli and Escherichia-Shigella) belonging to the phylum Proteobacteria were decreased. Alterations of microbial functional genes and metabolites were also observed. In conclusion, the response to FMT was associated with the gut microbiota and their metabolites. The pre-FMT microbial features of recipients, the comparison of pre- and post-FMT microbiota, and the relationship between recipients and donors at baseline should be further investigated using uniform and standardized methods.},
}
@article {pmid35720843,
year = {2022},
author = {Baholet, D and Skalickova, S and Batik, A and Malyugina, S and Skladanka, J and Horky, P},
title = {Importance of Zinc Nanoparticles for the Intestinal Microbiome of Weaned Piglets.},
journal = {Frontiers in veterinary science},
volume = {9},
number = {},
pages = {852085},
doi = {10.3389/fvets.2022.852085},
pmid = {35720843},
issn = {2297-1769},
abstract = {The scientific community is closely monitoring the replacement of antibiotics with doses of ZnO in weaned piglets. Since 2022, the use of zinc in medical doses has been banned in the European Union. Therefore, pig farmers are looking for other solutions. Some studies have suggested that zinc nanoparticles might replace ZnO for the prevention of diarrhea in weaning piglets. Like ZnO, zinc nanoparticles are effective against pathogenic microorganisms, e.g., Enterobacteriaceae family in vitro and in vivo. However, the effect on probiotic Lactobacillaceae appears to differ for ZnO and zinc nanoparticles. While ZnO increases their numbers, zinc nanoparticles act in the opposite way. These phenomena have been also confirmed by in vitro studies that reported a strong antimicrobial effect of zinc nanoparticles against Lactobacillales order. Contradictory evidence makes this topic still controversial, however. In addition, zinc nanoparticles vary in their morphology and properties based on the method of their synthesis. This makes it difficult to understand the effect of zinc nanoparticles on the intestinal microbiome. This review is aimed at clarifying many circumstances that may affect the action of nanoparticles on the weaning piglets' microbiome, including a comprehensive overview of the zinc nanoparticles in vitro effects on bacterial species occurring in the digestive tract of weaned piglets.},
}
@article {pmid35720594,
year = {2022},
author = {Kong, Z and Liu, H},
title = {Modification of Rhizosphere Microbial Communities: A Possible Mechanism of Plant Growth Promoting Rhizobacteria Enhancing Plant Growth and Fitness.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {920813},
doi = {10.3389/fpls.2022.920813},
pmid = {35720594},
issn = {1664-462X},
abstract = {Plant beneficial bacteria, defined as plant growth-promoting rhizobacteria (PGPR), play a crucial role in plants' growth, stress tolerance and disease prevention. In association with the rhizosphere of plants, PGPR facilitate plant growth and development either directly or indirectly through multiple mechanisms, including increasing available mineral nutrients, moderating phytohormone levels and acting as biocontrol agents of phytopathogens. It is generally accepted that the effectiveness of PGPR inoculants is associated with their ability to colonize, survive and persist, as well as the complex network of interactions in the rhizosphere. Despite the promising plant growth promotion results commonly reported and mostly attributed to phytohormones or other organic compounds produced by PGPR inoculants, little information is available on the potential mechanisms underlying such positive effects via modifying rhizosphere microbial community and soil functionality. In this review, we overviewed the effects of PGPR inoculants on rhizosphere microbial ecology and soil function, hypothesizing that PGPR may indirectly promote plant growth and health via modifying the composition and functioning of rhizosphere microbial community, and highlighting the further directions for investigating the role of PGPR in rhizosphere from an ecological perspective.},
}
@article {pmid35720593,
year = {2022},
author = {Toghueo, RMK and Zabalgogeazcoa, I and Pereira, EC and Vazquez de Aldana, BR},
title = {A Diaporthe Fungal Endophyte From a Wild Grass Improves Growth and Salinity Tolerance of Tritordeum and Perennial Ryegrass.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {896755},
doi = {10.3389/fpls.2022.896755},
pmid = {35720593},
issn = {1664-462X},
abstract = {Some microbiome components can provide functions that extend the capabilities of plants, increasing the environmental adaptability and performance of holobionts. Festuca rubra subsp. pruinosa is a perennial grass adapted to rocky sea cliffs, where soil and nutrients are very limited, and exposure to salinity is continuous. This study aimed to investigate if a Diaporthe fungal endophyte belonging to the core microbiome of Festuca rubra roots could improve the performance of two agricultural grasses. In a greenhouse experiment, plants of tritordeum (Triticum durum x Hordeum chilense) and perennial ryegrass (Lolium perenne) were inoculated with Diaporthe strain EB4 and subjected to two salinity conditions (0 and 200 mM NaCl). Biomass production, mineral elements, proline, hormone profiles, antioxidant capacity, and total phenolic compounds were examined in plants, and fungal functions potentially related to the promotion of plant growth were determined. The inoculation with Diaporthe promoted plant growth of both grasses, increasing leaf biomass (84% in tritordeum and 29% in perennial ryegrass), root biomass, nutrient content (N, Ca, Mg, and Fe), and the production of indole 3-acetic acid, regardless of the salinity treatment. Improved growth and nutrient uptake might occur because Diaporthe produces several extracellular enzymes capable of recycling organic nutrient pools. In addition, the fungus produced indole 3-acetic acid in vitro and modulated the production of this phytohormone in the plant. Under salinity, the activity of Diaporthe ameliorated the stress, increasing proline, nutrient uptake in roots, gibberellins, and indole 3-acetic acid, which in turn results into improved growth. Thus, this fungus can transfer to alternative hosts some advantages useful at its original habitat.},
}
@article {pmid35720372,
year = {2022},
author = {Krawczyk, KT and Locht, C and Kowalewicz-Kulbat, M},
title = {Halophilic Archaea Halorhabdus Rudnickae and Natrinema Salaciae Activate Human Dendritic Cells and Orient T Helper Cell Responses.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {833635},
doi = {10.3389/fimmu.2022.833635},
pmid = {35720372},
issn = {1664-3224},
mesh = {Cytokines ; Dendritic Cells ; *Halobacteriaceae ; Humans ; *Interleukin-13/pharmacology ; T-Lymphocytes, Helper-Inducer ; },
abstract = {Halophilic archaea are procaryotic organisms distinct from bacteria, known to thrive in hypersaline environments, including salt lakes, salterns, brines and salty food. They have also been identified in the human microbiome. The biological significance of halophiles for human health has rarely been examined. The interactions between halophilic archaea and human dendritic cells (DCs) and T cells have not been identified so far. Here, we show for the first time that the halophilic archaea Halorhabdus rudnickae and Natrinema salaciae activate human monocyte-derived DCs, induce DC maturation, cytokine production and autologous T cell activation. In vitro both strains induced DC up-regulation of the cell-surface receptors CD86, CD80 and CD83, and cytokine production, including IL-12p40, IL-10 and TNF-α, but not IL-23 and IL-12p70. Furthermore, autologous CD4+ T cells produced significantly higher amounts of IFN-γ and IL-13, but not IL-17A when co-cultured with halophile-stimulated DCs in comparison to T cells co-cultured with unstimulated DCs. IFN-γ was almost exclusively produced by naïve T cells, while IL-13 was produced by both naïve and memory CD4+ T cells. Our findings thus show that halophilic archaea are recognized by human DCs and are able to induce a balanced cytokine response. The immunomodulatory functions of halophilic archaea and their potential ability to re-establish the immune balance may perhaps participate in the beneficial effects of halotherapies.},
}
@article {pmid35720165,
year = {2022},
author = {Georgiou, K and Belev, NA and Koutouratsas, T and Katifelis, H and Gazouli, M},
title = {Gut microbiome: Linking together obesity, bariatric surgery and associated clinical outcomes under a single focus.},
journal = {World journal of gastrointestinal pathophysiology},
volume = {13},
number = {3},
pages = {59-72},
doi = {10.4291/wjgp.v13.i3.59},
pmid = {35720165},
issn = {2150-5330},
abstract = {Obesity is increasingly prevalent in the post-industrial era, with increased mortality rates. The gut microbiota has a central role in immunological, nutritional and metabolism mediated functions, and due to its multiplexity, it is considered an independent organ. Modern high-throughput sequencing techniques have allowed phylogenetic exploration and quantitative analyses of gut microbiome and improved our current understanding of the gut microbiota in health and disease. Its role in obesity and its changes following bariatric surgery have been highlighted in several studies. According to current literature, obesity is linked to a particular microbiota profile that grants the host an augmented potential for calorie release, while limited diversity of gut microbiome has also been observed. Moreover, bariatric surgery procedures represent effective interventions for sustained weight loss and restore a healthier microbiota, contributing to the observed fat mass reduction and lean mass increase. However, newer evidence has shown that gut microbiota is only partially recovered following bariatric surgery. Moreover, several targets including FGF15/19 (a gut-derived peptide), could be responsible for the favorable metabolic changes of bariatric surgery. More randomized controlled trials and larger prospective studies that include well-defined cohorts are required to better identify associations between gut microbiota, obesity, and bariatric surgery.},
}
@article {pmid35719363,
year = {2022},
author = {Xue, J and Dominguez Rieg, JA and Thomas, L and White, JR and Rieg, T},
title = {Intestine-Specific NHE3 Deletion in Adulthood Causes Microbial Dysbiosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {896309},
doi = {10.3389/fcimb.2022.896309},
pmid = {35719363},
issn = {2235-2988},
mesh = {Adult ; Animals ; Bacteroidetes ; Dysbiosis/microbiology ; Firmicutes ; *Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases/microbiology ; Intestines/microbiology ; Mice ; Sodium-Hydrogen Exchanger 3/genetics ; },
abstract = {In the intestine, the Na+/H+ exchanger 3 (NHE3) plays a critical role for Na+ and fluid absorption. NHE3 deficiency predisposes patients to inflammatory bowel disease (IBD). In mice, selective deletion of intestinal NHE3 causes various local and systemic pathologies due to dramatic changes in the intestinal environment, which can influence microbiota colonization. By using metagenome shotgun sequencing, we determined the effect of inducible intestinal epithelial cell-specific deletion of NHE3 (NHE3IEC-KO) in adulthood on the gut microbiome in mice. Compared with control mice, NHE3IEC-KO mice show a significantly different gut microbiome signature, with an unexpected greater diversity. At the phylum level, NHE3IEC-KO mice showed a significant expansion in Proteobacteria and a tendency for lower Firmicutes/Bacteroidetes (F/B) ratio, an indicator of dysbiosis. At the family level, NHE3IEC-KO mice showed significant expansions in Bacteroidaceae, Rikenellaceae, Tannerellaceae, Flavobacteriaceae and Erysipelotrichaceae, but had contractions in Lachnospiraceae, Prevotellaceae and Eubacteriaceae. At the species level, after removing those with lowest occurrence and abundance, we identified 23 species that were significantly expanded (several of which are established pro-inflammatory pathobionts); whereas another 23 species were found to be contracted (some of which are potential anti-inflammatory probiotics) in NHE3IEC-KO mice. These results reveal that intestinal NHE3 deletion creates an intestinal environment favoring the competitive advantage of inflammophilic over anti-inflammatory species, which is commonly featured in conventional NHE3 knockout mice and patients with IBD. In conclusion, our study emphasizes the importance of intestinal NHE3 for gut microbiota homeostasis, and provides a deeper understanding regarding interactions between NHE3, dysbiosis, and IBD.},
}
@article {pmid35719352,
year = {2022},
author = {Hobson, CA and Vigué, L and Magnan, M and Chassaing, B and Naimi, S and Gachet, B and Claraz, P and Storme, T and Bonacorsi, S and Tenaillon, O and Birgy, A},
title = {A Microbiota-Dependent Response to Anticancer Treatment in an In Vitro Human Microbiota Model: A Pilot Study With Hydroxycarbamide and Daunorubicin.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {886447},
doi = {10.3389/fcimb.2022.886447},
pmid = {35719352},
issn = {2235-2988},
mesh = {Daunorubicin/pharmacology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Background: Anticancer drug efficacy is linked to the gut microbiota's composition, and there is a dire need to better understand these interactions for personalized medicine. In vitro microbiota models are promising tools for studies requiring controlled and repeatable conditions. We evaluated the impact of two anticancer drugs on human feces in the MiniBioReactor Array (MBRA) in vitro microbiota system.<br><br>Methods: The MBRA is a single-stage continuous-flow culture model, hosted in an anaerobic chamber. We evaluated the effect of a 5-day treatment with hydroxycarbamide or daunorubicine on the fecal bacterial communities of two healthy donors. 16S microbiome profiling allowed analysis of microbial richness, diversity, and taxonomic changes.<br><br>Results: In this host-free setting, anticancer drugs diversely affect gut microbiota composition. Daunorubicin was associated with significant changes in alpha- and beta-diversity as well as in the ratio of Firmicutes/Bacteroidetes in a donor-dependent manner. The impact of hydroxycarbamide on microbiota composition was not significant.<br><br>Conclusion: We demonstrated, for the first time, the impact of anticancer drugs on human microbiota composition, in a donor- and molecule-dependent manner in an in vitro human microbiota model. We confirm the importance of personalized studies to better predict drug-associated-dysbiosis in vivo, linked to the host's response to treatment.},
}
@article {pmid35719350,
year = {2022},
author = {Shin, J and Li, T and Zhu, L and Wang, Q and Liang, X and Li, Y and Wang, X and Zhao, S and Li, L and Li, Y},
title = {Obese Individuals With and Without Phlegm-Dampness Constitution Show Different Gut Microbial Composition Associated With Risk of Metabolic Disorders.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {859708},
doi = {10.3389/fcimb.2022.859708},
pmid = {35719350},
issn = {2235-2988},
mesh = {Bacteria/genetics ; *Diabetes Mellitus, Type 2/complications ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Obesity/complications/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Background: Obesity is conventionally considered a risk factor for multiple metabolic diseases, such as dyslipidemia, type 2 diabetes, hypertension, and cardiovascular disease (CVD). However, not every obese patient will progress to metabolic disease. Phlegm-dampness constitution (PDC), one of the nine TCM constitutions, is considered a high-risk factor for obesity and its complications. Alterations in the gut microbiota have been shown to drive the development and progression of obesity and metabolic disease, however, key microbial changes in obese patients with PDC have a higher risk for metabolic disorders remain elusive.<br><br>Methods: We carried out fecal 16S rRNA gene sequencing in the present study, including 30 obese subjects with PDC (PDC), 30 individuals without PDC (non-PDC), and 30 healthy controls with balanced constitution (BC). Metagenomic functional prediction of bacterial taxa was achieved using PICRUSt.<br><br>Results: Obese individuals with PDC had higher BMI, waist circumference, hip circumference, and altered composition of their gut microbiota compared to non-PDC obese individuals. At the phylum level, the gut microbiota was characterized by increased abundance of Bacteroidetes and decreased levels of Firmicutes and Firmicutes/Bacteroidetes ratio. At the genus level, Faecalibacterium, producing short-chain fatty acid, achieving anti-inflammatory effects and strengthening intestinal barrier functions, was depleted in the PDC group, instead, Prevotella was enriched. Most PDC-associated bacteria had a stronger correlation with clinical indicators of metabolic disorders rather than more severe obesity. The PICRUSt analysis demonstrated 70 significantly different microbiome community functions between the two groups, which were mainly involved in carbohydrate and amino acid metabolism, such as promoting Arachidonic acid metabolism, mineral absorption, and Lipopolysaccharide biosynthesis, reducing Arginine and proline metabolism, flavone and flavonol biosynthesis, Glycolysis/Gluconeogenesis, and primary bile acid biosynthesis. Furthermore, a disease classifier based on microbiota was constructed to accurately discriminate PDC individuals from all obese people.<br><br>Conclusion: Our study shows that obese individuals with PDC can be distinguished from non-PDC obese individuals based on gut microbial characteristics. The composition of the gut microbiome altered in obese with PDC may be responsible for their high risk of metabolic diseases.},
}
@article {pmid35719348,
year = {2022},
author = {Ling, Z and Jin, G and Yan, X and Cheng, Y and Shao, L and Song, Q and Liu, X and Zhao, L},
title = {Fecal Dysbiosis and Immune Dysfunction in Chinese Elderly Patients With Schizophrenia: An Observational Study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {886872},
doi = {10.3389/fcimb.2022.886872},
pmid = {35719348},
issn = {2235-2988},
mesh = {Aged ; Bacteria/genetics ; China ; Cytokines ; Dysbiosis/microbiology ; Feces/microbiology ; Humans ; *Immune System Diseases ; RNA, Ribosomal, 16S/genetics ; *Schizophrenia ; },
abstract = {Schizophrenia (SZ) is a severe neuropsychiatric disorder with largely unknown etiology and pathogenesis. Mounting preclinical and clinical evidence suggests that the gut microbiome is a vital player in SZ. However, the gut microbiota characteristics and its host response in elderly SZ patients are still not well understood. A total of 161 samples was collected, including 90 samples from elderly SZ patients and 71 samples from healthy controls. We explored the gut microbiota profiles targeting the V3-V4 region of the 16S rRNA gene by MiSeq sequencing, and to analyze their associations with host immune response. Our data found that bacterial β-diversity analyses could divide the SZ patients and healthy controls into two different clusters. The Linear discriminant analysis Effect Size (LEfSe) identified the compositional changes in SZ-associated bacteria, including Faecalibacterium, Roseburia, Actinomyces, Butyricicoccus, Prevotella and so on. In addition, the levels of pro-inflammatory cytokines such as IL-1β were greatly increased in SZ patients while the levels of anti-inflammatory cytokines such as IFN-γ were markedly decreased. Correlation analysis suggested that these bacteria contributed to immune disturbances in the host that could be used as non-invasive biomarkers to distinguish the SZ patients from healthy controls. Moreover, several predicted functional modules, including increased lipopolysaccharide biosynthesis, folate biosynthesis, lipoic acid metabolism, and decreased bile acid biosynthesis, fatty acid biosynthesis in SZ-associated microbiota, could be utilized by the bacteria to produce immunomodulatory metabolites. This study, for the first time, demonstrated the structural and functional dysbiosis of the fecal microbiota in Chinese elderly SZ patients, suggesting the potential for using gut key functional bacteria for the early, non-invasive diagnosis of SZ, personalized treatment, and the development of tailor-made probiotics designed for Chinese elderly SZ patients.},
}
@article {pmid35719342,
year = {2022},
author = {Kahl, BC and Moreau, K},
title = {Editorial: Co-Infection and Consequences in Cystic Fibrosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {924527},
doi = {10.3389/fcimb.2022.924527},
pmid = {35719342},
issn = {2235-2988},
mesh = {Adaptation, Biological ; *Coinfection ; *Cystic Fibrosis/complications ; Humans ; Pseudomonas aeruginosa ; },
}
@article {pmid35719339,
year = {2022},
author = {Xi, Y and Liu, F and Qiu, B and Li, Y and Xie, X and Guo, J and Wu, L and Liang, T and Wang, D and Wang, J and Chen, M and Xue, L and Ding, Y and Zhang, J and Wu, Q and Liu, H},
title = {Analysis of Gut Microbiota Signature and Microbe-Disease Progression Associations in Locally Advanced Non-Small Cell Lung Cancer Patients Treated With Concurrent Chemoradiotherapy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {892401},
doi = {10.3389/fcimb.2022.892401},
pmid = {35719339},
issn = {2235-2988},
mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Carcinoma, Non-Small-Cell Lung/drug therapy/genetics ; Chemoradiotherapy ; *Diabetes Mellitus, Type 2 ; Disease Progression ; Fatty Acids ; *Gastrointestinal Microbiome/genetics ; Humans ; *Lung Neoplasms/drug therapy/genetics ; Retrospective Studies ; },
abstract = {Purpose: To evaluate the association of gut microbiome signature and disease progression in locally advanced non-small cell lung cancer (LA-NSCLC) patients treated with concurrent chemoradiotherapy (CCRT) by fecal metagenome analysis.<br><br>Methods: Metagenome-wide association studies on baseline fecal samples from 18 LA-NSCLC patients before CCRT and 13 controls from healthy first-degree relatives were performed. Among the 18 LA-NSCLC patients, six patients were defined as the long progression-free survival (long-PFS) group (PFS≥11 months) while another 12 were in the short-PFS group (PFS<11 months). Alpha diversity, taxonomic composition, and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways were compared between groups.<br><br>Results: The Firmicutes/Bacteroidetes value of long-PFS group was higher than those of short-PFS (p=0.073) and healthy individual groups (p=0.009). Meanwhile, long-PFS group had significantly higher diversities in Fungi, Archaea, and Viruses than short-PFS group. The KEGG pathways overrepresented in short-PFS group included fructose and mannose metabolism (p=0.028), streptomycin biosynthesis (p=0.028), acarbose and validamycin biosynthesis (p=0.013), ribosome biogenesis in eukaryotes (p=0.035), biosynthesis of vancomycin group antibiotics (p=0.004), apoptosis-fly (p=0.044), and tetracycline biosynthesis (p=0.044), while those overrepresented in long-PFS group included fatty acid biosynthesis (p=0.035), fatty acid metabolism (p=0.008), vancomycin resistance (p=0.008), longevity regulating pathway-worm (p=0.028), type II diabetes mellitus (p=0.004), and viral carcinogenesis (p=0.003). Further analysis of antibiotic resistome demonstrated that the short-PFS group had a trend with more antibiotic resistance genes than healthy control (p=0.070) and long-PFS groups (p=0.218). The vancomycin resistance sequences were significantly enriched in the long-PFS group compared to the short-PFS group (p=0.006).<br><br>Conclusions: The baseline gut microbiome composition and functionality might be associated with PFS in LA-NSCLC treated with CCRT. The outcome of CCRT might be modulated through bacterial metabolic pathways. The antibiotic resistance genes might play a role in disease progression and provide potential information on the relationship between the use of antibiotics and treatment efficacy of CCRT in LA-NSCLC.},
}
@article {pmid35719331,
year = {2022},
author = {Ji, L and Hao, S and Wang, J and Zou, J and Wang, Y},
title = {Roles of Toll-Like Receptors in Radiotherapy- and Chemotherapy-Induced Oral Mucositis: A Concise Review.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {831387},
doi = {10.3389/fcimb.2022.831387},
pmid = {35719331},
issn = {2235-2988},
mesh = {*Antineoplastic Agents/adverse effects ; Humans ; Immunity, Innate ; Quality of Life ; *Stomatitis/chemically induced ; Toll-Like Receptors/metabolism ; },
abstract = {Radiotherapy and/or chemotherapy-induced oral mucositis (RIOM/CIOM) is a common complication in cancer patients, leading to negative clinical manifestations, reduced quality of life, and impacting compliance with anticancer treatment. The composition and metabolic function of the oral microbiome, as well as the innate immune response of the oral mucosa are severely altered during chemotherapy or radiotherapy, promoting the expression of inflammatory mediators by direct and indirect mechanisms. Commensal oral bacteria-mediated innate immune signaling via Toll-like receptors (TLRs) ambiguously shapes radiotherapy- and/or chemotherapy-induced oral damage. To date, there has been no comprehensive overview of the role of TLRs in RIOM/CIOM. This review aims to provide a narrative of the involvement of TLRs, including TLR2, TLR4, TLR5, and TLR9, in RIOM/CIOM, mainly by mediating the interaction between the host and microorganisms. As such, we suggest that these TLR signaling pathways are a novel mechanism of RIOM/CIOM with considerable potential for use in therapeutic interventions. More studies are needed in the future to investigate the role of different TLRs in RIOM/CIOM to provide a reference for the precise control of RIOM/CIOM.},
}
@article {pmid35719163,
year = {2022},
author = {Shen, W and Qiu, W and Lin, Q and Zeng, C and Liu, Y and Huang, W and Zhou, H},
title = {The Gut Microbiome of Preterm Infants Treated With Aminophylline Is Closely Related to the Occurrence of Feeding Intolerance and the Weight Gain.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {905839},
doi = {10.3389/fnut.2022.905839},
pmid = {35719163},
issn = {2296-861X},
abstract = {Background: Aminophylline is widely used in the treatment of preterm infants, but it can cause feeding intolerance events, in which gut microbial dysbiosis may have a role. This study aims to investigate the relationship between the gut microbiome of preterm infants treated with aminophylline and the occurrence of feeding intolerance and weight gain rate.<br><br>Methods: This study included a cohort of 118 preterm infants. Survival analysis and multivariate Cox regression were used to evaluate the relationship between aminophylline treatment and the occurrence of feeding intolerance. 16S rRNA V4 region gene sequencing was used to characterize the microbiome of fecal samples from the cohort. Linear discriminant analysis effect size was used to analyze the differential abundance of bacteria related to aminophylline treatment. Wilcoxon test, Kruskal-Wallis test, Spearman correlation coefficients and generalized linear mixed models were used to analyze the correlation between the differential bacteria and feeding intolerance events as well as the weight gain.<br><br>Results: The results showed that the use of aminophylline could significantly increase the occurrence of feeding intolerance. The relative abundances of Streptococcus and Rothia in the gut microbiome of preterm infants were positively correlated with both the occurrence of feeding intolerance and the use of aminophylline, while the relative abundance of Staphylococcus was negatively correlated. In particular, preterm infants with a lower relative abundance of Rothia were more likely to develop feeding intolerance associated with aminophylline, and this difference existed before the onset of feeding intolerance. Moreover, it took longer for individuals with a lower relative abundance of Streptococcus to reach 2 kg weight. The contribution of Streptococcus to weight gain was greater than that of Bifidobacterium or Lactobacillus.<br><br>Conclusion: The gut microbiome in preterm infants treated with aminophylline was characterized by a decrease in Streptococcus and Rothia and an increase in Staphylococcus. These microbes, especially Rothia, were positively correlated with the occurrence of feeding intolerance. Streptococcus but not Bifidobacter likely participated in the weight gain of preterm infants in early life.},
}
@article {pmid35719048,
year = {2022},
author = {Li, K and Liu, J and Qin, X},
title = {Research progress of gut microbiota in hepatocellular carcinoma.},
journal = {Journal of clinical laboratory analysis},
volume = {},
number = {},
pages = {e24512},
doi = {10.1002/jcla.24512},
pmid = {35719048},
issn = {1098-2825},
support = {//Liaoning Provincial Central Government's special project to guide local scientific and technological development (2019 JH6/10400009)./ ; //The National Science and Technology Major Project of China (2018ZX10302205)./ ; //"345 Talent Project" of Shengjing Hospital of China Medical University./ ; },
abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) is the sixth most common cancer and the fourth leading cause of cancer-related death in the world. A number of challenges remain for the early detection and effective treatment of HCC. In recent years, microbiota have been proven to be associated with the development of HCC. Many studies have explored the pathogenesis, diagnostic marker, and therapeutic target potential of microbiota in hepatocellular carcinoma. Therefore, we aimed to introduce the research methods and achievements of gut microbiota in hepatocellular carcinoma and discuss the value of gut microbiota in the pathogenesis, diagnosis, and treatment of hepatocellular carcinoma.<br><br>METHODS: Keywords are used to search relevant articles which were mainly published from 2010 to 2021, and we further selected targeted articles and read the full text.<br><br>RESULTS: Gut microbiota involved in promoting the formation and development of hepatocellular carcinoma, and differential gut microbiota and microbial metabolites have the potential to be the biomarkers of hepatocellular carcinoma. Purposefully regulated gut microbiota can improve the prognosis of patients, which is expected to be used in hepatocellular carcinoma.<br><br>CONCLUSION: The study of gut microbiota in hepatocellular carcinoma is definitely worthy of study. In-depth and elaborate research design is crucial for the study of the mechanism of gut microbiota involved in hepatocellular carcinoma, which can provide new directions and targets for the diagnosis, treatment, and prognosis of hepatocellular carcinoma.},
}
@article {pmid35719046,
year = {2022},
author = {Wei, L and Singh, R and Ghoshal, UC},
title = {Enterochromaffin Cells-Gut Microbiota Crosstalk: Underpinning the Symptoms, Pathogenesis, and Pharmacotherapy in Disorders of Gut-Brain Interaction.},
journal = {Journal of neurogastroenterology and motility},
volume = {},
number = {},
pages = {},
doi = {10.5056/jnm22008},
pmid = {35719046},
issn = {2093-0879},
abstract = {Disorders of gut-brain interaction (DGBIs) are common conditions in community and clinical practice. As specialized enteroendocrine cells, enterochromaffin (EC) cells produce up to 95% of total body serotonin and coordinate luminal and basolateral communication in the gastrointestinal (GI) tract. EC cells affect a broad range of gut physiological processes, such as motility, absorption, secretion, chemo/mechanosensation, and pathologies, including visceral hypersensitivity, immune dysfunction, and impaired gastrointestinal barrier function. We aim to review EC cell and serotonin-mediated physiology and pathophysiology with particular emphasis on DGBIs. We explored the knowledge gap and attempted to suggest new perspectives of physiological and pathophysiological insights of DGBIs, such as (1) functional heterogeneity of regionally distributed EC cells throughout the entire GI tract; (2) potential pathophysiological mechanisms mediated by EC cell defect in DGBIs; (3) cellular and molecular mechanisms characterizing EC cells and gut microbiota bidirectional communication; (4) differential modulation of EC cells through GI segment-specific gut microbiota; (5) uncover whether crosstalk between EC cells and (i) luminal contents; (ii) enteric nervous system; and (iii) central nervous system are core mechanisms modulating gut-brain homeostasis; and (6) explore the therapeutic modalities for physiological and pathophysiological mechanisms mediated through EC cells. Insights discussed in this review will fuel the conception and realization of pathophysiological mechanisms and therapeutic clues to improve the management and clinical care of DGBIs.},
}
@article {pmid35718965,
year = {2022},
author = {Sohrabi, M and Sahu, B and Kaur, H and Hasler, W and Prakash, A and Combs, CK},
title = {Gastrointestinal Changes and Alzheimer's Disease.},
journal = {Current Alzheimer research},
volume = {},
number = {},
pages = {},
doi = {10.2174/1567205019666220617121255},
pmid = {35718965},
issn = {1875-5828},
abstract = {BACKGROUND: There is a well-described mechanism of communication between the brain and gastrointestinal system in which both organs influence the function of the other. This bi-directional communication suggests that disease in either organ may affect function in the other.<br><br>OBJECTIVE: To assess whether the evidence supports gastrointestinal system inflammatory or degenerative pathophysiology as a characteristic of Alzheimer's disease [AD].<br><br>METHODS: A review of both rodent and human studies implicating gastrointestinal changes in AD was performed.<br><br>RESULTS: Numerous studies indicate that AD changes are not unique to the brain but also occur at various levels of the gastrointestinal tract involving both immune and neuronal changes. In addition, it appears that numerous conditions and diseases affecting regions of the tract may communicate to the brain to influence disease.<br><br>CONCLUSION: Gastrointestinal changes represent a perhaps overlooked aspect of AD, representing a more system influence of this disease.},
}
@article {pmid35718835,
year = {2022},
author = {Bao, S and Wang, H and Li, W and Ji, L and Wang, X and Shen, Q and Yang, S and Zhou, C and Zhang, W},
title = {Dynamic alterations of the mice gut virome after Coxsackievirus B3 infection.},
journal = {Journal of medical virology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jmv.27946},
pmid = {35718835},
issn = {1096-9071},
abstract = {The gut microbiome plays an essential role in the human health and dysbiosis has been implicated in numerous diseases. Coxsackievirus B3 infects millions of humans yearly and yet limited research has explored dynamic alterations of the gut virome after infection. Here, we established the mouse model of Coxsackievirus B3 infection and collected fecal samples at several time points to investigate alterations of the gut virome using viral metagenomic analysis. We found that the mice virome was dominated by Caudovirales and Microviridae, and phylogenetic analyses showed that both Caudovirales and Microviridae had high diversity. The gut virome had significant variations with the increase of Caudovirales and the decrease of Microviridae after infection. We proposed that Caudovirales and Microviridae may be biomarkers for the Coxsackievirus infection process. This study provides a reference for the dynamic changes of the gut virome after human Enterovirus infection, which may help guide the rational drug use in clinical treatment and provide new ideas for preventing Enterovirus infection. This article is protected by copyright. All rights reserved.},
}
@article {pmid35718778,
year = {2022},
author = {Sadoughi, B and Schneider, D and Daniel, R and Schülke, O and Ostner, J},
title = {Aging gut microbiota of wild macaques are equally diverse, less stable, but progressively personalized.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {95},
pmid = {35718778},
issn = {2049-2618},
mesh = {Aging ; Animals ; Bacteria/genetics ; Cross-Sectional Studies ; Female ; *Gastrointestinal Microbiome/genetics ; Macaca/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Pronounced heterogeneity of age trajectories has been identified as a hallmark of the gut microbiota in humans and has been explained by marked changes in lifestyle and health condition. Comparatively, age-related personalization of microbiota is understudied in natural systems limiting our comprehension of patterns observed in humans from ecological and evolutionary perspectives.<br><br>RESULTS: Here, we tested age-related changes in the diversity, stability, and composition of the gut bacterial community using 16S rRNA gene sequencing with dense repeated sampling over three seasons in a cross-sectional age sample of adult female Assamese macaques (Macaca assamensis) living in their natural forest habitat. Gut bacterial composition exhibited a personal signature which became less stable as individuals aged. This lack of stability was not explained by differences in microbiota diversity but rather linked to an increase in the relative abundance of rare bacterial taxa. The lack of age-related changes in core taxa or convergence with age to a common state of the community hampered predicting gut bacterial composition of aged individuals. On the contrary, we found increasing personalization of the gut bacterial composition with age, indicating that composition in older individuals was increasingly divergent from the rest of the population. Reduced direct transmission of bacteria resulting from decreasing social activity may contribute to, but not be sufficient to explain, increasing personalization with age.<br><br>CONCLUSIONS: Together, our results challenge the assumption of a constant microbiota through adult life in a wild primate. Within the limits of this study, the fact that increasing personalization of the aging microbiota is not restricted to humans suggests the underlying process to be evolved instead of provoked only by modern lifestyle of and health care for the elderly. Video abstract.},
}
@article {pmid35718272,
year = {2022},
author = {Li, Z and Liu, Y and Zhang, L},
title = {Role of the microbiome in oral cancer occurrence, progression and therapy.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {105638},
doi = {10.1016/j.micpath.2022.105638},
pmid = {35718272},
issn = {1096-1208},
abstract = {The oral cavity, like other digestive or mucosal sites, contains a site-specific microbiome that plays a significant role in maintaining health and homeostasis. Strictly speaking, the gastrointestinal tract starts from the oral cavity, with special attention paid to the specific flora of the oral cavity. In healthy people, the microbiome of the oral microenvironment is governed by beneficial bacteria, that benefit the host by symbiosis. When a microecological imbalance occurs, changes in immune and metabolic signals affect the characteristics of cancer, as well as chronic inflammation, disruption of the epithelial barrier, changes in cell proliferation and cell apoptosis, genomic instability, angiogenesis, and epithelial barrier destruction and metabolic regulation. These pathophysiological changes could result in oral cancer. Rising evidence suggests that oral dysbacteriosis and particular microbes may play a positive role in the evolution, development, progression, and metastasis of oral cancer, for instance, oral squamous cell carcinoma (OSCC) through direct or indirect action.},
}
@article {pmid35718258,
year = {2022},
author = {Kloepfer, KM and McCauley, KE and Kirjavainen, PV},
title = {The Microbiome as a Gateway to Prevention of Allergic Disease Development.},
journal = {The journal of allergy and clinical immunology. In practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaip.2022.05.033},
pmid = {35718258},
issn = {2213-2201},
abstract = {Allergic diseases exclusively affect tissues that face environmental challenges and harbor endogenous bacterial microbiota. The microbes inhabiting the affected tissues may not be mere bystanders in this process but actively affect the risk of allergic sensitization, disease development and exacerbation or abatement of symptoms. Experimental evidence provides several plausible means by which the human microbiota could influence the development of allergic diseases including, but not limited to, effects on antigen presentation and induction of tolerance and allergen permeation by endorsing or disrupting epithelial barrier integrity. Epidemiological evidence attests to the significance of age-appropriate, non-pathogenic microbiota development in skin, gastrointestinal tract and airways for protection against allergic disease development. Thus, there exists potential targets for preventive actions either in the prenatal or postnatal period. These could include maternal dietary interventions, antibiotic stewardship both for the mother and infant, reducing elective cesarean deliveries, and understanding barriers to breastfeeding and timing of food diversification. In here, we will review the current understanding and evidence of allergy-associated human microbiota patterns, their role in development of allergic diseases, and how we could harness these associations to our benefit against allergies.},
}
@article {pmid35718251,
year = {2022},
author = {Juarez, VM and Montalbine, AN and Singh, A},
title = {Microbiome as an immune regulator in health, disease, and therapeutics.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {114400},
doi = {10.1016/j.addr.2022.114400},
pmid = {35718251},
issn = {1872-8294},
abstract = {New discoveries in drugs and drug delivery systems are focused on identifying and delivering a pharmacologically effective agent, potentially targeting a specific molecular component. However, current drug discovery and therapeutic delivery approaches do not necessarily exploit the complex regulatory network of an indispensable microbiota that has been engineered through evolutionary processes in humans or has been altered by environmental exposure or diseases. The human microbiome, in all its complexity, plays an integral role in the maintenance of host functions such as metabolism and immunity. However, dysregulation in this intricate ecosystem has been linked with a variety of diseases, ranging from inflammatory bowel disease to cancer. Therapeutics and bacteria have an undeniable effect on each other and understanding the interplay between microbes and drugs could lead to new therapies, or to changes in how existing drugs are delivered. In addition, targeting the human microbiome using engineered therapeutics has the potential to address global health challenges. Here, we present the challenges and cutting-edge developments in microbiome-immune cell interactions and outline novel targeting strategies to advance drug discovery and therapeutics, which are defining a new era of personalized and precision medicine.},
}
@article {pmid35718139,
year = {2022},
author = {Irizar, H and Chun, Y and Arditi, Z and Do, A and Grishina, G and Grishin, A and Vicencio, A and Bunyavanich, S},
title = {Examination of host genetic effects on nasal microbiome composition.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2022.06.004},
pmid = {35718139},
issn = {1097-6825},
abstract = {BACKGROUND: Genetic predisposition increases risk for asthma, and distinct nasal microbial compositions are associated with asthma. Host genetics might shape nasal microbiome composition.<br><br>OBJECTIVE: We examined associations between host genetics and nasal microbiome composition.<br><br>METHODS: Nasal samples were collected from 584 participants from the Mount Sinai Health System, New York, USA. Seventy-seven follow-up samples were collected from a subset of forty participants. 16S rRNA sequencing and RNA-sequencing were performed on nasal samples. Beta-diversity was calculated, variant calling on RNA-seq data was performed, and genetic relatedness between individuals was determined. Using linear regression models, we tested for associations between genetic relatedness and nasal microbiome composition.<br><br>RESULTS: The median age of the cohort was 14.6 years (IQR 11.2-19.5), with participants representing diverse ancestries and 52.7% of the cohort female. For participants who provided follow-up samples, the median time between samples was 5.1 months (IQR 1.4-7.2). Nasal microbiome composition similarity as reflected by beta diversity was significantly higher within subjects over time vs. between subjects (coefficient=0.091, p-value=2.84-07). There was no significant association between genetic relatedness and beta diversity (coefficient=-0.05, p-value=0.29). Additional analyses exploring the relationship between beta-diversity and genetic variance yielded similar results.<br><br>CONCLUSION: Our results suggest that host genetics has little influence on nasal microbiome composition.},
}
@article {pmid35718049,
year = {2022},
author = {Zhang, L and He, Y and Lin, D and Yao, Y and Song, N and Wang, F},
title = {Co-application of biochar and nitrogen fertilizer promotes rice performance, decreases cadmium availability, and shapes rhizosphere bacterial community in paddy soil.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {119624},
doi = {10.1016/j.envpol.2022.119624},
pmid = {35718049},
issn = {1873-6424},
abstract = {Cadmium (Cd) contamination in soil has posed a great threat to crop safety and yield as well as soil quality. Biochar blended with nitrogen fertilizer have been reported to be effective in remediating Cd-contaminated soil. However, the influence of co-application of biochar and nitrogen fertilizer on the Cd bioavailability, rice yield and soil microbiome remains unclear. In this study, eight different treatments including control (CK), 5% biochar (B), 2.6, 3.5, 4.4 g/pot nitrogen fertilizers (N1, N2 and N3), and co-application of biochar and nitrogen fertilizers (BN1, BN2, BN3) were performed in a pot experiment with paddy soil for observations in an entire rice cycle growth period. Results showed single N increased soil available Cd content and Cd uptake in edible part of rice, while the soil available Cd content significantly decreased by 14.8% and 7.4%-11.1% under the B, BN treatments, and the Cd content in edible part of rice was significantly reduced by 35.1% and 18.5%-26.5%, respectively. Besides, B, N and BN treatments significantly increased the yield of rice by 14.3%-86.6% compared with CK, and the highest yield was gained under BN3 treatment. Soil bacterial diversity indices (Shannon, Chao1, observed species and PD whole tree index) under N2, N3 were generally improved. Cluster analysis indicated that bacterial community structures under BN treatments differed from those of CK and single N treatments. BN treatments enhanced the abundances of key bacterial phylum such as Acidobacteria, positively associated with yield, and increased the abundance of Spirochaetes, negatively correlated to soil available Cd and Cd uptake of rice. Furthermore, the regression path analysis (RPA) revealed that pH, organic matter (OM), alkaline hydrolysis of nitrogen (AHN) and available Cd were the major properties influencing Cd content in edible part of rice. Redundancy analysis (RDA) revealed that pH and available Cd played key role in shaping soil bacterial community. Thus, BN is a feasible practice for the improvements of rice growth and remediation of Cd-polluted soil.},
}
@article {pmid35718002,
year = {2022},
author = {Ye, Z and Huang, L and Zhang, J and Zhao, Q and Zhang, W and Yan, B},
title = {Biodegradation of arsenobetaine to inorganic arsenic regulated by specific microorganisms and metabolites in mice.},
journal = {Toxicology},
volume = {475},
number = {},
pages = {153238},
doi = {10.1016/j.tox.2022.153238},
pmid = {35718002},
issn = {1879-3185},
abstract = {Arsenobetaine (AsB) is a primary arsenic (As) compound found in marine organisms. However, in mammals, the metabolic mechanism of AsB remains indistinct. Therefore, in this study, we investigated the biotransformation and regulatory mechanism of AsB, particularly the biodegradation process, in a mouse model to assess the underlying health hazards of AsB. We studied the biotransformation process of AsB in mice through the food chain [AsB feed-marine fish (Epinephelus fuscoguttatus)-mice (Mus musculus)]. Our results showed the significant bioaccumulation of total As, AsB, and, in particular, arsenate [As(V)] through biodegradation in mice tissues. As the abundance of Staphylococcus and Blautia (phylum, Firmicutes) increased, the expression of aqp7 (absorption) and methyltransferase (as3mt) (methylation) was upregulated. In contrast, the expression of S-adenosyl methionine (sam) (methylation) was downregulated. These findings suggest that demethylation and methylation occurred simultaneously in the intestines, with demethylation capacity being greater than that of methylation. Furthermore, Firmicutes such as Staphylococcus and Blautia showed a significant inverse relationship with arachidonic acid, choline, and sphingosine. Gene, microbiome, and metabolomics analyses indicated that Staphylococcus and Blautia and arachidonic acid, choline, and sphingosine participated in the degradation of AsB to As(V) in mouse intestines. Therefore, long-term AsB ingestion through marine fish consumption could cause potential health hazards in humans.},
}
@article {pmid35717933,
year = {2022},
author = {Oshiro, T and Harada, Y and Kubota, K and Sadatomi, D and Sekine, H and Nishiyama, M and Fujitsuka, N},
title = {Associations between intestinal microbiota, fecal properties, and dietary fiber conditions: The Japanese traditional medicine Junchoto ameliorates dietary fiber deficit-induced constipation with F/B ratio alteration in rats.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {152},
number = {},
pages = {113263},
doi = {10.1016/j.biopha.2022.113263},
pmid = {35717933},
issn = {1950-6007},
mesh = {Animals ; Bacteroidetes ; Cellulose ; Constipation ; Dietary Fiber ; Firmicutes ; *Gastrointestinal Microbiome ; Humans ; Japan ; Medicine, Traditional ; RNA, Ribosomal, 16S/genetics ; Rats ; },
abstract = {Changes in the intestinal microbiota are known to occur in constipated patients. Dietary fiber restriction presents obstacles to appropriate defecation and affects fecal properties, but the relationship between fecal microbiota and fecal morphological properties remains obscure. Therefore, we examined the influence of fiber diets on the fecal microbiome and properties in rats, and the effectiveness of the Japanese traditional medicine Junchoto (JCT) in rats with fiber deficit-induced constipation. Rats were fed three different fiber diets with varying cellulose contents (0 %, FFD; 5 %, ND; 15 %, HFD), respectively, as follows: study 1: 21 days of feeding; study 2: 14 days of feeding followed by 7 days of ND (fiber normalization in all groups); study 3: FFD for 21 days, followed by JCT administration from 14 days. Fecal properties and 16S rRNA amplicon sequencing results were examined. We observed that the fecal frequency, dry weight, and length were increased, and water ratio were decreased in a cellulose dose-dependent manner. The difference in several kinds of fecal microbiota, but not the α-diversity Chao1 index and the Firmicutes/Bacteroidetes ratio (F/B ratio), between groups were observed. The change in fecal property in both the HFD and FFD groups was ameliorated with fiber normalization, accompanied by alteration of the Chao1 index and/or F/B ratio. JCT administration reversed the fecal morphological changes in FFD group, accompanied by F/B ratio increasing. In conclusion, short-term dietary changes modulated microbial homeostasis, which is linked to fecal property. JCT may alter the F/B ratio and improve fecal properties to facilitate easier excretion.},
}
@article {pmid35717815,
year = {2022},
author = {Li, W and He, E and Zhang, P and Li, Y and Qiu, H},
title = {Multiomics analyses uncover nanoceria triggered oxidative injury and nutrient imbalance in earthworm Eisenia fetida.},
journal = {Journal of hazardous materials},
volume = {437},
number = {},
pages = {129354},
doi = {10.1016/j.jhazmat.2022.129354},
pmid = {35717815},
issn = {1873-3336},
abstract = {The toxic stress caused by nanoceria remains vague owing to the limited efforts scrutinizing its molecular mechanisms. Herein, we investigated the impacts of nanoceria on earthworm Eisenia fetida, at the molecular level using the multiomics-based profiling approaches (transcriptomics, metabolomics, and 16 S rRNA sequencing). Nanoceria (50 and 500 mg/kg) significantly increased the contents of malondialdehyde (MDA), Fe, and K in worms, suggesting oxidative injury and nutrient imbalance. This was corroborated by the transcriptomic and metabolomic analyses. Nanoceria decreased the levels of certain genes and metabolites associated with glycerolipid and glycerophospholipid metabolisms, suggesting the production of reactive oxygen species and subsequent oxidative stress. Additionally, the ABCD3 gene belonging to ABC transporter family was upregulated, facilitating Fe uptake by worms. Moreover, the higher contents of MDA, Fe, and K after exposure were tightly associated with the imbalanced intestinal flora. Specifically, a higher relative abundance of Actinobacteriota and a lower relative abundance of Proteobacteria and Patescibacteria were induced. This study, for the first time, revealed that nanoceria at nonlethal levels caused oxidative stress and nutrient imbalance of earthworms from the perspective of genes, metabolites, and gut microbiome perturbations, and also established links between the gut microbiome and the overall physiological responses of the host.},
}
@article {pmid35717707,
year = {2022},
author = {Han, SW and Yoshikuni, Y},
title = {Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes.},
journal = {Current opinion in microbiology},
volume = {68},
number = {},
pages = {102172},
doi = {10.1016/j.mib.2022.102172},
pmid = {35717707},
issn = {1879-0364},
abstract = {Plants benefit from symbiotic relationships with their microbiomes. Modifying these microbiomes to further promote plant growth and improve stress tolerance in crops is a promising strategy. However, such efforts have had limited success, perhaps because the original microbiomes quickly re-establish. Since the complex biological networks involved are little understood, progress through conventional means is time-consuming. Synthetic biology, with its practical successes in multiple industries, could speed up this research considerably. Some fascinating candidates for production by synthetic microbiomes are organic nitrogen metabolites and related pyridoxal-5'-phosphate-dependent enzymes, which have pivotal roles in microbe-microbe and plant-microbe interactions. This review summarizes recent studies of these metabolites and enzymes and discusses prospective synthetic biology platforms for sustainable agriculture.},
}
@article {pmid35717574,
year = {2022},
author = {Parshukov, AN and Fokina, NN and Sukhovskaya, IV and Kantserova, NP and Lysenko, LA},
title = {Infection and antibiotic treatment have prolonged effect on gut microbiota, muscle and hepatic fatty acids in rainbow trout (Oncorhynchus mykiss).},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jam.15674},
pmid = {35717574},
issn = {1365-2672},
abstract = {AIMS: The aim of the present study was to investigate the gastrointestinal (GI) microbiota and bacterium-specific fatty acid occurrence in the muscle and hepatic lipids of rainbow trout Oncorhynchus mykiss (Walbaum, 1792), both healthy and those naturally infected with bacterial pathogens.<br><br>METHODS AND RESULTS: From June 2017 (L1) to September 2018 (L8), 74 specimens of rainbow trout Oncorhynchus mykiss (with the average weight from 139.2 ± 7.1 g (L1) to 2191.7 ± 85.1 g (L8)) were studied. Amplicon sequencing targeted to the V3-V4 region of 16S rRNA gene fragments is used for identification of taxonomic composition of gut bacterial communities. Firmicutes, Bacteroidetes, Proteobacteria, Tenericutes, and Fusobacteria were the major phyla. Besides behavioural and physiological manifestations of the bacterial mixed disease (yersiniosis, pseudomonosis, and flavobacteriosis), some disorders induced both the infection and followed antibiotic treatment were detected in the host organism, including (1) a progressive decrease in the content of odd-chain saturated fatty acids of bacterial origin within the trout lipid molecules and (2) abnormalities in trout GI tract microbiota, such as the elimination of LAB and progressive occurrence of certain bacterial taxa, particularly Mycoplasmataceae.<br><br>CONCLUSIONS: The GI bacterial flora varied principally due to Mycoplasmataceae and Lactobacillaceae, which could be considered in the search for bioindicators. The content of specific bacterium-derived fatty acids incorporated into the lipids of trout muscle and hepatic seems to be related to the prevalence of bacterial taxa, and their deficit could be regarded as an early warning sign of microbiota disturbance.<br><br>Our results demonstrated that infectious disease and antibiotic treatment of reared species can cause pertinent imbalance in their gut microbiota and reduce the abundance of specific fatty acids. This can be useful for the sustainable aquaculture industry due to development of early indication technologies for rapid disease diagnosis.},
}
@article {pmid35717483,
year = {2022},
author = {Moroishi, Y and Gui, J and Nadeau, KC and Morrison, HG and Madan, J and Karagas, MR},
title = {A prospective study of the infant gut microbiome in relation to vaccine response.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {35717483},
issn = {1530-0447},
abstract = {BACKGROUND: The establishment of the gut microbiome plays a key symbiotic role in the developing immune system; however, its influence on vaccine response is yet uncertain. We prospectively investigated the composition and diversity of the early-life gut microbiome in relation to infant antibody response to two routinely administered vaccines.<br><br>METHODS: Eighty-three infants enrolled in the New Hampshire Birth Cohort Study were included in the analysis. We collected blood samples at 12 months of age and assayed the isolated serum to quantify total IgG and measured antibody to pneumococcal capsular polysaccharide and tetanus toxoid. Stool samples were collected from infants at 6 weeks of age and sequenced using 16S rRNA, and a subset of 61 samples were sequenced using shotgun metagenomics sequencing.<br><br>RESULTS: We observed differences in beta diversity for 16S 6-week stool microbiota and pneumococcal and tetanus IgG antibody responses. Metagenomics analyses identified species and metabolic pathways in 6-week stool associated with tetanus antibody response, in particular, negative associations with the relative abundance of Aeriscardovia aeriphila species and positive associations with the relative abundance of species associated with CDP-diacylglycerol biosynthesis pathways.<br><br>CONCLUSIONS: The early gut microbiome composition may influence an infant's vaccine response.<br><br>IMPACT: Early intestinal microbiome acquisition plays a critical role in immune maturation and in both adaptive and innate immune response in infancy. We identified associations between early life microbiome composition and response to two routinely administered vaccines-pneumococcal capsular polysaccharide and tetanus toxoid-measured at approximately 1 year of age. Our findings highlight the potential impact of the gut microbiome on infant immune response that may open up opportunities for future interventions.},
}
@article {pmid35717467,
year = {2022},
author = {Shetty, SA and Kostopoulos, I and Geerlings, SY and Smidt, H and de Vos, WM and Belzer, C},
title = {Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {35717467},
issn = {1751-7370},
support = {NRGWI.obrug.2018.005//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; },
abstract = {Microbe-microbe interactions in the human gut are influenced by host-derived glycans and diet. The high complexity of the gut microbiome poses a major challenge for unraveling the metabolic interactions and trophic roles of key microbes. Synthetic minimal microbiomes provide a pragmatic approach to investigate their ecology including metabolic interactions. Here, we rationally designed a synthetic microbiome termed Mucin and Diet based Minimal Microbiome (MDb-MM) by taking into account known physiological features of 16 key bacteria. We combined 16S rRNA gene-based composition analysis, metabolite measurements and metatranscriptomics to investigate community dynamics, stability, inter-species metabolic interactions and their trophic roles. The 16 species co-existed in the in vitro gut ecosystems containing a mixture of complex substrates representing dietary fibers and mucin. The triplicate MDb-MM's followed the Taylor's power law and exhibited strikingly similar ecological and metabolic patterns. The MDb-MM exhibited resistance and resilience to temporal perturbations as evidenced by the abundance and metabolic end products. Microbe-specific temporal dynamics in transcriptional niche overlap and trophic interaction network explained the observed co-existence in a competitive minimal microbiome. Overall, the present study provides crucial insights into the co-existence, metabolic niches and trophic roles of key intestinal microbes in a highly dynamic and competitive in vitro ecosystem.},
}
@article {pmid35717012,
year = {2022},
author = {Penyalver, R and Roesch, LFW and Piquer-Salcedo, JE and Forner-Giner, MA and Alguacil, MDM},
title = {From the bacterial citrus microbiome to the selection of potentially host-beneficial microbes.},
journal = {New biotechnology},
volume = {70},
number = {},
pages = {116-128},
doi = {10.1016/j.nbt.2022.06.002},
pmid = {35717012},
issn = {1876-4347},
abstract = {Citrus is the most cultivated fruit crop worldwide. The modern citrus industry needs new bioproducts to overcome phytopathological threats, tolerate stresses and increase yield and quality. Mutualistic microbes from roots significantly impact host physiology and health and are a potentially beneficial resource. The bacterial microbiome can be surveyed to select potentially host-beneficial microbes. To achieve this goal, a prevalent "core-citrus" bacterial microbiome was obtained by picking those operational taxonomic units (OTUs) shared among samples within and across two Citrus rootstock genotypes grown in the same soil for more than 20 years. A sub-selection of main OTUs from the defined "core-citrus" microbiome was made based on abundance, host-enriched versus bulk soil, and rhizosphere-indicator species. In parallel, an extensive census of the cultivable microbiota was performed to collect a large number of bacterial citrus isolates. Metataxonomic data were linked to cultured microbes, matching 16S rRNA gene sequences from bacterial isolates with those counterpart OTU reference sequences from the selected bacterial "core-citrus" microbiome. This approach allowed selection of potentially host-beneficial bacteria to mine for agricultural probiotics in future biotechnological applications required for the citrus industry.},
}
@article {pmid35716742,
year = {2022},
author = {Perrotta, BG and Kidd, KA and Walters, DM},
title = {PCB exposure is associated with reduction of endosymbionts in riparian spider microbiomes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {156726},
doi = {10.1016/j.scitotenv.2022.156726},
pmid = {35716742},
issn = {1879-1026},
abstract = {Microbial communities, including endosymbionts, play diverse and critical roles in host biology and reproduction, but contaminant exposure may cause an imbalance in the microbiome composition with subsequent impacts on host health. Here, we examined whether there was a significant alteration of the microbiome community within two taxa of riparian spiders (Tetragnathidae and Araneidae) from a site with historical polychlorinated biphenyl (PCB) contamination in southern Ontario, Canada. Riparian spiders specialize in the predation of adult aquatic insects and, as such, their contaminant levels closely track those of nearby aquatic ecosystems. DNA from whole spiders from sites with either low or high PCB contamination was extracted, and spider microbiota profiled by partial 16S rRNA gene amplicon sequencing. The most prevalent shift in microbial communities we observed was a large reduction in endosymbionts in spiders at the high PCB site. The abundance of endosymbionts at the high PCB site was 63 % and 98 % lower for tetragnathids and araneids, respectively, than at the low PCB site. Overall, this has potential implications for spider reproductive success and food webs, as riparian spiders are critical gatekeepers of energy and material fluxes at the land-water interface.},
}
@article {pmid35716597,
year = {2022},
author = {Huang, TY and Lim, HL},
title = {Electrogenic Staphylococcus warneri in lactate-rich skin.},
journal = {Biochemical and biophysical research communications},
volume = {618},
number = {},
pages = {67-72},
doi = {10.1016/j.bbrc.2022.06.020},
pmid = {35716597},
issn = {1090-2104},
abstract = {The electrogenicity of environmental bacteria has been thoroughly explored and has been known to have the unique capability of decomposing hazardous chemicals for environmental remediation. However, electrogenic bacteria in human skin in regards to their electrical properties and locations have not yet been determined. Here, electrodermal activities and metabolite compositions at different locations of arm skin were assessed. Compared to the uppermost part of arm, we found that the forearm elicited high electrodermal activity and carried abundant lactate and alpha-ketoglutarate, two components commonly present in sweat. Upon culturing bacteria from the forearm, an iron-resistant strain of Staphylococcus warneri (S. warneri) was identified through 16S ribosomal RNA sequencing. Voltage changes induced by S. warneri in the presence of glucose were detected by two voltmeters of different electrode materials, demonstrating the electrogenicity of skin bacteria. Furthermore, we discovered that S. warneri has the ability to metabolize lactate to generate electricity. The results of this study reveal changes in skin conductance caused by bacterial electricity that are mediated by skin endogenous molecules and may provide a novel method of monitoring environmental skin insults.},
}
@article {pmid35715947,
year = {2022},
author = {Facchin, S and Calgaro, M and Pandolfo, M and Caldart, F and Ghisa, M and Greco, E and Sattin, E and Valle, G and Dellon, E and Vitulo, N and Savarino, EV},
title = {Salivary microbiota composition may discriminate between patients with eosinophilic oesophagitis (EoE) and non-EoE subjects.},
journal = {Alimentary pharmacology &amp; therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.17091},
pmid = {35715947},
issn = {1365-2036},
support = {Research grant 2019/2020//Department of Surgery, Oncology and Gastroenterology University of Padua/ ; STARS@Unipd2019//Department of Surgery, Oncology and Gastroenterology University of Padua/ ; },
abstract = {BACKGROUND: Data on the role of the microbiome in adult patients with eosinophilic oesophagitis (EoE) are limited.<br><br>AIMS: To prospectively collect and characterise the salivary, oesophageal and gastric microbiome in patients with EoE, further correlating the findings with disease activity.<br><br>METHODS: Adult patients with symptoms of oesophageal dysfunction undergoing upper endoscopy were consecutively enrolled. Patients were classified as EoE patients, in case of more than 15 eosinophils per high-power field, or non-EoE controls, in case of lack of eosinophilic infiltration. Before and during endoscopy, saliva, oesophageal and gastric fundus biopsies were collected. Microbiota assessment was performed by 16 s rRNA analysis. A Sparse Partial Least Squares Discriminant Analysis (sPLS-DA) was implemented to identify biomarkers.<br><br>RESULTS: Saliva samples were collected from 29 EoE patients and 20 non-EoE controls;, biopsies from 25 EoE and 5 non-EoE controls. In saliva samples, 23 Amplicon Sequence Variants (ASVs) were positively associated with EoE and 27 ASVs with controls, making it possible to discriminate between EoE and non-EoE patients with a classification error (CE) of 24%. In a validation cohort, the accuracy, sensitivity, specificity, positive predictive value and negative predictive value of this model were 78.6%, 80%, 75%, 80% and 60%, respectively. Moreover, the analysis of oesophageal microbiota samples observed a clear microbial pattern able to discriminate between active and inactive EoE (CE = 8%).<br><br>CONCLUSION: Our preliminary data suggest that salivary metabarcoding analysis in combination with machine learning approaches could become a valid, cheap, non-invasive test to segregate between EoE and non-EoE patients.},
}
@article {pmid35504561,
year = {2022},
author = {Yang, K and Tabung, FK and Whitehead, WE and Giovannucci, EL and Chan, AT and Staller, K},
title = {Proinflammatory Diet Is Associated With Increased Risk of Fecal Incontinence Among Older Women: Prospective Results From the Nurses' Health Study.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2022.04.011},
pmid = {35504561},
issn = {1542-7714},
abstract = {Fecal incontinence (FI) is a debilitating gastrointestinal disorder with a devastating impact on quality of life,1,2 particularly on older women, partly because of unique risk factors including parity and menopause.2,3 Therefore, identifying modifiable factors, such as diet, are crucial for developing effective prevention strategies for FI among those at risk. We previously found higher dietary fiber intake was associated with lower FI risk,4 providing the first population-based data to connect diet and FI prevention. However, prospective evidence on other dietary factors and FI risk has been limited. Dietary patterns may be associated with gut microbiome characteristics, which may influence inflammatory responses in the gastrointestinal tract5 and drive neurosensory disturbances.6 Moreover, chronic inflammation may drive reduced muscle mass and function,7 and pelvic floor dysfunction is an established FI risk factor.1,2 We hypothesized that a proinflammatory dietary pattern may be associated with increased FI risk and tested this hypothesis in the Nurses' Health Study.},
}
@article {pmid35714791,
year = {2022},
author = {Premke, K and Wurzbacher, C and Felsmann, K and Fabian, J and Taube, R and Bodmer, P and Attermeyer, K and Nitzsche, KN and Schroer, S and Koschorreck, M and Hübner, E and Mahmoudinejad, TH and Kyba, CCM and Monaghan, MT and Hölker, F},
title = {Large-scale sampling of the freshwater microbiome suggests pollution-driven ecosystem changes.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {308},
number = {},
pages = {119627},
doi = {10.1016/j.envpol.2022.119627},
pmid = {35714791},
issn = {1873-6424},
abstract = {Freshwater microbes play a crucial role in the global carbon cycle. Anthropogenic stressors that lead to changes in these microbial communities are likely to have profound consequences for freshwater ecosystems. Using field data from the coordinated sampling of 617 lakes, ponds, rivers, and streams by citizen scientists, we observed linkages between microbial community composition, light and chemical pollution, and greenhouse gas concentration. All sampled water bodies were net emitters of CO2, with higher concentrations in running waters, and increasing concentrations at higher latitudes. Light pollution occurred at 75% of sites, was higher in urban areas and along rivers, and had a measurable effect on the microbial alpha diversity. Genetic elements suggestive of chemical stress and antimicrobial resistances (IntI1, blaOX58) were found in 85% of sites, and were also more prevalent in urban streams and rivers. Light pollution and CO2 were significantly related to microbial community composition, with CO2 inversely related to microbial phototrophy. Results of synchronous nationwide sampling indicate that pollution-driven alterations to the freshwater microbiome lead to changes in CO2 production in natural waters and highlight the vulnerability of running waters to anthropogenic stressors.},
}
@article {pmid35714467,
year = {2022},
author = {Chen, C and Pan, J and Xiao, S and Wang, J and Gong, X and Yin, G and Hou, L and Liu, M and Zheng, Y},
title = {Microplastics alter nitrous oxide production and pathways through affecting microbiome in estuarine sediments.},
journal = {Water research},
volume = {221},
number = {},
pages = {118733},
doi = {10.1016/j.watres.2022.118733},
pmid = {35714467},
issn = {1879-2448},
abstract = {Increasing microplastics (MPs) pollution in estuaries profoundly impacts microbial ecosystems and biogeochemical processes. Nitrous oxide (N2O), a powerful greenhouse gas, is an important intermediate product of microbial nitrogen cycling. However, how MPs regulate N2O production and its pathways remain poorly understood. Here, impacts of traditional petroleum-based and emerging biodegradable MPs on microbial N2O production and its pathways were studied through dual-isotope (15N-18O) labeling technique and molecular methods. Results indicated that both traditional petroleum-based and emerging biodegradable MPs promoted sedimentary N2O production, whereas pathways varied. Biodegradable polylactic acid (PLA) MPs displayed greater promotion of N2O production than petroleum-based MPs, polyvinyl chloride (PVC) and polyethylene (PE), of which PLA promoted through nitrifier nitrification (NN) and heterotrophic denitrification (HD), PE through nitrifier denitrification and HD, and PVC through NN. By combining the analysis of N2O production rates with sediment chemical and microbiological properties, we demonstrated that the enrichment of nitrifying and denitrifying bacteria, as well as related functional genes directly and/or indirectly increased N2O production primarily by interacting with carbon and nitrogen substrates. Different response of nitrogen cycling microbes to MPs led to the difference in N2O increase pathways, of which nitrifying bacteria significantly enriched in all MPs treatments due to the niches provided by MPs. However, part of denitrifying bacteria significantly enriched in treatments containing PLA and PE MPs, which may serve as organic carbon substrates. This work highlights that the presence of MPs can promote sedimentary N2O production, and the emerging biodegradable MPs represented by PLA may have a greater potential to enhance estuarine N2O emissions and accelerate global climate change.},
}
@article {pmid35714435,
year = {2022},
author = {Borker, SS and Thakur, A and Khatri, A and Kumar, R},
title = {Quality assessment, safety evaluation, and microbiome analysis of night-soil compost from Lahaul valley of northwestern Himalaya.},
journal = {Waste management (New York, N.Y.)},
volume = {149},
number = {},
pages = {42-52},
doi = {10.1016/j.wasman.2022.06.003},
pmid = {35714435},
issn = {1879-2456},
abstract = {The Himalayan dry toilet system prevalent in the northwestern Himalaya is a traditional practice of converting human faeces into a compost-like soil amendment. The current study evaluated night-soil compost (NSC) for agricultural use by assessing the compost quality, safety, and microbiome properties. Based on the fertility and clean indices determined by the fertility and heavy metal parameters, NSC was categorized as good quality compost with high fertilizing potential and moderate concentration of heavy metals. With respect to pathogens, the faecal coliform levels in the NSC were categorized as safe according to the U.S. Environmental Protection Agency standards. The bacterial community structure based on 16S rRNA gene amplicons revealed a diverse taxonomy with 14 phyla and 54 genera in NSC. Compared to publicly available 16S rRNA gene amplicon data, NSC exhibited predominant phyla (Proteobacteria, Bacteriodetes, Actinobacteria, and Firmicutes) similar to human faeces, cattle manure, food waste compost, vermicompost, and activated sludge. However, statistically, NSC was distinct at the genus level from all other groups. Additionally, pathogenic bacteria with antimicrobial resistance (AMR) genes in the NSC metagenome were determined by performing a standalone BLASTN against the PATRIC database. The analysis revealed 139 pathogenic strains with most pathogens susceptible to antibiotics, indicating lower AMR in the predicted strains. The phytotoxicity of NSC with Pisum sativum var. AS-10 seeds showed a germination index of > 85%, indicating NSC's non-harmful effects on seed germination and root growth. Overall, NSC from Himalayan dry toilets can be used as a soil amendment for food and non-food plants.},
}
@article {pmid35713962,
year = {2022},
author = {Joean, O and Welte, T},
title = {Vaccination and modern management of chronic obstructive pulmonary disease - a narrative review.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2022.2092099},
pmid = {35713962},
issn = {1747-6356},
abstract = {INTRODUCTION: Chronic obstructive pulmonary disease (COPD) carries a tremendous societal and individual burden posing significant challenges for public health systems worldwide due to its high morbidity and mortality. Due to aging, multimorbidity but also in the wake of important progress in deciphering the heterogeneous disease endotypes, an individualized approach to the prevention and management of COPD is necessary.<br><br>AREAS COVERED: This article tackles relevant immunization strategies that are available or still under development with a focus on latest evidence but also controversies around different regional immunization approaches. Further, we present the crossover between chronic lung inflammation and lung microbiome disturbance as well as its role in delineating COPD endotypes. Moreover, the article attempts to underline endotype-specific treatment approaches. Lastly, we highlight non-pharmacologic prevention and management programs in view of the challenges and opportunities of the COVID-19 era.<br><br>EXPERT OPINION: Despite remaining challenges, personalised medicine has the potential to offer tailored approaches to prevention and therapy and promises to improve the care of patients living with COPD.},
}
@article {pmid35713682,
year = {2022},
author = {Sandy, M and Bui, TI and Abá, KS and Ruiz, N and Paszalek, J and Connor, EW and Hawkes, CV},
title = {Plant Host Traits Mediated by Foliar Fungal Symbionts and Secondary Metabolites.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {35713682},
issn = {1432-184X},
support = {2017-67013-29207//National Institute of Food and Agriculture/ ; HATCH accesssion no 1018688//National Institute of Food and Agriculture/ ; },
abstract = {Fungal symbionts living inside plant leaves ("endophytes") can vary from beneficial to parasitic, but the mechanisms by which the fungi affect the plant host phenotype remain poorly understood. Chemical interactions are likely the proximal mechanism of interaction between foliar endophytes and the plant, as individual fungal strains are often exploited for their diverse secondary metabolite production. Here, we go beyond single strains to examine commonalities in how 16 fungal endophytes shift plant phenotypic traits such as growth and physiology, and how those relate to plant metabolomics profiles. We inoculated individual fungi on switchgrass, Panicum virgatum L. This created a limited range of plant growth and physiology (2-370% of fungus-free controls on average), but effects of most fungi overlapped, indicating functional similarities in unstressed conditions. Overall plant metabolomics profiles included almost 2000 metabolites, which were broadly correlated with plant traits across all the fungal treatments. Terpenoid-rich samples were associated with larger, more physiologically active plants and phenolic-rich samples were associated with smaller, less active plants. Only 47 metabolites were enriched in plants inoculated with fungi relative to fungus-free controls, and of these, Lasso regression identified 12 metabolites that explained from 14 to 43% of plant trait variation. Fungal long-chain fatty acids and sterol precursors were positively associated with plant photosynthesis, conductance, and shoot biomass, but negatively associated with survival. The phytohormone gibberellin, in contrast, was negatively associated with plant physiology and biomass. These results can inform ongoing efforts to develop metabolites as crop management tools, either by direct application or via breeding, by identifying how associations with more beneficial components of the microbiome may be affected.},
}
@article {pmid35713550,
year = {2022},
author = {Katanski, CD and Watkins, CP and Zhang, W and Reyer, M and Miller, S and Pan, T},
title = {Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkac517},
pmid = {35713550},
issn = {1362-4962},
support = {RM1HG008935/GF/NIH HHS/United States ; BC191198//DoD/CDMRP/ ; },
abstract = {Queuosine (Q) is a conserved tRNA modification at the wobble anticodon position of tRNAs that read the codons of amino acids Tyr, His, Asn, and Asp. Q-modification in tRNA plays important roles in the regulation of translation efficiency and fidelity. Queuosine tRNA modification is synthesized de novo in bacteria, whereas in mammals the substrate for Q-modification in tRNA is queuine, the catabolic product of the Q-base of gut bacteria. This gut microbiome dependent tRNA modification may play pivotal roles in translational regulation in different cellular contexts, but extensive studies of Q-modification biology are hindered by the lack of high throughput sequencing methods for its detection and quantitation. Here, we describe a periodate-treatment method that enables single base resolution profiling of Q-modification in tRNAs by Nextgen sequencing from biological RNA samples. Periodate oxidizes the Q-base, which results in specific deletion signatures in the RNA-seq data. Unexpectedly, we found that periodate-treatment also enables the detection of several 2-thio-modifications including τm5s2U, mcm5s2U, cmnm5s2U, and s2C by sequencing in human and E. coli tRNA. We term this method periodate-dependent analysis of queuosine and sulfur modification sequencing (PAQS-seq). We assess Q- and 2-thio-modifications at the tRNA isodecoder level, and 2-thio modification changes in stress response. PAQS-seq should be widely applicable in the biological studies of Q- and 2-thio-modifications in mammalian and microbial tRNAs.},
}
@article {pmid35713407,
year = {2022},
author = {Shaffer, JP and Carpenter, CS and Martino, C and Salido, RA and Minich, JJ and Bryant, M and Sanders, K and Schwartz, T and Humphrey, G and Swafford, AD and Knight, R},
title = {A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities.},
journal = {BioTechniques},
volume = {},
number = {},
pages = {},
doi = {10.2144/btn-2022-0032},
pmid = {35713407},
issn = {1940-9818},
support = {3022//Emerald Foundation/ ; 675191//Crohn's and Colitis Foundation of America/ ; 1DP1AT010885, 1RF1-AG058942-01, 5K12GM068524-17, R01DK102932, R01HL134887, R01HL140976, U01AI124316, U19AG063744/NH/NIH HHS/United States ; 2019-67013-29137//National Institute of Food and Agriculture/ ; GI18518//Semiconductor Research Corporation/ ; 2011004//National Science Foundation/ ; N00014-15-1-2809//Office of Naval Research/ ; },
abstract = {Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority of methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems and are potentially important members of the human microbiome, beyond those that can cause disease. To expand our analysis of microbial communities to include data from the fungal internal transcribed spacer (ITS) region, five candidate DNA extraction kits were compared against our standardized protocol for describing bacteria and archaea using 16S rRNA gene amplicon- and shotgun metagenomics sequencing. The results are presented considering a diverse panel of host-associated and environmental sample types and comparing the cost, processing time, well-to-well contamination, DNA yield, limit of detection and microbial community composition among protocols. Across all criteria, the MagMAX Microbiome kit was found to perform best. The PowerSoil Pro kit performed comparably but with increased cost per sample and overall processing time. The Zymo MagBead, NucleoMag Food and Norgen Stool kits were included.},
}
@article {pmid35713100,
year = {2022},
author = {Dixit, S and Kumar, S and Sharma, R and Banakar, PS and Singh, M and Keshri, A and Tyagi, AK},
title = {Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review.},
journal = {Animal biotechnology},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/10495398.2022.2078979},
pmid = {35713100},
issn = {1532-2378},
abstract = {Continuous improvement in the living standards of developing countries, calls for an urgent need of high quality meat and dairy products. The farm animals have a micro-ecosystem in gastro-intestinal tract, comprising of a wide variety of flora and fauna which converts roughages and agricultural byproducts as well as nutrient rich concentrate sources into the useful products such as volatile fatty acids and microbial crude proteins. The microbial diversity changes according to composition of the feed, host species/breed and host's individual genetic makeup. From culture methods to next-generation sequencing technologies, the knowledge has emerged a lot to know-how of microbial world viz. their identification, enzymatic activities and metabolites which are the keys of ruminant's successful existence. The structural composition of ruminal community revealed through metagenomics can be elaborated by metatranscriptomics and metabolomics through deciphering their functional role in metabolism and their responses to the external and internal stimuli. These highly sophisticated analytical tools have made possible to correlate the differences in the feed efficiency, nutrients utilization and methane emissions to their rumen microbiome. The comprehensively understood rumen microbiome will enhance the knowledge in the fields of animal nutrition, biotechnology and climatology through deciphering the significance of each and every domain of residing microbial entity. The present review undertakes the recent investigations regarding rumen multi-omics viz. taxonomic and functional potential of microbial populations, host-diet-microbiome interactions and correlation with metabolic dynamics.},
}
@article {pmid35712658,
year = {2022},
author = {Oinam, L and Tateno, H},
title = {Glycan Profiling by Sequencing to Uncover Multicellular Communication: Launching Glycobiology in Single Cells and Microbiomes.},
journal = {Frontiers in cell and developmental biology},
volume = {10},
number = {},
pages = {919168},
doi = {10.3389/fcell.2022.919168},
pmid = {35712658},
issn = {2296-634X},
abstract = {Glycans are essential building blocks of life that are located at the outermost surface of all cells from mammals to bacteria and even viruses. Cell surface glycans mediate multicellular communication in diverse biological processes and are useful as "surface markers" to identify cells. Various single-cell sequencing technologies have already emerged that enable the high-throughput analysis of omics information, such as transcriptome and genome profiling on a cell-by-cell basis, which has advanced our understanding of complex multicellular interactions. However, there has been no robust technology to analyze the glycome in single cells, mainly because glycans with branched and heterogeneous structures cannot be readily amplified by polymerase chain reactions like nucleic acids. We hypothesized that the generation of lectins conjugated with DNA barcodes (DNA-barcoded lectins) would enable the conversion of glycan information to gene information, which may be amplified and measured using DNA sequencers. This technology will enable the simultaneous analysis of glycan and RNA in single cells. Based on this concept, we developed a technology to analyze glycans and RNA in single cells, which was referred to as scGR-seq. Using scGR-seq, we acquired glycan and gene expression profiles of individual cells constituting heterogeneous cell populations, such as tissues. We further extended Glycan-seq to the profiling of the surface glycans of bacteria and even gut microbiota. Glycan-seq and scGR-seq are new technologies that enable us to elucidate the function of glycans in cell-cell and cell-microorganism communication, which extends glycobiology to the level of single cells and microbiomes.},
}
@article {pmid35712561,
year = {2022},
author = {Mierzejewska, E and Urbaniak, M and Zagibajło, K and Vangronsveld, J and Thijs, S},
title = {The Effect of Syringic Acid and Phenoxy Herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) on Soil, Rhizosphere, and Plant Endosphere Microbiome.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {882228},
doi = {10.3389/fpls.2022.882228},
pmid = {35712561},
issn = {1664-462X},
abstract = {The integration of phytoremediation and biostimulation can improve pollutant removal from the environment. Plant secondary metabolites (PSMs), which are structurally related to xenobiotics, can stimulate the presence of microbial community members, exhibiting specialized functions toward detoxifying, and thus mitigating soil toxicity. In this study, we evaluated the effects of enrichment of 4-chloro-2-methylphenoxyacetic acid (MCPA) contaminated soil (unplanted and zucchini-planted) with syringic acid (SA) on the bacterial community structure in soil, the rhizosphere, and zucchini endosphere. Additionally, we measured the concentration of MCPA in soil and fresh biomass of zucchini. The diversity of bacterial communities differed significantly between the studied compartments (i.e., unplanted soil, rhizospheric soil, and plant endosphere: roots or leaves) and between used treatments (MCPA or/and SA application). The highest diversity indices were observed for unplanted soil and rhizosphere. Although the lowest diversity was observed among leaf endophytes, this community was significantly affected by MCPA or SA: the compounds applied separately favored the growth of Actinobacteria (especially Pseudarthrobacter), while their simultaneous addition promoted the growth of Firmicutes (especially Psychrobacillus). The application of MCPA + SA together lead also to enhanced growth of Pseudomonas, Burkholderia, Sphingomonas, and Pandoraea in the rhizosphere, while SA increased the occurrence of Pseudomonas in leaves. In addition, SA appeared to have a positive influence on the degradative potential of the bacterial communities against MCPA: its addition, followed by zucchini planting, significantly increased the removal of the herbicide (50%) from the soil without affecting, neither positively nor negatively, the plant growth.},
}
@article {pmid35712333,
year = {2022},
author = {Popa, CM and Ianosi, SL and Dorobantu, SC and Saftoiu, A},
title = {Gut Microbiota Imbalance in Metastatic Colorectal Patients Treated With EGFRI and Long-Term Antibiotic Therapy for Cutaneous Toxicity: A Pilot Study.},
journal = {Cureus},
volume = {14},
number = {5},
pages = {e25007},
doi = {10.7759/cureus.25007},
pmid = {35712333},
issn = {2168-8184},
abstract = {Patients with metastatic colorectal cancer (mCRC) frequently experience epidermal growth factor inhibitors (EGFRI)-induced skin side effects. Antibiotic treatment with doxycycline is often required in order to manage the skin and mucosal toxicity. Since these patients already have significant gut dysbiosis, the long-term antibiotic treatment may destabilize their gut microbiome. Objectives The assessment of intestinal dysbiosis in patients undergoing treatment with EGFRI, who require antibiotic treatment with doxycycline in order to manage adverse skin effects. Methods We conducted a prospective pilot study between 2020 and 2021 involving 10 patients with mCRC. These patients were undergoing treatment with EGFRI and required either short-term or long-term treatment with doxycycline in order to manage skin toxicity. Results The patients with mCRC who were treated with doxycycline for 8 weeks showed overexpression of Escherichia coli, Candida, and Geotrichum species compared to the patients who only received doxycycline treatment for two weeks. Conclusions The elevated levels of Escherichia coli and Candida species in the patients who received doxycycline for eight weeks compared to the patients who received the treatment for two weeks could provide a starting point for the development of a standardized guideline regarding the use of pre-active or reactive antibiotic treatment. We also highlight the importance of analyzing the intestinal microbiome of these patients. The identification of overexpressed species, as well as the deficiency of certain protective species, could guide the administration of probiotics to cover and repair the affected intestinal flora.},
}
@article {pmid35711786,
year = {2022},
author = {Srivastava, AK and Kashyap, PL and Santoyo, G and Newcombe, G},
title = {Editorial: Plant Microbiome: Interactions, Mechanisms of Action, and Applications, Volume II.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {915684},
doi = {10.3389/fmicb.2022.915684},
pmid = {35711786},
issn = {1664-302X},
}
@article {pmid35711777,
year = {2022},
author = {Jiang, Y and Luo, J and Huang, D and Liu, Y and Li, DD},
title = {Machine Learning Advances in Microbiology: A Review of Methods and Applications.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {925454},
doi = {10.3389/fmicb.2022.925454},
pmid = {35711777},
issn = {1664-302X},
abstract = {Microorganisms play an important role in natural material and elemental cycles. Many common and general biology research techniques rely on microorganisms. Machine learning has been gradually integrated with multiple fields of study. Machine learning, including deep learning, aims to use mathematical insights to optimize variational functions to aid microbiology using various types of available data to help humans organize and apply collective knowledge of various research objects in a systematic and scaled manner. Classification and prediction have become the main achievements in the development of microbial community research in the direction of computational biology. This review summarizes the application and development of machine learning and deep learning in the field of microbiology and shows and compares the advantages and disadvantages of different algorithm tools in four fields: microbiome and taxonomy, microbial ecology, pathogen and epidemiology, and drug discovery.},
}
@article {pmid35711772,
year = {2022},
author = {Chen, J and Sharifi, R and Khan, MSS and Islam, F and Bhat, JA and Kui, L and Majeed, A},
title = {Corrigendum: Wheat Microbiome: Structure, Dynamics, and Role in Improving Performance Under Stress Environments.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {940368},
doi = {10.3389/fmicb.2022.940368},
pmid = {35711772},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2021.821546.].},
}
@article {pmid35711771,
year = {2022},
author = {Patra, S and Sahu, N and Saxena, S and Pradhan, B and Nayak, SK and Roychowdhury, A},
title = {Effects of Probiotics at the Interface of Metabolism and Immunity to Prevent Colorectal Cancer-Associated Gut Inflammation: A Systematic Network and Meta-Analysis With Molecular Docking Studies.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {878297},
doi = {10.3389/fmicb.2022.878297},
pmid = {35711771},
issn = {1664-302X},
abstract = {Background: Dysbiosis/imbalance in the gut microbial composition triggers chronic inflammation and promotes colorectal cancer (CRC). Modulation of the gut microbiome by the administration of probiotics is a promising strategy to reduce carcinogenic inflammation. However, the mechanism remains unclear.<br><br>Methods: In this study, we presented a systematic network, meta-analysis, and molecular docking studies to determine the plausible mechanism of probiotic intervention in diminishing CRC-causing inflammations.<br><br>Results: We selected 77 clinical, preclinical, in vitro, and in vivo articles (PRISMA guidelines) and identified 36 probiotics and 135 training genes connected to patients with CRC with probiotic application. The meta-analysis rationalizes the application of probiotics in the prevention and treatment of CRC. An association network is generated with 540 nodes and 1,423 edges. MCODE cluster analysis identifies 43 densely interconnected modules from the network. Gene ontology (GO) and pathway enrichment analysis of the top scoring and functionally significant modules reveal stress-induced metabolic pathways (JNK, MAPK), immunomodulatory pathways, intrinsic apoptotic pathways, and autophagy as contributors for CRC where probiotics could offer major benefits. Based on the enrichment analyses, 23 CRC-associated proteins and 7 probiotic-derived bacteriocins were selected for molecular docking studies. Results indicate that the key CRC-associated proteins (e.g., COX-2, CASP9, PI3K, and IL18R) significantly interact with the probiotic-derived bacteriocins (e.g., plantaricin JLA-9, lactococcin A, and lactococcin mmfii). Finally, a model for probiotic intervention to reduce CRC-associated inflammation has been proposed.<br><br>Conclusion: Probiotics and/or probiotic-derived bacteriocins could directly interact with CRC-promoting COX2. They could modulate inflammatory NLRP3 and NFkB pathways to reduce CRC-associated inflammation. Probiotics could also activate autophagy and apoptosis by regulating PI3K/AKT and caspase pathways in CRC. In summary, the potential mechanisms of probiotic-mediated CRC prevention include multiple signaling cascades, yet pathways related to metabolism and immunity are the crucial ones.},
}
@article {pmid35711748,
year = {2022},
author = {Sun, Y and Chen, L and Zhang, S and Miao, Y and Zhang, Y and Li, Z and Zhao, J and Yu, L and Zhang, J and Qin, X and Yao, Y},
title = {Plant Interaction Patterns Shape the Soil Microbial Community and Nutrient Cycling in Different Intercropping Scenarios of Aromatic Plant Species.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {888789},
doi = {10.3389/fmicb.2022.888789},
pmid = {35711748},
issn = {1664-302X},
abstract = {Intercropping systems improve the soil nutrient cycle through microbial community activity and then land productivity. However, their interactions mechanism underlying that the mixed aromatic plant species intercropping regulate the soil microbiome and nutrient cycling on the perennial woody orchard is still uncovered. We designed treatments with 0, 1, and 3 aromatic plant species intercropped in two scenarios of clean tillage (T model, T1, T2, and T4) and natural grass (G model, G1, G2, and G4) in apple orchards, and investigated intercrops effects at the branch growing stage (BGS) and fruit development stage (FDS), respectively. Compared with T model, G model in FDS increased alpha diversity of bacterial community and Shannon index fungal community, the relative abundance of dominant taxa, such as Acidobacteria and Actinobacteria, and also the numbers of up and down-regulated OTUs, the most of indices of co-occurrence network in both bacterial and fungal community, and then improved invertase activity and available nitrogen content. Relative to G1, G2 and G4 reduced diversity bacterial community in FDS, the relative abundance of dominant taxa, the most of indices of co-occurrence network, and then improved soil invertase activity and total phosphorus content in soil. Moreover, Shannon index of fungal community, the altered number of OTUs and the most indices of co-occurrence network were higher in G4 than those in G2 in FDS. These changes above in FDS were more markedly than those in BGS, suggesting that chemical diversity of litter from mixed species of aromatic plants in natural grass scenario led to diversity, complexity, and stability of soil microbial community and then nutrient cycling. It provided a novel highlight and method to modulate biocenosis and then improve the soil nutrient cycling.},
}
@article {pmid35711746,
year = {2022},
author = {Korth, B and Pous, N and Hönig, R and Haus, P and Corrêa, FB and Nunes da Rocha, U and Puig, S and Harnisch, F},
title = {Electrochemical and Microbial Dissection of Electrified Biotrickling Filters.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {869474},
doi = {10.3389/fmicb.2022.869474},
pmid = {35711746},
issn = {1664-302X},
abstract = {Electrified biotrickling filters represent sustainable microbial electrochemical technology for treating organic carbon-deficient ammonium-contaminated waters. However, information on the microbiome of the conductive granule bed cathode remains inexistent. For uncovering this black box and for identifying key process parameters, minimally invasive sampling units were introduced, allowing for the extraction of granules from different reactor layers during reactor operation. Sampled granules were analyzed using cyclic voltammetry and molecular biological tools. Two main redox sites [-288 ± 18 mV and -206 ± 21 mV vs. standard hydrogen electrode (SHE)] related to bioelectrochemical denitrification were identified, exhibiting high activity in a broad pH range (pH 6-10). A genome-centric analysis revealed a complex nitrogen food web and the presence of typical denitrifiers like Pseudomonas nitroreducens and Paracoccus versutus with none of these species being identified as electroactive microorganism so far. These are the first results to provide insights into microbial structure-function relationships within electrified biotrickling filters and underline the robustness and application potential of bioelectrochemical denitrification for environmental remediation.},
}
@article {pmid35711624,
year = {2022},
author = {Reis, RM and Carlo, HL and Dos Santos, RL and Sabella, FM and Parisotto, TM and de Carvalho, FG},
title = {Possible Relationship Between the Oral and Gut Microbiome, Caries Development, and Obesity in Children During the COVID-19 Pandemic.},
journal = {Frontiers in oral health},
volume = {3},
number = {},
pages = {887765},
doi = {10.3389/froh.2022.887765},
pmid = {35711624},
issn = {2673-4842},
abstract = {The COVID-19 pandemic has brought health damage and socioeconomic disruptions, together with lifestyle disorders around the world. Children are one of the most commonly affected, mainly due to social isolation and changes in eating habits and physical activities. This way, the risk of weight gain and obesity is possibly enhanced, as well as poor oral hygiene conditions and early childhood caries (ECC) development during the lockdown. In children under 6 years of age, ECC is defined as carious lesions in one or more primary teeth, with or without cavitation. Importantly, alterations in the oral microbiome caused by changes in children lifestyles have much more than a local impact on oral tissues, interplaying with the gut microbiome and influencing systemic environments. Recent studies have been exploring the oral health conditions, eating habits, and weight gain in the childhood population during the COVID-19 pandemic; however, there is a lack of information concerning the association among oral and gut microbiome, dental caries, and obesity in the COVID-19 era. In this context, this review aimed at analyzing a possible relationship between the oral and gut microbiome, caries, and obesity in children during the COVID-19 pandemic.},
}
@article {pmid35711547,
year = {2022},
author = {Paul, P and Kaul, R and Abdellatif, B and Arabi, M and Upadhyay, R and Saliba, R and Sebah, M and Chaari, A},
title = {The Promising Role of Microbiome Therapy on Biomarkers of Inflammation and Oxidative Stress in Type 2 Diabetes: A Systematic and Narrative Review.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {906243},
doi = {10.3389/fnut.2022.906243},
pmid = {35711547},
issn = {2296-861X},
abstract = {Background: One in 10 adults suffer from type 2 diabetes (T2D). The role of the gut microbiome, its homeostasis, and dysbiosis has been investigated with success in the pathogenesis as well as treatment of T2D. There is an increasing volume of literature reporting interventions of pro-, pre-, and synbiotics on T2D patients.<br><br>Methods: Studies investigating the effect of pro-, pre-, and synbiotics on biomarkers of inflammation and oxidative stress in T2D populations were extracted from databases such as PubMed, Scopus, Web of Science, Embase, and Cochrane from inception to January 2022.<br><br>Results: From an initial screening of 5,984 hits, 47 clinical studies were included. Both statistically significant and non-significant results have been compiled, analyzed, and discussed. We have found various promising pro-, pre-, and synbiotic formulations. Of these, multistrain/multispecies probiotics are found to be more effective than monostrain interventions. Additionally, our findings show resistant dextrin to be the most promising prebiotic, followed closely by inulin and oligosaccharides. Finally, we report that synbiotics have shown excellent effect on markers of oxidative stress and antioxidant enzymes. We further discuss the role of metabolites in the resulting effects in biomarkers and ultimately pathogenesis of T2D, bring attention toward the ability of such nutraceuticals to have significant role in COVID-19 therapy, and finally discuss few ongoing clinical trials and prospects.<br><br>Conclusion: Current literature of pro-, pre- and synbiotic administration for T2D therapy is promising and shows many significant results with respect to most markers of inflammation and oxidative stress.},
}
@article {pmid35711426,
year = {2022},
author = {Hua, H and Meydan, C and Afshin, EE and Lili, LN and D'Adamo, CR and Rickard, N and Dudley, JT and Price, ND and Zhang, B and Mason, CE},
title = {A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {889702},
doi = {10.3389/fimmu.2022.889702},
pmid = {35711426},
issn = {1664-3224},
mesh = {DNA, Bacterial/genetics ; Feces/microbiology ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Specimen Handling/methods ; },
abstract = {While a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20°C, room temperature storage, a commercial DNA preservation kit, and a dissolvable wipe used with DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, bacterial metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R2 of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R2 of 0.98), and samples consistently clustered by subject across each method. These data support that the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.},
}
@article {pmid35711332,
year = {2022},
author = {Sadik, KW and Hranjec, T and Bonatti, HJR and Sawyer, RG},
title = {Incidence of Early and Late-Onset Clostridioides difficile Infection following Appendectomy Compared to Other Common Abdominal Surgical Procedures.},
journal = {Surgery research and practice},
volume = {2022},
number = {},
pages = {8720144},
doi = {10.1155/2022/8720144},
pmid = {35711332},
issn = {2356-7759},
abstract = {Introduction: Clostridioides difficile associated diarrhea (CDAD) is a major public health issue. The appendix may function as a reservoir for the intestinal microbiome, which may repopulate the intestine following enteric infections including CDAD. Patients/Methods. This retrospective cohort study includes a total of 12,039 patients undergoing appendectomy, hemicolectomy, and cholecystectomy at a single center between 1992 and 2011 who were diagnosed with early and late-onset CDAD and were followed for a minimum of two years.<br><br>Results: Cumulative CDAD rates were 2.3% after appendectomy, 6.4% after left and 6.8% after right hemicolectomy, and 4% after cholecystectomy with a median onset of 76 (range 1-6011) days after the procedure. Median time to CDAD onset was 76 days after appendectomy, 23 days after left, 54 days after right hemicolectomy, and 122 days after cholecystectomy (p < 0.05). Late-onset CDAD (>1 year) was significantly more common following appendectomy (37%) and cholecystectomy (39%) than after left (17%) and right (21%) hemicolectomy. Significant differences in age, gender, complication rate, and length of hospitalization between the four groups need to be considered when interpreting the results.<br><br>Conclusion: The incidence of CDAD after various abdominal surgeries ranged between 2% and 7% in this study. Whereas, hemicolectomy patients had predominantly early onset CDAD, and appendectomy and cholecystectomy may increase the risk for late-onset CDAD. Appendectomy per se does not seem to increase the risk for late-onset CDAD.},
}
@article {pmid35711125,
year = {2022},
author = {Bjerregaard, P and Larsen, CVL and Olesen, I and Ottendahl, CB and Backer, V and Senftleber, N and Christensen, MMB and Larsen, TJ and Byberg, S and Hansen, T and Jørgensen, ME},
title = {The Greenland population health survey 2018 - methods of a prospective study of risk factors for lifestyle related diseases and social determinants of health amongst Inuit.},
journal = {International journal of circumpolar health},
volume = {81},
number = {1},
pages = {2090067},
doi = {10.1080/22423982.2022.2090067},
pmid = {35711125},
issn = {2242-3982},
mesh = {*Cardiovascular Diseases/epidemiology ; Glucose ; Greenland/epidemiology ; Hand Strength ; Humans ; Inuits ; Life Style ; *Population Health ; Prospective Studies ; Risk Factors ; Social Determinants of Health ; Surveys and Questionnaires ; },
abstract = {Since 1993, regular population health surveys in Greenland have supported and monitored the public health strategy of Greenland and have monitored cardiometabolic and lung diseases. The most recent of these surveys included 2539 persons aged 15+ from 20 communities spread over the whole country. The survey instruments included personal interviews, self-administered questionnaires, blood sampling, anthropometric measurements, blood pressure, ECG, oral glucose test, pulmonary function, hand grip strength and chair stand test. Blood samples were analysed for glucose, glycated haemoglobin (HbA1c), insulin, incretin hormones, cholesterol, kidney function, fatty acids in erythrocyte membranes and mercury, urine for albumin-creatinine ratio, and aliquots were stored at -80°C for future use. Data were furthermore collected for studies of the gut microbiome and diabetes complications. Survey participants were followed up with register data. The potential of the study is to contribute to the continued monitoring of risk factors and health conditions as part of Greenland's public health strategy and to study the epidemiology of cardiometabolic diseases and other chronic diseases and behavioural risk factors. The next population health survey is planned for 2024. The emphasis of the article is on the methods of the study and results will be presented in other publications.},
}
@article {pmid35711026,
year = {2022},
author = {Kim, A and Zisman, CR and Holingue, C},
title = {Influences of the Immune System and Microbiome on the Etiology of ASD and GI Symptomology of Autistic Individuals.},
journal = {Current topics in behavioral neurosciences},
volume = {},
number = {},
pages = {},
pmid = {35711026},
issn = {1866-3370},
abstract = {Autism Spectrum Disorder is a developmental condition associated with impairments in communication and social interactions, and repetitive and restricted behavior or interests. Autistic individuals are more likely to experience gastrointestinal (GI) symptoms than neurotypical individuals. This may be partially due to dysbiosis of the gut microbiome. In this article, we describe the interaction of the microbiome and immune system on autism etiology. We also summarize the links between the microbiome and gastrointestinal and related symptoms among autistic individuals. We report that microbial interventions, including diet, probiotics, antibiotics, and fecal transplants, and immune-modulating therapies such as cytokine blockade during the preconception, pregnancy, and postnatal period may impact the neurodevelopment, behavior, and gastrointestinal health of autistic individuals.},
}
@article {pmid35711021,
year = {2022},
author = {Siddiqui, R and Makhlouf, Z and Khan, NA},
title = {The increasing importance of the gut microbiome in acne vulgaris.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {35711021},
issn = {1874-9356},
abstract = {Acne is a frequently presented dermatological condition brought about by an interplay among inflammation, increased sebum production, hyperkeratinisation, and predominantly Propionibacterium acnes (renamed as Cutibacterium acnes) proliferation, leading to debilitating psychological scars. However, it has been shown that it is the loss of microbial diversity in the skin and the imbalance among C. acnes phylotypes that brings about acne rather than the C. acnes species as a whole. Interestingly, recent evidence suggests that other microorganisms may be implicated, such as the fungi Malassezia and the bacteria Cutibacterium granulosum. A plethora of scientific evidence suggests that the gut microbiome is implicated in the overall health and physiology of the host; studies show that the gut microbiome of acne patients is distinct and depicts less microbial diversity compared to individuals without acne. Herein, using the key terms: acne, C. acnes, IGF-1, sebum, and gut microbiome, we carried out a review of the literature, using Google Scholar and PubMed, and discussed the role of the gut and skin microbiome in relation to acne, as a narrative review. The role of hormones, diet, sebum, and stress in relation to the gut microbiome was also investigated. Therapeutic implications and the use of pre-/postbiotics are also deliberated upon. In this light, future research should investigate the relationship between the gut microbiome and the agreed upon factors of acne pathology, potentially leading to the discovery of novel acne treatments with milder side effects.},
}
@article {pmid35710863,
year = {2022},
author = {Bhanja, A and Nayak, N and Mukherjee, S and Sutar, PP and Mishra, M},
title = {Treating the Onset of Diabetes Using Probiotics Along with Prebiotic from Pachyrhizus erosus in High-Fat Diet Fed Drosophila melanogaster.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {35710863},
issn = {1867-1314},
support = {IMP/2018/002120/EC//Science and Engineering Research Board/ ; EMR/2017/003054//Science and Engineering Research Board/ ; BT/PR21857/NNT/28/1238/2017//Department of Biotechnology/ ; },
abstract = {The increasing mortality due to hypertension and hypercholesterolemia is directly linked with type-2 diabetes. This shows the lethality of the disease. Reports suggest that the prebiotics along with probiotics help in lowering the effects of type-2 diabetes. Prebiotic like inulin is best known for its anti-diabetic effect. The current study utilizes jicama extract as prebiotic source of inulin along with the bacterial strains with probiotic properties (Lactiplantibacillus plantarum and Enterococcus faecium) for treating type-2 diabetes in high-fat diet-induced Drosophila melanogaster model. The high-fat diet-induced Drosophila showed deposition of lipid droplets and formation of micronuclei in the gut. The larva and adult treated with probiotics and synbiotic (probiotic + prebiotic- inulin) comparatively reduced the lipid deposition and micronuclei number in the gut. The increased amount of triglyceride in the whole body of the fatty larva and adult indicated the onset of diabetes. The overexpression of insulin-like genes (Dilp 2) and (Dilp 5) confirmed the insulin resistance, whereas the expression was reduced in the larva and adult supplemented with probiotics and synbiotic. The reactive oxygen species level was reduced with the supplementation of probiotics. The weight, larva size, crawling speed and climbing were also altered in high-fat diet-induced Drosophila melanogaster. The study confirmed the effects of probiotics and synbiotic in successfully lowering diabetes in Drosophila. The study also proved the anti-diabetic potential of the probiotics. Further, it was also confirmed that the probiotics work better in the presence of prebiotic.},
}
@article {pmid35710793,
year = {2022},
author = {Park, S and You, YA and Kim, YH and Kwon, E and Ansari, A and Kim, SM and Lee, G and Hur, YM and Jung, YJ and Kim, K and Kim, YJ},
title = {Ureaplasma and Prevotella colonization with Lactobacillus abundance during pregnancy facilitates term birth.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10148},
pmid = {35710793},
issn = {2045-2322},
support = {2020R1A2C3011850//National Research Foundation of Korea/ ; BK21 Fostering Outstanding Universities for Research//Ministry of Education/ ; },
mesh = {Case-Control Studies ; Female ; Humans ; Infant, Newborn ; Lactobacillus/genetics ; Pregnancy ; *Premature Birth/microbiology ; Prevotella/genetics ; RNA, Ribosomal, 16S/genetics ; Term Birth ; Ureaplasma/genetics ; *Ureaplasma Infections ; Vagina/microbiology ; },
abstract = {Ureaplasma and Prevotella infections are well-known bacteria associated with preterm birth. However, with the development of metagenome sequencing techniques, it has been found that not all Ureaplasma and Prevotella colonizations cause preterm birth. The purpose of this study was to determine the association between Ureaplasma and Prevotella colonization with the induction of preterm birth even in the presence of Lactobacillus. In this matched case-control study, a total of 203 pregnant Korean women were selected and their cervicovaginal fluid samples were collected during mid-pregnancy. The microbiome profiles of the cervicovaginal fluid were analyzed using 16S rRNA gene amplification. Sequencing data were processed using QIIME1.9.1. Statistical analyses were performed using R software, and microbiome analysis was performed using the MicrobiomeAnalyst and Calypso software. A positive correlation between Ureaplasma and other genera was highly related to preterm birth, but interestingly, there was a negative correlation with Lactobacillus and term birth, with the same pattern observed with Prevotella. Ureaplasma and Prevotella colonization with Lactobacillus abundance during pregnancy facilitates term birth, although Ureaplasma and Prevotella are associated with preterm birth. Balanced colonization between Lactobacillus and Ureaplasma and Prevotella is important to prevent preterm birth.},
}
@article {pmid35710629,
year = {2022},
author = {Oyserman, BO and Flores, SS and Griffioen, T and Pan, X and van der Wijk, E and Pronk, L and Lokhorst, W and Nurfikari, A and Paulson, JN and Movassagh, M and Stopnisek, N and Kupczok, A and Cordovez, V and Carrión, VJ and Ligterink, W and Snoek, BL and Medema, MH and Raaijmakers, JM},
title = {Disentangling the genetic basis of rhizosphere microbiome assembly in tomato.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3228},
pmid = {35710629},
issn = {2041-1723},
mesh = {Iron/metabolism ; *Lycopersicon esculentum/metabolism ; *Microbiota/genetics ; Plant Breeding ; Plants/metabolism ; Rhizosphere ; },
abstract = {Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31 Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating 'microbiomics' and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs.},
}
@article {pmid35707452,
year = {2021},
author = {Werbin, ZR and Hackos, B and Lopez-Nava, J and Dietze, MC and Bhatnagar, JM},
title = {The National Ecological Observatory Network's soil metagenomes: assembly and basic analysis.},
journal = {F1000Research},
volume = {10},
number = {},
pages = {299},
doi = {10.12688/f1000research.51494.2},
pmid = {35707452},
issn = {2046-1402},
mesh = {Computational Biology/methods ; *Metagenome ; Metagenomics/methods ; Neon ; *Soil ; },
abstract = {The largest dataset of soil metagenomes has recently been released by the National Ecological Observatory Network (NEON), which performs annual shotgun sequencing of soils at 47 sites across the United States. NEON serves as a valuable educational resource, thanks to its open data and programming tutorials, but there is currently no introductory tutorial for accessing and analyzing the soil shotgun metagenomic dataset. Here, we describe methods for processing raw soil metagenome sequencing reads using a bioinformatics pipeline tailored to the high complexity and diversity of the soil microbiome. We describe the rationale, necessary resources, and implementation of steps such as cleaning raw reads, taxonomic classification, assembly into contigs or genomes, annotation of predicted genes using custom protein databases, and exporting data for downstream analysis. The workflow presented here aims to increase the accessibility of NEON's shotgun metagenome data, which can provide important clues about soil microbial communities and their ecological roles.},
}
@article {pmid35705822,
year = {2022},
author = {Ley, R},
title = {The human microbiome: there is much left to do.},
journal = {Nature},
volume = {606},
number = {7914},
pages = {435},
doi = {10.1038/d41586-022-01610-5},
pmid = {35705822},
issn = {1476-4687},
mesh = {Humans ; *Microbiota ; },
}
@article {pmid35705744,
year = {2022},
author = {García-Sánchez, JC and Arredondo-Centeno, J and Segovia-Ramírez, MG and Tenorio Olvera, AM and Parra-Olea, G and Vredenburg, VT and Rovito, SM},
title = {Factors Influencing Bacterial and Fungal Skin Communities of Montane Salamanders of Central Mexico.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {35705744},
issn = {1432-184X},
support = {221614//Conacyt/ ; 2015-01-721//Conacyt/ ; 1633948//National Science Foundation/ ; },
abstract = {Host microbial communities are increasingly seen as an important component of host health. In amphibians, the first land vertebrates that are threatened by a fungal skin disease globally, our understanding of the factors influencing the microbiome of amphibian skin remains incomplete because recent studies have focused almost exclusively on bacteria, and little information exists on fungal communities associated with wild amphibian species. In this study, we describe the effects of host phylogeny, climate, geographic distance, and infection with a fungal pathogen on the composition and structure of bacterial and fungal communities in seven tropical salamander species that occur in the Trans-Mexican Volcanic Belt of Central Mexico. We find that host phylogenetic relatedness is correlated with bacterial community composition while a composite climatic variable of temperature seasonality and precipitation is significantly associated with fungal community composition. We also estimated co-occurrence networks for bacterial and fungal taxa and found differences in the degree of connectivity and the distribution of negative associations between the two networks. Our results suggest that different factors may be responsible for structuring the bacterial and fungal communities of amphibian skin and that the inclusion of fungi in future studies could shed light on important functional interactions within the microbiome.},
}
@article {pmid35705585,
year = {2022},
author = {Yun, BR and Truong, AT and Choi, YS and Lee, MY and Kim, BY and Seo, M and Yoon, SS and Yoo, MS and Van Quyen, D and Cho, YS},
title = {Comparison of the gut microbiome of sacbrood virus-resistant and -susceptible Apis cerana from South Korea.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10010},
pmid = {35705585},
issn = {2045-2322},
support = {B-1543081-2019-21-03//Animal and Plant Quarantine Agency/ ; B-1543081-2019-21-03//Animal and Plant Quarantine Agency/ ; B-1543081-2019-21-03//Animal and Plant Quarantine Agency/ ; B-1543081-2019-21-03//Animal and Plant Quarantine Agency/ ; B-1543081-2019-21-03//Animal and Plant Quarantine Agency/ ; },
mesh = {Animals ; Bacteria/genetics ; Bees ; Disease Susceptibility ; Ecosystem ; *Gastrointestinal Microbiome ; Larva ; *RNA Viruses ; *Virus Diseases ; },
abstract = {Honey bees are important pollinators for the conservation of the ecosystem and agricultural products and provide a variety of products important for human use, such as honey, pollen, and royal jelly. Sacbrood disease (SD) is a devastating viral disease in Apis cerana; an effective preventive measure for SD is urgently needed. In this study, the relationship between the gut microbiome of honey bees and SD was investigated by pyrosequencing. Results revealed that sacbrood virus (SBV)-resistant A. cerana strains harbour a unique acetic acid bacterium, Bombella intestini, and the lactic acid bacteria (LAB) Lactobacillus (unclassified)_uc, Bifidobacterium longum, B. catenulatum, Lactococcus lactis, and Leuconostoc mesenteroides in larvae and Hafnia alvei, B. indicum, and the LAB L. mellifer and Lactobacillus HM215046_s in adult bees. Changes in the gut microbiome due to SBV infection resulted in loss of bacteria that could affect host nutrients and inhibit honey bee pathogens, such as Gilliamella JFON_s, Gilliamella_uc, Pseudomonas putida, and L. kunkeei in A. cerana larvae and Frischella_uc, Pantoea agglomerans, Snodgrassella_uc, and B. asteroides in adult bees. These findings provide important information for the selection of probiotics for A. cerana larvae and adults to prevent pathogenic infections and keep honey bees healthy.},
}
@article {pmid35705580,
year = {2022},
author = {Shelkey, E and Oommen, D and Stirling, ER and Soto-Pantoja, DR and Cook, KL and Lu, Y and Votanopoulos, KI and Soker, S},
title = {Immuno-reactive cancer organoid model to assess effects of the microbiome on cancer immunotherapy.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {9983},
pmid = {35705580},
issn = {2045-2322},
support = {2T32EB014836//U.S. Department of Health &amp; Human Services | NIH | National Institute of Biomedical Imaging and Bioengineering (NIBIB)/ ; 5T32AI007401//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {Animals ; Humans ; Immunomodulation ; Immunotherapy/methods ; Mice ; *Microbiota ; Organoids/metabolism ; *Triple Negative Breast Neoplasms/metabolism ; },
abstract = {Immune checkpoint blockade (ICB) therapy has demonstrated good efficacy in many cancer types. In cancers such as non-resectable advanced or metastatic triple-negative breast cancer (TNBC), it has recently been approved as a promising treatment. However, clinical data shows overall response rates (ORRs) from ~ 3-40% in breast cancer patients, depending on subtype, previous treatments, and mutation status. Composition of the host-microbiome has a significant role in cancer development and therapeutic responsiveness. Some bacterial families are conducive to oncogenesis and progression, while others aid innate and therapeutically induced anti-tumor immunity. Modeling microbiome effects on anti-tumor immunity in ex vivo systems is challenging, forcing the use of in vivo models, making it difficult to dissect direct effects on immune cells from combined effects on tumor and immune cells. We developed a novel immune-enhanced tumor organoid (iTO) system to study factors affecting ICB response. Using the 4T1 TNBC murine cell line and matched splenocytes, we demonstrated ICB-induced response. Further administration of bacterial-derived metabolites from species found in the immunomodulatory host-microbiome significantly increased ICB-induced apoptosis of tumor cells and altered immune cell receptor expression. These outcomes represent a method to isolate individual factors that alter ICB response and streamline the study of microbiome effects on ICB efficacy.},
}
@article {pmid35710395,
year = {2022},
author = {Karolkiewicz, J and Nieman, DC and Cisoń, T and Szurkowska, J and Gałęcka, M and Sitkowski, D and Szygula, Z},
title = {No effects of a 4-week post-exercise sauna bathing on targeted gut microbiota and intestinal barrier function, and hsCRP in healthy men: a pilot randomized controlled trial.},
journal = {BMC sports science, medicine &amp; rehabilitation},
volume = {14},
number = {1},
pages = {107},
pmid = {35710395},
issn = {2052-1847},
support = {PB.501-1/2018//State University of Applied Sciences in Nowy Sącz/ ; },
abstract = {BACKGROUND: Body temperature fluctuations induced by acute exercise bouts may influence the intestinal barrier with related effects on epithelial permeability, immune responses, and release of metabolites produced by the gut microbiota. This study evaluated the effects of post-exercise sauna bathing in young men undergoing endurance training on gut bacteria inflammation and intestinal barrier function.<br><br>METHODS: Fifteen (15) untrained males aged 22 ± 1.5 years were randomly assigned to exercise training (ET) with or without post-exercise sauna treatments (S). Participants in the group ET + S (n = 8) exercised 60 min, 3 times per week, on a bicycle ergometer followed by a 30-min dry Finish sauna treatment. The control group (ET, n = 7) engaged in the same exercise training program without the sauna treatments. Blood and stool samples were collected before and after the 4-week training program. Blood samples were analysed for the concentration of high-sensitivity C-reactive protein (hsCRP) and complete blood counts. Stool samples were analysed for pH, quantitative and qualitative measures of targeted bacteria, zonulin, and secretory immunoglobulin A.<br><br>RESULTS: Interaction effects revealed no differences in the pattern of change over time between groups for the abundance of selected gut microbiome bacteria and stool pH, zonulin, sIgA, and hsCRP. Pre- and post-study fecal concentrations of Bifidobacterium spp., Faecalibacterium prausnitzii, and Akkermansia muciniphila were below reference values for these bacteria in both groups.<br><br>CONCLUSIONS: The combination of 4-weeks exercise followed by passive heat exposure did not have a measurable influence on targeted gut microbiota, intestinal barrier function, and hsCRP levels in young males.<br><br>TRIAL REGISTRATION: The study was retrospectively registered in the clinical trials registry (Clinicaltrials.gov) under the trial registration number: NCT05277597. Release Date: March 11, 2022.},
}
@article {pmid35710335,
year = {2022},
author = {Zapién-Campos, R and Bansept, F and Sieber, M and Traulsen, A},
title = {On the effect of inheritance of microbes in commensal microbiomes.},
journal = {BMC ecology and evolution},
volume = {22},
number = {1},
pages = {75},
pmid = {35710335},
issn = {2730-7182},
support = {CRC 1182//German Research Foundation (FB, AT)/ ; CRC 1182//German Research Foundation (FB, AT)/ ; },
mesh = {Biological Evolution ; Humans ; Infant, Newborn ; Inheritance Patterns ; *Microbiota/genetics ; Symbiosis/genetics ; },
abstract = {BACKGROUND: Our current view of nature depicts a world where macroorganisms dwell in a landscape full of microbes. Some of these microbes not only transit but establish themselves in or on hosts. Although hosts might be occupied by microbes for most of their lives, a microbe-free stage during their prenatal development seems to be the rule for many hosts. The questions of who the first colonizers of a newborn host are and to what extent these are obtained from the parents follow naturally.<br><br>RESULTS: We have developed a mathematical model to study the effect of the transfer of microbes from parents to offspring. Even without selection, we observe that microbial inheritance is particularly effective in modifying the microbiome of hosts with a short lifespan or limited colonization from the environment, for example by favouring the acquisition of rare microbes.<br><br>CONCLUSION: By modelling the inheritance of commensal microbes to newborns, our results suggest that, in an eco-evolutionary context, the impact of microbial inheritance is of particular importance for some specific life histories.},
}
@article {pmid35710137,
year = {2022},
author = {Highley, MS and Landuyt, B and Prenen, H and Harper, PG and De Bruijn, EA},
title = {The Nitrogen Mustards.},
journal = {Pharmacological reviews},
volume = {74},
number = {3},
pages = {552-599},
doi = {10.1124/pharmrev.120.000121},
pmid = {35710137},
issn = {1521-0081},
mesh = {*Antineoplastic Agents/adverse effects ; Cyclophosphamide/therapeutic use ; Humans ; *Neoplasms/drug therapy ; Nitrogen/therapeutic use ; *Nitrogen Mustard Compounds/therapeutic use ; },
abstract = {The nitrogen mustards are powerful cytotoxic and lymphoablative agents and have been used for more than 60 years. They are employed in the treatment of cancers, sarcomas, and hematologic malignancies. Cyclophosphamide, the most versatile of the nitrogen mustards, also has a place in stem cell transplantation and the therapy of autoimmune diseases. Adverse effects caused by the nitrogen mustards on the central nervous system, kidney, heart, bladder, and gonads remain important issues. Advances in analytical techniques have facilitated the investigation of the pharmacokinetics of the nitrogen mustards, especially the oxazaphosphorines, which are prodrugs requiring metabolic activation. Enzymes involved in the metabolism of cyclophosphamide and ifosfamide are very polymorphic, but a greater understanding of the pharmacogenomic influences on their activity has not yet translated into a personalized medicine approach. In addition to damaging DNA, the nitrogen mustards can act through other mechanisms, such as antiangiogenesis and immunomodulation. The immunomodulatory properties of cyclophosphamide are an area of current exploration. In particular, cyclophosphamide decreases the number and activity of regulatory T cells, and the interaction between cyclophosphamide and the intestinal microbiome is now recognized as an important factor. New derivatives of the nitrogen mustards continue to be assessed. Oxazaphosphorine analogs have been synthesized in attempts to both improve efficacy and reduce toxicity, with varying degrees of success. Combinations of the nitrogen mustards with monoclonal antibodies and small-molecule targeted agents are being evaluated. SIGNIFICANCE STATEMENT: The nitrogen mustards are important, well-established therapeutic agents that are used to treat a variety of diseases. Their role is continuing to evolve.},
}
@article {pmid35710008,
year = {2022},
author = {Afonso, M and Coelho, L and Jesus, F and Campos, I and Abrantes, N and Gonçalves, FJM and Marques, S and Serpa, D},
title = {Effects of Pine and Eucalypt ashes on bacterial isolates from the skin microbiome of the fire salamander (Salamandra salamandra).},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {156677},
doi = {10.1016/j.scitotenv.2022.156677},
pmid = {35710008},
issn = {1879-1026},
abstract = {Environmental contamination influences the diversity of the resident skin microbial community of amphibians, ultimately affecting the individual's immune system. Wildfires are expected to impact the skin microbiome, since post-fire runoff typically transports hazardous substances, that can affect terrestrial and aquatic ecosystems. The present study is the first to assess the effects of Eucalypt and Pine wildfire ash on cultivable bacterial isolates from the skin microbiome of amphibians, in particular the fire salamander (Salamandra salamandra), a common species in fire-prone Mediterranean ecosystems. To achieve this goal, samples of skin bacteria of adult individuals of S. salamandra were collected at a site without influence of wildfires. The bacterial isolates were tested against the pathogenic agent Aeromonas salmonicida for assessing their antimicrobial activity, before exposing them to a series of dilutions of aqueous extracts of Eucalypt and Pine ashes (AAEs) from high severity wildfires. From the 80 bacterial isolates collected, 48 (mostly Pseudomonas spp.) showed antimicrobial activity. Exposure of bacteria with antimicrobial activity to the Eucalypt and Pine AAEs at concentrations of 0, 6.25, 12.5, 25, 50, 75, and 100%, revealed that bacterial growth could be significantly inhibited, stimulated or unaffected by ash. Growth inhibition was found for Pine and Eucalypt AAEs at concentrations as low as 6.25% and 12.5%, respectively, but were more expressive at concentrations equal or above 50%. Eucalypt AAEs had a higher negative impact on bacterial growth than Pine AAEs, likely due to differences in metal concentrations between ash types. These findings raise concern about the future of amphibians in fire-prone regions since the foreseen increase in fire frequency and severity owing to climate changes are likely to alter the skin microbiome of amphibians, weaken the immune system and consequently increasing the incidence of infections or diseases, further contributing to the decline of the populations.},
}
@article {pmid35709757,
year = {2022},
author = {Ignacio, A and Shah, K and Bernier-Latmani, J and Köller, Y and Coakley, G and Moyat, M and Hamelin, R and Armand, F and Wong, NC and Ramay, H and Thomson, CA and Burkhard, R and Wang, H and Dufour, A and Geuking, MB and McDonald, B and Petrova, TV and Harris, NL and McCoy, KD},
title = {Small intestinal resident eosinophils maintain gut homeostasis following microbial colonization.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2022.05.014},
pmid = {35709757},
issn = {1097-4180},
abstract = {The intestine harbors a large population of resident eosinophils, yet the function of intestinal eosinophils has not been explored. Flow cytometry and whole-mount imaging identified eosinophils residing in the lamina propria along the length of the intestine prior to postnatal microbial colonization. Microscopy, transcriptomic analysis, and mass spectrometry of intestinal tissue revealed villus blunting, altered extracellular matrix, decreased epithelial cell turnover, increased gastrointestinal motility, and decreased lipid absorption in eosinophil-deficient mice. Mechanistically, intestinal epithelial cells released IL-33 in a microbiota-dependent manner, which led to eosinophil activation. The colonization of germ-free mice demonstrated that eosinophil activation in response to microbes regulated villous size alterations, macrophage maturation, epithelial barrier integrity, and intestinal transit. Collectively, our findings demonstrate a critical role for eosinophils in facilitating the mutualistic interactions between the host and microbiota and provide a rationale for the functional significance of their early life recruitment in the small intestine.},
}
@article {pmid35709728,
year = {2022},
author = {Lenfestey, MW and Li, N and Gauthier, J and Winglee, K and Fodor, A and Zeng, K and Jobin, C and Neu, J and Parker, LA},
title = {Effect of Routine Gastric Residual Aspiration on the Preterm Infant Fecal Microbiome.},
journal = {American journal of perinatology},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-1877-6306},
pmid = {35709728},
issn = {1098-8785},
support = {National Institute of Nursing Research//R01DK088244/ ; },
abstract = {OBJECTIVE: Enteral feeding tubes are used in neonatal intensive care units (NICU) to assess feeding tolerance by utilizing pre-prandial gastric residual aspiration. This study evaluates the effect of gastric residual aspiration on the preterm infant fecal microbiome and gastrointestinal inflammation.<br><br>STUDY DESIGN: Fifty-one very low birth weight (VLBW) infants (<32 weeks gestational age and <1250g) enrolled in a larger single-center randomized controlled trial evaluating the effects of routine and non-routine gastric residual aspiration were selected for further analysis. Of those infants, 30 infants had microbiome analysis performed on stools collected at 6 weeks by sequencing the bacterial V1-V3 variable regions of the genes encoding for 16S rRNA. In an additional 21 infants, stool samples collected at 3- and 6-weeks were analyzed for intestinal inflammation using a cytokine multiplex panel.<br><br>RESULTS: Microbial communities between groups were not distinct from each other and there was no difference in intestinal inflammation between groups. Analyses using gene expression packages DESeq2 and edgeR produced statistically significant differences in several taxa possibly indicating a more commensal intestinal microbiome in infants not undergoing gastric residual aspiration.<br><br>CONCLUSION: Omission of routine gastric residual aspiration was not associated with intestinal dysbiosis or inflammation, providing additional evidence that monitoring pre-prandial gastric residuals is unnecessary.},
}
@article {pmid35709624,
year = {2022},
author = {Chen, C and Li, Y and Yin, G and Hou, L and Liu, M and Jiang, Y and Zheng, D and Wu, H and Zheng, Y and Sun, D},
title = {Antibiotics sulfamethoxazole alter nitrous oxide production and pathways in estuarine sediments: Evidenced by the N15-O18 isotopes tracing.},
journal = {Journal of hazardous materials},
volume = {437},
number = {},
pages = {129281},
doi = {10.1016/j.jhazmat.2022.129281},
pmid = {35709624},
issn = {1873-3336},
abstract = {Estuarine antibiotic residues are profoundly impacting microbial nitrogen (N) cycling and associated N2O production, but the response of N2O production pathways to antibiotics remains poorly understood. Here, 15N-18O labeling technique combined with molecular methods were used to investigate the impacts of sulfamethoxazole on the contribution of ammonia oxidation (nitrifier nitrification, nitrifier denitrification, and nitrification-coupled denitrification) and heterotrophic denitrification (HD) to N2O production in estuarine sediments. Results showed that environmental concentration of sulfamethoxazole (4 ng/g) promoted the total N2O production by 17.1% through nitrifier denitrification. Environmentally relevant (40-4000 ng/g) and irrelevant (40,000 ng/g) concentration of sulfamethoxazole drove nitrification denitrification to gradually lose the dominant role in total N2O production and ammonia oxidation-derived N2O, replaced by HD and nitrifier nitrification, while total N2O production were inhibited. Furthermore, when HD dominated the total N2O production, the HD-derived N2O increased by 63.6% with sulfamethoxazole concentration reaching 40,000 ng/g. The mechanistic investigation further showed that nitrifying bacteria were more susceptible to sulfamethoxazole than nitrifying archaea and denitrifiers. The increased expression of nirS gene carried by non-dominant denitrifiers improved the ratio of nirS:nosZ and hence increased HD-derived N2O under high sulfamethoxazole stresses. Overall, our results provide a comprehensive view into how antibiotics regulate N2O production and its pathways in estuarine sediments.},
}
@article {pmid35709613,
year = {2022},
author = {Alimena, S and Davis, J and Fichorova, RN and Feldman, S},
title = {The vaginal microbiome: A complex milieu affecting risk of human papillomavirus persistence and cervical cancer.},
journal = {Current problems in cancer},
volume = {46},
number = {4},
pages = {100877},
doi = {10.1016/j.currproblcancer.2022.100877},
pmid = {35709613},
issn = {1535-6345},
abstract = {The purpose of this review is to describe the existing literature regarding the relationship between the vaginal microbiome, human papillomavirus persistence, and cervical cancer risk, as well as to discuss factors that mediate these relationships. Data suggest that alterations in the vaginal microbiome affect the risk of human papillomavirus infection and persistence, which has downstream effects on cervical dysplasia and cancer risk. The homeostatic Lactobillus species L. crispatus, L. gasseri, L. jensenii act to promote a healthy vaginal environment, while L. iners and pathogens causing bacterial vaginosis are associated with increased inflammation, human papillomavirus infection, cervical dysplasia, and potentially cancer. There are, however, still several large gaps in the literature, particularly related to the modifiable and non-modifiable factors that affect the vaginal microbiome and ensuing risk of pre-cancerous and cancerous lesions. Evidence currently suggests that endogenous and exogenous hormones, tobacco products, and sexual practices influence vaginal microbiome composition, but the nuances of these relationships and how changes in these factors affect dysplasia risk are yet to be delineated. Other studies examining how diet, exercise, race, socioeconomic status, and genetic factors influence the vaginal microbiome are difficult to interpret in the setting of multiple confounders. Future studies should focus on how changes in these modulatory factors might promote a healthy vaginal microbiome to prevent or treat dysplasia in the lower female genital tract.},
}
@article {pmid35709584,
year = {2022},
author = {Ferrocino, I and Rantsiou, K and Cocolin, L},
title = {Microbiome and -omics application in food industry.},
journal = {International journal of food microbiology},
volume = {377},
number = {},
pages = {109781},
doi = {10.1016/j.ijfoodmicro.2022.109781},
pmid = {35709584},
issn = {1879-3460},
abstract = {The enormous potential of multi-omics approaches to unravel microbiome-related links between food quality, sustainability and safety still requires experimental work and extensive data integration to increase knowledge and understand the biological and ecological processes involved in the assembly and dynamics of microbial communities along the production chains. Data spanning from DNA sequences to transcripts and metabolites need to be integrated in order to be translated at industrial level and literature showed several successful examples. The application of microbiome studies in food systems has shown the potential to improve food quality. Nevertheless, classical microbiological methods are still highly relevant even if isolation and characterization of strains in pure culture is often laborious and time-consuming and requires the use of several specific growth media that take into the account microbial growth characteristics as well as food characteristics. Studies on microbiomes have become a popular topic in the food industry since it can be used as a tool to improve quality and safety in the food chain.},
}
@article {pmid35709423,
year = {2022},
author = {Shaikh, SR and Virk, R and Van Dyke, TE},
title = {Potential Mechanisms by Which Hydroxyeicosapentaenoic Acids Regulate Glucose Homeostasis In Obesity.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/advances/nmac073},
pmid = {35709423},
issn = {2156-5376},
abstract = {Dysregulation of glucose metabolism in response to diet-induced obesity contributes toward numerous complications such as insulin resistance and hepatic steatosis. Therefore, there is a need to develop effective strategies to improve glucose homeostasis. In this review, we first discuss emerging evidence from epidemiological studies and rodent experiments that increased consumption of eicosapentaenoic acid (EPA), (either as oily fish, or dietary/pharmacological supplements) may have a role in preventing impairments to insulin and glucose homeostasis. We then review the current evidence on how EPA derived metabolites known as hydroxyeicosapentaenoic acids (HEPE), may be a major mode of action by which EPA exerts its beneficial effects on glucose and lipid metabolism. Notably, cell culture and rodent studies show that HEPEs prevent fat accumulation in metabolic tissues through peroxisome proliferator activated receptor (PPAR)-mediated mechanisms. In addition, activation of resolvin E1 pathway, either by administration of EPA in the diet or via intraperitoneal administration of resolvin E1, improves hyperglycemia, hyperinsulinemia, and liver steatosis through multiple mechanisms. These mechanisms include shifting immune cell phenotypes toward resolution of inflammation and preventing dysbiosis of the gut microbiome. Finally, we present the next steps for this line of research that will drive future precision randomized clinical trials with EPA and its downstream metabolites. These include dissecting the variables that drive heterogeneity in the response to EPA such as the baseline microbiome profile and fatty acid status, circadian rhythm, genetic variation, sex, and age. In addition, there is a critical need to further investigate mechanisms of action for HEPEs and to establish the concentration of HEPEs in differing tissues, particularly in response to consumption of oily fish and EPA-enriched supplements.},
}
@article {pmid35708632,
year = {2022},
author = {Byeon, HR and Jang, SY and Lee, Y and Kim, D and Hong, MG and Lee, D and Shin, JH and Seo, JG},
title = {New Strains of Akkermansia muciniphila and Faecalibacterium prausnitzii are Effective for Improving the Muscle Strength of Mice with Immobilization-Induced Muscular Atrophy.},
journal = {Journal of medicinal food},
volume = {25},
number = {6},
pages = {565-575},
doi = {10.1089/jmf.2021.K.0148},
pmid = {35708632},
issn = {1557-7600},
mesh = {Akkermansia ; Animals ; *Faecalibacterium prausnitzii/metabolism ; Mice ; Muscle Strength ; Muscular Atrophy/etiology ; *Proteasome Endopeptidase Complex ; Ubiquitins/metabolism ; Verrucomicrobia/physiology ; },
abstract = {Muscular atrophy is a muscle disease in which muscle mass and strength decrease due to aging, injury, metabolic disorders, or chronic conditions. Proteins in muscle tissue are degraded by the ubiquitin-proteasome pathway, and atrophy accelerates this pathway. Akkermansia muciniphila and Faecalibacterium prausnitzii strains are effective agents against metabolic and inflammatory diseases in next-generation probiotic research. In this study, we evaluated the efficacy of A. muciniphila strain EB-AMDK19 and F. prausnitzii strain EB-FPDK11 in a mouse model of muscular atrophy, since atrophy inhibits energy metabolism and immune activation. After oral administration of each strain for 4 weeks, the hind legs of the mice were fixed with a plaster cast to immobilize them for a week. As a result, the administration of EB-AMDK19 and EB-FPDK11 strains improved grip strength but did not increase muscle mass. At the molecular level, A. muciniphila and F. prausnitzii treatments decreased the expression levels of ubiquitin-proteasome genes, atrogin-1, MuRF, and cathepsin L. They increased the expression level of the mitochondrial biogenesis regulatory gene, PGC-1α. The effect of the strains was confirmed by a decrease in myostatin. Furthermore, A. muciniphila and F. prausnitzii modulated the immune function by enhancing ZO-1 and inhibiting IL-6. In particular, EB-AMDK19 promoted the expression of IL-10, an anti-inflammatory cytokine. These results suggest that A. muciniphila and F. prausnitzii may have beneficial effects on muscular atrophy, verified by newly isolated EB-AMDK19 and EB-FPDK11 as potential next-generation probiotics.},
}
@article {pmid35708472,
year = {2022},
author = {Li, X and Kiprowska, M and Kansara, T and Kansara, P and Li, P},
title = {Neuroinflammation: A Distal Consequence of Periodontitis.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345221102084},
doi = {10.1177/00220345221102084},
pmid = {35708472},
issn = {1544-0591},
abstract = {Periodontitis, a chronic, inflammatory disease, induces systemic inflammation and contributes to the development of neurodegenerative diseases. The precise etiology of the most common neurodegenerative disorders, such as sporadic Alzheimer's, Parkinson's diseases and multiple sclerosis (AD, PD, and MS, respectively), remains to be revealed. Chronic neuroinflammation is a well-recognized component of these disorders, and evidence suggests that systemic inflammation is a possible stimulus for neuroinflammation development. Systemic inflammation can lead to deleterious consequences on the brain if the inflammation is sufficiently severe or if the brain shows vulnerabilities due to genetic predisposition, aging, or neurodegenerative diseases. It has been proposed that periodontal disease can initiate or contribute to the AD pathogenesis through multiple pathways, including key periodontal pathogens. Dysbiotic oral bacteria can release bacterial products into the bloodstream and eventually cross the brain-blood barrier; these bacteria can also cause alterations to gut microbiota that enhance inflammation and potentially affect brain function via the gut-brain axis. The trigeminal nerve has been suggested as another route for connecting oral bacterial products to the brain. PD and MS are often preceded by gastrointestinal symptoms or aberrant gut microbiome composition, and alterations in the enteric nervous system accompany the disease. Clinical evidence has suggested that patients with periodontitis are at a higher risk of developing PD and MS. This nexus among the brain, periodontal disease, and systemic inflammation heralds new ways in which microglial cells, the main innate immune cells, and astrocytes, the crucial regulators of innate and adaptive immune responses in the brain, contribute to brain pathology. Currently, the lack of understanding of the pathogenesis of neurodegeneration is hindering treatment development. However, we may prevent this pathogenesis by tackling one of its possible contributors (periodontitis) for systemic inflammation through simple preventive oral hygiene measures.},
}
@article {pmid35708337,
year = {2022},
author = {Bhute, SS and Mefferd, CC and Phan, JR and Ahmed, M and Fox-King, AE and Alarcia, S and Villarama, JV and Abel-Santos, E and Hedlund, BP},
title = {A High-Carbohydrate Diet Prolongs Dysbiosis and Clostridioides difficile Carriage and Increases Delayed Mortality in a Hamster Model of Infection.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0180421},
doi = {10.1128/spectrum.01804-21},
pmid = {35708337},
issn = {2165-0497},
abstract = {Studies using mouse models of Clostridioides difficile infection (CDI) have demonstrated a variety of relationships between dietary macronutrients on antibiotic-associated CDI; however, few of these effects have been examined in more susceptible hamster models of CDI. In this study, we investigated the effect of a high-carbohydrate diet previously shown to protect mice from CDI on the progression and resolution of CDI in a hamster disease model, with 10 animals per group. Hamsters fed the high-carbohydrate diet developed distinct diet-specific microbiomes during antibiotic treatment and CDI, with lower diversity, persistent C. difficile carriage, and delayed microbiome restoration. In contrast to CDI protection in mice, most hamsters fed a high-carbohydrate diet developed fulminant CDI including several cases of late-onset CDI, that were not observed in hamsters fed a standard lab diet. We speculate that prolonged high-carbohydrate diet-specific dysbiosis in these animals allowed C. difficile to persist in the gut of the animals where they could proliferate postvancomycin treatment, leading to delayed CDI onset. This study, along with similar studies in mouse models of CDI, suggests some high-carbohydrate diets may promote antibiotic-associated dysbiosis and long-term C. difficile carriage, which may later convert to symptomatic CDI. IMPORTANCE The effects of diet on CDI are not completely known. Here, we used a high-carbohydrate diet previously shown to protect mice against CDI to assess its effect on a hamster model of CDI and paradoxically found that it promoted dysbiosis, C. difficile carriage, and higher mortality. A common thread in both mouse and hamster experimental models was that the high-carbohydrate diet promoted dysbiosis and long-term carriage of C. difficile, which may have converted to fulminant CDI only in the highly susceptible hamster model system. If diets high in carbohydrates also promote dysbiosis and C. difficile carriage in humans, then these diets might paradoxically increase chances of CDI relapse despite their protective effects against primary CDI.},
}
@article {pmid35708124,
year = {2022},
author = {Otuya, DO and Dechene, NM and Poshtupaka, D and Judson, S and Carlson, CJ and Zemlok, SK and Sevieri, E and Choy, P and Shore, RE and De León-Peralta, E and Cirio, AA and Rihm, TW and Krall, AA and Gavgiotaki, E and Dong, J and Silva, SL and Baillargeon, A and Baldwin, G and Gao, AH and Jansa, Z and Barrios, A and Ryan, E and Bhat, NGM and Balmasheva, I and Chung, A and Grant, CN and Bablouzian, AL and Beatty, M and Ahsen, OO and Zheng, H and Tearney, GJ},
title = {Passively scanned, single-fiber optical coherence tomography probes for gastrointestinal devices.},
journal = {Lasers in surgery and medicine},
volume = {},
number = {},
pages = {},
doi = {10.1002/lsm.23576},
pmid = {35708124},
issn = {1096-9101},
abstract = {BACKGROUND/OBJECTIVES: Optical coherence tomography (OCT) uses low coherence interferometry to obtain depth-resolved tissue reflectivity profiles (M-mode) and transverse beam scanning to create images of two-dimensional tissue morphology (B-mode). Endoscopic OCT imaging probes typically employ proximal or distal mechanical beam scanning mechanisms that increase cost, complexity, and size. Here, we demonstrate in the gastrointestinal (GI) tracts of unsedated human patients, that a passive, single-fiber probe can be used to guide device placement, conduct device-tissue physical contact sensing, and obtain two-dimensional OCT images via M-to-B-mode conversion.<br><br>MATERIALS AND METHODS: We designed and developed ultrasmall, manually scannable, side- and forward-viewing single fiber-optic probes that can capture M-mode OCT data. Side-viewing M-mode OCT probes were incorporated into brush biopsy devices designed to harvest the microbiome and forward-viewing M-mode OCT probes were integrated into devices that measure intestinal potential difference (IPD). The M-mode OCT probe-coupled devices were utilized in the GI tract in six unsedated patients in vivo. M-mode data were converted into B-mode images using an M-to-B-mode conversion algorithm. The effectiveness of physical contact sensing by the M-mode OCT probes was assessed by comparing the variances of the IPD values when the probe was in physical contact with the tissue versus when it was not. The capacity of forward- and side-viewing M-mode OCT probes to produce high-quality B-mode images was compared by computing the percentages of the M-to-B-mode images that showed close contact between the probe and the luminal surface. Passively scanned M-to-B-mode images were qualitatively compared to B-mode images obtained by mechanical scanning OCT tethered capsule endomicroscopy (TCE) imaging devices.<br><br>RESULTS: The incorporation of M-mode OCT probes in these nonendoscopic GI devices safely and effectively enabled M-mode OCT imaging, facilitating real-time device placement guidance and contact sensing in vivo. Results showed that M-mode OCT contact sensing improved the variance of IPD measurements threefold and side-viewing probes increased M-to-B-mode image visibility by 10%. Images of the esophagus, stomach, and duodenum generated by the passively scanned probes and M-to-B-mode conversion were qualitatively superior to B-mode images obtained by mechanically scanning OCT TCE devices.<br><br>CONCLUSION: These results show that passive, single optical fiber OCT probes can be effectively utilized for nonendoscopic device placement guidance, device contact sensing, and two-dimensional morphologic imaging in the human GI tract in vivo. Due to their small size, lower cost, and reduced complexity, these M-mode OCT probes may provide an easier avenue for the incorporation of OCT functionality into endoscopic/nonendoscopic devices.},
}
@article {pmid35707722,
year = {2022},
author = {Feng, Y and Liu, D and Liu, Y and Yang, X and Zhang, M and Wei, F and Li, D and Hu, Y and Guo, Y},
title = {Host-genotype-dependent cecal microbes are linked to breast muscle metabolites in Chinese chickens.},
journal = {iScience},
volume = {25},
number = {6},
pages = {104469},
doi = {10.1016/j.isci.2022.104469},
pmid = {35707722},
issn = {2589-0042},
abstract = {In chickens, the effect of host genetics on the gut microbiota is not fully understood, and the extent to which the heritable gut microbes affect chicken metabolism and physiology is still an open question. Here, we explored the interactions among chicken genetics, the cecal microbiota and metabolites in breast muscle from ten chicken breeds in China. We found that different chicken breeds displayed distinct cecal microbial community structures and functions, and 15 amplicon sequence variants (ASVs) were significantly associated with host genetics through different genetic loci, such as those related to the intestinal barrier function. We identified five heritable ASVs significantly associated with 53 chicken muscle metabolites, among which the Megamonas probably affected lipid metabolism through the production of propionate. Our study revealed that the chicken genetically associated cecal microbes may have the potential to affect the bird's physiology and metabolism.},
}
@article {pmid35707172,
year = {2022},
author = {Sumithra, TG and Sharma, KSR and Gangadharan, S and Suresh, G and Prasad, V and Amala, PV and Sayooj, P and Gop, AP and Anil, MK and Patil, PK and Achamveetil, G},
title = {Dysbiosis and Restoration Dynamics of the Gut Microbiome Following Therapeutic Exposure to Florfenicol in Snubnose Pompano (Trachinotus blochii) to Aid in Sustainable Aquaculture Production Strategies.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {881275},
doi = {10.3389/fmicb.2022.881275},
pmid = {35707172},
issn = {1664-302X},
abstract = {Information on unintended effects of therapeutic exposure of antibiotics on the fish gut microbiome is a vital prerequisite for ensuring fish and environmental health during sustainable aquaculture production strategies. The present study forms the first report on the impact of florfenicol (FFC), a recommended antibiotic for aquaculture, on the gut microbiome of snubnose pompano (Trachinotus blochii), a high-value marine aquaculture candidate. Both culture-dependent and independent techniques were applied to identify the possible dysbiosis and restoration dynamics, pointing out the probable risks to the host and environment health. The results revealed the critical transient dysbiotic events in the taxonomic and functional metagenomic profiles and significant reductions in the bacterial load and diversity measures. More importantly, there was a complete restoration of gut microbiome density, diversity, functional metagenomic profiles, and taxonomic composition (up to class level) within 10-15 days of antibiotic withdrawal, establishing the required period for applying proper management measures to ensure animal and environment health, following FFC treatment. The observed transient increase in the relative abundance of opportunistic pathogens suggested the need to apply proper stress management measures and probiotics during the period. Simultaneously, the results demonstrated the inhibitory potential of FFC against marine pathogens (vibrios) and ampicillin-resistant microbes. The study pointed out the possible microbial signatures of stress in fish and possible probiotic microbes (Serratia sp., Methanobrevibacter sp., Acinetobacter sp., and Bacillus sp.) that can be explored to design fish health improvisation strategies. Strikingly, the therapeutic exposure of FFC neither caused any irreversible increase in antibiotic resistance nor promoted the FFC resistant microbes in the gut. The significant transient increase in the numbers of kanamycin-resistant bacteria and abundance of two multidrug resistance encoding genes (K03327 and K03585) in the treated fish gut during the initial 10 days post-withdrawal suggested the need for implementing proper aquaculture effluent processing measures during the period, thus, helps to reduce the spillover of antibiotic-resistant microbes from the gut of the treated fish to the environment. In brief, the paper generates interesting and first-hand insights on the implications of FFC treatment in the gut microbiome of a marine aquaculture candidate targeting its safe and efficient application in unavoidable circumstances. Implementation of mitigation strategies against the identified risks during the initial 15 days of withdrawal period is warranted to ensure cleaner and sustainable aquaculture production from aquatic animal and ecosystem health perspectives.},
}
@article {pmid35638605,
year = {2022},
author = {Dillard, BA and Chung, AK and Gunderson, AR and Campbell-Staton, SC and Moeller, AH},
title = {Humanization of wildlife gut microbiota in urban environments.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
doi = {10.7554/eLife.76381},
pmid = {35638605},
issn = {2050-084X},
support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; R35 GM138284/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Animals, Wild ; Bacteria/genetics ; Cities ; *Gastrointestinal Microbiome ; Humans ; *Lizards ; Urbanization ; },
abstract = {Urbanization is rapidly altering Earth's environments, demanding investigation of the impacts on resident wildlife. Here, we show that urban populations of coyotes (Canis latrans), crested anole lizards (Anolis cristatellus), and white-crowned sparrows (Zonotrichia leucophrys) acquire gut microbiota constituents found in humans, including gut bacterial lineages associated with urbanization in humans. Comparisons of urban and rural wildlife and human populations revealed significant convergence of gut microbiota among urban populations relative to rural populations. All bacterial lineages overrepresented in urban wildlife relative to rural wildlife and differentially abundant between urban and rural humans were also overrepresented in urban humans relative to rural humans. Remarkably, the bacterial lineage most overrepresented in urban anoles was a Bacteroides sequence variant that was also the most significantly overrepresented in urban human populations. These results indicate parallel effects of urbanization on human and wildlife gut microbiota and suggest spillover of bacteria from humans into wildlife in cities.},
}
@article {pmid35705309,
year = {2022},
author = {Prekrasna, I and Pavlovska, M and Miryuta, N and Dzhulai, A and Dykyi, E and Convey, P and Kozeretska, I and Bedernichek, T and Parnikoza, I},
title = {Antarctic Hairgrass Rhizosphere Microbiomes: Microscale Effects Shape Diversity, Structure, and Function.},
journal = {Microbes and environments},
volume = {37},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME21069},
pmid = {35705309},
issn = {1347-4405},
abstract = {The rhizosphere microbiome of the native Antarctic hairgrass Deschampsia antarctica from the central maritime Antarctic was investigated using 16S RNA metagenomics and compared to those of the second native Antarctic plant Colobanthus quitensis and closely related temperate D. cespitosa. The rhizosphere microbial communities of D. antarctica and D. cespitosa had high taxon richness, while that of C. quitensis had markedly lower diversity. The majority of bacteria in the rhizosphere communities of the hairgrass were affiliated to Proteobacteria, Bacteroidetes, and Actinobacteria. The rhizosphere of C. quitensis was dominated by Actinobacteria. All microbial communities included high proportions of unique amplicon sequence variants (ASVs) and there was high heterogeneity between samples at the ASV level. The soil parameters examined did not explain this heterogeneity. Bacteria belonging to Actinobacteria, Bacteroidetes, and Proteobacteria were sensitive to fluctuations in the soil surface temperature. The values of the United Soil Surface Temperature Influence Index (UTII, Iti) showed that variations in most microbial communities from Galindez Island were associated with microscale variations in temperature. Metabolic predictions in silico using PICRUSt 2.0, based on the taxonomically affiliated part of the microbiomes, showed similarities with the rhizosphere community of D. antarctica in terms of the predicted functional repertoire. The results obtained indicate that these communities are involved in the primary processes of soil development (particularly the degradation of lignin and lignin-derived compounds) in the central maritime Antarctic and may be beneficial for the growth of Antarctic vascular plants. However, due to the limitations associated with interpreting PICRUSt 2.0 outputs, these predictions need to be verified experimentally.},
}
@article {pmid35705000,
year = {2022},
author = {Schneider, KM and Thaiss, CA},
title = {When the brain feels the bugs.},
journal = {Immunity},
volume = {55},
number = {6},
pages = {976-978},
doi = {10.1016/j.immuni.2022.05.008},
pmid = {35705000},
issn = {1097-4180},
abstract = {The microbiome modulates brain function, but the precise routes of gut-brain communication remain unclear. In a recent issue of Science, Gabanyi et al. discover that hypothalamic GABAergic neurons directly recognize microbial muropeptides via NOD2, leading to reduced neuronal activity, loss of appetite, and aberrant thermoregulation.},
}
@article {pmid35704900,
year = {2022},
author = {Thomas, MS and Blesso, CN and Calle, MC and Chun, OK and Puglisi, M and Fernandez, ML},
title = {Dietary Influences on Gut Microbiota with a Focus on Metabolic Syndrome.},
journal = {Metabolic syndrome and related disorders},
volume = {},
number = {},
pages = {},
doi = {10.1089/met.2021.0131},
pmid = {35704900},
issn = {1557-8518},
abstract = {There is a clear correlation between gut microbiota, diet, and metabolic outcomes. A diet high in fiber has been shown to decrease inflammation, increase insulin sensitivity, and reduce dyslipidemias whereas a diet high in fat and sugar leads to dyslipidemia, insulin resistance, and low-grade inflammation. There is recent evidence suggesting that the human gut microbiota has a significant role in the development or the resolution of metabolic syndrome (MetS) and associated conditions. Leading a stressful, sedentary lifestyle with limited or no physical activity and consuming an unhealthy diet high in saturated fat, simple carbohydrates, and sodium and low in dietary fiber and in high-quality protein are some of the contributing factors. Unhealthy diets have been shown to induce alterations in the gut microbiota and contribute to the pathogenesis of MetS by altering microbiota composition and disrupting the intestinal barrier, which leads to low-grade systemic inflammation. In contrast, healthy diets can lead to changes in microbiota that increase gut barrier function and increase the production of anti-inflammatory biomarkers. This review aims at providing a more in-depth discussion of diet-induced dysbiosis of the gut microbiota and its effect on MetS. Here, we discuss the possible mechanisms involved in the development of the metabolic biomarkers that define MetS, with an emphasis on the role of sugar and dietary fiber in microbiome-mediated changes in low-grade systemic inflammation and metabolic dysfunction.},
}
@article {pmid35704763,
year = {2022},
author = {Woehle, C and Roy, AS and Glock, N and Michels, J and Wein, T and Weissenbach, J and Romero, D and Hiebenthal, C and Gorb, SN and Schönfeld, J and Dagan, T},
title = {Denitrification in foraminifera has an ancient origin and is complemented by associated bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {25},
pages = {e2200198119},
doi = {10.1073/pnas.2200198119},
pmid = {35704763},
issn = {1091-6490},
support = {281357//EC | European Research Council (ERC)/ ; SFB754//German Research Foundation/ ; The Future Ocean//German Research Foundation/ ; Christian Woehle//Kiel Life Science Young Scientist Programme/ ; },
abstract = {Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origin. However, the prevalence of denitrification genes in foraminifera remains unknown, and the missing denitrification pathway components are elusive. Analyzing transcriptomes and metagenomes of 10 foraminiferal species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer the last common ancestor of denitrifying foraminifera, which enables us to predict the ability to denitrify for additional foraminiferal species. Additionally, an examination of the foraminiferal microbiota reveals evidence for a stable interaction with Desulfobacteraceae, which harbor genes that complement the foraminiferal denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera-associated microbiome. The interaction of foraminifera with their resident bacteria is at the basis of foraminiferal adaptation to anaerobic environments that manifested in ecological success in oxygen depleted habitats.},
}
@article {pmid35704681,
year = {2022},
author = {Clancy, RM and Marion, MC and Ainsworth, HC and Chang, M and Howard, TD and Izmirly, PM and Masson, M and Buyon, JP and Langefeld, CD},
title = {Gut dysbiosis and the clinical spectrum in anti-Ro positive mothers of children with neonatal lupus.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2081474},
doi = {10.1080/19490976.2022.2081474},
pmid = {35704681},
issn = {1949-0984},
abstract = {Anti-SSA/Ro antibodies, while strongly linked to fetal cardiac injury and neonatal rash, can associate with a spectrum of disease in the mother, ranging from completely asymptomatic to overt Systemic Lupus Erythematosus (SLE) or Sjögren's Syndrome (SS). This study was initiated to test the hypothesis that the microbiome, influenced in part by genetics, contributes to disease state. The stool microbiome of healthy controls (HC) was compared to that of anti-SSA/Ro positive women whose children had neonatal lupus. At the time of sampling, these women were either asymptomatic (Asym), had minor rheumatic symptoms or signs considered as an undifferentiated autoimmune syndrome (UAS), or were diagnosed with SLE or SS. Differences in microbial relative abundances among these three groups were tested assuming an ordering in clinical severity (HC<Asym/UAS<SS/SLE) and then again without the ordinal assumption. Those taxa that showed differential relative abundances were then tested for whether the effect size differed depending on the women's HLA SLE-risk allele genotype (DRB1*03:01, DRB1*15:01, DQB1*02:01 and DQB1*06:02) or anti-SSA/Ro autoantibody levels. Multiple genera within the families Ruminococcaceae and Lachnospiraceae showed evidence of an HLA-by-genus interaction (P < .05). Four genera exhibited evidence of an interaction with anti-Ro52 IgA: Lachnoclostridium, Romboutsia, Bacteroides and Actinomyces (P < .01). In addition to documenting differences in microbial relative abundances across clinical severity of disease, these data provide a first-time demonstration that microbial differences are correlated with HLA SLE-risk alleles. Taken together, these data suggest that the clinical spectrum from benign to overt clinical autoimmunity may partially result from or trigger a complex interplay among specific microbial profiles, anti-Ro autoantibodies, and genetics.},
}
@article {pmid35704501,
year = {2022},
author = {Zavala-Norzagaray, AA and Aguirre, AA and Angulo-Zamudio, UA and Ley-Quiñonez, CP and Flores-Villaseñor, H and León-Sicairos, N and Velázquez-Román, J and Elorriaga-Verplancken, FR and Zavala-Félix, KA and Hart, CE and Canizalez-Román, A},
title = {ISOLATION, CHARACTERIZATION, AND ANTIMICROBIAL SUSCEPTIBILITY OF BACTERIA ISOLATED FROM SEA LION (ZALOPHUS CALIFORNIANUS) PUPS IN NORTHWESTERN MEXICO.},
journal = {Journal of wildlife diseases},
volume = {},
number = {},
pages = {},
doi = {10.7589/JWD-D-21-00183},
pmid = {35704501},
issn = {1943-3700},
abstract = {Bacterial infections have been documented in marine mammals for decades, and some are considered emerging pathogens with zoonotic potential. The aerobic oral (n=16) and rectal (n=17) bacterial microbiota and their antimicrobial resistance were characterized for 17 apparently healthy California sea lion pups (Zalophus californianus) captured with a hoop net in Farallon Island, Sinaloa, Mexico, in 2016. Bacteriologic cultures, API, and PCR were used to identify bacterial species. The Escherichia coli phylogenetic groups were identified by PCR, Salmonella serotypes were identified, and resistance to antibiotics was evaluated. Overall, 39 bacterial species were isolated, including E. coli and Salmonella spp. (35.9% each) and Pseudomonas aeruginosa (28.2%). For E. coli, UNKNOWN phylogroup was the most prevalent (57.7%), followed by the A phylogroup (37.1%). Most Salmonella serotypes were identified as Newport (92.8%); serotype Saintpaul was also identified (7.2%). Sea lions with bacterial cocolonization included 24.2%, from which two bacterial species were isolated, and 3% with three species. Overall, 59% of bacteria were resistant to at least one antibiotic tested, and 25.6% were extensively drug resistant. Bacteria were highly resistant to ampicillin and cefotaxime. This study demonstrates the importance of characterizing the microbiome of sea lions, and the potential effect of pathogens with antimicrobial resistance on wildlife conservation and public health.},
}
@article {pmid35704266,
year = {2022},
author = {Kapsetaki, SE and Marquez Alcaraz, G and Maley, CC and Whisner, CM and Aktipis, A},
title = {Diet, Microbes, and Cancer Across the Tree of Life: a Systematic Review.},
journal = {Current nutrition reports},
volume = {},
number = {},
pages = {},
pmid = {35704266},
issn = {2161-3311},
support = {U54CA217376/NH/NIH HHS/United States ; U2CCA233254/NH/NIH HHS/United States ; P01CA91955/NH/NIH HHS/United States ; R01CA140657/NH/NIH HHS/United States ; BC132057//CDMRP Breast Cancer Research Program/ ; ADHS18-198847//Arizona Biomedical Research Commission/ ; },
abstract = {PURPOSE OF REVIEW: Cancers are a leading cause of death in humans and for many other species. Diet has often been associated with cancers, and the microbiome is an essential mediator between diet and cancers. Here, we review the work on cancer and the microbiome across species to search for broad patterns of susceptibility associated with different microbial species.<br><br>RECENT FINDINGS: Some microbes, such as Helicobacter bacteria, papillomaviruses, and the carnivore-associated Fusobacteria, consistently induce tumorigenesis in humans and other species. Other microbes, such as the milk-associated Lactobacillus, consistently inhibit tumorigenesis in humans and other species. We systematically reviewed over a thousand published articles and identified links between diet, microbes, and cancers in several species of mammals, birds, and flies. Future work should examine a larger variety of host species to discover new model organisms for human preclinical trials, to better understand the observed variance in cancer prevalence across species, and to discover which microbes and diets are associated with cancers across species. Ultimately, this could help identify microbial and dietary interventions to diagnose, prevent, and treat cancers in humans as well as other animals.},
}
@article {pmid35703919,
year = {2022},
author = {Ji, Y and Yang, Y and Sun, S and Dai, Z and Ren, F and Wu, Z},
title = {Insights into diet-associated oxidative pathomechanisms in inflammatory bowel disease and protective effects of functional amino acids.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuac039},
pmid = {35703919},
issn = {1753-4887},
support = {31625025//National Natural Science Foundation of China/ ; 00109016//2115 Talent Development Program of China Agricultural University/ ; 2016XT016//Zhengzhou 1125 Talent Program/ ; //Jinxinnong Animal Science Development Foundation/ ; },
abstract = {There has been a substantial rise in the incidence and prevalence of clinical patients presenting with inflammatory bowel disease (IBD), which includes Crohn's disease and ulcerative colitis. Accumulating evidence has corroborated the view that dietary factors (particularly diets with high levels of saturated fat or sugar) are involved in the development and progression of IBD, which is predominately associated with changes in the composition of the gut microbiota and an increase in the generation of reactive oxygen species. Notably, the ecological imbalance of the gut microbiome exacerbates oxidative stress and inflammatory responses, leading to perturbations of the intestinal redox balance and immunity, as well as mucosal integrity. Recent findings have revealed that functional amino acids, including L-glutamine, glycine, L-arginine, L-histidine, L-tryptophan, and hydroxyproline, are effectively implicated in the maintenance of intestinal redox and immune homeostasis. These amino acids and their metabolites have oxygen free-radical scavenging and inflammation-relieving properties, and they participate in modulation of the microbial community and the metabolites in the gut. The principal focus of this article is a review of recent advances in the oxidative pathomechanisms of IBD development and progression in relation to dietary factors, with a particular emphasis on the redox and signal transduction mechanisms of host cells in response to unbalanced diets and enterobacteria. In addition, an update on current understanding of the protective effects of functional amino acids against IBD, together with the underlying mechanisms for this protection, have been provided.},
}
@article {pmid35703559,
year = {2022},
author = {Churcheward, B and Millet, M and Bihouée, A and Fertin, G and Chaffron, S},
title = {MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0043222},
doi = {10.1128/msystems.00432-22},
pmid = {35703559},
issn = {2379-5077},
abstract = {Metagenome-assembled genomes (MAGs) represent individual genomes recovered from metagenomic data. MAGs are extremely useful to analyze uncultured microbial genomic diversity, as well as to characterize associated functional and metabolic potential in natural environments. Recent computational developments have considerably improved MAG reconstruction but also emphasized several limitations, such as the nonbinning of sequence regions with repetitions or distinct nucleotidic composition. Different assembly and binning strategies are often used; however, it still remains unclear which assembly strategy, in combination with which binning approach, offers the best performance for MAG recovery. Several workflows have been proposed in order to reconstruct MAGs, but users are usually limited to single-metagenome assembly or need to manually define sets of metagenomes to coassemble prior to genome binning. Here, we present MAGNETO, an automated workflow dedicated to MAG reconstruction, which includes a fully-automated coassembly step informed by optimal clustering of metagenomic distances, and implements complementary genome binning strategies, for improving MAG recovery. MAGNETO is implemented as a Snakemake workflow and is available at: https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto. IMPORTANCE Genome-resolved metagenomics has led to the discovery of previously untapped biodiversity within the microbial world. As the development of computational methods for the recovery of genomes from metagenomes continues, existing strategies need to be evaluated and compared to eventually lead to standardized computational workflows. In this study, we compared commonly used assembly and binning strategies and assessed their performance using both simulated and real metagenomic data sets. We propose a novel approach to automate coassembly, avoiding the requirement for a priori knowledge to combine metagenomic information. The comparison against a previous coassembly approach demonstrates a strong impact of this step on genome binning results, but also the benefits of informing coassembly for improving the quality of recovered genomes. MAGNETO integrates complementary assembly-binning strategies to optimize genome reconstruction and provides a complete reads-to-genomes workflow for the growing microbiome research community.},
}
@article {pmid35703548,
year = {2022},
author = {Honeyman, AS and Fegel, TS and Peel, HF and Masters, NA and Vuono, DC and Kleiber, W and Rhoades, CC and Spear, JR},
title = {Statistical Learning and Uncommon Soil Microbiota Explain Biogeochemical Responses after Wildfire.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0034322},
doi = {10.1128/aem.00343-22},
pmid = {35703548},
issn = {1098-5336},
abstract = {Wildfires are a perennial event globally, and the biogeochemical underpinnings of soil responses at relevant spatial and temporal scales are unclear. Soil biogeochemical processes regulate plant growth and nutrient losses that affect water quality, yet the response of soil after variable intensity fire is difficult to explain and predict. To address this issue, we examined two wildfires in Colorado, United States, across the first and second postfire years and leveraged statistical learning (SL) to predict and explain biogeochemical responses. We found that SL predicts biogeochemical responses in soil after wildfire with surprising accuracy. Of the 13 biogeochemical analytes analyzed in this study, 9 are best explained with a hybrid microbiome + biogeochemical SL model. Biogeochemical-only models best explain 3 features, and 1 feature is explained equally well with the hybrid and biogeochemical-only models. In some cases, microbiome-only SL models are also effective (such as predicting NH4+). Whenever a microbiome component is employed, selected features always involve uncommon soil microbiota (i.e., the "rare biosphere" [existing at <1% mean relative abundance]). Here, we demonstrate that SL paired with DNA sequence and biogeochemical data predicts environmental features in postfire soils, although this approach could likely be applied to any biogeochemical system. IMPORTANCE Soil biogeochemical processes are critical to plant growth and water quality and are substantially disturbed by wildfire. However, soil responses to fire are difficult to predict. To address this issue, we developed a large environmental data set that tracks postfire changes in soil and used statistical learning (SL) to build models that exploit complex data to make predictions about biogeochemical responses. Here, we show that SL depends upon uncommon microbiota in soil (the "rare biosphere") to make surprisingly accurate predictions about soil biogeochemical responses to wildfire. Using SL to explain variation in a natively chaotic environmental system is mechanism independent. Likely, the approach that we describe for combining SL with microbiome and biogeochemical parameters has practical applications across a range of issues in the environmental sciences where predicting responses would be useful.},
}
@article {pmid35703536,
year = {2022},
author = {Wang, H and Shankar, V and Jiang, X},
title = {Compositional and Functional Changes in Microbial Communities of Composts Due to the Composting-Related Factors and the Presence of Listeria monocytogenes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0184521},
doi = {10.1128/spectrum.01845-21},
pmid = {35703536},
issn = {2165-0497},
abstract = {Listeria monocytogenes is a leading foodborne pathogen that can contaminate fresh produce in farm environment, resulting in deadly outbreaks. Composts contain a diversity of microorganisms, and some of them may be compost-adapted competitive exclusion microorganisms against L. monocytogenes. To understand interactions between compost microflora and the pathogen, both dairy- and poultry-wastes based composts (n = 12) were inoculated with L. monocytogenes, and then analyzed by next-generation sequencing approaches along with culturing methods. DNA extraction and enumeration of L. monocytogenes were performed at 0 and 72 h post-incubation at room temperature. The major bacterial phyla were identified as Firmicutes (23%), Proteobacteria (23%), Actinobacteria (19%), Chloroflexi (13%), Bacteroidetes (12%), Gemmatimonadetes (2%), and Acidobacteria (2%). The top three indicator genera enriched in different compost types were identified by LEfSe with LDA score > 2. The interactions between L. monocytogenes and indigenous microflora were limited as no significant changes in the dominant microbial members in compost ecosystem, but some discriminatory species such as Bacillus, Geobacillus, and Brevibacterium were identified by Random Forest analysis. Besides, changes in metabolic pathways and the increased abundance of bacteriocins category in the compost samples containing L. monocytogenes after 72 h postinoculation were revealed by metatranscriptomic sequencing. Taken together, the compost-related factors such as compost types, composting stages, and the collection farms are major drivers that affect compost microbial compositions, and the analysis of compost metagenome implied that interactions between L. monocytogenes and compost microflora may include competition for nutrients and the presence of antimicrobials. IMPORTANCE Listeria monocytogenes has been recognized as the etiological agent causing foodborne disease outbreaks, with fresh produce as vulnerable for contamination at even preharvest stage. Owing to the richness in microbial community, compost may mediate suppression of pathogens. In this study, the impact of compost-related factors and L. monocytogenes intrusion on dynamic changes in compost microbiome was investigated by next generation sequencing techniques. The compost-related factors such as compost types, composting stages, and the collection farms are major drivers that affect compost microbiome. The interactions between L. monocytogenes and compost microflora may include the competition for nutrients and the presence of antimicrobials produced by native compost microorganisms as potential competitive exclusion microorganisms. Findings from this study are important for the composting industry to understand the composition and functionality of microbial community in their products and help developing organic fertilizers fortified with anti-L. monocytogenes competitive exclusion microorganisms.},
}
@article {pmid35703535,
year = {2022},
author = {Tandon, K and Chiou, YJ and Yu, SP and Hsieh, HJ and Lu, CY and Hsu, MT and Chiang, PW and Chen, HJ and Wada, N and Tang, SL},
title = {Microbiome Restructuring: Dominant Coral Bacterium Endozoicomonas Species Respond Differentially to Environmental Changes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0035922},
doi = {10.1128/msystems.00359-22},
pmid = {35703535},
issn = {2379-5077},
abstract = {Bacteria in the coral microbiome play a crucial role in determining coral health and fitness, and the coral host often restructures its microbiome composition in response to external factors. An important but often neglected factor determining this microbiome restructuring is the ability of microbiome members to respond to changes in the environment. To address this issue, we examined how the microbiome structure of Acropora muricata corals changed over 9 months following a reciprocal transplant experiment. Using a combination of metabarcoding, genomics, and comparative genomics approaches, we found that coral colonies separated by a small distance harbored different dominant Endozoicomonas-related phylotypes belonging to two different species, including a novel species, "Candidatus Endozoicomonas penghunesis" 4G, whose chromosome-level (complete) genome was also sequenced in this study. Furthermore, the two dominant Endozoicomonas species had different potentials to scavenge reactive oxygen species, suggesting potential differences in responding to the environment. Differential capabilities of dominant members of the microbiome to respond to environmental change can (i) provide distinct advantages or disadvantages to coral hosts when subjected to changing environmental conditions and (ii) have positive or negative implications for future reefs. IMPORTANCE The coral microbiome has been known to play a crucial role in host health. In recent years, we have known that the coral microbiome changes in response to external stressors and that coral hosts structure their microbiome in a host-specific manner. However, an important internal factor, the ability of microbiome members to respond to change, has been often neglected. In this study, we combine metabarcoding, culturing, and genomics to delineate the differential ability of two dominant Endozoicomonas species, including a novel "Ca. Endozoicomonas penghunesis" 4G, to respond to change in the environment following a reciprocal transplant experiment.},
}
@article {pmid35702801,
year = {2022},
author = {Xavier, J and M, A and A S, F and Ravichandiran, V and Kumar, N},
title = {Intriguing role of Gut-Brain Axis on cognition with emphasis on interaction with Papez circuit.},
journal = {CNS &amp; neurological disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/1871527321666220614124145},
pmid = {35702801},
issn = {1996-3181},
abstract = {The gut microbiome is a complicated ecosystem of around a hundred billion symbiotic bacteria cells. Bidirectional communication between the gut and the brain is facilitated by the immune system, the enteric nervous system, the vagus nerve, and microbial compounds such as tryptophan metabolites and short-chain fatty acids (SCFAs). The current study emphasises the relationship of the gut-brain axis with cognitive performance and elucidates the underlying biological components, with a focus on neurotransmitters such as serotonin, indole derivatives, and catecholamine. These biological components play important roles in both the digestive and brain systems. Recent research has linked the gut microbiome to a variety of cognitive disorders, including Alzheimer's (AD). The review describes the intriguing role of the gut-brain axis in recognition memory depending on local network connections within the hippocampal as well as other additional hippocampal portions of the Papez circuit. The available data from various research papers show how the gut microbiota might alter brain function and hence psychotic and cognitive illnesses. The role of supplementary probiotics is emphasized for the reduction of brain-related dysfunction as a viable strategy in handling cognitive disorders. Further, the study elucidates the mode of action of probiotics with reported adverse effects.},
}
@article {pmid35702576,
year = {2022},
author = {Roy, S and Nag, S and Saini, A and Choudhury, L},
title = {Association of human gut microbiota with rare diseases: A close peep through.},
journal = {Intractable &amp; rare diseases research},
volume = {11},
number = {2},
pages = {52-62},
doi = {10.5582/irdr.2022.01025},
pmid = {35702576},
issn = {2186-3644},
abstract = {The human body harbors approximately 1014 cells belonging to a diverse group of microorganisms. Bacteria outnumbers protozoa, fungi and viruses inhabiting our gastrointestinal tract (GIT), commonly referred to as the "human gut microbiome". Dysbiosis occurs when the balanced relationship between the host and the gut microbiota is disrupted, altering the usual microbial population there. This increases the susceptibility of the host to pathogens, and chances of its morbidity. It is due to the fact that the gut microbiome plays an important role in human health; it influences the progression of conditions varying from colorectal cancer to GIT disorders linked with the nervous system, autoimmunity, metabolism and inheritance. A rare disease is a lethal and persistent condition affecting 2-3 people per 5,000 populaces. This review article intends to discuss such rare neurological, autoimmune, cardio-metabolic and genetic disorders of man, focusing on the fundamental mechanism that links them with their gut microbiome. Ten rare diseases, including Pediatric Crohn's disease (PCD), Lichen planus (LP), Hypophosphatasia (HPP), Discitis, Cogan's syndrome, Chancroid disease, Sennetsu fever, Acute cholecystitis (AC), Grave's disease (GD) and Tropical sprue (TS) stands to highlight as key examples, along with personalized therapeutics meant for them. This medicinal approach addresses the individual's genetic and genomic pathography, and tackles the illness with specific and effective treatments.},
}
@article {pmid35702504,
year = {2022},
author = {Laiho, JE and Laitinen, OH and Malkamäki, J and Puustinen, L and Sinkkonen, A and Pärkkä, J and Hyöty, H},
title = {Exposomic determinants of immune-mediated diseases: Special focus on type 1 diabetes, celiac disease, asthma, and allergies: The HEDIMED project approach.},
journal = {Environmental epidemiology (Philadelphia, Pa.)},
volume = {6},
number = {3},
pages = {e212},
doi = {10.1097/EE9.0000000000000212},
pmid = {35702504},
issn = {2474-7882},
abstract = {The incidence of immune-mediated diseases (IMDs) is increasing rapidly in the developed countries constituting a huge medical, economic, and societal challenge. The exposome plays an important role since genetic factors cannot explain such a rapid change. In the Human Exposomic Determinants of Immune Mediated Diseases (HEDIMED) project, altogether 22 academic and industrial partners join their multidisciplinary forces to identify exposomic determinants that are driving the IMD epidemic. The project is based on a combination of data and biological samples from large clinical cohorts constituting about 350,000 pregnant women, 30,000 children prospectively followed from birth, and 7,000 children from cross-sectional studies. HEDIMED focuses on common chronic IMDs that cause a significant disease burden, including type 1 diabetes, celiac disease, allergy, and asthma. Exposomic disease determinants and the underlying biological pathways will be identified by an exploratory approach using advanced omics and multiplex technologies combined with cutting-edge data mining technologies. Emphasis is put on fetal and childhood exposome since the IMD disease processes start early. Inclusion of several IMDs makes it possible to identify common exposomic determinants for the diseases, thus facilitating the development of widely operating preventive and curative treatments. HEDIMED includes data and samples from birth cohorts and clinical trials that have used exposomic interventions and cell and organ culture models to identify mechanisms of the observed associations. Importantly, HEDIMED generates a toolbox that offers science-based functional tools for key stakeholders to control the IMD epidemic. Altogether, HEDIMED aims at innovations, which become widely exploited in diagnostic, therapeutic, preventive, and health economic approaches.},
}
@article {pmid35702356,
year = {2022},
author = {Davidson, AL and Driscoll, CR and Luther, VP and Katz, AJ},
title = {Recurrent Skin and Soft Tissue Infection following Breast Reduction Surgery Caused by Gordonia bronchialis: A Case Report.},
journal = {Plastic and reconstructive surgery. Global open},
volume = {10},
number = {6},
pages = {e4395},
doi = {10.1097/GOX.0000000000004395},
pmid = {35702356},
issn = {2169-7574},
abstract = {The expanding knowledge of the breast microbiome and its constituents necessitates understanding of how it plays into human disease. Consideration of how to identify novel organisms in breast tissue is a topic of hot debate. We report a case of a 26-year-old woman with repeat incisional break-down and sanguinopurulent drainage who required repeat incision and drainage procedures after bilateral breast reduction. Cultures revealed no growth until 4 months postoperation when matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) revealed Gordonia bronchialis, a fastidious, slow-growing organism. To date, there are fewer than 30 reported cases of G. bronchialis infections and only one with breast involvement. Our patient required 6 weeks of amoxicillin-clavulanate therapy and frequent follow-up for symptom resolution. This case demonstrates the need for additional microbiologic data in patients with delayed, persistent infections after breast surgery.},
}
@article {pmid35702150,
year = {2022},
author = {Wang, C and Segal, LN and Hu, J and Zhou, B and Hayes, R and Ahn, J and Li, H},
title = {Microbial Risk Score for Capturing Microbial Characteristics, Integrating Multi-omics Data, and Predicting Disease Risk.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2022.06.07.495127},
pmid = {35702150},
abstract = {Background: With the rapid accumulation of microbiome-wide association studies, a great amount of microbiome data are available to study the microbiome's role in human disease and advance the microbiome's potential use for disease prediction. However, the unique features of microbiome data hinder its utility for disease prediction.<br><br>Methods: Motivated from the polygenic risk score framework, we propose a microbial risk score (MRS) framework to aggregate the complicated microbial profile into a summarized risk score that can be used to measure and predict disease susceptibility. Specifically, the MRS algorithm involves two steps: 1) identifying a sub-community consisting of the signature microbial taxa associated with disease, and 2) integrating the identified microbial taxa into a continuous score. The first step is carried out using the existing sophisticated microbial association tests and pruning and thresholding method in the discovery samples. The second step constructs a community-based MRS by calculating alpha diversity on the identified sub-community in the validation samples. Moreover, we propose a multi-omics data integration method by jointly modeling the proposed MRS and other risk scores constructed from other omics data in disease prediction.<br><br>Results: Through three comprehensive real data analyses using the NYU Langone Health COVID-19 cohort, the gut microbiome health index (GMHI) multi-study cohort, and a large type 1 diabetes cohort separately, we exhibit and evaluate the utility of the proposed MRS framework for disease prediction and multi-omics data integration. In addition, the disease-specific MRSs for colorectal adenoma, colorectal cancer, Crohn's disease, and rheumatoid arthritis based on the relative abundances of 5, 6, 12, and 6 microbial taxa respectively are created and validated using the GMHI multi-study cohort. Especially, Crohn's disease MRS achieves AUCs of 0.88 ([0.85-0.91]) and 0.86 ([0.78-0.95]) in the discovery and validation cohorts, respectively.<br><br>Conclusions: The proposed MRS framework sheds light on the utility of the microbiome data for disease prediction and multi-omics integration, and provides great potential in understanding the microbiome's role in disease diagnosis and prognosis.},
}
@article {pmid35702025,
year = {2022},
author = {Chelluboina, B and Kieft, K and Breister, A and Anantharaman, K and Vemuganti, R},
title = {Gut virome dysbiosis following focal cerebral ischemia in mice.},
journal = {Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism},
volume = {},
number = {},
pages = {271678X221107702},
doi = {10.1177/0271678X221107702},
pmid = {35702025},
issn = {1559-7016},
abstract = {Stroke leads to gut bacterial dysbiosis that impacts the post-stroke outcome. The gut microbiome also contains a high abundance of viruses which might play a crucial role in disease progression and recovery by modulating the metabolism of both host and host's gut bacteria. We presently analyzed the virome composition (viruses and phages) by shotgun metagenomics in the fecal samples obtained at 1 day of reperfusion following transient focal ischemia in adult mice. Viral genomes, viral auxiliary metabolic genes, and viral protein networks were compared between stroke and sham conditions (stroke vs sham, exclusive to sham and exclusive to stroke). Following focal ischemia, abundances of 2 viral taxa decreased, and 5 viral taxa increased compared with the sham. Furthermore, the abundance of Clostridia-like phages and Erysipelatoclostridiaceae-like phages were altered in the stroke compared with the sham cohorts. This is the first report to show that the gut virome responds acutely to stroke.},
}
@article {pmid35701845,
year = {2022},
author = {Miao, Z and Du, W and Xiao, C and Su, C and Gou, W and Shen, L and Zhang, J and Fu, Y and Jiang, Z and Wang, Z and Jia, X and Zheng, JS and Wang, H},
title = {Gut microbiota signatures of long-term and short-term plant-based dietary pattern and cardiometabolic health: a prospective cohort study.},
journal = {BMC medicine},
volume = {20},
number = {1},
pages = {204},
pmid = {35701845},
issn = {1741-7015},
support = {R01-HD30880/NH/NIH HHS/United States ; DK056350/NH/NIH HHS/United States ; R24 HD050924/NH/NIH HHS/United States ; R01-HD38700/NH/NIH HHS/United States ; 82073529//National Natural Science Foundation of China/ ; 81903316//National Natural Science Foundation of China/ ; 2019R52039//Zhejiang Ten-thousand Talents Program/ ; },
abstract = {BACKGROUND: The interplay among the plant-based dietary pattern, gut microbiota, and cardiometabolic health is still unclear, and evidence from large prospective cohorts is rare. We aimed to examine the association of long-term and short-term plant-based dietary patterns with gut microbiota and to assess the prospective association of the identified microbial features with cardiometabolic biomarkers.<br><br>METHODS: Using a population-based prospective cohort study: the China Health and Nutrition Survey, we included 3096 participants from 15 provinces/megacities across China. We created an overall plant-based diet index (PDI), a healthful plant-based diet index (hPDI), and an unhealthful plant-based diet index (uPDI). The average PDIs were calculated using repeat food frequency questionnaires collected in 2011 and 2015 to represent a long-term dietary pattern. Short-term dietary pattern was estimated using 3-day 24-h dietary recalls collected in 2015. Fecal samples were collected in 2015 and measured using 16S rRNA sequencing. We investigated the association of long-term and short-term plant-based dietary patterns with gut microbial diversity, taxonomies, and functional pathways using linear mixed models. Furthermore, we assessed the prospective associations between the identified gut microbiome signatures and cardiometabolic biomarkers (measured in 2018) using linear regression.<br><br>RESULTS: We found a significant association of short-term hPDI with microbial alpha-diversity. Both long-term and short-term plant-based diet indices were correlated with microbial overall structure, whereas long-term estimates explained more variance. Long-term and short-term PDIs were differently associated with microbial taxonomic composition, yet only microbes related to long-term estimates showed association with future cardiometabolic biomarkers. Higher long-term PDI was associated with the lower relative abundance of Peptostreptococcus, while this microbe was positively correlated with the high-sensitivity C-reactive protein and inversely associated with high-density lipoprotein cholesterol.<br><br>CONCLUSIONS: We found shared and distinct gut microbial signatures of long-term and short-term plant-based dietary patterns. The identified microbial genera may provide insights into the protective role of long-term plant-based dietary pattern for cardiometabolic health, and replication in large independent cohorts is needed.},
}
@article {pmid35701831,
year = {2022},
author = {Herremans, KM and Riner, AN and Cameron, ME and McKinley, KL and Triplett, EW and Hughes, SJ and Trevino, JG},
title = {The oral microbiome, pancreatic cancer and human diversity in the age of precision medicine.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {93},
pmid = {35701831},
issn = {2049-2618},
support = {T32 HG0008958/HG/NHGRI NIH HHS/United States ; T32 HG0008958/HG/NHGRI NIH HHS/United States ; U01DK108320-06/DK/NIDDK NIH HHS/United States ; R01CA242003/CA/NCI NIH HHS/United States ; U54CA233444/CA/NCI NIH HHS/United States ; U54CA233444-03S1/CA/NCI NIH HHS/United States ; },
abstract = {Pancreatic cancer is a deadly disease with limited diagnostic and treatment options. Not all populations are affected equally, as disparities exist in pancreatic cancer prevalence, treatment and outcomes. Recently, next-generation sequencing has facilitated a more comprehensive analysis of the human oral microbiome creating opportunity for its application in precision medicine. Oral microbial shifts occur in patients with pancreatic cancer, which may be appreciated years prior to their diagnosis. In addition, pathogenic bacteria common in the oral cavity have been found within pancreatic tumors. Despite these findings, much remains unknown about how or why the oral microbiome differs in patients with pancreatic cancer. As individuals develop, their oral microbiome reflects both their genotype and environmental influences. Genetics, race/ethnicity, smoking, socioeconomics and age affect the composition of the oral microbiota, which may ultimately play a role in pancreatic carcinogenesis. Multiple mechanisms have been proposed to explain the oral dysbiosis found in patients with pancreatic cancer though they have yet to be confirmed. With a better understanding of the interplay between the oral microbiome and pancreatic cancer, improved diagnostic and therapeutic approaches may be implemented to reduce healthcare disparities. Video Abstract.},
}
@article {pmid35701804,
year = {2022},
author = {Park, T and Ma, L and Gao, S and Bu, D and Yu, Z},
title = {Heat stress impacts the multi-domain ruminal microbiota and some of the functional features independent of its effect on feed intake in lactating dairy cows.},
journal = {Journal of animal science and biotechnology},
volume = {13},
number = {1},
pages = {71},
pmid = {35701804},
issn = {1674-9782},
support = {31872383//National Natural Science Foundation of China/ ; ASTIP-IAS07-1//Scientific Research Project for Major Achievements of The Agricultural Science and Technology Innovation Program/ ; BAIC06-2021//Beijing Dairy Industry Innovation Team/ ; },
abstract = {BACKGROUND: Heat stress (HS) affects the ruminal microbiota and decreases the lactation performance of dairy cows. Because HS decreases feed intake, the results of previous studies were confounded by the effect of HS on feed intake. This study examined the direct effect of HS on the ruminal microbiota using lactating Holstein cows that were pair-fed and housed in environmental chambers in a 2 × 2 crossover design. The cows were pair-fed the same amount of identical total mixed ration to eliminate the effect of feed or feed intake. The composition and structure of the microbiota of prokaryotes, fungi, and protozoa were analyzed using metataxonomics and compared between two thermal conditions: pair-fed thermoneutrality (PFTN, thermal humidity index: 65.5) and HS (87.2 for daytime and 81.8 for nighttime).<br><br>RESULTS: The HS conditions altered the structure of the prokaryotic microbiota and the protozoal microbiota, but not the fungal microbiota. Heat stress significantly increased the relative abundance of Bacteroidetes (primarily Gram-negative bacteria) while decreasing that of Firmicutes (primarily Gram-positive bacteria) and the Firmicutes-to-Bacteroidetes ratio. Some genera were exclusively found in the heat-stressed cows and thermal control cows. Some co-occurrence and mutual exclusion between some genera were also found exclusively for each thermal condition. Heat stress did not significantly affect the overall functional features predicted using the 16S rRNA gene sequences and ITS1 sequences, but some enzyme-coding genes altered their relative abundance in response to HS.<br><br>CONCLUSIONS: Overall, HS affected the prokaryotes, fungi, and protozoa of the ruminal microbiota in lactating Holstein cows to a different extent, but the effect on the structure of ruminal microbiota and functional profiles was limited when not confounded by the effect on feed intake. However, some genera and co-occurrence were exclusively found in the rumen of heat-stressed cows. These effects should be attributed to the direct effect of heat stress on the host metabolism, physiology, and behavior. Some of the "heat-stress resistant" microbes may be useful as potential probiotics for cows under heat stress.},
}
@article {pmid35701733,
year = {2022},
author = {Hoang, T and Kim, MJ and Park, JW and Jeong, SY and Lee, J and Shin, A},
title = {Nutrition-wide association study of microbiome diversity and composition in colorectal cancer patients.},
journal = {BMC cancer},
volume = {22},
number = {1},
pages = {656},
pmid = {35701733},
issn = {1471-2407},
support = {0420190530//Seoul National University Hospital/ ; 0420190530//Seoul National University Hospital/ ; 0420190530//Seoul National University Hospital/ ; },
abstract = {BACKGROUND: The effects of diet on the interaction between microbes and host health have been widely studied. However, its effects on the gut microbiota of patients with colorectal cancer (CRC) have not been elucidated. This study aimed to investigate the association between diet and the overall diversity and different taxa levels of the gut microbiota in CRC patients via the nutrition-wide association approach.<br><br>METHODS: This hospital-based study utilized data of 115 CRC patients who underwent CRC surgery in Department of Surgery, Seoul National University Hospital. Spearman correlation analyses were conducted for 216 dietary features and three alpha-diversity indices, Firmicutes/Bacteroidetes ratio, and relative abundance of 439 gut microbial taxonomy. To identify main enterotypes of the gut microbiota, we performed the principal coordinate analysis based on the β-diversity index. Finally, we performed linear regression to examine the association between dietary intake and main microbiome features, and linear discriminant analysis effect size (LEfSe) to identify bacterial taxa phylogenetically enriched in the low and high diet consumption groups.<br><br>RESULTS: Several bacteria were enriched in patients with higher consumption of mature pumpkin/pumpkin juice (ρ, 0.31 to 0.41) but lower intake of eggs (ρ, -0.32 to -0.26). We observed negative correlations between Bacteroides fragilis abundance and intake of pork (belly), beef soup with vegetables, animal fat, and fatty acids (ρ, -0.34 to -0.27); an inverse correlation was also observed between Clostridium symbiosum abundance and intake of some fatty acids, amines, and amino acids (ρ, -0.30 to -0.24). Furthermore, high intake of seaweed was associated with a 6% (95% CI, 2% to 11%) and 7% (95% CI, 2% to 11%) lower abundance of Rikenellaceae and Alistipes, respectively, whereas overall beverage consumption was associated with an 10% (95% CI, 2% to 18%) higher abundance of Bacteroidetes, Bacteroidia, and Bacteroidales, compared to that in the low intake group. LEfSe analysis identified phylogenetically enriched taxa associated with the intake of sugars and sweets, legumes, mushrooms, eggs, oils and fats, plant fat, carbohydrates, and monounsaturated fatty acids.<br><br>CONCLUSIONS: Our data elucidates the diet-microbe interactions in CRC patients. Additional research is needed to understand the significance of these results in CRC prognosis.},
}
@article {pmid35701607,
year = {2022},
author = {Cho, S and Stroup, BM and Britto, SL and Ruan, W and Schady, D and Hoffman, KL and Kellermayer, R},
title = {Increased number of children in households may protect against inflammatory bowel disease.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {35701607},
issn = {1530-0447},
abstract = {BACKGROUND: The increasing incidence of inflammatory bowel disease (IBD: Crohn's disease and ulcerative colitis) around the world has coincided with a wide array of environmental and epidemiologic changes. The relationship between IBD incidence and household or family size decline, however, has not been examined before. Our background epidemiological analyses suggested an inverse association between household size and IBD incidence. We aimed to examine this further in a murine model.<br><br>METHODS: We designed a unique two-generation cohousing model of family size and IBD susceptibility in C57BL/6J mice. Serial fecal microbiomes during cohousing were examined by high-throughput 16S rRNA sequencing. After cohousing for 10 days, mice were exposed to dextran sulfate sodium (DSS) to induce acute colitis. Body weight as a significant correlate of colitis severity was measured.<br><br>RESULTS: Mice in a large household arrangement demonstrated less weight loss than mice in the small household arrangement in the DSS model. Age- and housing-dependent microbiome shifts were found.<br><br>CONCLUSIONS: Larger households may be protective against intestinal inflammation through intergenerational microbiome modulation. Our observations may set the foundation for age-dependent, microbiome-directed future prevention against IBD.<br><br>IMPACT: Epidemiological analyses in this study suggested that IBD incidence may inversely correlate with household size (an indicator of family size/children per family), which has not been examined before. A uniquely designed two-generation cohousing model of family size and IBD susceptibility in mice supported our epidemiologic observations. Microbiome changes in our cohousing model may set the foundation for age-dependent, microbiome-directed prevention against IBD.},
}
@article {pmid35701595,
year = {2022},
author = {Png, CW and Chua, YK and Law, JH and Zhang, Y and Tan, KK},
title = {Alterations in co-abundant bacteriome in colorectal cancer and its persistence after surgery: a pilot study.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {9829},
pmid = {35701595},
issn = {2045-2322},
support = {NUHSRO/2020/142/RO5+6/Seed-Sep/02//National University Health System/ ; },
abstract = {There is growing interest in the role of gut microbiome in colorectal cancer (CRC), ranging from screening to disease recurrence. Our study aims to identify microbial markers characteristic of CRC and to examine if changes in bacteriome persist after surgery. Forty-nine fecal samples from 25 non-cancer (NC) individuals and 12 CRC patients, before and 6-months after surgery, were collected for analysis by bacterial 16S rRNA gene sequencing. Bacterial richness and diversity were reduced, while pro-carcinogenic bacteria such as Bacteroides fragilis and Odoribacter splanchnicus were increased in CRC patients compared to NC group. These differences were no longer observed after surgery. Comparison between pre-op and post-op CRC showed increased abundance of probiotic bacteria after surgery. Concomitantly, bacteria associated with CRC progression were observed to have increased after surgery, implying persistent dysbiosis. In addition, functional pathway predictions based on the bacterial 16S rRNA gene data showed that various pathways were differentially enriched in CRC compared to NC. Microbiome signatures characteristic of CRC comprise altered bacterial composition. Elements of these dysbiotic signatures persists even after surgery, suggesting possible field-change in remnant non-diseased colon. Future studies should involve a larger sample size with microbiome data collected at multiple time points after surgery to examine if these dysbiotic patterns truly persist and also correlate with disease outcomes.},
}
@article {pmid35701558,
year = {2022},
author = {Ruotsalainen, AL and Tejesvi, MV and Vänni, P and Suokas, M and Tossavainen, P and Pirttilä, AM and Talvensaari-Mattila, A and Nissi, R},
title = {Child type 1 diabetes associated with mother vaginal bacteriome and mycobiome.},
journal = {Medical microbiology and immunology},
volume = {},
number = {},
pages = {},
pmid = {35701558},
issn = {1432-1831},
abstract = {Mother vaginal microbes contribute to microbiome of vaginally delivered neonates. Child microbiome can be associated with autoimmune diseases, such as type 1 diabetes (T1D). We collected vaginal DNA samples from 25 mothers with a vaginally delivered child diagnosed with T1D and samples from 24 control mothers who had vaginally delivered a healthy child and analyzed bacteriome and mycobiome of the samples. The total DNA of the samples was extracted, and ribosomal DNA regions (16S for bacteria, ITS2 for fungi) were amplified, followed by next-generation sequencing and machine learning. We found that alpha-diversity of bacteriome was increased (P < 0.002), whereas alpha-diversity of mycobiome was decreased (P < 0.001) in mothers with a diabetic child compared to the control mothers. Beta-diversity analysis suggested differences in mycobiomes between the mother groups (P = 0.001). Random forest models were able to effectively predict diabetes and control status of unknown samples (bacteria: 0.86 AUC, fungi: 0.96 AUC). Our data indicate several fungal genera and bacterial metabolic pathways of mother vaginal microbiome to be associated with child T1D. We suggest that early onset of T1D in a child has a relationship with altered mother vaginal microbiome and that both bacteriome and mycobiome contribute to this shift.},
}
@article {pmid35701291,
year = {2022},
author = {Jing, J and Cong, WF and Bezemer, TM},
title = {Legacies at work: plant-soil-microbiome interactions underpinning agricultural sustainability.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2022.05.007},
pmid = {35701291},
issn = {1878-4372},
abstract = {Agricultural intensification has had long-lasting negative legacies largely because of excessive inputs of agrochemicals (e.g., fertilizers) and simplification of cropping systems (e.g., continuous monocropping). Conventional agricultural management focuses on suppressing these negative legacies. However, there is now increasing attention for creating positive above- and belowground legacies through selecting crop species/genotypes, optimizing temporal and spatial crop combinations, improving nutrient inputs, developing intelligent fertilizers, and applying soil or microbiome inoculations. This can lead to enhanced yields and reduced pest and disease pressure in cropping systems, and can also mitigate greenhouse gas emissions and enhance carbon sequestration in soils. Strengthening positive legacies requires a deeper understanding of plant-soil-microbiome interactions and innovative crop, input, and soil management which can help to achieve agricultural sustainability.},
}
@article {pmid35701123,
year = {2022},
author = {Zhang, JH and Shi, JQ and Chen, ZJ and Jia, G},
title = {[Effects of nano titanium dioxide on gut microbiota based on human digestive tract microecology simulation system in vitro].},
journal = {Beijing da xue xue bao. Yi xue ban = Journal of Peking University. Health sciences},
volume = {54},
number = {3},
pages = {468-476},
pmid = {35701123},
issn = {1671-167X},
abstract = {OBJECTIVE: To explore the effects of oral exposure to titanium dioxide nanoparticles (TiO2 NPs) on the composition and structure of human gut microbiota.<br><br>METHODS: The particle size, shape, crystal shape and degree of agglomeration in ultrapure water of TiO2 NPs were characterized. The in vitro human digestive tract microecological simulation system was established by simulating the fluid environment and physical conditions of stomach, small intestine and colon, and the stability of the simulation system was evaluated. The bacterial communities were extracted from human feces and cultured stably in the simulated system. They were exposed to 0, 20, 100 and 500 mg/L TiO2 NPs, respectively, and the bacterial fluids were collected after 24 h of exposure. The effect of TiO2 NPs on the composition and structure of human gut microbiota was analyzed by 16S rRNA sequencing technology. Linear discriminant analysis effect size (LEfSe) was used to screen differential bacteria, and the Kyoto encyclopedia of genes and genomes (KEGG) database for functional prediction.<br><br>RESULTS: The spherical and anatase TiO2 NPs were (25.12±5.64) nm in particle size, while in ultra-pure water hydrated particle size was (609.43±60.35) nm and Zeta potential was (-8.33±0.22) mV. The in vitro digestive tract microecology simulation system reached a relatively stable state after 24 hours, and the counts of Enterococci, Enterobacte-rium, and Lactobacillus reached (1.6±0.85)×107, (5.6±0.82)×107 and (2.7±1.32)×107, respectively. 16S rRNA sequencing results showed that compared with the control group, the number and evenness of gut microbiota were not significantly affected at phylum, class, order, family and genus levels in TiO2 NPs groups (20, 100 and 500 mg/L). The relative abundance of some species was significantly changed, and a total of 42 different bacteria were screened between the TiO2 NPs groups (20, 100 and 500 mg/L) and the control group [linear discriminant analysis(LDA) score>3], represented by Enterobacter, Bacteroidaceae, Lactobacillaceae, Bifidobacteriaceae and Clostridium. Further predictive analysis of gut microbiota function showed that TiO2 NPs might affect oxidative phosphorylation, energy meta-bolism, phosphonate and phosphonate metabolism, and methane metabolism (P < 0.05).<br><br>CONCLUSION: In human digestive tract microecological simulation system, TiO2 NPs could significantly change the composition and structure of human gut microbiota, represented by Enterobacter and probiotics, and may further affect a variety of metabolism and function of the body.},
}
@article {pmid35643340,
year = {2022},
author = {Benincasa, G and Coscioni, E and Napoli, C},
title = {Cardiovascular risk factors and molecular routes underlying endothelial dysfunction: Novel opportunities for primary prevention.},
journal = {Biochemical pharmacology},
volume = {202},
number = {},
pages = {115108},
doi = {10.1016/j.bcp.2022.115108},
pmid = {35643340},
issn = {1873-2968},
abstract = {One of the major challenges of cardiovascular primary prevention approach is the absence of early biomarkers of endothelial dysfunction which may be useful for identifying at-risk subjects. Endothelial dysfunction is a systemic disorder in which traditional cardiovascular risk factors, such as aging, gender, hypertension, smoking, hyperglycemia, and dyslipidemia, as well as emerging risk determinants, such as fetal factors, gut microbiome alteration, clonal hematopoiesis, air pollution, and sleep disorders act synergistically to tip the endothelial balance in favor of vasoconstrictive, pro-inflammatory, and pro-thrombotic phenotypes. Endothelial dysfunction can start already in fetal life and may be regained once detrimental stimuli are removed. The hallmark of endothelial dysfunction is a marked reduction of nitric oxide (NO) bioavailability owing to epigenetic-sensitive dysregulation of the endothelial nitric oxide synthase (eNOS) gene and upregulation of reactive oxygen species (ROS) in endothelial cells (ECs). Advance in liquid-based assays and molecular biology tools are providing novel potential EC-specific biomarkers for prediction and diagnosis of endothelial dysfunction. Significant associations between clinically useful indexes of endothelial dysfunction, mainly brachial artery flow-mediated dilation (FMD), and increased number of endothelial microparticles (EMPs), increased levels of endoglin and endocan, as well as reduced levels of irisin were observed in subjects with one or more traditional risk factors. However, none entered in clinical practice yet. Smoking cessation, weight loss, physical exercise, and diet control are the milestones of cardiovascular primary prevention, and they may restore endothelial function via epigenetic-sensitive pathways able to reduce inflammation and oxidative stress and increase NO production . We briefly summarize well-known and novel molecular routes driving early endothelial dysfunction mainly in human ECs and related potential biomarkers which may add predictive or diagnostic value to the traditional non-invasive techniques. Also, we focus on clinical trials investigating lifestyle modifications and their impact on molecular routes involved in restoring endothelial function.},
}
@article {pmid35700918,
year = {2022},
author = {Wang, Z and Xiao, H and Dong, J and Li, Y and Wang, B and Chen, Z and Zeng, X and Liu, J and Dong, Y and Ma, L and Xu, J and Cheng, L and Li, C and Liu, X and Cui, M},
title = {Sexual dimorphism in gut microbiota dictates therapeutic efficacy of intravenous immunoglobulin on radiotherapy complications.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2022.06.002},
pmid = {35700918},
issn = {2090-1224},
abstract = {INTRODUCTION: With the mounting number of cancer survivors, the complications following cancer treatment become novel conundrums and starve for countermeasures. Intravenous immunoglobulin (IVIg) is a purified preparation for immune-deficient and autoimmune conditions.<br><br>OBJECTIVES: Here, we investigated whether IVIg could be employed to fight against radiation injuries and explored the underlying mechanism.<br><br>METHODS: Hematopoietic or gastrointestinal (GI) tract toxicity was induced by total body or abdominal local irradiation. High-throughput sequencing was performed to analyze the gut microbiota configurations and gene expression profile of small intestine. The untargeted metabolomics of gut microbiome was assessed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) analyses. Hydrodynamic-based gene delivery was used to knockdown the target genes in vivo.<br><br>RESULTS: Intravenous injection of IVIg protected against radiation-induced hematopoietic and GI tract toxicity in female mice but not in males. IVIg structured sex-characteristic gut microbiota configurations in abdominal irradiated mice. The irradiation enriched gut Lachnospiraceae in female mice but reduced those in males. IVIg injection combined with oral gavage of Lachnospiraceae or its metabolite hypoxanthine, alleviated radiation toxicity in male mice however, Lachnospiraceae or hypoxanthine alone failed to ameliorate the injuries. Abdominal local irradiation drove sex-distinct gene expression signatures in small intestine. Mechanistic investigation showed that replenishment of Lachnospiraceae or hypoxanthine offset abdominal radiation-reduced PLD1 expression in male mice. In females, irradiation elevated PLD1 expression. Deletion of PLD1 in GI tract of female mice erased the radioprotective effects of IVIg.<br><br>CONCLUSION: IVIg battles against radiation injuries in a sex-specific, gut microbiome-dependent way through Lachnospiraceae/hypoxanthine/PLD1 axis. Our findings provide a sex-precise therapeutic avenue to improve the prognosis of cancer patients with radiotherapy in pre-clinical settings.},
}
@article {pmid35700748,
year = {2022},
author = {Gaire, TN and Noyes, NR and Scott, HM and Ericsson, AC and Dunmire, K and Tokach, MD and Paulk, CB and Vinasco, J and Roenne, B and Nagaraja, TG and Volkova, VV},
title = {A Longitudinal Investigation of the Effects of Age, Dietary Fiber Type and Level and Injectable Antimicrobials on the Fecal Microbiome and Antimicrobial Resistance of Finisher Pigs.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skac217},
pmid = {35700748},
issn = {1525-3163},
abstract = {Age and diet are among the factors that influence the community composition of the fecal microbiome. Additionally, antimicrobial use can alter the composition of bacterial communities. An 86-d study with finisher pigs aimed to evaluate age-related dynamics (d 98-177 of age), effects of types and levels of dietary fiber, and injectable antimicrobials on the fecal microbiome and antimicrobial resistance (AMR) was conducted. A total of 287 pigs, housed in 36 pens, with 7 to 8 pigs per pen, fed a corn grain and soybean meal-based basal diet, formulated to contain 8.7% neutral detergent fiber (NDF), were randomly assigned to one of three treatments: 1. basal diet with no supplement, 2. basal diet supplemented with 20% distillers dried grains with solubles (DDGS) formulated to contain 13.6% NDF, or 3. basal diet supplemented with 14.5% sugar beet pulp (SBP) formulated to contain 13.6% NDF. Five finisher pigs from each treatment group were selected randomly, and fecal samples were collected on d 98, 110, 144, and 177 of age. In addition, fecal samples were collected from pigs that were injected intramuscularly ceftiofur hydrochloride or penicillin G on d 1 and 3 along with pen-mate untreated controls on d 1. Fecal samples were subjected to 16S rRNA amplicon-based microbiome analysis and culture methods to quantify the abundance of total and AMR coliforms and enterococci populations. The alpha diversity, such as species richness, increased with age, and the overall bacterial composition changed with age (P =0.001) and diet (P = 0.001). Diet-associated shifts in the specific bacterial taxa were observed. The richness, diversity, and evenness of bacterial taxa did not differ between pigs that were injected with ceftiofur versus their untreated pen mates or by dietary treatments, but differed in pigs that received penicillin G injection. Both antimicrobial treatments contributed to changes in the overall fecal bacterial composition at the genus level. Collectively, the data demonstrate that both age and the diet (control vs. DDGS-, control vs. SBP- or DDGS- vs. SBP-based diets) were associated with overall bacterial community composition and the impact of age on variations in fecal microbiome composition was greater than the diet. Antibiotic treatment had minimal effect on bacterial diversity and relative abundance of taxa. Further, diets and antimicrobial treatment had minimal impact on the overall counts of AMR coliforms and enterococci populations in feces.},
}
@article {pmid35700706,
year = {2022},
author = {Polyak, K},
title = {Bacterial Darth Vader: May the force be with you.},
journal = {Cancer cell},
volume = {40},
number = {6},
pages = {600-602},
doi = {10.1016/j.ccell.2022.05.008},
pmid = {35700706},
issn = {1878-3686},
abstract = {The microbiome has a major impact on tumor progression, yet the mechanisms are poorly defined. Fu et al. report in Cell that intracellular bacteria in a breast cancer model promote metastasis via reorganizing the cytoskeleton to enhance resistance to mechanical stress, thereby facilitating survival in the circulation during dissemination.},
}
@article {pmid35700606,
year = {2022},
author = {Rohde, RL and North, LM and Murray, M and Khalili, S and Poetker, DM},
title = {Pott's puffy tumor: A comprehensive review of the literature.},
journal = {American journal of otolaryngology},
volume = {43},
number = {5},
pages = {103529},
doi = {10.1016/j.amjoto.2022.103529},
pmid = {35700606},
issn = {1532-818X},
abstract = {PURPOSE: Pott's puffy tumor (PPT) is a rare clinical entity characterized by osteomyelitis of the frontal bone with subperiosteal abscess collection. The frequency of reported cases of PPT in the literature has increased in recent years. Previous reviews of PPT exist primarily in the form of small, retrospective case series and anecdotal case reports. Therefore, the aim of this study is to provide the literature's largest comprehensive, up-to-date review of the essential clinical findings, diagnostic modalities, microbiologic considerations, and treatment approaches utilized in the management of PPT, both in pediatric and adult populations.<br><br>MATERIALS AND METHODS: We searched MEDLINE, PubMed, and Embase databases for English-language studies published from January 1950 through January 30, 2022. The authors reviewed all cases of PPT, focusing specifically on those describing therapeutic management of PPT. A total of 321 patients were included, consisting of 318 patients (from 216 articles) and an additional 3 adult cases from our institution.<br><br>RESULTS: PPT most often results from untreated rhinosinusitis, as well as direct head trauma, substance use, and odontogenic disease. Infections are classically polymicrobial with an anaerobe-predominant microbiome. Both CT and MRI imaging modalities are commonly obtained for presurgical assessment of sinusitis and intracranial extension. The core of treatment is an early and aggressive approach to prevent long-term complications. A significant association exists between surgical management and clinical outcomes for patients with PPT. Recent literature suggests endoscopic sinus surgery is essential for successful disease resolution.<br><br>CONCLUSIONS: PPT is an important and relatively morbid disease process that is often underrecognized and misdiagnosed at presentation due to its variable clinical presentation. Management of PPT includes both antimicrobial therapy and surgical intervention. Determination of the optimal approach depends on patient clinical features including age, history of prior endoscopic sinus surgery, and presence of intracranial involvement on presentation. An individualized, targeted, and interdisciplinary approach to the treatment of PPT is critical for successful disease resolution.},
}
@article {pmid35700403,
year = {2022},
author = {Dahshan, D and Gallagher, N and Workman, A and Perdue, J and Aikens, J and Schmicker, T and Shuler, FD},
title = {Targeting the Gut Microbiome for Inflammation and Pain Management in Orthopedic Conditions.},
journal = {Orthopedics},
volume = {},
number = {},
pages = {1-13},
doi = {10.3928/01477447-20220608-07},
pmid = {35700403},
issn = {1938-2367},
abstract = {The human gut microbiome can be altered with probiotics, prebiotics, synbiotics, and anti-inflammatory foods and spices as part of an evidence-based strategy that targets inflammation and pain in common orthopedic conditions. Implementing these strategies avoids adverse effects associated with nonsteroidal anti-inflammatory drugs and minimizes the potential for opioid use. This review focuses exclusively on human trials studying the effects of gut microbiome alterations to address pain and inflammatory markers in common orthopedic conditions: osteoarthritis, rheumatoid arthritis, fractures/osteoporosis, and bone pain associated with chemotherapy. Individualized supplementation strategies can be further explored with the information in this review. [Orthopedics. 20XX;XX(X):xx-xx.].},
}
@article {pmid35700319,
year = {2022},
author = {Luo, Y and Tan, L and Zhang, H and Bi, W and Zhao, L and Wang, X and Lu, X and Xu, X and Sun, R and Alvarez, PJJ},
title = {Characteristics of Wild Bird Resistomes and Dissemination of Antibiotic Resistance Genes in Interconnected Bird-Habitat Systems Revealed by Similarity of blaTEM Polymorphic Sequences.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.2c01633},
pmid = {35700319},
issn = {1520-5851},
abstract = {Wild birds are known to harbor and discharge antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs). However, assessments of their contribution to the dissemination of antibiotic resistance in the environment are limited to culture-dependent bacterial snapshots. Here, we present a high-throughput sequencing study that corroborates extensive ARG exchange between wild bird feces and their habitats and implies the need to scrutinize high-mobility birds as potential vectors for global propagation of ARGs. We characterized the resistome (281 ARGs) and microbiome of seven wild bird species and their terrestrial and aquatic habitats. The resistomes of bird feces were influenced by the microbial community structure, mobile genetic elements (MGEs), and residual antibiotics. We designated 33 ARGs found in more than 90% of the bird fecal samples as core ARGs of wild bird feces, among which 16 ARGs were shared as core ARGs in both wild bird feces and their habitats; these genes represent a large proportion of both the bird feces (35.0 ± 15.9%) and the environmental resistome (29.9 ± 21.4%). One of the most detected β-lactam resistance genes (blaTEM, commonly harbored by multidrug resistant "superbugs") was used as molecular marker to demonstrate the high interconnectivity of ARGs between the microbiomes of wild birds and their habitats. Overall, this work provides a comprehensive analysis of the wild bird resistome and underscores the importance to consider genetic exchange between animals and the environment in the One Health approach.},
}
@article {pmid35700195,
year = {2022},
author = {Severgnini, M and Morselli, S and Camboni, T and Ceccarani, C and Salvo, M and Zagonari, S and Patuelli, G and Pedna, MF and Sambri, V and Foschi, C and Consolandi, C and Marangoni, A},
title = {Gardnerella vaginalis clades in pregnancy: New insights into the interactions with the vaginal microbiome.},
journal = {PloS one},
volume = {17},
number = {6},
pages = {e0269590},
doi = {10.1371/journal.pone.0269590},
pmid = {35700195},
issn = {1932-6203},
abstract = {Gardnerella vaginalis (GV) is an anaerobic bacterial species involved in the pathogenesis of bacterial vaginosis (BV), a condition of vaginal dysbiosis associated with adverse pregnancy outcomes. GV strains are categorized into four clades, characterized by a different ability to produce virulence factors, such as sialidase. We investigated the distribution of GV clades and sialidase genes in the vaginal ecosystem of a cohort of pregnant women, assessing the correlations between GV clades and the whole vaginal microbiome. A total of 61 Caucasian pregnant women were enrolled. Their vaginal swabs, collected both at the first and third trimester of pregnancy, were used for (i) evaluation of the vaginal status by Nugent score, (ii) vaginal microbiome profiling by 16S rRNA sequencing, (iii) detection and quantification of GV clades and sialidase A gene by qPCR assays. DNA of at least one GV clade was detected in most vaginal swabs, with clade 4 being the most common one. GV clade 2, together with the presence of multiple clades (>2 simultaneously), were significantly associated with a BV condition. Significantly higher GV loads and sialidase gene levels were found in BV cases, compared to the healthy status. Clade 2 was related to the major shifts in the vaginal microbial composition, with a decrease in Lactobacillus and an increase in several BV-related taxa. As the number of GV clades detected simultaneously increased, a group of BV-associated bacteria tended to increase as well, while Bifidobacterium tended to decrease. A negative correlation between sialidase gene levels and Lactobacillus, and a positive correlation with Gardnerella, Atopobium, Prevotella, Megasphaera, and Sneathia were observed. Our results added knowledge about the interactions of GV clades with the inhabitants of the vaginal microbiome, possibly helping to predict the severity of BV and opening new perspectives for the prevention of pregnancy-related complications.},
}
@article {pmid35700129,
year = {2022},
author = {Tiamani, K and Luo, S and Schulz, S and Xue, J and Costa, R and Mirzaei, MK and Deng, L},
title = {The role of virome in the gastrointestinal tract and beyond.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuac027},
pmid = {35700129},
issn = {1574-6976},
abstract = {The human gut virome is comprised of diverse commensal and pathogenic viruses. The colonization by these viruses begins right after birth through vaginal delivery, then continues through breastfeeding, and broader environmental exposure. Their constant interaction with their bacterial hosts in the body shapes not only our microbiomes but us. In addition, these viruses interact with the immune cells, trigger a broad range of immune responses, and influence different metabolic pathways. Besides its key role in regulating the human gut homeostasis, the intestinal virome contributes to disease development in distant organs, both directly and indirectly. In this review, we will describe the changes in the gut virome through life, health, and disease, followed by discussing the interactions between the virome, the microbiome, and the human host as well as providing an overview of their contribution to gut disease and disease of distant organs.},
}
@article {pmid35699800,
year = {2022},
author = {Haq, FU and Imran, M and Saleem, S and Aftab, U and Ghazal, A},
title = {Investigation of Morchella esculenta and Morchella conica for their antibacterial potential against methicillin-susceptible Staphylococcus aureus, methicillin-resistant Staphylococcus aureus and Streptococcus pyogenes.},
journal = {Archives of microbiology},
volume = {204},
number = {7},
pages = {391},
pmid = {35699800},
issn = {1432-072X},
abstract = {Antimicrobial resistance is an alarming problem, especially due to emergence of methicillin-resistance Staphylococcus aureus (MRSA). World Health Organization (WHO) has already listed MRSA as a top priority pathogen for the development of novel antibacterial agents. Presently, different therapeutic approaches against bacterial infections are in practice which includes targeting bacterial virulence factors, bacteriophage therapy, and manipulation of the microbiome. Natural products have been efficiently used for centuries to combat bacterial infections. Morchella is a natural fungal product which has been reported to possess broad-spectrum biological activities against bacterial infections. Hence, this study was aimed to evaluate the antibacterial efficacy of two macro-fungi against S. aureus, MRSA, and Streptococcus pyogenes (S. pyogenes). The antibacterial potential of both fungal extracts (Morchella esculenta and Morchella conica) was evaluated using disk diffusion and standard broth microdilution methods. The chemical compounds of both fungi were investigated using ultra-performance liquid chromatography mass spectroscopy (UPLC-MS) analysis. All fungal extracts inhibited growth of tested bacteria with inhibitory zone ranging from 10.66 ± 0.3 to 21.00 ± 1.5 mm. The minimum inhibitory concentration (MIC) of tested bacterial growth ranged from 03.33 to 16.0 mg/ml. It was noteworthy that Morchella extracts prevented S. aureus growth in a bactericidal manner with minimal bactericidal concentration (MBC) of 8-16 mg/ml. The extracts were also more effective against MRSA than currently available antibiotics. In conclusion, the growth inhibition of tested bacteria by fungal extracts revealed their potential as antibacterial agents and their compounds may be used as drug candidates.},
}
@article {pmid35699597,
year = {2022},
author = {Stafford, IS and Gosink, MM and Mossotto, E and Ennis, S and Hauben, M},
title = {A Systematic Review of Artificial Intelligence and Machine Learning Applications to Inflammatory Bowel Disease, with Practical Guidelines for Interpretation.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izac115},
pmid = {35699597},
issn = {1536-4844},
support = {//Institute for Life Sciences, University of Southampton/ ; //National Institute for Health Research/ ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a gastrointestinal chronic disease with an unpredictable disease course. Computational methods such as machine learning (ML) have the potential to stratify IBD patients for the provision of individualized care. The use of ML methods for IBD was surveyed, with an additional focus on how the field has changed over time.<br><br>METHODS: On May 6, 2021, a systematic review was conducted through a search of MEDLINE and Embase databases, with the search structure ("machine learning" OR "artificial intelligence") AND ("Crohn* Disease" OR "Ulcerative Colitis" OR "Inflammatory Bowel Disease"). Exclusion criteria included studies not written in English, no human patient data, publication before 2001, studies that were not peer reviewed, nonautoimmune disease comorbidity research, and record types that were not primary research.<br><br>RESULTS: Seventy-eight (of 409) records met the inclusion criteria. Random forest methods were most prevalent, and there was an increase in neural networks, mainly applied to imaging data sets. The main applications of ML to clinical tasks were diagnosis (18 of 78), disease course (22 of 78), and disease severity (16 of 78). The median sample size was 263. Clinical and microbiome-related data sets were most popular. Five percent of studies used an external data set after training and testing for additional model validation.<br><br>DISCUSSION: Availability of longitudinal and deep phenotyping data could lead to better modeling. Machine learning pipelines that consider imbalanced data and that feature selection only on training data will generate more generalizable models. Machine learning models are increasingly being applied to more complex clinical tasks for specific phenotypes, indicating progress towards personalized medicine for IBD.},
}
@article {pmid35699474,
year = {2022},
author = {Geesink, P and Taubert, M and Jehmlich, N and von Bergen, M and Küsel, K},
title = {Bacterial Necromass Is Rapidly Metabolized by Heterotrophic Bacteria and Supports Multiple Trophic Levels of the Groundwater Microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0043722},
doi = {10.1128/spectrum.00437-22},
pmid = {35699474},
issn = {2165-0497},
abstract = {Pristine groundwater is a highly stable environment with microbes adapted to dark, oligotrophic conditions. Input events like heavy rainfalls can introduce the excess particulate organic matter, including surface-derived microorganisms, thereby disturbing the groundwater microbiome. Some surface-derived bacteria will not survive this translocation, leading to an input of necromass to the groundwater. Here, we investigated the effects of necromass addition to the microbial community in fractured bedrock groundwater, using groundwater mesocosms as model systems. We followed the uptake of 13C-labeled necromass by the bacterial and eukaryotic groundwater community quantitatively and over time using a complementary protein-stable and DNA-stable isotope probing approach. Necromass was rapidly depleted in the mesocosms within 4 days, accompanied by a strong decrease in Shannon diversity and a 10-fold increase in bacterial 16S rRNA gene copy numbers. Species of Flavobacterium, Massilia, Rheinheimera, Rhodoferax, and Undibacterium dominated the microbial community within 2 days and were identified as key players in necromass degradation, based on a 13C incorporation of >90% in their peptides. Their proteomes comprised various proteins for uptake and transport functions and amino acid metabolization. After 4 and 8 days, the autotrophic and mixotrophic taxa Nitrosomonas, Limnohabitans, Paucibacter, and Acidovorax increased in abundance with a 13C incorporation between 0.5% and 23%. Likewise, eukaryotes assimilated necromass-derived carbon either directly or indirectly. Our data point toward a fast and exclusive uptake of labeled necromass by a few specialists followed by a concerted action of groundwater microorganisms, including autotrophs presumably fueled by released, reduced nitrogen and sulfur compounds generated during necromass degradation. IMPORTANCE Subsurface microbiomes provide essential ecosystem services, like the generation of drinking water. These ecosystems are devoid of light-driven primary production, and microbial life is adapted to the resulting oligotrophic conditions. Modern groundwater is most vulnerable to anthropogenic and climatic impacts. Heavy rainfalls, which will increase with climate change, can result in high surface inputs into shallow aquifers by percolation or lateral flow. These inputs include terrestrial organic matter and surface-derived microbes that are not all capable to flourish in aquatic subsurface habitats. Here, we investigated the response of groundwater mesocosms to the addition of bacterial necromass, simulating event-driven surface input. We found that the groundwater microbiome responds with a rapid bloom of only a few primary degraders, followed by the activation of typical groundwater autotrophs and mixotrophs, as well as eukaryotes. Our results suggest that this multiphase strategy is essential to maintain the balance of the groundwater microbiome to provide ecosystem services.},
}
@article {pmid35699432,
year = {2022},
author = {Tlais, AZA and Lemos Junior, WJF and Filannino, P and Campanaro, S and Gobbetti, M and Di Cagno, R},
title = {How Microbiome Composition Correlates with Biochemical Changes during Sauerkraut Fermentation: a Focus on Neglected Bacterial Players and Functionalities.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0016822},
doi = {10.1128/spectrum.00168-22},
pmid = {35699432},
issn = {2165-0497},
abstract = {This study provided a new perspective on the bacterial community succession during sauerkraut fermentation, and on resulting metabolic functions. While culture-dependent methods confirmed the key role of the well-known core microbiome species, metagenomic approach (shotgun) revealed Secundilactobacillus malefermentans as a species of the core microbiome, especially during the last weeks of fermentation. Although the potentiality of S. malefermentans has not yet fully explored, it held core functional genes usually attributed to others lactic acid bacteria driving sauerkraut fermentation. Based on our results it is arguable that S. malefermentans might have a key a role during sauerkraut fermentation carried out at low temperature. Under our experimental conditions, the profile of phenolic compounds changed throughout sauerkraut fermentation. The amount of free phenolics, including free phenolic acids, increased at the beginning of the fermentation, whereas the conversion of phenolic acids into microbial derivatives was consistent during the last part of the sauerkraut fermentation. We pioneered correlating changes in the phenolics profile to changes in the microbiome, although the framework presented is still fragmentary. Annotated genes linked to the phenolic compounds metabolism (VprA and padA) were found in many core species during the whole process. A high metabolic potential for phenolics bioconversion emerged for lactobacilli and Pediococcus spp. through correlation analysis between microbiome composition and phenolics profile. IMPORTANCE Our study was not limited to describe the succession pattern of the microbial community during sauerkraut fermentation, but also revealed how some neglected bacterial players belong to the core species during sauerkrauts processing, especially at low temperature. Such species might have a role as potential starters to optimize the fermentation processes and to obtain sauerkrauts with improved and standardized nutritional and sensory features. Furthermore, our correlations between microbiome composition and phenolics profile might also represent new references for sauerkraut biotechnology, aiming to identify new metabolic drivers of potential sauerkraut functionalities. Finally, sauerkraut ecosystem is a tractable model, although with high level of complexity, and resultant ecological information might be extended to other plant ecosystems.},
}
@article {pmid35699005,
year = {2021},
author = {Bello, S and Vengoechea, JJ and Ponce-Alonso, M and Figueredo, AL and Mincholé, E and Rezusta, A and Gambó, P and Pastor, JM and Javier Galeano, and Del Campo, R},
title = {Core Microbiota in Central Lung Cancer With Streptococcal Enrichment as a Possible Diagnostic Marker.},
journal = {Archivos de bronconeumologia},
volume = {57},
number = {11},
pages = {681-689},
doi = {10.1016/j.arbr.2020.05.017},
pmid = {35699005},
issn = {1579-2129},
abstract = {BACKGROUND: Dysbiosis in lung cancer has been underexplored. The aim of this study was to define the bacterial and fungal microbiota of the bronchi in central lung cancer and to compare it with that of the oral and intestinal compartments.<br><br>METHODS: Twenty-five patients with central lung cancer and sixteen controls without antimicrobial intake during the previous month were recruited. Bacterial and fungal distribution was determined by massive sequencing of bronchial biopsies and saliva and faecal samples. Complex computational analysis was performed to define the core lung microbiota.<br><br>RESULTS: Affected and contralateral bronchi of patients have almost identical microbiota dominated by Streptococcus, whereas Pseudomonas was the dominant genera in controls. Oral and pulmonary ecosystems were significantly more similar in patients, probably due to microaspirations. Streptococcal abundance in the bronchi differentiated patients from controls according to a ROC curve analysis (90.9% sensitivity, 83.3% specificity, AUC=0.897). The saliva of patients characteristically showed a greater abundance of Streptococcus, Rothia, Gemella and Lactobacillus. The mycobiome of controls (Candida) was significantly different from that of patients (Malassezia). Cancer patients' bronchial mycobiome was similar to their saliva, but different from their contralateral bronchi.<br><br>CONCLUSIONS: The central lung cancer microbiome shows high levels of Streptococcus, and differs significantly in its composition from that of control subjects. Changes are not restricted to tumour tissue, and seem to be the consequence of microaspirations from the oral cavity. These findings could be useful in the screening and even diagnosis of this disease.},
}
@article {pmid35698733,
year = {2022},
author = {Iglesia, S and Kononov, T and Zahr, AS},
title = {A Multi-Functional Anti-Aging Moisturizer Maintains a Diverse and Balanced Facial Skin Microbiome.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jam.15663},
pmid = {35698733},
issn = {1365-2672},
abstract = {AIMS: To assess the effect of a 28-day skincare regimen in healthy female subjects on the facial skin microbiome composition and to determine if the skincare regimen including a gentle cleansing lotion, a multi-functional anti-aging moisturizer formulated with prebiotics and postbiotics at skin neutral pH, and bland sunscreen pushed the microbiome to a healthier state and improved skin aging measured by self-assessment and clinical photography.<br><br>METHODS AND RESULTS: The study protocol was in accordance with the EU Scientific Committee on Consumer Safety (SCCS) guidance and met all international standards. Twenty-five female subjects between 35 to 65 years old with Fitzpatrick skin type I - VI, moderate crow's feet wrinkles and global face photodamage were enrolled. After 28 days the skincare regimen improved microbial facial diversity and shifted the microbiota composition when compared to baseline.<br><br>CONCLUSIONS: After 28-days, the skincare regimen treatment shifted the distribution of the facial skin microbiome, positively influencing the skin microbiome diversity and balance, to promote long term skin health and protect from further skin aging.<br><br>These results suggest that incorporating prebiotics and postbiotics into a skincare regimen may have a positive impact on the facial skin microbiome in healthy women.},
}
@article {pmid35698690,
year = {2022},
author = {Anipindi, M and Bitetto, D},
title = {Diagnostic and Therapeutic Uses of the Microbiome in the Field of Oncology.},
journal = {Cureus},
volume = {14},
number = {5},
pages = {e24890},
doi = {10.7759/cureus.24890},
pmid = {35698690},
issn = {2168-8184},
abstract = {Cancer is a leading cause of death worldwide and it can affect almost every part of the human body. Effective screening and early diagnosis of cancers is extremely difficult due to the multifactorial etiology of the disease and delayed presentation of the patients. The available treatments are usually not specific to the affected organ system, leading to intolerable systemic side effects and early withdrawal from therapies. In vivo and in vitro studies have revealed an association of specific microbiome signatures with individual cancers. The cancer-related human microbiome has also been shown to affect the response of tissues to chemotherapy, immunotherapy, and radiation. This is an excellent opportunity for us to design specific screening markers using the microbiome to prevent cancers and diagnose them early. We can also develop precise treatments that can target cancer-affected specific organ systems and probably use a lesser dose of chemotherapy or radiation for the same effect. This prevents adverse effects and early cessation of treatments. However, we need further studies to exactly clarify and characterize these associations. In this review article, we focus on the association of the microbiome with individual cancers and highlight its future role in cancer screenings, diagnosis, prognosis, and treatments.},
}
@article {pmid35698622,
year = {2022},
author = {Padda, KP and Puri, A and Nguyen, NK and Philpott, TJ and Chanway, CP},
title = {Evaluating the rhizospheric and endophytic bacterial microbiome of pioneering pines in an aggregate mining ecosystem post-disturbance.},
journal = {Plant and soil},
volume = {474},
number = {1-2},
pages = {213-232},
doi = {10.1007/s11104-022-05327-2},
pmid = {35698622},
issn = {0032-079X},
abstract = {Aims: Despite little soil development and organic matter accumulation, lodgepole pine (Pinus contorta var. latifolia) consistently shows vigorous growth on bare gravel substrate of aggregate mining pits in parts of Canadian sub-boreal forests. This study aimed to investigate the bacterial microbiome of lodgepole pine trees growing at an unreclaimed gravel pit in central British Columbia and suggest their potential role in tree growth and survival following mining activity.<br><br>Methods: We characterized the diversity, taxonomic composition, and relative abundance of bacterial communities in rhizosphere and endosphere niches of pine trees regenerating at the gravel pit along with comparing them with a nearby undisturbed forested site using 16S rRNA high-throughput sequencing. Additionally, the soil and plant nutrient contents at both sites were also analyzed.<br><br>Results: Although soil N-content at the gravel pit was drastically lower than the forest site, pine tissue N-levels at both sites were identical. Beta-diversity was affected by site and niche-type, signifying that the diversity of bacterial communities harboured by pine trees was different between both sites and among various plant-niches. Bacterial alpha-diversity was comparable at both sites but differed significantly between belowground and aboveground plant-niches. In terms of composition, pine trees predominantly associated with taxa that appear plant-beneficial including phylotypes of Rhizobiaceae, Acetobacteraceae, and Beijerinckiaceae at the gravel pit and Xanthobacteraceae, Acetobacteraceae, Beijerinckiaceae and Acidobacteriaceae at the forest site.<br><br>Conclusions: Our results suggest that, following mining activity, regenerating pine trees recruit bacterial communities that could be plant-beneficial and support pine growth in an otherwise severely N-limited disturbed environment.<br><br>Supplementary Information: The online version contains supplementary material available at 10.1007/s11104-022-05327-2.},
}
@article {pmid35698614,
year = {2022},
author = {Li, Y and Bi, Y and Yang, L and Jin, K},
title = {Comparative study on intestinal microbiome composition and function in young and adult Hainan gibbons (Nomascus hainanus).},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13527},
doi = {10.7717/peerj.13527},
pmid = {35698614},
issn = {2167-8359},
abstract = {The Hainan gibbon is one of the most endangered primates in the world, with a small population size, narrow distribution range, and high inbreeding risk, which retains the risk of species extinction. To explore the composition and functional differences of the intestinal microbiome of Hainan gibbons at different ages, the faecal microbiomes of young and adult Hainan gibbons were analysed using metagenome sequencing. The results showed that the dominant phyla in the intestinal tract of young and adult Hainan gibbons were Firmicutes and Bacteroidetes, and the dominant genus was Prevotella. Linear discriminant analysis effect size analysis showed that Firmicutes, Ruminococcus, Clostridium, and Butyrivibrio were significantly more abundant in adults than in young, whereas Bacteroidetes, Proteobacteria, Prevotella, and Bacteroides were significantly more abundant in young than in adults. In terms of gene function, the adult Hainan gibbon intestinal microbiome generally harboured a higher abundance of genes related to metabolic processes, such as carbohydrate, amino acid, and nucleotide metabolism. This may be due to adaptive advantages for adult Hainan gibbons, such as stable and mature intestinal microbiome composition, which allows them to utilise diverse foods efficiently. In summary, this study helps understand the dynamic changes in the intestinal microbiome of young and adult Hainan gibbons and plays a key role in the health monitoring and rejuvenation of their population.},
}
@article {pmid35698548,
year = {2022},
author = {Shao, L and Jiang, S and Li, Y and Shi, Y and Wang, M and Liu, T and Yang, S and Ma, L},
title = {Regular Late Bedtime Significantly Affects the Skin Physiological Characteristics and Skin Bacterial Microbiome.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {15},
number = {},
pages = {1051-1063},
doi = {10.2147/CCID.S364542},
pmid = {35698548},
issn = {1178-7015},
abstract = {Background: Late bedtime is a common form of unhealthy sleep pattern in adulthood, which influences circadian rhythm, and negatively affects health. However, little is known about the effect of regular late bedtime on skin characteristics, particularly on skin microbiome.<br><br>Objective: To investigate the changes and effects of the regular late bedtime on skin physiological parameters and facial bacterial microbiome of 219 cases of Chinese women aged 18-38 years living in Shanghai.<br><br>Methods: Based on the Self-Evaluation Questionnaire, bedtime was categorized as 11:00 PM; thus, the volunteers were divided into early bedtime group (S0) and late bedtime group (S1). The physiological parameters of facial skin were measured by non-invasive instrumental methods, and the skin microbiome was analyzed by 16S rRNA high-throughput sequencing.<br><br>Results: The skin physiological parameters of the late bedtime group exhibited significant decrease in skin hydration content, skin firmness (F4) and elasticity (R2), while TEWL, sebum and wrinkle significantly increased. The result indicated that late bedtime significantly impaired the integrity of skin barrier, damaged skin structure, and disrupted water-oil balance. Furthermore, the analysis of α-diversity, Sobs, Ace and Chao index were found to significantly decrease (P < 0.05) in the late bedtime group, suggesting that late bedtime reduced both the abundance and the diversity of facial bacterial microbiota. Moreover, the abundance of Pseudomonas increased significantly, while Streptococcus, Stenotrophomonas, Acinetobacter, Haemophilus, Actinomyces and Neisseria decreased significantly. In addition, Spearman correlation analysis revealed strong correlations between the microbiota and the physiological parameters. Notably, the abundance of Pseudomonas significantly positively correlated with skin firmness and elasticity, but significantly negatively correlated with skin hemoglobin content, melanin content and skin hydration.<br><br>Conclusion: Bedtime is an important factor in maintaining skin health. Regular late bedtime not only damages the skin barrier and skin structure but also reduces the diversity and composition of facial bacterial microbiome.},
}
@article {pmid35698449,
year = {2022},
author = {Shiffler, JA and Goerger, KA and Gorres-Martens, BK},
title = {Estrogen receptor α activation modulates the gut microbiome and type 2 diabetes risk factors.},
journal = {Physiological reports},
volume = {10},
number = {11},
pages = {e15344},
doi = {10.14814/phy2.15344},
pmid = {35698449},
issn = {2051-817X},
support = {IIA-1355423//National Science Foundation/EPSCoR/ ; P20GM103443//Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health/ ; },
abstract = {Estradiol and exercise can decrease risk factors associated with type 2 diabetes (T2D) including total body weight gain and abdominal fat gain. Estradiol functions through estrogen receptor (ER) α and ERβ. Some studies suggest that activation of ERα may provide protection against T2D. Female Wistar rats were ovariectomized and fed a high-fat diet for 10 weeks and divided into the following 5 experimental groups: (1) no treatment (control), (2) exercise, (3) estradiol, (4) propylpyrazoletriyl (a selective ERα agonist), and (5) diarylpropionitrile (a selective ERβ agonist). ERα activation decreased the abundance of Firmicutes, and ERα and ERβ activation increased the abundance of Bacteroidetes. ERα activation decreased food consumption, and ERα and ERβ activation increased voluntary activity. Exercise was the only treatment to decrease the blood glucose and serum insulin levels. ERα activation, but not ERβ, increased hepatic protein expression of ACC and FAS and decreased hepatic protein expression of LPL. ERα activation also decreased hepatic mRNA expression of PPARα and PPARγ. This study elucidates the functions of estradiol by assessing specific activation of ERα and ERβ. As obesity increases the abundance of Firmicutes and decreases the abundance of Bacteroidetes, our study shows that ERα activation can restore the gut microbiome to non-obese abundances. This study further provides novel insights into ERα's role in hepatic fat metabolism via regulation of ACC, FAS, LPL, PPARα, and PPARγ.},
}
@article {pmid35698389,
year = {2022},
author = {Zheng, J and Xu, H and Fang, J and Zhang, X},
title = {Enzymatic and chemoenzymatic synthesis of human milk oligosaccharides and derivatives.},
journal = {Carbohydrate polymers},
volume = {291},
number = {},
pages = {119564},
doi = {10.1016/j.carbpol.2022.119564},
pmid = {35698389},
issn = {1879-1344},
abstract = {Human milk oligosaccharides (HMOs) are complex glycans that are the third largest solid component in human milk. It has attracted great interest in recent years due to their critical role in boosting infant health. These oligosaccharides play an important role in a variety of physiological processes, such as shaping the infant gut microbiome, preventing pathogenic infections and promoting the development of immune system. However, limited availability of HMOs hampered their use in food and medical areas. Moreover, most of the HMOs are unique to human milk and difficult to isolate. The strategies, chemical synthesis, whole-cell fermentation, and purification from human milk, have their advantages and come with their own challenges. In this review, we examined the remarkable progress that has been made in the enzymatic and chemoenzymatic synthesis of HMOs, and discussed the challenges and opportunities in large-scale synthesis of HMOs.},
}
@article {pmid35698246,
year = {2022},
author = {Ratiner, K and Shapiro, H and Goldenberg, K and Elinav, E},
title = {Time-limited diets and the gut microbiota in cardiometabolic disease.},
journal = {Journal of diabetes},
volume = {},
number = {},
pages = {},
doi = {10.1111/1753-0407.13288},
pmid = {35698246},
issn = {1753-0407},
support = {//N/A/ ; },
abstract = {In recent years, intermittent fasting (IF), including periodic fasting and time-restricted feeding (TRF), has been increasingly suggested to constitute a promising treatment for cardiometabolic diseases (CMD). A deliberate daily pause in food consumption influences the gut microbiome and the host circadian clock, resulting in improved cardiometabolic health. Understanding the molecular mechanisms by which circadian host-microbiome interactions affect host metabolism and immunity may add a potentially important dimension to effective implementation of IF diets. In this review, we discuss emerging evidence potentially linking compositional and functional alterations of the gut microbiome with IF impacts on mammalian metabolism and risk of development of hypertension, type 2 diabetes (T2D), obesity, and their long-term micro- and macrovascular complications. We highlight the challenges and unknowns in causally linking diurnal bacterial signals with dietary cues and downstream metabolic consequences and means of harnessing these signals toward future microbiome integration into precision medicine.},
}
@article {pmid35698170,
year = {2022},
author = {Wang, K and Gao, P and Geng, L and Liu, C and Zhang, J and Shu, C},
title = {Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {90},
pmid = {35698170},
issn = {2049-2618},
support = {32070511//National Natural Science Foundation of China/ ; 31972336//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The Scarabaeidae insect Protaetia brevitarsis (PB) has recently gained increasing research interest as a resource insect because its larvae can effectively convert decaying organic matter to plant growth-promoting frass with a high humic acid content and produce healthy, nutritional insect protein sources. Lignocellulose is the main component of PB larvae (PBL) feed, but PB genome annotation shows that PBL carbohydrate-active enzymes are not able to complete the lignocellulose degradation process. Thus, the mechanism by which PBL efficiently degrade lignocellulose is worthy of further study.<br><br>RESULTS: Herein, we used combined host genomic and gut metagenomic datasets to investigate the lignocellulose degradation activity of PBL, and a comprehensive reference catalog of gut microbial genes and host gut transcriptomic genes was first established. We characterized a gene repertoire comprising highly abundant and diversified lignocellulose-degrading enzymes and demonstrated that there was unique teamwork between PBL and their gut bacterial microbiota for efficient lignocellulose degradation. PBL selectively enriched lignocellulose-degrading microbial species, mainly from Firmicutes and Bacteroidetes, which are capable of producing a broad array of cellulases and hemicellulases, thus playing a major role in lignocellulosic biomass degradation. In addition, most of the lignocellulose degradation-related module sequences in the PBL microbiome were novel. PBL provide organic functional complementarity for lignocellulose degradation via their evolved strong mouthparts, alkaline midgut, and mild stable hindgut microenvironment to facilitate lignocellulosic biomass grinding, dissolving, and symbiotic microbial fermentation, respectively.<br><br>CONCLUSIONS: This work shows that PBL are a promising model to study lignocellulose degradation, which can provide highly abundant novel enzymes and relevant lignocellulose-degrading bacterial strains for biotechnological biomass conversion industries. The unique teamwork between PBL and their gut symbiotic bacterial microbiota for efficient lignocellulose degradation will expand the knowledge of holobionts and open a new beginning in the theory of holobionts. Video Abstract.},
}
@article {pmid35697586,
year = {2022},
author = {Ayeni, KI and Berry, D and Wisgrill, L and Warth, B and Ezekiel, CN},
title = {Early-life chemical exposome and gut microbiome development: African research perspectives within a global environmental health context.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2022.05.008},
pmid = {35697586},
issn = {1878-4380},
abstract = {The gut microbiome of neonates, infants, and toddlers (NITs) is very dynamic, and only begins to stabilize towards the third year of life. Within this period, exposure to xenobiotics may perturb the gut environment, thereby driving or contributing to microbial dysbiosis, which may negatively impact health into adulthood. Despite exposure of NITs globally, but especially in Africa, to copious amounts and types of xenobiotics - such as mycotoxins, pesticide residues, and heavy metals - little is known about their influence on the early-life microbiome or their effects on acute or long-term health. Within the African context, the influence of fermented foods, herbal mixtures, and the delivery environment on the early-life microbiome are often neglected, despite being potentially important factors that influence the microbiome. Consequently, data on in-depth understanding of the microbiome-exposome interactions is lacking in African cohorts. Collecting and evaluating such data is important because exposome-induced gut dysbiosis could potentially favor disease progression.},
}
@article {pmid35697549,
year = {2022},
author = {Laÿna, D and Jannel, R and Rupprecht, CDD},
title = {Living through multispecies societies: Approaching the microbiome with Imanishi Kinji.},
journal = {Endeavour},
volume = {},
number = {},
pages = {100814},
doi = {10.1016/j.endeavour.2022.100814},
pmid = {35697549},
issn = {1873-1929},
abstract = {Recent research about the microbiome points to a picture in which we, humans, are 'living through' nature, and nature itself is living in us. Our bodies are hosting-and depend on-the multiple species that constitute human microbiota. This article will discuss current research on the microbiome through the ideas of Japanese ecologist Imanishi Kinji (1902-1992). First, some of Imanishi's key ideas regarding the world of living beings and multispecies societies are presented. Second, seven types of relationships concerning the human microbiome, human beings, and the environment are explored. Third, inspired by Imanishi's work, this paper develops the idea of dynamic, porous, and complex multispecies societies in which different living beings or species are codependent on others, including microbiota and human beings.},
}
@article {pmid35676264,
year = {2022},
author = {Chen, L and Zhao, N and Cao, J and Liu, X and Xu, J and Ma, Y and Yu, Y and Zhang, X and Zhang, W and Guan, X and Yu, X and Liu, Z and Fan, Y and Wang, Y and Liang, F and Wang, D and Zhao, L and Song, M and Wang, J},
title = {Short- and long-read metagenomics expand individualized structural variations in gut microbiomes.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3175},
pmid = {35676264},
issn = {2041-1723},
support = {91857101//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Metabolome/genetics ; Metagenome ; Metagenomics ; *Nanopores ; },
abstract = {In-depth profiling of genetic variations in the gut microbiome is highly desired for understanding its functionality and impacts on host health and disease. Here, by harnessing the long read advantage provided by Oxford Nanopore Technology (ONT), we characterize fine-scale genetic variations of structural variations (SVs) in hundreds of gut microbiomes from healthy humans. ONT long reads dramatically improve the quality of metagenomic assemblies, enable reliable detection of a large, expanded set of structural variation types (notably including large insertions and inversions). We find SVs are highly distinct between individuals and stable within an individual, representing gut microbiome fingerprints that shape strain-level differentiations in function within species, complicating the associations to metabolites and host phenotypes such as blood glucose. In summary, our study strongly emphasizes that incorporating ONT reads into metagenomic analyses expands the detection scope of genetic variations, enables profiling strain-level variations in gut microbiome, and their intricate correlations with metabolome.},
}
@article {pmid35697165,
year = {2022},
author = {Huang, Y and Chen, H and Zhang, K and Lu, Y and Wu, Q and Chen, J and Li, Y and Wu, Q and Chen, Y},
title = {Extraction, purification, structural characterization, and gut microbiota relationship of polysaccharides: A review.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijbiomac.2022.06.049},
pmid = {35697165},
issn = {1879-0003},
abstract = {Intestinal dysbiosis is one of the major causes of the occurrence of metabolic syndromes, such as obesity, diabetes, nonalcoholic fatty liver disease, and cardiovascular diseases. Polysaccharide-based microbial therapeutic strategies have excellent potential in the treatment of metabolic syndromes, but the underlying regulatory mechanisms remain elusive. Identification of the internal regulatory mechanism of the gut microbiome and the interaction mechanisms involving bacteria and the host are essential to achieve precise control of the gut microbiome and obtain valuable clinical data. Polysaccharides cannot be directly digested; the behavior in the intestinal tract is considered a "bridge" between microbiota and host communication. To provide a relatively comprehensive reference for researchers in the field, we will discuss the polysaccharide extraction and purification processes and chemical and structural characteristics, focusing on the polysaccharides in gut microbiota through the immune system, gut-liver axis, gut-brain axis, energy axis interactions, and potential applications.},
}
@article {pmid35697161,
year = {2022},
author = {de Vries, LP and van de Weijer, MP and Bartels, M},
title = {The human physiology of well-being: A systematic review on the association between neurotransmitters, hormones, inflammatory markers, the microbiome and well-being.},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {104733},
doi = {10.1016/j.neubiorev.2022.104733},
pmid = {35697161},
issn = {1873-7528},
abstract = {To understand the pathways through which well-being contributes to health, we performed a systematic review according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines on the association between well-being and physiological markers in four categories, neurotransmitters, hormones, inflammatory markers, and microbiome. We identified 91 studies. Neurotransmitter studies (knumber of studies=9) reported only a possible positive association between serotonin and well-being. For the hormone studies (k=48), a lower momentary cortisol level was related to higher well-being (meta-analytic r=-.06), and a steeper diurnal slope of cortisol levels. Inflammatory marker studies (k=36) reported negative or non-significant relations with well-being, with meta-analytic estimates of respectively r=-.07 and r=-.05 for C-reactive protein and interleukin-6. Microbiome studies (k=4) reported inconsistent associations between different bacteria abundance and well-being. The results indicate possible but small roles of serotonin, cortisol, and inflammatory markers in explaining differences in well-being. The inconsistent and limited results for other markers and microbiome require further research. Future directions for a complete picture of the physiological factors underlying well-being are proposed.},
}
@article {pmid35697110,
year = {2022},
author = {Liu, J and Liu, J and Xu, B and Xu, A and Cao, S and Wei, R and Zhou, J and Jiang, M and Dong, W},
title = {Biodegradation of polyether-polyurethane foam in yellow mealworms (Tenebrio molitor) and effects on the gut microbiome.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {135263},
doi = {10.1016/j.chemosphere.2022.135263},
pmid = {35697110},
issn = {1879-1298},
abstract = {Polyurethane (PU) is one of the mass-produced recalcitrant plastics with a high environmental resistance but extremely low biodegradability. Therefore, improperly disposed PU waste adds significantly to plastic pollution, which must be addressed immediately. In recent years, there has been an increasing number of reports on plastic biodegradation in insect larvae, especially those that can feed on polyethylene and polystyrene. This study revealed that yellow mealworm (Tenebrio molitor) larvae can chew and ingest polyether-PU foams efficiently, resulting in a significant mass loss of nearly 67% after 35 days at a similar survival rate compared to when fed on bran. However, polyether-PU fragments were found in the frass of T. molitor, indicating that polyether-PU biodegradation and bioconversion in intestinal tracts were not complete. The scission of ether and urethane bonds in the polyether-PU can be evidenced by comparing polymer fragments recovered from frass with the pristine ones using Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy. Gel permeation chromatography suggested the release of low-molecular-weight oligomers as a result of the biodegradation, which also resulted in poor thermal stability of the polyether-PU foam as determined by thermogravimetric analysis. High-throughput sequencing of the gut microbiome revealed significant changes in the microbial community populations due to the polyether-PU diet, for example, an increase in the families Enterobacteriaceae and Streptococcaceae, suggesting that these microorganisms may contribute to the polyether-PU biodegradation.},
}
@article {pmid35696962,
year = {2022},
author = {Wu, H and Zheng, L and Tan, M and Li, Y and Xu, J and Yan, S and Jiang, D},
title = {Cd exposure-triggered susceptibility to Bacillus thuringiensis in Lymantria dispar involves in gut microbiota dysbiosis and hemolymph metabolic disorder.},
journal = {Ecotoxicology and environmental safety},
volume = {241},
number = {},
pages = {113763},
doi = {10.1016/j.ecoenv.2022.113763},
pmid = {35696962},
issn = {1090-2414},
abstract = {The immunotoxicity induced by heavy metals on herbivorous insects reflect the alterations of the susceptibility to entomopathogenic agents in herbivorous insects exposed to heavy metal. In the present study, the susceptibility of gypsy moth larvae to Bacillus thuringiensis under Cd treatment at low and high dosages was investigated, and the gut microbiome-hemolymph metabolome responses that affected larval disease susceptibility caused by Cd exposure were examined. Our results showed that mortality of gypsy moth larvae caused by B. thuringiensis was significantly higher in larvae pre-exposed to Cd stress, and there was a synergistic effect between Cd pre-exposure and bacterial infection. Exposure to Cd significantly decreased the abundance of several probiotics (e.g., Serratia for the low Cd dosage and Weissella, Aeroonas, and Serratia for the high Cd dosage) and increased the abundances of several pathogenic bacteria (e.g., Stenotrophomonas, Gardnerella, and Cutibacterium for the low Cd dosage and Pluralibacter and Tsukamurella for the high Cd dosage) compared to the controls. Moreover, metabolomics analysis indicated that amino acid biosynthesis and metabolism were significantly perturbed in larval hemolymph under Cd exposure at both the low and high dosages. Correlation analysis demonstrated that several altered metabolites in larval hemolymph were significantly correlated with changes in the gut microbial community. The results demonstrate that prior exposure to Cd increases the susceptibility of gypsy moth larvae to B. thuringiensis in a synergistic fashion due to gut microbiota dysbiosis and hemolymph metabolic disorder, and thus microbial-based biological control may be the best pest control strategy in heavy metal-polluted areas.},
}
@article {pmid35696589,
year = {2022},
author = {Zhang, Y and Horne, RN and Hawkins, AJ and Primo, JC and Gorbatenko, O and Dekas, AE},
title = {Geological activity shapes the microbiome in deep-subsurface aquifers by advection.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {25},
pages = {e2113985119},
doi = {10.1073/pnas.2113985119},
pmid = {35696589},
issn = {1091-6490},
abstract = {Subsurface environments host diverse microorganisms in fluid-filled fractures; however, little is known about how geological and hydrological processes shape the subterranean biosphere. Here, we sampled three flowing boreholes weekly for 10 mo in a 1478-m-deep fractured rock aquifer to study the role of fracture activity (defined as seismically or aseismically induced fracture aperture change) and advection on fluid-associated microbial community composition. We found that despite a largely stable deep-subsurface fluid microbiome, drastic community-level shifts occurred after events signifying physical changes in the permeable fracture network. The community-level shifts include the emergence of microbial families from undetected to over 50% relative abundance, as well as the replacement of the community in one borehole by the earlier community from a different borehole. Null-model analysis indicates that the observed spatial and temporal community turnover was primarily driven by stochastic processes (as opposed to deterministic processes). We, therefore, conclude that the observed community-level shifts resulted from the physical transport of distinct microbial communities from other fracture(s) that outpaced environmental selection. Given that geological activity is a major cause of fracture activity and that geological activity is ubiquitous across space and time on Earth, our findings suggest that advection induced by geological activity is a general mechanism shaping the microbial biogeography and diversity in deep-subsurface habitats across the globe.},
}
@article {pmid35696443,
year = {2022},
author = {Yang, QY and Yang, YL and Tang, YX and Qin, P and Wang, G and Xie, JY and Chen, SX and Ding, C and Huang, YW and Zhu, SJ},
title = {Bile acids promote the caveolae-associated entry of swine acute diarrhea syndrome coronavirus in porcine intestinal enteroids.},
journal = {PLoS pathogens},
volume = {18},
number = {6},
pages = {e1010620},
doi = {10.1371/journal.ppat.1010620},
pmid = {35696443},
issn = {1553-7374},
abstract = {Intestinal microbial metabolites have been increasingly recognized as important regulators of enteric viral infection. However, very little information is available about which specific microbiota-derived metabolites are crucial for swine enteric coronavirus (SECoV) infection in vivo. Using swine acute diarrhea syndrome (SADS)-CoV as a model, we were able to identify a greatly altered bile acid (BA) profile in the small intestine of infected piglets by untargeted metabolomic analysis. Using a newly established ex vivo model-the stem cell-derived porcine intestinal enteroid (PIE) culture-we demonstrated that certain BAs, cholic acid (CA) in particular, enhance SADS-CoV replication by acting on PIEs at the early phase of infection. We ruled out the possibility that CA exerts an augmenting effect on viral replication through classic farnesoid X receptor or Takeda G protein-coupled receptor 5 signaling, innate immune suppression or viral attachment. BA induced multiple cellular responses including rapid changes in caveolae-mediated endocytosis, endosomal acidification and dynamics of the endosomal/lysosomal system that are critical for SADS-CoV replication. Thus, our findings shed light on how SECoVs exploit microbiome-derived metabolite BAs to swiftly establish viral infection and accelerate replication within the intestinal microenvironment.},
}
@article {pmid35696250,
year = {2022},
author = {Niu, K and Bai, P and Yang, B and Feng, X and Qiu, F},
title = {Asiatic acid alleviates metabolism disorders in ob/ob mice: mechanistic insights.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d2fo01069k},
pmid = {35696250},
issn = {2042-650X},
abstract = {Glucolipid metabolism disorders pose a serious and global health problem, and more effective prevention and treatment methods are urgently needed. In this study, ob/ob mice were used to explore the potential mechanism explaining how asiatic acid (AA) regulates glucolipid metabolism disorders. Five-week AA treatment (30 mg kg-1) significantly improved a host of metabolic factors in ob/ob mice, including hyperglycemia, hyperlipidemia, insulin resistance, and liver histopathology. Combined analysis of untargeted liver metabolomics, liver transcriptomics, and the gut microbiome was conducted, and the results showed that AA alleviates metabolic disorders in ob/ob mice through regulating pyrimidine metabolism, activating PPAR-γ, and modulating gut microbiota. AA treatment remarkedly increased the levels of cytosine and cytidine, two crucial endogenous metabolites related to pyrimidine metabolism, which were significantly decreased in ob/ob mice. AA treatment also affected the levels of 13-S-hydroxyoctadecadienoic acid, an endogenous PPAR-γ agonist. The abundances of Lachnospiraceae_NK4A136_group and norank_f__norank_o__Clostridia_UCG-014 were increased after AA treatment. Meanwhile, correlation analysis showed that endogenous metabolites and gut microbiota were strongly correlated. These findings indicated that AA supplements might be beneficial for the prevention of metabolic disorders.},
}
@article {pmid35695806,
year = {2022},
author = {Nakano, S and Kawamoto, Y and Komatsu, Y and Saito, R and Ito, K and Yamamura, T and Harada, K and Yuki, S and Kawakubo, K and Sugiura, R and Kato, S and Hirata, K and Hirata, H and Nakajima, M and Furukawa, R and Takishin, Y and Nagai, K and Yokota, I and Ota, KH and Nakaoka, S and Kuwatani, M and Sakamoto, N},
title = {Analysis of the Pancreatic Cancer Microbiome Using Endoscopic Ultrasound-Guided Fine-Needle Aspiration-Derived Samples.},
journal = {Pancreas},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPA.0000000000002028},
pmid = {35695806},
issn = {1536-4828},
abstract = {OBJECTIVES: Most previous studies have analyzed bacteria in tumors using resected pancreatic cancer (PC) tissues, because it is difficult to obtain tissue samples from unresectable advanced PC. We aimed to determine whether minimal tissue obtained by endoscopic ultrasound-guided fine-needle aspiration is useful for microbiome analysis.<br><br>METHODS: Thirty PC and matched duodenal and stomach tissues (N = 90) were prospectively collected from 30 patients who underwent endoscopic ultrasound-guided fine-needle aspiration. Bacterial DNA was extracted, and 16S rRNA sequencing was performed. The primary outcome was the success rate of bacterial detection in tumors. Bacterial diversity and structure were investigated.<br><br>RESULTS: The bacterial detection rates were 80%, 100%, and 97% in PC, gastric, and duodenal samples, respectively. Pancreatic cancer tissues showed a lower α-diversity and a significantly different microbial structure than stomach and duodenal tissues. Proteobacteria were more abundant, whereas Firmicutes, Bacteroidetes, and Fusobacteria were less abundant in PC tissues than in stomach and duodenal tissues. Acinetobacter was more abundant in PC tissues than in stomach and duodenal tissues, and Delftia was more frequently detected in resectable PC.<br><br>CONCLUSIONS: Endoscopic ultrasound-guided fine-needle aspiration samples were valuable for PC microbiome analysis, revealing that the bacterial composition of PC is different from that of the stomach and duodenum.},
}
@article {pmid35695679,
year = {2022},
author = {Bouzid, F and Gtif, I and Alfadhli, S and Charfeddine, S and Ghorbel, W and Abdelhédi, R and Benmarzoug, R and Abid, L and Bouayed Abdelmoula, N and Elloumi, I and Masmoudi, S and Rebai, A and Kharrat, N},
title = {A potential oral microbiome signature associated with coronary artery disease in Tunisia.},
journal = {Bioscience reports},
volume = {},
number = {},
pages = {},
doi = {10.1042/BSR20220583},
pmid = {35695679},
issn = {1573-4935},
abstract = {The coronary artery disease is a chronic inflammatory disease involving genetic as well as environmental factors. Recent evidence suggests that the oral microbiome has a significant role in triggering atherosclerosis. The present study assessed the oral microbiome composition variation between coronary patients and healthy subjects in order to identify a potential pathogenic signature associated with coronary artery disease (CAD). We performed metagenomic profiling of salivary microbiomes by 16S rRNA next-generation sequencing. Oral microbiota profiling was performed for 30 individuals including 20 patients with CAD and 10 healthy individuals without carotid plaques or previous stroke or myocardial infarction.We found that oral microbial communities in patients and healthy controls are represented by similar global core oral microbiome. The predominant taxa belonged to Firmicutes (genus Streptococcus, Veillonella, Granulicatella, Selenomonas), Proteobacteria (genus Neisseria, Haemophilus), Actinobacteria (genus Rothia), Bacteroidetes (genus Prevotella, Porphyromonas) and Fusobacteria (genus Fusobacterium, Leptotrichia). More than 60% relative abundance of each sample for both CAD patients and controls is represented by three major genera including Streptococcus (24.97% and 26.33%), Veillonella (21.43% and 19.91%) and Neisseria (14.23% and 15.33%). Using penalized regression analysis, the bacterial genus Eikenella was involved as the major discriminant genus for both status and Syntax score of CAD. We also reported a significant negative correlation between Syntax score and Eikenella abundance in coronary patients' group (Spearman rho =-0.68, p= 0.00094). In conclusion, the abundance of Eikenella in oral coronary patient samples compared to controls could be a prominent pathological indicator for the development of CAD.},
}
@article {pmid35695645,
year = {2021},
author = {Swafford, AD and Khandelwal, S and Bhute, S},
title = {Potential Immune-Microbiome Interactions in Breast Cancer May Advance Treatment: What's Holding Us Back?.},
journal = {Critical reviews in immunology},
volume = {41},
number = {6},
pages = {27-42},
doi = {10.1615/CritRevImmunol.2022043153},
pmid = {35695645},
issn = {1040-8401},
abstract = {The impact of the human microbiome, the diverse collection of microorganisms that inhabit nearly every niche in the human body, in shaping the immune response to dysbiotic events is apparent if poorly understood, particularly in complex, evolving disease states such as breast cancer. The impacts can be both indirect via metabolites and immune-interactions along the skin, gut, and oral cavities where the microbial communities are most abundant, or direct in the tumor microenvironment where microbial activities can promote growth or clearance of cancerous cells. Based on reports of using gut microbial signatures to predict therapeutic efficacy, the role that gut microbes and their metabolites may play in shaping the success or failure of immunotherapy has been extensively reviewed. In this review, we dissect the evidence for the direct and distal impact of microbes on oncogenesis, tumor growth and the immune responses to combat or promote tolerance of breast cancer tumors. Implementation of robust, valid analyses and methods are lacking in the field, and we provide recommendations for researchers and clinicians to work together to characterize the micro-biome-immune-breast cancer interactions that will hopefully enable the next generation of biomarkers and targets for improving disease outcomes.},
}
@article {pmid35695644,
year = {2021},
author = {Maslinska, M and Kostyra-Grabczak, K and Królicki, L and Kwiatkowska, B},
title = {The Role of the Microbiome in Sjogren's Syndrome.},
journal = {Critical reviews in immunology},
volume = {41},
number = {6},
pages = {13-26},
doi = {10.1615/CritRevImmunol.2022043083},
pmid = {35695644},
issn = {1040-8401},
abstract = {The human microbiome is a living ecosystem existing within the host organism, determined by a balance between pathogenic microorganisms, symbionts, and commensals. The disturbance of microbiome composition-dysbiosis-often resulting in the excess of commensal numbers, may push the immune system towards activation of inflammatory and autoimmune processes. Changes in the microbiome of gut, eyes, and mouth may play a significant role in the development and course of autoimmune diseases, including primary Sjogren's syndrome. This autoimmune disease is associated with changes in the protective barrier of the epithelium, which is an important part of the antimicrobial defense. The development of pSS may be influenced by a mechanism of molecular mimicry between microbial antigens and self antigens leading to the initiation of anti-Ro60 antibody response. The knowledge of the influence of the state of microbiome on pSS may translate into the prophylaxis of the progression of dryness symptoms. The aim of this review is to present various aspects related to the human microbiome and Sjogren's syndrome.},
}
@article {pmid35695643,
year = {2021},
author = {Galant-Swafford, J},
title = {Selective Immunoglobulin A Deficiency and the Microbiome.},
journal = {Critical reviews in immunology},
volume = {41},
number = {6},
pages = {1-12},
doi = {10.1615/CritRevImmunol.2022042293},
pmid = {35695643},
issn = {1040-8401},
abstract = {Selective immunoglobulin A (IgA) deficiency (SIgAD) is the most common primary immunodeficiency disease with a prevalence of about 1:500 individuals. SIgAD is heterogeneous, though thought to be due to a defect in the differentiation of IgA-bearing B lymphocytes into IgA-secreting plasma cells which provide a first line of defense against bacterial and viral pathogens. Although SIgAD was for a long time considered asymptomatic, longitudinal studies have revealed that about 80% of patients are symptomatic and can present with a range of phenotypes including allergic disease, recurrent bacterial respiratory tract infections, gastrointestinal disorders, and autoimmune diseases. Secretory IgA has been shown to play a critical role in maintaining immune homeostasis in the gut by determining the composition of and directing the function of gut microbiota. Patients with SIgAD demonstrate gut dysbiosis with enriched proinflammatory phyla that is only partially compensated for by IgM and IgG. In this review, we will discuss what is known about the microbiome of individuals with SIgAD and how this might provide insights into therapeutics and monitoring in these patients.},
}
@article {pmid35695642,
year = {2021},
author = {Passos, GA and Chaturvedi, VK},
title = {Preface Special Issue: Microbiome-Immune System Interactions.},
journal = {Critical reviews in immunology},
volume = {41},
number = {6},
pages = {v},
doi = {10.1615/CritRevImmunol.2022043499},
pmid = {35695642},
issn = {1040-8401},
abstract = {Body homeostasis, immune response to microbial infections or vaccination, control of cancer onset or autoimmune or inflammatory diseases, as well as autism or other behavioral disorders, among other examples, are now recognized to be associated with the complex constitution of the body's microbiome. Recent findings demonstrate that the microbial composition, i.e., pathogenic, symbionts, and commensal viruses, bacteria, or yeast mainly in the gut, is strongly associated with susceptibility/resistance to several classes of diseases or its therapeutic response. This Special Issue focuses on the processes that link the human microbiome to three classes of diseases; immunodeficiency, autoimmunity, and cancer. Review articles cover aspects of the recent progress in selective immunoglobulin A (IgA) deficiency, Sjörgren's syndrome, breast cancer.},
}
@article {pmid35695620,
year = {2022},
author = {Vliex, LMM and Le, GN and Fassarella, M and Reijnders, D and Goossens, GH and Zoetendal, EG and Penders, J and Blaak, EE},
title = {Fecal carriage of vanB antibiotic resistance gene affects adipose tissue function under vancomycin use.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2083905},
doi = {10.1080/19490976.2022.2083905},
pmid = {35695620},
issn = {1949-0984},
abstract = {Detrimental consequences of antibiotic treatment may include long-lasting disruption of the gut microbiota. Previous studies found no negative effects of antibiotics on metabolic health, although individualized responses were observed. Here, we aimed to investigate the subject-specific response to vancomycin use in tissue-specific insulin sensitivity by stratifying individuals based on the presence of antibiotic resistance genes (ARGs) or opportunistic pathogens (OPs) in the baseline fecal microbiota. Quantitative Polymerase Chain Reaction (qPCR) was used to detect ARGs and OPs in DNA isolated from fecal samples of 56 males with overweight/obesity (Body Mass Index: 25-35 kg/m2) and impaired glucose metabolism (fasting plasma glucose ≥5.6 mmol/L and/or 2-hour glucose 7.8-11.1 mmol/L). A two-step hyperinsulinemic-euglycemic clamp was performed to determine tissue-specific insulin sensitivity. Abdominal subcutaneous adipose tissue (AT) gene expression was assessed using Affymetrix microarray. Gut microbial composition was determined using the Human Intestinal Tract Chip (HITChip) microarray. At baseline, the vancomycin resistance gene vanB was present in 60% of our population. In individuals that were vanB-negative at baseline, AT insulin sensitivity (insulin-mediated suppression of plasma free fatty acids) improved during vancomycin use, while it decreased among vanB-positive individuals (% change post versus baseline: 14.1 ± 5.6 vs. -6.7 ± 7.5% (p = .042)). The vancomycin-induced increase in AT insulin sensitivity was accompanied by downregulation of inflammatory pathways and enrichment of extracellular matrix remodeling pathways in AT. In the vanB-positive group, well-known vanB-carrying bacteria, Enterococcus and Streptococcus, expanded in the gut microbiome. In conclusion, microbiome composition and adipose tissue biology were differentially affected by vancomycin treatment based on fecal vanB carriage.},
}
@article {pmid35695567,
year = {2022},
author = {Tinker, K and Lipus, D and Gardiner, J and Stuckman, M and Gulliver, D},
title = {The Microbial Community and Functional Potential in the Midland Basin Reveal a Community Dominated by Both Thiosulfate and Sulfate-Reducing Microorganisms.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0004922},
doi = {10.1128/spectrum.00049-22},
pmid = {35695567},
issn = {2165-0497},
abstract = {The Permian Basin is the highest producing oil and gas reservoir in the United States. Hydrocarbon resources in this region are often accessed by unconventional extraction methods, including horizontal drilling and hydraulic fracturing. Despite the importance of the Permian Basin, there is no publicly available microbiological data from this region. We completed an analysis of Permian produced water samples to understand the dynamics present in hydraulically fractured wells in this region. We analyzed produced water samples taken from 10 wells in the Permian region of the Midland Basin using geochemical measurements, 16S rRNA gene sequencing, and metagenomic sequencing. Compared to other regions, we found that Permian Basin produced water was characterized by higher sulfate and lower total dissolved solids (TDS) concentrations, with a median of 1,110 mg/L and 107,000 mg/L. Additionally, geochemical measurements revealed the presence of frac hits, or interwell communication events where an established well is affected by the pumping of fracturing fluid into a new well. The occurrence of frac hits was supported by correlations between the microbiome and the geochemical parameters. Our 16S rRNA gene sequencing identified a produced water microbiome characterized by anaerobic, halophilic, and sulfur reducing taxa. Interestingly, sulfate and thiosulfate reducing taxa including Halanaerobium, Orenia, Marinobacter, and Desulfohalobium were the most prevalent microbiota in most wells. We further investigated the metabolic potential of microorganisms in the Permian Basin with metagenomic sequencing. We recovered 15 metagenome assembled genomes (MAGs) from seven different samples representing 6 unique well sites. These MAGs corroborated the high presence of sulfate and thiosulfate reducing genes across all wells, especially from key taxa including Halanaerobium and Orenia. The observed microbiome composition and metabolic capabilities in conjunction with the high sulfate concentrations demonstrate a high potential for hydrogen sulfide production in the Permian Basin. Additionally, evidence of frac hits suggests the possibility for the exchange of microbial cells and/or genetic information between wells. This exchange would increase the likelihood of hydrogen sulfide production and has implications for the oil and gas industry. IMPORTANCE The Permian Basin is the largest producing oil and gas region in the United States and plays a critical role supplying national energy needs. Previous work in other basins has demonstrated that the geochemistry and microbiology of hydrocarbon regions can have a major impact on well infrastructure and production. Despite that, little work has been done to understand the complex dynamics present in the Permian Basin. This study characterizes and analyzes 10 unique wells and one groundwater sample in the Permian Basin using geochemical and microbial techniques. Across all wells we found a high number of classic and thiosulfate reducers, suggesting that hydrogen sulfide production may be especially prevalent in the Permian Basin. Additionally, our analysis revealed a biogeochemical signal impacted by the presence of frac hits, or interwell communication events where an established well is affected by the pumping of fracturing fluid into a new well. This information can be utilized by the oil and gas industry to improve oil recovery efforts and minimize commercial and environmental costs.},
}
@article {pmid35695565,
year = {2022},
author = {Sun, Z and Wang, W and Li, L and Zhang, X and Ning, Z and Mayne, J and Walker, K and Stintzi, A and Figeys, D},
title = {Comprehensive Assessment of Functional Effects of Commonly Used Sugar Substitute Sweeteners on Ex Vivo Human Gut Microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0041222},
doi = {10.1128/spectrum.00412-22},
pmid = {35695565},
issn = {2165-0497},
abstract = {The composition and function of the human gut microbiome are often associated with health and disease status. Sugar substitute sweeteners are widely used food additives, although many studies using animal models have linked sweetener consumption to gut microbial changes and health issues. Whether sugar substitute sweeteners directly change the human gut microbiome functionality remains largely unknown. In this study, we systematically investigated the responses of five human gut microbiomes to 21 common sugar substitute sweeteners, using an approach combining high-throughput in vitro microbiome culturing and metaproteomic analyses to quantify functional changes in different taxa. Hierarchical clustering based on metaproteomic responses of individual microbiomes resulted in two clusters. The noncaloric artificial sweetener (NAS) cluster was composed of NASs and two sugar alcohols with shorter carbon backbones (4 or 5 carbon atoms), and the carbohydrate (CHO) cluster was composed of the remaining sugar alcohols. The metaproteomic functional responses of the CHO cluster were clustered with those of the prebiotics fructooligosaccharides and kestose. The sugar substitute sweeteners in the CHO cluster showed the ability to modulate the metabolism of Clostridia. This study provides a comprehensive evaluation of the direct effects of commonly used sugar substitute sweeteners on the functions of the human gut microbiome using a functional metaproteomic approach, improving our understanding of the roles of sugar substitute sweeteners on microbiome-associated human health and disease issues. IMPORTANCE The human gut microbiome is closely related to human health. Sugar substitute sweeteners as commonly used food additives are increasingly consumed and have potential impacts on microbiome functionality. Although many studies have evaluated the effects of a few sweeteners on gut microbiomes using animal models, the direct effect of sugar substitute sweeteners on the human gut microbiome remains largely unknown. Our results revealed that the sweetener-induced metaproteomic responses of individual microbiomes had two major patterns, which were associated with the chemical properties of the sweeteners. This study provided a comprehensive evaluation of the effects of commonly used sugar substitute sweeteners on the human gut microbiome.},
}
@article {pmid35695538,
year = {2022},
author = {Morrill, SR and Agarwal, K and Saha, S and Lewis, WG and Gilbert, NM and Lewis, AL},
title = {Models of Murine Vaginal Colonization by Anaerobically Grown Bacteria.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {183},
pages = {},
doi = {10.3791/64032},
pmid = {35695538},
issn = {1940-087X},
abstract = {The mammalian vagina can be colonized by many bacterial taxa. The human vaginal microbiome is often dominated by Lactobacillus species, but one-in-four women experience bacterial vaginosis, in which a low level of lactobacilli is accompanied by an overgrowth of diverse anaerobic bacteria. This condition has been associated with many health complications, including risks to reproductive and sexual health. While there is growing evidence showing the complex nature of microbial interactions in human vaginal health, the individual roles of these different anaerobic bacteria are not fully understood. This is complicated by the lack of adequate models to study anaerobically grown vaginal bacteria. Mouse models allow us to investigate the biology and virulence of these organisms in vivo. Other mouse models of vaginal bacterial inoculation have previously been described. Here, we describe methods for the inoculation of anaerobically grown bacteria and their viable recovery in conventionally raised C57Bl/6 mice. A new, less stressful procedural method for vaginal inoculation and washing is also described. Inoculation and viable recovery of Gardnerella are outlined in detail, and strategies for additional anaerobes such as Prevotella bivia and Fusobacterium nucleatum are discussed.},
}
@article {pmid35695500,
year = {2022},
author = {Newell, PD and Preciado, LM and Murphy, CG},
title = {A Functional Analysis of the Purine Salvage Pathway in Acetobacter fabarum.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0004122},
doi = {10.1128/jb.00041-22},
pmid = {35695500},
issn = {1098-5530},
abstract = {Acetobacter species are a major component of the gut microbiome of the fruit fly Drosophila melanogaster, a widely used model organism. While a range of studies have illuminated impacts of Acetobacter on their hosts, less is known about how association with the host impacts bacteria. A previous study identified that a purine salvage locus was commonly found in Acetobacter associated with Drosophila. In this study, we sought to verify the functions of predicted purine salvage genes in Acetobacter fabarum DsW_054 and to test the hypothesis that these bacteria can utilize host metabolites as a sole source of nitrogen. Targeted gene deletion and complementation experiments confirmed that genes encoding xanthine dehydrogenase (xdhB), urate hydroxylase (urhA), and allantoinase (puuE) were required for growth on their respective substrates as the sole source of nitrogen. Utilization of urate by Acetobacter is significant because this substrate is the major nitrogenous waste product of Drosophila, and its accumulation in the excretory system is detrimental to both flies and humans. The potential significance of our findings for host purine homeostasis and health are discussed, as are the implications for interactions among microbiota members, which differ in their capacity to utilize host metabolites for nitrogen. IMPORTANCE Acetobacter are commonly found in the gut microbiota of fruit flies, including Drosophila melanogaster. We evaluated the function of purine salvage genes in Acetobacter fabarum to test the hypothesis that this bacterium can utilize host metabolites as a source of nitrogen. Our results identify functions for three genes required for growth on urate, a major host waste product. The utilization of this and other Drosophila metabolites by gut bacteria may play a role in their survival in the host environment. Future research into how microbial metabolism impacts host purine homeostasis may lead to therapies because urate accumulation in the excretory system is detrimental to flies and humans.},
}
@article {pmid35695459,
year = {2022},
author = {Smith, CJ and Dethlefsen, L and Gardner, C and Nguyen, L and Feldman, M and Costello, EK and Kolodny, O and Relman, DA},
title = {Short-Term Dairy Product Elimination and Reintroduction Minimally Perturbs the Gut Microbiota in Self-Reported Lactose-Intolerant Adults.},
journal = {mBio},
volume = {},
number = {},
pages = {e0105122},
doi = {10.1128/mbio.01051-22},
pmid = {35695459},
issn = {2150-7511},
abstract = {An outstanding question regarding the human gut microbiota is whether and how microbiota-directed interventions influence host phenotypic traits. Here, we employed a dietary intervention to probe this question in the context of lactose intolerance. To assess the effects of dietary dairy product elimination and (re)introduction on the microbiota and host phenotype, we studied 12 self-reported mildly lactose-intolerant adults with triweekly collection of fecal samples over a 12-week study period: 2 weeks of baseline diet, 4 weeks of dairy product elimination, and 6 weeks of gradual whole cow milk (re)introduction. Of the 12 subjects, 6 reported either no dairy or only lactose-free dairy product consumption. A clinical assay for lactose intolerance, the hydrogen breath test, was performed before and after each of these three study phases, and 16S rRNA gene amplicon sequencing was performed on all fecal samples. We found that none of the subjects showed change in a clinically defined measure of lactose tolerance. Similarly, fecal microbiota structure resisted modification. Although the mean fraction of the genus Bifidobacterium, a group known to metabolize lactose, increased slightly with milk (re)introduction (from 0.0125 to 0.0206; Wilcoxon P = 0.068), the overall structure of each subject's gut microbiota remained highly individualized and largely stable in the face of diet manipulation. IMPORTANCE Lactose intolerance is a gastrointestinal disorder diagnosed with a lactose hydrogen breath test. Lifestyle changes such as diet interventions can impact the gut microbiome; however, the role of the microbiome in lactose intolerance is unclear. Our study assessed the effects of a 12-week dietary dairy product elimination and (re)introduction on the microbiome and clinical lactose intolerance status in 12 adult self-reported lactose-intolerant individuals. We found each subject's gut microbiome remained highly individualized and largely stable in the face of this diet manipulation. We also report that none of the subjects showed change in a clinically defined measure of lactose tolerance.},
}
@article {pmid35695455,
year = {2022},
author = {Ma, B and Sundararajan, S and Nadimpalli, G and France, M and McComb, E and Rutt, L and Lemme-Dumit, JM and Janofsky, E and Roskes, LS and Gajer, P and Fu, L and Yang, H and Humphrys, M and Tallon, LJ and Sadzewicz, L and Pasetti, MF and Ravel, J and Viscardi, RM},
title = {Highly Specialized Carbohydrate Metabolism Capability in Bifidobacterium Strains Associated with Intestinal Barrier Maturation in Early Preterm Infants.},
journal = {mBio},
volume = {},
number = {},
pages = {e0129922},
doi = {10.1128/mbio.01299-22},
pmid = {35695455},
issn = {2150-7511},
abstract = {"Leaky gut," or high intestinal barrier permeability, is common in preterm newborns. The role of the microbiota in this process remains largely uncharacterized. We employed both short- and long-read sequencing of the 16S rRNA gene and metagenomes to characterize the intestinal microbiome of a longitudinal cohort of 113 preterm infants born between 240/7 and 326/7 weeks of gestation. Enabled by enhanced taxonomic resolution, we found that a significantly increased abundance of Bifidobacterium breve and a diet rich in mother's breastmilk were associated with intestinal barrier maturation during the first week of life. We combined these factors using genome-resolved metagenomics and identified a highly specialized genetic capability of the Bifidobacterium strains to assimilate human milk oligosaccharides and host-derived glycoproteins. Our study proposes mechanistic roles of breastmilk feeding and intestinal microbial colonization in postnatal intestinal barrier maturation; these observations are critical toward advancing therapeutics to prevent and treat hyperpermeable gut-associated conditions, including necrotizing enterocolitis (NEC). IMPORTANCE Despite improvements in neonatal intensive care, necrotizing enterocolitis (NEC) remains a leading cause of morbidity and mortality. "Leaky gut," or intestinal barrier immaturity with elevated intestinal permeability, is the proximate cause of susceptibility to NEC. Early detection and intervention to prevent leaky gut in "at-risk" preterm neonates are critical for decreasing the risk of potentially life-threatening complications like NEC. However, the complex interactions between the developing gut microbial community, nutrition, and intestinal barrier function remain largely uncharacterized. In this study, we reveal the critical role of a sufficient breastmilk feeding volume and the specialized carbohydrate metabolism capability of Bifidobacterium in the coordinated postnatal improvement of the intestinal barrier. Determining the clinical and microbial biomarkers that drive the intestinal developmental disparity will inform early detection and novel therapeutic strategies to promote appropriate intestinal barrier maturation and prevent NEC and other adverse health conditions in preterm infants.},
}
@article {pmid35695433,
year = {2022},
author = {Reemst, K and Tims, S and Yam, KY and Mischke, M and Knol, J and Brul, S and Schipper, L and Korosi, A},
title = {The Role of the Gut Microbiota in the Effects of Early-Life Stress and Dietary Fatty Acids on Later-Life Central and Metabolic Outcomes in Mice.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0018022},
doi = {10.1128/msystems.00180-22},
pmid = {35695433},
issn = {2379-5077},
abstract = {Early-life stress (ELS) leads to increased vulnerability for mental and metabolic disorders. We have previously shown that a low dietary ω-6/ω-3 polyunsaturated fatty acid (PUFA) ratio protects against ELS-induced cognitive impairments. Due to the importance of the gut microbiota as a determinant of long-term health, we here study the impact of ELS and dietary PUFAs on the gut microbiota and how this relates to the previously described cognitive, metabolic, and fatty acid profiles. Male mice were exposed to ELS via the limited bedding and nesting paradigm (postnatal day (P)2 to P9 and to an early diet (P2 to P42) with an either high (15) or low (1) ω-6 linoleic acid to ω-3 alpha-linolenic acid ratio. 16S rRNA was sequenced and analyzed from fecal samples at P21, P42, and P180. Age impacted α- and β-diversity. ELS and diet together predicted variance in microbiota composition and affected the relative abundance of bacterial groups at several taxonomic levels in the short and long term. For example, age increased the abundance of the phyla Bacteroidetes, while it decreased Actinobacteria and Verrucomicrobia; ELS reduced the genera RC9 gut group and Rikenella, and the low ω-6/ω-3 diet reduced the abundance of the Firmicutes Erysipelotrichia. At P42, species abundance correlated with body fat mass and circulating leptin (e.g., Bacteroidetes and Proteobacteria taxa) and fatty acid profiles (e.g., Firmicutes taxa). This study gives novel insights into the impact of age, ELS, and dietary PUFAs on microbiota composition, providing potential targets for noninvasive (nutritional) modulation of ELS-induced deficits. IMPORTANCE Early-life stress (ELS) leads to increased vulnerability to develop mental and metabolic disorders; however, the biological mechanisms leading to such programming are not fully clear. Increased attention has been given to the importance of the gut microbiota as a determinant of long-term health and as a potential target for noninvasive nutritional strategies to protect against the negative impact of ELS. Here, we give novel insights into the complex interaction between ELS, early dietary ω-3 availability, and the gut microbiota across ages and provide new potential targets for (nutritional) modulation of the long-term effects of the early-life environment via the microbiota.},
}
@article {pmid35695430,
year = {2022},
author = {Fansler, RT and Zhu, W},
title = {Mind the Gap: Bridging the Divide from Sequencing Data to Empiric Phenotypes in the Human Gut Microbiota.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0020722},
doi = {10.1128/msystems.00207-22},
pmid = {35695430},
issn = {2379-5077},
abstract = {The gut microbiome exerts a powerful influence on human health and disease. Elucidating the underlying mechanisms of the microbiota's influence is hindered by the immense complexity of the gut microbial community and the glycans they forage. Despite a wealth of genomic and metagenomic sequencing information, there remains a lack of informative phenotypic measurements. Pudlo NA, Urs K, Crawford R, Pirani A, et al. (mSystems 7: e00947-21, 2022, https://doi.org/10.1128/msystems.00947-21) decode this complexity by introducing a scalable assay to measure specific carbohydrate utilization in the dominant microbiota phylum Bacteroidetes. The results reveal a mosaic structure of glycan utilization, both genetic and functional, underpinning niche construction in the human gastrointestinal tract. This Commentary highlights the significance of their findings in connection to the field's growing appreciation for competition, cooperation, and horizontal gene transfer in shaping the highly complex microbial community.},
}
@article {pmid35695425,
year = {2022},
author = {Li, J and Zou, Y and Yang, J and Li, Q and Bourne, DG and Sweet, M and Liu, C and Guo, A and Zhang, S},
title = {Cultured Bacteria Provide Insight into the Functional Potential of the Coral-Associated Microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0032722},
doi = {10.1128/msystems.00327-22},
pmid = {35695425},
issn = {2379-5077},
abstract = {Improving the availability of representative isolates from the coral microbiome is essential for investigating symbiotic mechanisms and applying beneficial microorganisms to improve coral health. However, few studies have explored the diversity of bacteria which can be isolated from a single species. Here, we isolated a total of 395 bacterial strains affiliated with 49 families across nine classes from the coral Pocillopora damicornis. Identification results showed that most of the strains represent potential novel bacterial species or genera. We also sequenced and assembled the genomes of 118 of these isolates, and then the putative functions of these isolates were identified based on genetic signatures derived from the genomes and this information was combined with isolate-specific phenotypic data. Genomic information derived from the isolates identified putative functions including nitrification and denitrification, dimethylsulfoniopropionate transformation, and supply of fixed carbon, amino acids, and B vitamins which may support their eukaryotic partners. Furthermore, the isolates contained genes associated with chemotaxis, biofilm formation, quorum sensing, membrane transport, signal transduction, and eukaryote-like repeat-containing and cell-cell attachment proteins, all of which potentially help the bacterium establish association with the coral host. Our work expands on the existing culture collection of coral-associated bacteria and provides important information on the metabolic potential of these isolates which can be used to refine understanding of the role of bacteria in coral health and are now available to be applied to novel strategies aimed at improving coral resilience through microbiome manipulation. IMPORTANCE Microbes underpin the health of corals which are the building blocks of diverse and productive reef ecosystems. Studying the culturable fraction of coral-associated bacteria has received less attention in recent times than using culture-independent molecular methods. However, the genomic and phenotypic characterization of isolated strains allows assessment of their functional role in underpinning coral health and identification of beneficial microbes for microbiome manipulation. Here, we isolated 395 bacterial strains from tissues of Pocillopora damicornis with many representing potentially novel taxa and therefore providing a significant contribution to coral microbiology through greatly enlarging the existing cultured coral-associated bacterial bank. Through analysis of the genomes obtained in this study for the coral-associated bacteria and coral host, we elucidate putative metabolic linkages and symbiotic establishment. The results of this study will help to elucidate the role of specific isolates in coral health and provide beneficial microbes for efforts aimed at improving coral health.},
}
@article {pmid35695265,
year = {2022},
author = {Chai, R and Tai, Z and Zhu, Y and Chai, C and Chen, Z and Zhu, Q},
title = {Symbiotic microorganisms: prospects for treating atopic dermatitis.},
journal = {Expert opinion on biological therapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14712598.2022.2089560},
pmid = {35695265},
issn = {1744-7682},
abstract = {INTRODUCTION: Atopic dermatitis (AD) is a common chronic recurrent inflammatory skin disease. The pathogenesis is unclear but may be related to genetic, immune, and environmental factors and abnormal skin barrier function. Symbiotic microorganisms in the gut and on the skin are associated with AD occurrence.<br><br>AREAS COVERED: We discuss the metabolism and distribution of intestinal and skin flora and review their relationship with AD, summarizing the recent applications of intestinal and skin flora in AD treatment, and discussing the prospect of research on these two human microbiota systems and their influence on AD treatment. The PubMed database was searched to identify relevant publications from 1949 to 2020 for the bibliometric analysis of atopic dermatitis and symbiotic microorganisms.<br><br>EXPERT OPINION: Many studies have suggested a potential contribution of microbes in the intestine and on the skin to AD. Bacteria living on the skin can aggravate AD by secreting numerous virulence factors. Moreover, the metabolism of intestinal flora can influence AD occurrence and development via the circulatory system. Current evidence suggests that by regulating intestinal and skin flora, AD can be treated and prevented.},
}
@article {pmid35695247,
year = {2022},
author = {Zhang, X and Yi, N},
title = {Analyzing the overall effects of the microbiome abundance data with a Bayesian predictive value approach.},
journal = {Statistical methods in medical research},
volume = {},
number = {},
pages = {9622802221107106},
doi = {10.1177/09622802221107106},
pmid = {35695247},
issn = {1477-0334},
abstract = {The microbiome abundance data is known to be over-dispersed and sparse count data. Among various zero-inflated models, zero-inflated negative binomial (ZINB) model and zero-inflated beta binomial (ZIBB) model are the methods to analyze the microbiome abundance data. ZINB and ZIBB have two sets of parameters, which are for modeling the zero-inflation part and the count part separately. Most previous methods have focused on making inferences in terms of separate case-control effect for the zero-inflation part and the count part. However, in a case-control study, the primary interest is normally focused on the inference and a single interpretation of the overall unconditional mean (also known as the overall effect) of the microbiome abundance in microbiome studies. Here, we propose a Bayesian predictive value (BPV) approach to estimate the overall effect of the microbiome abundance. This approach is implemented based on R package brms. Hence, the parameters in the models will be estimated with two Markov chain Monte Carlo (MCMC) algorithms used in Stan. We performed simulations and real data applications to compare the proposed approach and R package glmmTMB with simulation method in the estimation and inference in terms of the ratio function between the overall effects from two groups in a case-control study. The results show that the performance of the BPV approach is better than R package glmmTMB with the simulation method in terms of lower absolute biases and relative absolute biases, and coverage probability being closer to the nominal level especially when the sample size is small and zero-inflation rate is high.},
}
@article {pmid35694883,
year = {2022},
author = {Ciriza de Los Ríos, C and Aparicio Cabezudo, M and Zatarain Vallés, A and Rey, E},
title = {Practical approach to irritable bowel syndrome-diarrhea beyond low-FODMAP diet.},
journal = {Revista espanola de enfermedades digestivas : organo oficial de la Sociedad Espanola de Patologia Digestiva},
volume = {114},
number = {},
pages = {},
doi = {10.17235/reed.2022.8749/2022},
pmid = {35694883},
issn = {1130-0108},
abstract = {Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder characterized by abdominal pain and altered defecation, usually accompanied by abdominal bloating or distension. The integrated model of bidirectional interaction between the central, autonomic, enteric nervous system, the microbiome, and the gut barrier allows a better understanding of the pathophysiology of IBS, as well as consideration of potential therapeutic strategies. IBS with predominant diarrhea (IBS-D) represents a therapeutic challenge. Dietary changes or restrictions are most commonly used by patients in an attempt at symptom control. Therefore, a number of diets, especially low-FODMAP diet, have increasingly gained interest as a therapy for IBS-D or mixed IBS. However, this kind of diet, while effective, is not exempt of problems. It is therefore necessary that other therapeutic options be considered while bearing pathophysiological mechanisms and general symptom management in mind.},
}
@article {pmid35694805,
year = {2022},
author = {Rana, A and Samtiya, M and Dhewa, T and Mishra, V and Aluko, RE},
title = {Health benefits of polyphenols: A concise review.},
journal = {Journal of food biochemistry},
volume = {},
number = {},
pages = {e14264},
doi = {10.1111/jfbc.14264},
pmid = {35694805},
issn = {1745-4514},
support = {//The author (Ananya) is thankful to the DST-INSPIRE Fellowship program (Application reference number- DST/INSPIRE/03/2021/001914) India for the award of Junior Research Fellowship (financial support). The author (Mrinal Samtiya) is thankful to the Haryana state council for science innovation and technology (HSCSIT/R&amp;D/2021/461) India, for the award of Junior Research Fellowship (financial support)./ ; },
abstract = {Plants produce polyphenols, which are considered highly essential functional foods in our diet. They are classified into several groups according to their diverse chemical structures. Flavanoids, lignans, stilbenes, and phenolic acids are the four main families of polyphenols. Several in vivo and in vitro research have been conducted so far to evaluate their health consequences. Polyphenols serve a vital function in the protection of the organism from external stimuli and in eliminating reactive oxygen species (ROS), which are instigators of several illnesses. Polyphenols are present in tea, chocolate, fruits, and vegetables with the potential to positively influence human health. For instance, cocoa flavan-3-ols have been associated with a decreased risk of myocardial infarction, stroke, and diabetes. Polyphenols in the diet also help to improve lipid profiles, blood pressure, insulin resistance, and systemic inflammation. Quercetin, a flavonoid, and resveratrol, a stilbene, have been linked to improved cardiovascular health. Dietary polyphenols potential to elicit therapeutic effects might be attributed, at least in part, to a bidirectional association with the gut microbiome. This is because polyphenols are known to affect the gut microbiome composition in ways that lead to better human health. Specifically, the gut microbiome converts polyphenols into bioactive compounds that have therapeutic effects. In this review, the antioxidant, cytotoxicity, anti-inflammatory, antihypertensive, and anti-diabetic actions of polyphenols are described based on findings from in vivo and in vitro experimental trials. PRACTICAL APPLICATIONS: The non-communicable diseases (NCDs) burden has been increasing worldwide due to the sedentary lifestyle and several other factors such as smoking, junk food, etc. Scientific literature evidence supports the use of plant-based food polyphenols as therapeutic agents that could help to alleviate NCD's burden. Thus, consuming polyphenolic compounds from natural sources could be an effective solution to mitigate NCDs concerns. It is also discussed how natural antioxidants from medicinal plants might help prevent or repair damage caused by free radicals, such as oxidative stress.},
}
@article {pmid35694772,
year = {2022},
author = {Watts, PC and Mappes, T and Tukalenko, E and Mousseau, TA and Boratyński, Z and Møller, AP and Lavrinienko, A},
title = {Interpretation of gut microbiota data in the 'eye of the beholder': A commentary and re-evaluation of data from 'Impacts of radiation exposure on the bacterial and fungal microbiome of small mammals in the Chernobyl Exclusion Zone'.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.13667},
pmid = {35694772},
issn = {1365-2656},
support = {287153//Academy of Finland/ ; 324602//Academy of Finland/ ; 268670//Academy of Finland/ ; 324604//Academy of Finland/ ; //Oskar Öflund Stiftelse/ ; //Samuel Freeman Charitable Trust/ ; //Scholarship Fund of the University of Oulu/ ; //University of Oulu Graduate School doctoral programme/ ; },
abstract = {Evidence that exposure to environmental pollutants can alter the gut microbiota composition of wildlife includes studies of rodents exposed to radionuclides. Antwis et al. (2021) used amplicon sequencing to characterise the gut microbiota of four species of rodent (Myodes glareolus, Apodemus agrarius, A. flavicollis and A. sylvaticus) inhabiting the Chernobyl Exclusion Zone (CEZ) to examine possible changes in gut bacteria (microbiota) and gut fungi (mycobiota) associated with exposure to radionuclides and whether the sample type (from caecum or faeces) affected the analysis. The conclusions derived from the analyses of gut mycobiota are based on data that represent a mixture of ingested fungi (e.g. edible macrofungi, polypores, lichens and ectomycorrhizae) and gut mycobiota (e.g. microfungi and yeasts), which mask the patterns of inter- and intraspecific variation in the authentic gut mycobiota. Implying that 'faecal samples are not an accurate indicator of gut composition' creates an unnecessary controversy about faecal sampling because the comparison of samples from the caecum and faeces confounds many other possible drivers (including different animals from different locations, sampled in different years) of variation in gut microbiota. It is relevant also that Antwis et al.'s (2021) data lack statistical power to detect an effect of exposure to radionuclides on the gut microbiota because (1) all of their samples of Apodemus mice had experienced a medium or high total absorbed dose rate and (2) they did not collect samples of bank voles (M. glareolus) from replicate contaminated and uncontaminated locations. Discussion of Antwis et al.'s (2021) analysis, especially the claims presented in the Abstract, is important to prevent controversy about the outcome of research on the biological impacts of wildlife inhabiting the CEZ.},
}
@article {pmid35694769,
year = {2022},
author = {Jackson, JA and Antwis, RE and Beresford, NA and Wood, MD},
title = {Some observations on meaningful and objective inference in radioecological field studies.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.13743},
pmid = {35694769},
issn = {1365-2656},
abstract = {Anthropogenic releases of radiation are of ongoing importance for environmental protection, but the radiation doses at which natural systems begin to show effects are controversial. More certainty is required in this area to achieve optimal regulation for radioactive substances. We recently carried out a large survey (268 sampled animals and 20 sites) of the association between environmental radiation exposures and small mammal gut-associated microbiomes (fungal and bacterial) in the Chornobyl Exclusion zone (CEZ). Using individual measurements of total absorbed dose rates and a study design and analyses that accounted for spatial non-independence, we found no, or only limited, association. Watts et al. have criticised our study: for not filtering candidate non-resident components prior to our fungal microbiome analyses, for our qualified speculations on the relative merits of faecal and gut samples, and for the design of our study which they felt lacked sufficient replication. The advantage of filtering non-resident-fungal taxa is not clear and it would not have changed the null (spatially adjusted) association we found between radioactive dose and mycobiome composition because the most discriminatory fungal taxa with regard to dose were non-resident taxa. We maintain that it was legitimate for us to make qualified discussion comments on the differences in results between our faecal and gut microbiome analyses and on the relative merits of these sample types. Most importantly, the criticism of our study design by Watts et al. and the designs and analysis of their recent studies in the CEZ show a misunderstanding of the true nature of independent replication in field studies. Recognising the importance of spatial non-independence is essential in the design and analysis of radioecological field surveys.},
}
@article {pmid35694547,
year = {2022},
author = {Huang, Y and Li, D and Cai, W and Zhu, H and Shane, MI and Liao, C and Pan, S},
title = {Distribution of Vaginal and Gut Microbiome in Advanced Maternal Age.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {819802},
doi = {10.3389/fcimb.2022.819802},
pmid = {35694547},
issn = {2235-2988},
abstract = {The distribution of the microbiome in women with advanced maternal age (AMA) is poorly understood. To gain insight into this, the vaginal and gut microbiota of 62 women were sampled and sequenced using the 16S rRNA technique. These women were divided into three groups, namely, the AMA (age ≥ 35 years, n = 13) group, the non-advanced maternal age (NMA) (age < 35 years, n = 38) group, and the control group (non-pregnant healthy women, age >35 years, n = 11). We found that the alpha diversity of vaginal microbiota in the AMA group significantly increased. However, the beta diversity significantly decreased in the AMA group compared with the control group. There was no significant difference in the diversity of gut microbiota among the three groups. The distributions of microbiota were significantly different among AMA, NMA, and control groups. In vaginal microbiota, the abundance of Lactobacillus was higher in the pregnant groups. Bifidobacterium was significantly enriched in the AMA group. In gut microbiota, Prevotella bivia was significantly enriched in the AMA group. Vaginal and gut microbiota in women with AMA were noticeably different from the NMA and non-pregnant women, and this phenomenon is probably related to the increased risk of complications in women with AMA.},
}
@article {pmid35694384,
year = {2022},
author = {Ene, A and Stegman, N and Wolfe, A and Putonti, C},
title = {Genomic insights into Lactobacillus gasseri and Lactobacillus paragasseri.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13479},
doi = {10.7717/peerj.13479},
pmid = {35694384},
issn = {2167-8359},
abstract = {Background: Antimicrobial and antifungal species are essential members of the healthy human microbiota. Several different species of lactobacilli that naturally inhabit the human body have been explored for their probiotic capabilities including strains of the species Lactobacillus gasseri. However, L. gasseri (identified by 16S rRNA gene sequencing) has been associated with urogenital symptoms. Recently a new sister taxon of L. gasseri was described: L. paragasseri. L. paragasseri is also posited to have probiotic qualities.<br><br>Methods: Here, we present a genomic investigation of all (n = 79) publicly available genome assemblies for both species. These strains include isolates from the vaginal tract, gastrointestinal tract, urinary tract, oral cavity, wounds, and lungs.<br><br>Results: The two species cannot be distinguished from short-read sequencing of the 16S rRNA as the full-length gene sequences differ only by two nucleotides. Based upon average nucleotide identity (ANI), we identified 20 strains deposited as L. gasseri that are in fact representatives of L. paragasseri. Investigation of the genic content of the strains of these two species suggests recent divergence and/or frequent gene exchange between the two species. The genomes frequently harbored intact prophage sequences, including prophages identified in strains of both species. To further explore the antimicrobial potential associated with both species, genome assemblies were examined for biosynthetic gene clusters. Gassericin T and S were identified in 46 of the genome assemblies, with all L. paragasseri strains including one or both bacteriocins. This suggests that the properties once ascribed to L. gasseri may better represent the L. paragasseri species.},
}
@article {pmid35694379,
year = {2022},
author = {Koorakula, R and Ghanbari, M and Schiavinato, M and Wegl, G and Dohm, JC and Domig, KJ},
title = {Storage media and RNA extraction approaches substantially influence the recovery and integrity of livestock fecal microbial RNA.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13547},
doi = {10.7717/peerj.13547},
pmid = {35694379},
issn = {2167-8359},
abstract = {Background: There is growing interest in understanding gut microbiome dynamics, to increase the sustainability of livestock production systems and to better understand the dynamics that regulate antibiotic resistance genes (i.e., the resistome). High-throughput sequencing of RNA transcripts (RNA-seq) from microbial communities (metatranscriptome) allows an unprecedented opportunity to analyze the functional and taxonomical dynamics of the expressed microbiome and emerges as a highly informative approach. However, the isolation and preservation of high-quality RNA from livestock fecal samples remains highly challenging. This study aimed to determine the impact of the various sample storage and RNA extraction strategies on the recovery and integrity of microbial RNA extracted from selected livestock (chicken and pig) fecal samples.<br><br>Methods: Fecal samples from pigs and chicken were collected from conventional slaughterhouses. Two different storage buffers were used at two different storage temperatures. The extraction of total RNA was done using four different commercially available kits and RNA integrity/quality and concentration were measured using a Bioanalyzer 2100 system with RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA). In addition, RT-qPCR was used to assess bacterial RNA quality and the level of host RNA contamination.<br><br>Results: The quantity and quality of RNA differed by sample type (i.e., either pig or chicken) and most significantly by the extraction kit, with differences in the extraction method resulting in the least variability in pig feces samples and the most variability in chicken feces. Considering a tradeoff between the RNA yield and the RNA integrity and at the same time minimizing the amount of host RNA in the sample, a combination of storing the fecal samples in RNALater at either 4 °C (for 24 h) or -80 °C (up to 2 weeks) with extraction with PM kit (RNEasy Power Microbiome Kit) had the best performance for both chicken and pig samples.<br><br>Conclusion: Our findings provided a further emphasis on using a consistent methodology for sample storage, duration as well as a compatible RNA extraction approach. This is crucial as the impact of these technical steps can be potentially large compared with the real biological variability to be explained in microbiome and resistome studies.},
}
@article {pmid35694307,
year = {2022},
author = {Wang, W and Liu, Z and Yue, W and Zhu, L and Zhong, H and Yang, C and He, T and Wan, P and Geng, J},
title = {Mucosa-Colonizing Microbiota Correlate With Host Autophagy Signaling in Patients With Inflammatory Bowel Disease.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {875238},
doi = {10.3389/fmicb.2022.875238},
pmid = {35694307},
issn = {1664-302X},
abstract = {Both bacteria and autophagy are implicated in inflammatory bowel disease (IBD) pathogenesis. However, how bacteria crosstalk with autophagy signaling remains largely known, especially in intestinal mucosa. This study aimed to profile the internal complex autophagy signaling cascade and their external correlation with these bacteria, and consequently provide a systematic and precise target for future IBD diagnosis and therapy. We found the Ulcerative colitis (UC) patients exhibited more severe dysbiosis than the Crohn's disease (CD) patients, as represented by alpha diversity, community phenotypes, and functional annotation compared with the control population. Meanwhile, CD patients showed greater transcriptional signaling activities of autophagy, endoplasmic reticulum (ER) stress, and bile acid production. Dominant bacteria (e.g., Rhodococcus, Escherichia, Shigella, and Enterococcus) were positively correlated and low-abundance bacteria (e.g., Bacillus, Acidovorax, Acinetobacter, and Stenotrophomonas) were negatively correlated with the autophagy signaling cascade (184 autophagy genes, 52 ER stress genes, and 22 bile acid production genes). Our observations suggested UC patients showed temporary and widespread microbiota turbulence and CD patients showed processive and local autophagy activity during IBD progression. Intestinal mucosa-colonizing bacteria were correlated with the bile/ER stress/autophagy signaling axis in IBD pathogenesis.},
}
@article {pmid35694302,
year = {2022},
author = {Teklebrhan, T and Tan, Z},
title = {Diet Supplementation With Sulfur Amino Acids Modulated Fermentation Metabolome and Gut Microbiome in Goats.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {870385},
doi = {10.3389/fmicb.2022.870385},
pmid = {35694302},
issn = {1664-302X},
abstract = {Dietary amino acids shift hydrogen metabolism to an alternative hydrogen sink consisting of dissolved hydrogen sulfur (dH2S) rather than methanogenesis; and influences the fermentation metabolome and microbiome associated with particles and liquid fractions in gut regions (foregut, small intestine, and hindgut) of goats. A completely randomized block design with a total of 20 goats (5 goats per treatment) was used to conduct the trial. The goats were fed on a diet that consisted of a concentrated mixture with maize stover roughage (50:50, on a dry matter basis) and randomly assigned to one of the four treatments: without amino acid supplementation (a basal diet), a basal diet supplemented with methionine (Met), a basal diet supplemented with lysine (Lys), and a basal diet supplemented with methionine and lysine (ML). Goats fed Met alone or in combination had less acetate, acetate to propionate ratio, and greater propionate (p < 0.05) in the foregut and hindgut than those fed control or Lys. Nonetheless, the goats fed on the amino acid supplements had higher levels of branched-chain VFA (p < 0.05) in the foregut and hindgut than the control goats. Goats fed on ML had the highest ammonia (p < 0.01), followed by Met or Lys, both in the foregut and hindgut, compared with the control. Those fed on Met alone or in combination, had lower dH2, dCH4 (p < 0.01), and higher dH2S (p < 0.01) in the foregut and hindgut than the control or Lys. The goats that were fed on Met alone or in combination, had higher 16S rRNA gene copies of total bacteria, methanogens, and 18S rRNA gene copies of protozoa, fungi, and fiber-utilizing bacterial species (p < 0.01) associated with particles vs. liquid, both in the foregut and hindgut than the control goats. This study gives insights into the use of sulfur-containing amino acids, as an alternative dietary mitigation strategy of methanogenesis in ruminants and highlights the need for further research in this direction.},
}
@article {pmid35694288,
year = {2022},
author = {Khan, I and Khan, I and Kakakhel, MA and Xiaowei, Z and Ting, M and Ali, I and Fei, Y and Jianye, Z and Zhiqiang, L and Lizhe, A},
title = {Comparison of Microbial Populations in the Blood of Patients With Myocardial Infarction and Healthy Individuals.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {845038},
doi = {10.3389/fmicb.2022.845038},
pmid = {35694288},
issn = {1664-302X},
abstract = {Increased bacterial translocation in the gut and bloodstream infections are both major comorbidities of heart failure and myocardial infarction (MI). However, the alterations in the microbiome of the blood of patients with MI remain unclear. To test this hypothesis, we conducted this case-control study to explore the microbiota compositions in the blood of Chinese patients with MI. Using high-throughput Illumina HiSeq sequencing targeting the V3-V4 region of the 16S ribosomal RNA (rRNA) gene, the microbiota communities in the blood of 29 patients with MI and 29 healthy controls were examined. In addition, the relationship between the blood microbiome and clinical features of MI was investigated. This study revealed a significant reduction in alpha diversity (Shannon index) in the MI group compared with the healthy controls. Also, a significant difference was detected in the structure and richness between the patients with MI and healthy controls. The members of the phylum Actinobacteria, class Actinobacteria, order Bifdobacteriales, family Bifidobacteriaceae, and genus Bifidobacterium were significantly abundant in the MI group, while the members of the phylum Bacteroidetes, class Bacteroidia, and order Bacteroidales were significantly enriched in the healthy controls (p < 0.05). Moreover, the functional analysis revealed a significant variation between both groups. For instance, the enrichment of genes involved in the metabolism pathways of three amino acids decreased, that is, nucleotide transport and metabolism, coenzyme transport and metabolism, and lipid transport and metabolism, among others. Our study will contribute to a better knowledge of the microbiota of blood, which will further lead to improved MI diagnosis and therapy. Further study is needed to determine the role of the blood microbiota in human health and disease.},
}
@article {pmid35694216,
year = {2022},
author = {Vieira Lima, CP and Grisi, DC and Guimarães, MDCM and Salles, LP and Kruly, PC and Do, T and Dos Anjos Borges, LG and Dame-Teixeira, N},
title = {Enrichment of sulphate-reducers and depletion of butyrate-producers may be hyperglycaemia signatures in the diabetic oral microbiome.},
journal = {Journal of oral microbiology},
volume = {14},
number = {1},
pages = {2082727},
doi = {10.1080/20002297.2022.2082727},
pmid = {35694216},
issn = {2000-2297},
abstract = {Objectives: This study aimed to investigate oral microbial signatures associated with hyperglycaemia, by correlating the oral microbiome with three glycaemic markers. Potential association between clinical parameters and oral bacterial taxa that could be modulating the hyperglycaemic microbiome was also explored.<br><br>Methods: Twenty-three individuals diagnosed with type 2 Diabetes Mellitus (T2D) and presenting periodontitis were included, as well as 25 systemically and periodontally healthy ones. Fasting blood glucose, glycated haemoglobin, salivary glucose, periodontitis classification, caries experience and activity and salivary pH were evaluated. The V4 region of the 16S rRNA gene was amplified from total salivary DNA, and amplicons were sequenced (Illumina MiSeq).<br><br>Results: Hyperglycaemia was correlated with proportions of Treponema, Desulfobulbus, Phocaiecola and Saccharimonadaceae. Desulfobulbus was ubiquitous and the most enriched organism in T2D individuals (log2FC = 4). The Firmicutes/Bacteroidetes ratio was higher at alkali salivary pH than acidic pH. In the network analysis, Desulfobulbus was clustered in a negative association with caries-associated and butyrate-producing bacteria.<br><br>Conclusion: The salivary microbiome is shaped by systemic hyperglycaemia, as well as changes in the salivary pH, which may be linked to local hyperglycaemia. The enrichment of predictive biomarkers of gut dysbiosis in the salivary microbiome can reflect its capacity for impairment of hyperglycaemia.},
}
@article {pmid35694215,
year = {2022},
author = {Qin, H and Li, G and Xu, X and Zhang, C and Zhong, W and Xu, S and Yin, Y and Song, J},
title = {The role of oral microbiome in periodontitis under diabetes mellitus.},
journal = {Journal of oral microbiology},
volume = {14},
number = {1},
pages = {2078031},
doi = {10.1080/20002297.2022.2078031},
pmid = {35694215},
issn = {2000-2297},
abstract = {Periodontitis is among most common human inflammatory diseases and characterized by destruction of tooth-supporting tissues that will eventually lead to tooth loss. Diabetes mellitus (DM) is a group of metabolic disorders characterized by chronic hyperglycemia which results from defects in insulin secretion and/or insulin resistance. Numerous studies have provided evidence for the inter-relationship between DM and periodontitis that has been considered as the sixth most frequent complication of DM. However, the mechanisms are not fully understood yet. The impact of DM on periodontitis through hyperglycemia and inflammatory pathways is well described, but the effects of DM on oral microbiota remain controversial according to previous studies. Recent studies using next-generation sequencing technology indicate that DM can alter the biodiversity and composition of oral microbiome especially subgingival microbiome. This may be another mechanism by which DM risks or aggravates periodontitis. Thus, to understand the role of oral microbiome in periodontitis of diabetics and the mechanism of shifts of oral microbiome under DM would be valuable for making specific therapeutic regimens for treating periodontitis patients with DM or preventing diabetic patients from periodontitis. This article reviews the role of oral microbiome in periodontal health (symbiosis) and disease (dysbiosis), highlights the oral microbial shifts under DM and summarizes the mechanism of the shifts.},
}
@article {pmid35694162,
year = {2022},
author = {Karl, CM and Vidakovic, A and Pjevac, P and Hausmann, B and Schleining, G and Ley, JP and Berry, D and Hans, J and Wendelin, M and König, J and Somoza, V and Lieder, B},
title = {Individual Sweet Taste Perception Influences Salivary Characteristics After Orosensory Stimulation With Sucrose and Noncaloric Sweeteners.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {831726},
doi = {10.3389/fnut.2022.831726},
pmid = {35694162},
issn = {2296-861X},
abstract = {Emerging evidence points to a major role of salivary flow and viscoelastic properties in taste perception and mouthfeel. It has been proposed that sweet-tasting compounds influence salivary characteristics. However, whether perceived differences in the sensory properties of structurally diverse sweet-tasting compounds contribute to salivary flow and saliva viscoelasticity as part of mouthfeel and overall sweet taste perception remains to be clarified. In this study, we hypothesized that the sensory diversity of sweeteners would differentially change salivary characteristics in response to oral sweet taste stimulation. Therefore, we investigated salivary flow and saliva viscoelasticity from 21 healthy test subjects after orosensory stimulation with sucrose, rebaudioside M (RebM), sucralose, and neohesperidin dihydrochalcone (NHDC) in a crossover design and considered the basal level of selected influencing factors, including the basal oral microbiome. All test compounds enhanced the salivary flow rate by up to 1.51 ± 0.12 g/min for RebM compared to 1.10 ± 0.09 g/min for water within the 1st min after stimulation. The increase in flow rate was moderately correlated with the individually perceived sweet taste (r = 0.3, p < 0.01) but did not differ between the test compounds. The complex viscosity of saliva was not affected by the test compounds, but the analysis of covariance showed that it was associated (p < 0.05) with mucin 5B (Muc5B) concentration. The oral microbiome was of typical composition and diversity but was strongly individual-dependent (permutational analysis of variance (PERMANOVA): R 2 = 0.76, p < 0.001) and was not associated with changes in salivary characteristics. In conclusion, this study indicates an impact of individual sweet taste impressions on the flow rate without measurable changes in the complex viscosity of saliva, which may contribute to the overall taste perception and mouthfeel of sweet-tasting compounds.},
}
@article {pmid35693832,
year = {2022},
author = {Bourgonje, AR and Roo-Brand, G and Lisotto, P and Sadaghian Sadabad, M and Reitsema, RD and de Goffau, MC and Faber, KN and Dijkstra, G and Harmsen, HJM},
title = {Patients With Inflammatory Bowel Disease Show IgG Immune Responses Towards Specific Intestinal Bacterial Genera.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {842911},
doi = {10.3389/fimmu.2022.842911},
pmid = {35693832},
issn = {1664-3224},
abstract = {Introduction: Inflammatory bowel disease (IBD) is characterized by a disturbed gut microbiota composition. Patients with IBD have both elevated mucosal and serum levels of IgG-antibodies directed against bacterial antigens, including flagellins. In this study, we aimed to determine to which intestinal bacteria the humoral immune response is directed to in patients with IBD.<br><br>Methods: Fecal and serum samples were collected from patients with IBD (n=55) and age- and sex-matched healthy controls (n=55). Fecal samples were incubated with autologous serum and IgG-coated fractions were isolated by magnetic-activated cell sorting (MACS) and its efficiency was assessed by flow cytometry. The bacterial composition of both untreated and IgG-coated fecal samples was determined by 16S rRNA-gene Illumina sequencing.<br><br>Results: IgG-coated fecal samples were characterized by significantly lower microbial diversity compared to the fecal microbiome. Both in patients with IBD and controls, serum IgG responses were primarily directed to Streptococcus, Lactobacillus, Lactococcus, Enterococcus, Veillonella and Enterobacteriaceae, as well as against specific Lachnospiraceae bacteria, including Coprococcus and Dorea (all P<0.001), and to Ruminococcus gnavus-like bacteria (P<0.05). In contrast, serological IgG responses against typical commensal, anaerobic and colonic microbial species were rather low, e.g. to the Lachnospiraceae members Roseburia and Blautia, to Faecalibacterium, as well as to Bacteroides. Patients with IBD showed more IgG-coating of Streptococcus, Lactobacillus, and Lactococcus bacteria compared to healthy controls (all P<0.05). No differences in IgG-coated bacterial fractions were observed between Crohn's disease and ulcerative colitis, between active or non-active disease, nor between different disease locations.<br><br>Conclusion: The IgG immune response is specifically targeted at distinct intestinal bacterial genera that are typically associated with the small intestinal microbiota, whereas responses against more colonic-type commensals are lower, which was particularly the case for patients with IBD. These findings may be indicative of a strong immunological exposure to potentially pathogenic intestinal bacteria in concordance with relative immune tolerance against commensal bacteria.},
}
@article {pmid35693821,
year = {2022},
author = {Augustine, T and Al-Aghbar, MA and Al-Kowari, M and Espino-Guarch, M and van Panhuys, N},
title = {Asthma and the Missing Heritability Problem: Necessity for Multiomics Approaches in Determining Accurate Risk Profiles.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {822324},
doi = {10.3389/fimmu.2022.822324},
pmid = {35693821},
issn = {1664-3224},
abstract = {Asthma is ranked among the most common chronic conditions and has become a significant public health issue due to the recent and rapid increase in its prevalence. Investigations into the underlying genetic factors predict a heritable component for its incidence, estimated between 35% and 90% of causation. Despite the application of large-scale genome-wide association studies (GWAS) and admixture mapping approaches, the proportion of variants identified accounts for less than 15% of the observed heritability of the disease. The discrepancy between the predicted heritable component of disease and the proportion of heritability mapped to the currently identified susceptibility loci has been termed the 'missing heritability problem.' Here, we examine recent studies involving both the analysis of genetically encoded features that contribute to asthma and also the role of non-encoded heritable characteristics, including epigenetic, environmental, and developmental aspects of disease. The importance of vertical maternal microbiome transfer and the influence of maternal immune factors on fetal conditioning in the inheritance of disease are also discussed. In order to highlight the broad array of biological inputs that contribute to the sum of heritable risk factors associated with allergic disease incidence that, together, contribute to the induction of a pro-atopic state. Currently, there is a need to develop in-depth models of asthma risk factors to overcome the limitations encountered in the interpretation of GWAS results in isolation, which have resulted in the missing heritability problem. Hence, multiomics analyses need to be established considering genetic, epigenetic, and functional data to create a true systems biology-based approach for analyzing the regulatory pathways that underlie the inheritance of asthma and to develop accurate risk profiles for disease.},
}
@article {pmid35693794,
year = {2022},
author = {Son, M and Park, IS and Kim, S and Ma, HW and Kim, JH and Kim, TI and Kim, WH and Han, J and Kim, SW and Cheon, JH},
title = {Novel Potassium-Competitive Acid Blocker, Tegoprazan, Protects Against Colitis by Improving Gut Barrier Function.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {870817},
doi = {10.3389/fimmu.2022.870817},
pmid = {35693794},
issn = {1664-3224},
abstract = {Inflammatory bowel disease (IBD) is a chronic immune-mediated disorder characterized by prolonged inflammation of the gastrointestinal tract. IBD can result from gut barrier dysfunction, altered gut microbiota, and abnormal intestinal immunity induced by environmental factors in genetically susceptible individuals. Proton pump inhibitors (PPIs) such as rabeprazole are frequently employed for gastric acid inhibition. However, long-term PPI administration can alter the intestinal microbiome composition, possibly worsening IBD severity. The present study revealed that tegoprazan, a potassium-competitive acid blocker, significantly improved colitis in mice and enhanced the intestinal epithelial barrier function. Tegoprazan alleviated gut microbiota dysbiosis and enhanced the growth of Bacteroides vulgatus. In turn, B. vulgatus alleviated intestinal inflammation by inhibiting epithelial adhesion of pathogenic bacteria. Unlike rabeprazole, tegoprazan did not induce gut dysbiosis. Our findings provide novel insights into the potential role of tegoprazan as an intestinal protectant for IBD and as a therapeutic agent for gastric acid-related diseases.},
}
@article {pmid35693372,
year = {2022},
author = {Gupta, K and Tappiti, M and Nazir, AM and Koganti, B and Memon, MS and Aslam Zahid, MB and Shantha Kumar, V and Mostafa, JA},
title = {Fecal Microbiota Transplant in Recurrent Clostridium Difficile Infections: A Systematic Review.},
journal = {Cureus},
volume = {14},
number = {5},
pages = {e24754},
doi = {10.7759/cureus.24754},
pmid = {35693372},
issn = {2168-8184},
abstract = {Fecal Microbiota Transplantation (FMT) is the process of transferring the fecal microbiome from a healthy donor to an individual with repeated multiple episodes of Clostridium difficile infection. It is also known as stool transplant. Fecal microbiota transplant is effective and safe in various studies, the approval from the Food and Drug Administration (FDA) remains pending. The main objective of this systemic review is to evaluate the efficacy and safety of stool transplant in studies with only treatment groups (FMT) and studies with treatment (FMT) and antibiotic (AB) groups and previous studies. Online databases PubMed, PubMed Central, Science Direct, Google Scholar, and Embase were searched for relevant articles in the last five years (2016 to 2021) using automation tools. Following the removal of duplicates, screening of eligibility criteria, titles/abstracts, and quality appraisal were done by two authors independently. In total, seven observational studies are in this review article. Out of the seven observational studies, five are retrospective and two prospective. Two of the five retrospective and one of two prospective studies have a control group. In both the prospective studies and one retrospective study, FMT efficacy of (68% to 93%) was demonstrated in the elderly population despite high index comorbidities. In the younger individuals with inflammatory bowel disease, and efficacy of 90% or above was found. The most common side effects were minor such as fever, abdominal pain, bloating, and flatulence. In one study, two cases of aspiration events occurred attributed to the gastroscopy route of donor feces delivery. There was no statistical significance in the incidence of diseases such as (allergies, autoimmune diseases, cancer, inflammatory bowel diseases, and neurological diseases like dementia and migraine). Fecal microbiota transplantation has shown to be effective and safe in recurrent Clostridium difficile infections. Since very few pragmatic studies have demonstrated its efficacy and safety, their application is not well established. Robust studies, both observation and experiment, are required in the future to well-establish its effectiveness, safety in the treatment of recurrent Clostridium difficile infection.},
}
@article {pmid35693079,
year = {2022},
author = {Kim, OH and Choi, BY and Kim, DK and Kim, NH and Rho, JK and Sul, WJ and Lee, SW},
title = {The microbiome of lung cancer tissue and its association with pathological and clinical parameters.},
journal = {American journal of cancer research},
volume = {12},
number = {5},
pages = {2350-2362},
pmid = {35693079},
issn = {2156-6976},
abstract = {Lung cancer is the primary cause of cancer-related deaths worldwide. Recently, although the microbiome has emerged as the key modulator of the carcinogenesis, it has not been evaluated in lung cancer. Here, we evaluated the microbial composition of lung cancer tissues according to the histologic type and genetic mutation, compared it with that of the adjacent normal lung tissues, and investigated the association between the lung microbiome and clinical parameters. We collected lung tissue samples from 162 patients with non-small cell lung cancer (NSCLC, 162 cancer and 54 adjacent normal tissues), surgically resected between January 2018 and December 2019, and analyzed their microbiome using 16S rRNA gene amplicon sequencing, the QIIME2 pipeline, and statistical analyses. NSCLC tissues had significantly lower alpha diversity than the normal tissues, and their microbial composition differed according to the histologic type and cancer genetic mutation. The genera Romboutsia, Novosphingobium, Acinetobacter, and Prevotella were significantly overrepresented in NSCLC tissues. Alpha diversity steadily declined from a normal to a more advanced stage, and microbial compositional differences were noted along with recurrence. Stenotrophomonas was the most predominant genus in the NSCLC tissues of patients with recurrence. The pathways related to the tricarboxylic acid cycle and L-glutamate and L-glutamine biosynthesis were predominant in adenocarcinoma, whereas those related to purine and pyrimidine nucleotide degradation and formaldehyde assimilation were predominant in squamous cell carcinoma. Our findings suggest that the altered lung cancer microbial composition might be associated with cancer initiation and/or progression.},
}
@article {pmid35693065,
year = {2022},
author = {Ozma, MA and Abbasi, A and Akrami, S and Lahouty, M and Shahbazi, N and Ganbarov, K and Pagliano, P and Sabahi, S and Köse, Ş and Yousefi, M and Dao, S and Asgharzadeh, M and Hosseini, H and Kafil, HS},
title = {Postbiotics as the key mediators of the gut microbiota-host interactions.},
journal = {Le infezioni in medicina},
volume = {30},
number = {2},
pages = {180-193},
doi = {10.53854/liim-3002-3},
pmid = {35693065},
issn = {2532-8689},
abstract = {The priority of the Sustainable Development Goals for 2022 is to reduce all causes related to mortality. In this regard, microbial bioactive compounds with characteristics such as optimal compatibility and close interaction with the host immune system are considered a novel therapeutic approach. The fermentation process is one of the most well-known pathways involved in the natural synthesis of a diverse range of postbiotics. However, some postbiotics are a type of probiotic response behavior to environmental stimuli that usually play well-known biological roles. Also, postbiotics with unique structure and function are key mediators between intestinal microbiota and host cellular processes/metabolic pathways that play a significant role in maintaining homeostasis. By further understanding the nature of parent microbial cells, factors affecting their metabolic pathways, and the development of compatible extraction and identification methods, it is possible to achieve certain formulations of postbiotics with special efficiencies, which in turn will significantly improve the performance of health systems (especially in developing countries) toward a wide range of acute/chronic diseases. The present review aims to describe the fundamental role of postbiotics as the key mediators of the microbiota-host interactions. Besides, it presents the available current evidence regarding the interaction between postbiotics and host cells through potential cell receptors, stimulation/improvement of immune system function, and the enhancement of the composition and function of the human microbiome.},
}
@article {pmid35692444,
year = {2022},
author = {You, L and Zhou, J and Xin, Z and Hauck, JS and Na, F and Tang, J and Zhou, X and Lei, Z and Ying, B},
title = {Novel directions of precision oncology: circulating microbial DNA emerging in cancer-microbiome areas.},
journal = {Precision clinical medicine},
volume = {5},
number = {1},
pages = {pbac005},
doi = {10.1093/pcmedi/pbac005},
pmid = {35692444},
issn = {2516-1571},
abstract = {Microbiome research has extended into the cancer area in the past decades. Microbes can affect oncogenesis, progression, and treatment response through various mechanisms, including direct regulation and indirect impacts. Microbiota-associated detection methods and agents have been developed to facilitate cancer diagnosis and therapy. Additionally, the cancer microbiome has recently been redefined. The identification of intra-tumoral microbes and cancer-related circulating microbial DNA (cmDNA) has promoted novel research in the cancer-microbiome area. In this review, we define the human system of commensal microbes and the cancer microbiome from a brand-new perspective and emphasize the potential value of cmDNA as a promising biomarker in cancer liquid biopsy. We outline all existing studies on the relationship between cmDNA and cancer and the outlook for potential preclinical and clinical applications of cmDNA in cancer precision medicine, as well as critical problems to be overcome in this burgeoning field.},
}
@article {pmid35692191,
year = {2022},
author = {Shin, SY and Kim, Y and Kim, WS and Moon, JM and Lee, KM and Jung, SA and Park, H and Huh, EY and Kim, BC and Lee, SC and Choi, CH and , },
title = {Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease.},
journal = {Intestinal research},
volume = {},
number = {},
pages = {},
doi = {10.5217/ir.2021.00168},
pmid = {35692191},
issn = {1598-9100},
abstract = {Background/Aims: The fecal microbiota of Korean patients with inflammatory bowel disease (IBD) was investigated with respect to disease phenotypes and taxonomic biomarkers for diagnosis and prognosis of IBD.<br><br>Methods: Fecal samples from 70 ulcerative colitis (UC) patients, 39 Crohn's disease (CD) patients, and 100 healthy control individuals (HC) were collected. The fecal samples were amplified via polymerase chain reaction and sequenced using Illumina MiSeq. The relationships between fecal bacteria and clinical phenotypes were analyzed using the EzBioCloud database and 16S microbiome pipeline.<br><br>Results: The alpha-diversity of fecal bacteria was significantly lower in UC and CD (P<0.05) compared to that in HC. Bacterial community compositions in UC and CD were significantly different from that of HC according to Bray-Curtis dissimilarities, and there was also a difference between community composition in UC and CD (P=0.01). In UC, alpha-diversity was further decreased when the disease was more severe and the extent of disease was greater, and community composition significantly differed depending on the extent of the disease. We identified 9 biomarkers of severity and 6 biomarkers of the extent of UC. We also identified 5 biomarkers of active disease and 3 biomarkers of ileocolonic involvement in CD. Lachnospiraceae and Ruminococcus gnavus were biomarkers for better prognosis in CD.<br><br>Conclusions: The fecal microbiota profiles of IBD patients were different from those of HC, and several bacterial taxa may be used as biomarkers to determine disease phenotypes and prognosis. These data may also help discover new therapeutic targets for IBD.},
}
@article {pmid35692123,
year = {2022},
author = {Mesas, C and Martínez, R and Doello, K and Ortiz, R and López-Jurado, M and Bermúdez, F and Quiñonero, F and Prados, J and Porres, JM and Melguizo, C},
title = {In vivo antitumor activity of Euphorbia lathyris ethanol extract in colon cancer models.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {149},
number = {},
pages = {112883},
doi = {10.1016/j.biopha.2022.112883},
pmid = {35692123},
issn = {1950-6007},
abstract = {Euphorbia lathyris seeds have been used to treat various medical conditions. We previously reported that ethanolic extract from the defatted seed of Euphorbia lathyris (EE) (variety S3201) possesses a potent in vitro antitumor activity against colon cancer (CRC) cell lines. However, the effects of EE on CRC in vivo models and its possible preventive activity have not been elucidated. The aim of this study is to develop an in vivo study to corroborate its efficacy. For this purpose, two tumor induction models have been developed. In orthotopic xenograft model, it has been shown that EE reduces tumor size without hematological toxicity. The ethanolic extract induced an intense apoptosis in tumors mediated by caspase 3. Using the Azoxymethane/Dextran Sulfate Sodium model, a reduction of dysplastic polyps has been demonstrated, showing its preventive power. Furthermore, EE promoted the presence of an eubiotic microbiotal environment in the mucosa of the colon and induced an increase in antioxidant enzyme activity. This fact was accompanied by a modulation of cytokine expression that could be related to its protective mechanism. Therefore, although further experiments will be necessary to determine its applicability in the treatment of CRC, ES could be a new prevention strategy as well as treatment for this type of tumor, being a powerful candidate for future clinical trials.},
}
@article {pmid35692051,
year = {2022},
author = {van Schooten, TS and Derks, S and Jiménez-Martí, E and Carneiro, F and Figueiredo, C and Ruiz, E and Alsina, M and Molero, C and Garrido, M and Riquelme, A and Caballero, C and Lezcano, E and O'Connor, JM and Esteso, F and Farrés, J and Mas, JM and Lordick, F and Vogt, J and Cardone, A and Girvalaki, C and Cervantes, A and Fleitas, T and , },
title = {The LEGACy study: a European and Latin American consortium to identify risk factors and molecular phenotypes in gastric cancer to improve prevention strategies and personalized clinical decision making globally.},
journal = {BMC cancer},
volume = {22},
number = {1},
pages = {646},
pmid = {35692051},
issn = {1471-2407},
support = {GA825832 LEGACy//Horizon 2020 Framework Programme/ ; },
abstract = {BACKGROUND: Gastric Cancer (GC) is the fourth most deadly cancer worldwide. Enhanced understanding of its key epidemiological and molecular drivers is urgently needed to lower the incidence and improve outcomes. Furthermore, tumor biology in European (EU) and Latin American (LATAM) countries is understudied. The LEGACy study is a Horizon 2020 funded multi-institutional research approach to 1) detail the epidemiological features including risk factors of GC in current time and 2) develop cost-effective methods to identify and integrate biological biomarkers needed to guide diagnostic and therapeutic approaches with the aim of filling the knowledge gap on GC in these areas.<br><br>METHODS: This observational study has three parts that are conducted in parallel during 2019-2023 across recruiting centers from four EU and four LATAM countries: Part 1) A case-control study (800 cases and 800 controls) using questionnaires on candidate risk factors for GC, which will be correlated with clinical, demographic and epidemiological parameters. Part 2) A case-control tissue sampling study (400 cases and 400 controls) using proteome, genome, microbiome and immune analyses to characterize advanced (stage III and IV) GC. Patients in this part of the study will be followed over time to observe clinical outcomes. The first half of samples will be used as training cohort to identify the most relevant risk factors and biomarkers, which will be selected to propose cost-effective diagnostic and predictive methods that will be validated with the second half of samples. Part 3) An educational study, as part of our prevention strategy (subjects recruited from the general public) to test and disseminate knowledge on GC risk factors and symptoms by a questionnaire and informative video. Patients could be recruited for more than one of the three LEGACy studies.<br><br>DISCUSSION: The LEGACy study aims to generate novel, in-depth knowledge on the tumor biological characteristics through integrating epidemiological, multi-omics and clinical data from GC patients at an EU-LATAM partnership. During the study, cost-effective panels with potential use in clinical decision making will be developed and validated.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov Identifiers: Part 1: NCT03957031 . Part 2: NCT04015466 . Part 3: NCT04019808 .},
}
@article {pmid35692009,
year = {2022},
author = {Ye, CC and Wu, YF},
title = {[Oral microbiome dysbiosis triggers gestational periodontal disease and adverse pregnancy outcomes].},
journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology},
volume = {57},
number = {6},
pages = {635-641},
doi = {10.3760/cma.j.cn112144-20220410-00166},
pmid = {35692009},
issn = {1002-0098},
support = {81600875//National Natural Science Foundation of China/ ; },
abstract = {Oral microbiome dysbiosis, triggered by increased oral pathogens or decreased commercial bacteria, leads to oral and systemic diseases. Recent ecological events suggest that periodontal disease is a risk factor of adverse pregnancy outcomes. The oral microbiome dysbiosis is believed to be associated with oral disease and adverse pregnancy outcomes (APO). However, the pathogenic mechanisms have not yet been elucidated. In this review, we summarize the recent literature on how pregnancy associated pathogenic oral microbiome dysbiosis can trigger gestational periodontal diseases and poor birth outcomes, especially the role of periodontal pathogenic bacteria in the mechanisms of how gestational periodontal diseases cause APO, and the effect of periodontal therapy during pregnancy on birth outcomes.},
}
@article {pmid35691891,
year = {2022},
author = {Inaba, T and Yamaguchi, M and Taniguchi, A and Sato, Y and Aoyagi, T and Hori, T and Inoue, H and Fujita, M and Iwata, M and Iwata, Y and Habe, H},
title = {Evaluation of dye decolorization using anaerobic granular sludge from an expanded granular sludge bed based on spectrometric and microbiome analyses.},
journal = {The Journal of general and applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.2323/jgam.2022.04.003},
pmid = {35691891},
issn = {1349-8037},
abstract = {The decolorization of 11 dyes by granular sludge from an anaerobic expanded granular sludge bed (EGSB) reactor was evaluated. Biological decolorization of Reactive Red 21, 23, and 180, and Reactive Yellow 15, 17, and 23 in model textile wastewater was observed for the first time after a 7-day incubation (over 94% decolorization). According to the sequencing analysis of 16S rRNA gene amplicons from EGSB granular sludge, the operational taxonomic unit related to Paludibacter propionicigenes showed the highest increase in relative abundance ratios in the presence of dyes (7.12 times on average over 11 dyes) compared to those without dyes.},
}
@article {pmid35691866,
year = {2022},
author = {Newman, KL and Kamada, N},
title = {Pathogenic associations between oral and gastrointestinal diseases.},
journal = {Trends in molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molmed.2022.05.006},
pmid = {35691866},
issn = {1471-499X},
abstract = {Both periodontitis and inflammatory bowel disease (IBD) are complex chronic conditions characterized by aberrant host immune response and dysregulated microbiota. Emerging data show an association between periodontitis and IBD, including direct and indirect mechanistic links between oral and intestinal inflammation. Direct pathways include translocation of proinflammatory microbes from the oral cavity to the gut and immune priming. Indirect pathways involve systemic immune activation with possible nonspecific effects on the gut. There are limited data on the effects of periodontal disease treatment on IBD course and vice versa, but early reports suggest that treatment of periodontitis decreases systemic immune activation and that treatment of IBD is associated with periodontitis healing, underscoring the importance of recognizing and treating both conditions.},
}
@article {pmid35691626,
year = {2022},
author = {Credille, B},
title = {High-Risk Cattle Management and Stocker Calf Health: Modulation of the Bovine Respiratory Microbiome from a Systems Perspective.},
journal = {The Veterinary clinics of North America. Food animal practice},
volume = {38},
number = {2},
pages = {229-243},
doi = {10.1016/j.cvfa.2022.03.001},
pmid = {35691626},
issn = {1558-4240},
abstract = {Bovine respiratory disease (BRD) affects animals in all segments of the North American beef industry. The segmented nature of the beef industry results in the marketing of cattle that are considered to be at high risk of developing BRD. The microbiota is the complex microbial ecosystem that exists in and on the body of all animals. The respiratory tract has its unique microbiota that is shaped by many factors. Stress reduction, appropriate nutritional management, strategic use of vaccines, and antimicrobial administration targeted to the highest risk individuals have the potential to stabilize an inherently unstable microbial population and enhance calf health.},
}
@article {pmid35691185,
year = {2022},
author = {Tabei, KI and Saji, N and Ogama, N and Abe, M and Omura, S and Sakurai, T and Tomimoto, H},
title = {Quantitative analysis of white matter hyperintensity: Comparison of magnetic resonance imaging image analysis software.},
journal = {Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association},
volume = {31},
number = {8},
pages = {106555},
doi = {10.1016/j.jstrokecerebrovasdis.2022.106555},
pmid = {35691185},
issn = {1532-8511},
abstract = {OBJECTIVE: White matter hyperintensity (WMH), defined as abnormal signals on magnetic resonance imaging (MRI), is an important clinical indicator of aging and dementia. Although MRI image analysis software can automatically detect WMH, the quantitative accuracy of periventricular hyperintensity (PVH) and deep white matter hyperintensity (DWMH) is unknown.<br><br>MATERIALS AND METHODS: This study was a sub-analysis of MRI data from an ongoing hospital-based prospective cohort study (the Gimlet study). Between March 2016 and March 2017, we enrolled patients who visited our memory clinic and agreed to undergo medical assessments of cognitive function and fecal examination to study the gut microbiome. Participants with a history of stroke were excluded. WMH was independently quantitatively analyzed using two MRI imaging analysis software modalities: SNIPER and FUSION. Intraclass correlation coefficients and the mean difference in volume were calculated and compared between modalities.<br><br>RESULTS: The data of 87 patients (49 women, mean age 74.8 ± 7.9 years) were analyzed. Both total WMH and DWMH volumes obtained using FUSION were greater (p < 0.001), and PVH volume was smaller (p < 0.001) than those obtained using SNIPER. Intraclass correlation coefficients for the lesion measurements of WMH, PVH, and DWMH between the different software were 0.726 (p < 0.001), 0.673 (p < 0.001), and 0.048 (p = 0.231), respectively.<br><br>CONCLUSIONS: There were significant differences in the quantitative data of WMH between the two MRI imaging analysis software modalities. Thus, care should be taken for quantitative assessments of WMH.},
}
@article {pmid35691183,
year = {2022},
author = {Apolzan, JW and Stein, JA and Rood, JC and Beyl, RA and Yang, S and Greenway, FL and Lieberman, HR},
title = {Applied nutritional investigationEffects of acute arginine supplementation on neuroendocrine, metabolic, cardiovascular, and mood outcomes in younger men: A double-blind, placebo-controlled trial.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {101},
number = {},
pages = {111658},
doi = {10.1016/j.nut.2022.111658},
pmid = {35691183},
issn = {1873-1244},
abstract = {OBJECTIVES: Arginine is an amino-acid supplement and precursor for nitric-oxide synthesis, which affects various biologic processes. The objective of this study was to determine the effects of arginine supplementation on growth hormone (GH) and metabolic parameters.<br><br>METHODS: Thirty physically active, healthy men (age 18-39 y; body mass index: 18.5-25 kg/m2) were randomized in a double-blind, placebo-controlled, crossover trial. Arginine (10 g) and placebo (0 g) beverages were consumed after an overnight fast. Blood samples were collected at baseline and 1.5, 3.0, and 24 h after supplementation. The primary outcomes were serum GH and metabolomics. Also, amino acids, glucose, insulin, triacylglycerols, thyroid hormones, testosterone, cortisol, dehydroepiandrosterone, and mood state were assessed. Individuals with detectable increases in GH were analyzed separately (responders: n = 16; < 0.05 ng/mL at 1.5 h). Repeated-measure analyses of variance estimated the treatment effects at each timepoint.<br><br>RESULTS: Arginine levels increased at 1.5 h (146%) and 3.0 h (95%; P ≤ 0.001) and GH (193%) and thyroid-stimulating hormone (TSH; 10%) levels at 24 h (P < 0.05) after arginine versus placebo consumption. Arginine versus placebo increased glucose levels at 1.5 h (5%) and 3.0 h (3%; P ≤ 0.001). Arginine versus placebo did not affect other dependent measures, including mood state (P > 0.05), but changes in the urea, glutamate, and citric-acid pathways were observed. Among responders, arginine versus placebo increased GH at 1.5 h (37%), glucose at 1.5 h (4%) and 3.0 h (4%), and TSH at 24 h (9%; P < 0.05). Responders had higher levels of benzoate metabolites at baseline and 1.5 h, and an unknown compound (X-16124) at baseline, 1.5 h, and 24 h that corresponds to a class of gut microbes (P < 0.05).<br><br>CONCLUSIONS: Arginine supplementation modestly increased GH, glucose, and TSH levels in younger men. Responders had higher benzoate metabolites and an unknown analyte attributed to the gut microbiome. Future studies should examine whether the increased prevalence of these gut microorganisms corresponds with GH response after arginine supplementation.},
}
@article {pmid35690527,
year = {2022},
author = {Huang, C and Yi, P and Zhu, M and Zhou, W and Zhang, B and Yi, X and Long, H and Zhang, G and Wu, H and Tsokos, GC and Zhao, M and Lu, Q},
title = {Safety and efficacy of fecal microbiota transplantation for treatment of systemic lupus erythematosus: An EXPLORER trial.},
journal = {Journal of autoimmunity},
volume = {},
number = {},
pages = {102844},
doi = {10.1016/j.jaut.2022.102844},
pmid = {35690527},
issn = {1095-9157},
abstract = {Gut microbiota dysbiosis is involved in the development of systemic lupus erythematosus (SLE). The safety and efficacy of fecal microbiota transplantation (FMT) for the treatment of SLE patients has not been explored. In this 12-week, single-arm pilot clinical trial of oral encapsulated fecal microbiome from healthy donors to patients with active SLE, we aimed to evaluate the safety and efficacy of FMT in patients with SLE (ChiCTR2000036352). 20 SLE patients with SLEDAI ≥6 were recruited. FMT was administered once a week for three consecutive weeks along with standard treatment and the patients were followed for 12 weeks. Safety was evaluated throughout the trial. The primary endpoint was the SLE Responder Index-4 (SRI-4) at week 12. Microbiome composition, levels of short chain fatty acids (SCFAs) in the gut and of cytokines in the sera were measured along with lymphocyte phenotyping. No serious adverse events were observed after FMT. At week 12, the SRI-4 response rate was 42.12%, and significant reductions in the SLEDAI-2K scores and the level of serum anti-dsDNA antibody were observed compared to baseline. Significant enrichment of SCFAs-producing bacterial taxa and reduction of inflammation-related bacterial taxa were observed, along with increased production of SCFAs in the gut and reduced levels of IL-6 and CD4+ memory/naïve ratio in the peripheral blood. Furthermore, SRI-4 responding patients displayed specific microbiota signatures both before and after FMT. The first clinical trial of FMT in active SLE patients provide supportive evidence that FMT might be a feasible, safe, and potentially effective therapy in SLE patients by modifying the gut microbiome and its metabolic profile.},
}
@article {pmid35690468,
year = {2022},
author = {Mueller, JL and Goldstein, AM},
title = {The science of Hirschsprung disease: What we know and where we are headed.},
journal = {Seminars in pediatric surgery},
volume = {31},
number = {2},
pages = {151157},
doi = {10.1016/j.sempedsurg.2022.151157},
pmid = {35690468},
issn = {1532-9453},
abstract = {The enteric nervous system (ENS) is a rich network of neurons and glial cells that comprise the gastrointestinal tract's intrinsic nervous system and are responsible for controlling numerous complex functions, including digestion, transit, secretion, barrier function, and maintenance of a healthy microbiome. Development of a functional ENS relies on the coordinated interaction between enteric neural crest-derived cells and their environment as the neural crest-derived cells migrate rostrocaudally along the embryonic gut mesenchyme. Congenital or acquired disruption of ENS development leads to various neurointestinal diseases. Hirschsprung disease is a congenital neurocristopathy, a disease of the neural crest. It is characterized by a variable length of distal colonic aganglionosis due to a failure in enteric neural crest-derived cell proliferation, migration, differentiation, and/or survival. In this review, we will review the science of Hirschsprung disease, targeting an audience of pediatric surgeons. We will discuss the basic biology of normal ENS development, as well as what goes awry in ENS development in Hirschsprung disease. We will review animal models that have been integral to studying this disease, as well as current hot topics and future research, including genetic risk profiling, stem cell therapy, non-invasive diagnostic techniques, single-cell sequencing techniques, and genotype-phenotype correlation.},
}
@article {pmid35690459,
year = {2022},
author = {Lewit, RA and Kuruvilla, KP and Fu, M and Gosain, A},
title = {Current understanding of Hirschsprung-associated enterocolitis: Pathogenesis, diagnosis and treatment.},
journal = {Seminars in pediatric surgery},
volume = {31},
number = {2},
pages = {151162},
doi = {10.1016/j.sempedsurg.2022.151162},
pmid = {35690459},
issn = {1532-9453},
abstract = {Hirschsprung-associated enterocolitis (HAEC) was described in 1886 by Harald Hirschsprung and is a potentially deadly complication of Hirschsprung Disease. HAEC is classically characterized by abdominal distension, fever, and diarrhea, although there can be a variety of other associated symptoms, including colicky abdominal pain, lethargy, and the passage of blood-stained stools. HAEC occurs both pre-operatively and post-operatively, is the presenting symptom of HSCR in up to 25% of infants and varies in overall incidence from 20 to 60%. This article reviews our current understanding of HAEC pathogenesis, diagnosis, and treatment with discussion of areas of ongoing research, controversy, and future investigation.},
}
@article {pmid35690059,
year = {2022},
author = {Wilmanski, T and Kornilov, SA and Diener, C and Conomos, MP and Lovejoy, JC and Sebastiani, P and Orwoll, ES and Hood, L and Price, ND and Rappaport, N and Magis, AT and Gibbons, SM},
title = {Heterogeneity in statin responses explained by variation in the human gut microbiome.},
journal = {Med (New York, N.Y.)},
volume = {3},
number = {6},
pages = {388-405.e6},
doi = {10.1016/j.medj.2022.04.007},
pmid = {35690059},
issn = {2666-6340},
abstract = {BACKGROUND: Statins remain one of the most prescribed medications worldwide. While effective in decreasing atherosclerotic cardiovascular disease risk, statin use is associated with adverse effects for a subset of patients, including disrupted metabolic control and increased risk of type 2 diabetes.<br><br>METHODS: We investigated the potential role of the gut microbiome in modifying patient responses to statin therapy across two independent cohorts (discovery n = 1,848, validation n = 991). Microbiome composition was assessed in these cohorts using stool 16S rRNA amplicon and shotgun metagenomic sequencing, respectively. Microbiome associations with markers of statin on-target and adverse effects were tested via a covariate-adjusted interaction analysis framework, utilizing blood metabolomics, clinical laboratory tests, genomics, and demographics data.<br><br>FINDINGS: The hydrolyzed substrate for 3-hydroxy-3-methylglutarate-coenzyme-A (HMG-CoA) reductase, HMG, emerged as a promising marker for statin on-target effects in cross-sectional cohorts. Plasma HMG levels reflected both statin therapy intensity and known genetic markers for variable statin responses. Through exploring gut microbiome associations between blood-derived measures of statin effectiveness and adverse metabolic effects of statins, we find that heterogeneity in statin responses was consistently associated with variation in the gut microbiome across two independent cohorts. A Bacteroides-enriched and diversity-depleted gut microbiome was associated with more intense statin responses, both in terms of on-target and adverse effects.<br><br>CONCLUSIONS: With further study and refinement, gut microbiome monitoring may help inform precision statin treatment.<br><br>FUNDING: This research was supported by the M.J. Murdock Charitable Trust, WRF, NAM Catalyst Award, and NIH grant U19AG023122 awarded by the NIA.},
}
@article {pmid35690054,
year = {2022},
author = {Eckel, RH and Bruce, KD},
title = {Statins, gut microbiome, LDL-C, glucose intolerance: Personalized medicine timely?.},
journal = {Med (New York, N.Y.)},
volume = {3},
number = {6},
pages = {355-357},
doi = {10.1016/j.medj.2022.05.006},
pmid = {35690054},
issn = {2666-6340},
abstract = {Statins are a mainstay in reducing cardiovascular disease risk by reducing circulating levels of plasma LDL-C. In this issue of Med, Wilmanski et al. demonstrate how the composition of the gut microbiome influences the pharmacological benefits and risks of statin therapy, an exciting additional step in personalized medicine.},
}
@article {pmid35690000,
year = {2022},
author = {Jia, L and Hsu, CY and Zhang, X and Li, X and Schilling, MW and Peebles, ED and Kiess, AS and Zhang, L},
title = {Effects of dietary bacitracin or Bacillus subtilis on the woody breast myopathy-associated gut microbiome of Eimeria spp. challenged and unchallenged broilers.},
journal = {Poultry science},
volume = {101},
number = {8},
pages = {101960},
doi = {10.1016/j.psj.2022.101960},
pmid = {35690000},
issn = {1525-3171},
abstract = {Study suggested that dysbiosis of the gut microbiota may affect the etiology of woody breast (WB). In the current study, the cecal microbiota and WB in chickens fed three different diets were investigated. A total of 504 male chicks were used in a randomized complete block design with a 3 (Diet) × 2 (Challenge) factorial arrangement of treatments with 6 replicates per treatment, 6 treatments per block, and 14 birds per treatment. The experimental diets were a control diet (corn-soybean meal basal diet), an antibiotic diet (basal diet + 6.075 mg bacitracin/kg feed), and a probiotic diet (basal diet + 2.2 × 108 CFU Bacillus subtilis PB6/kg feed). On d 14, birds that were assigned to the challenge treatment received a 20 × live cocci vaccine. On d 41, breast muscle hardness in live birds was palpated and grouped into normal (NB) and WB phenotypes. Cecal contents were collected and their bacterial compositions were analyzed and compared. The genomic DNA of the cecal contents was extracted and the V3 and V4 regions of 16S rRNA gene were amplified and sequenced via an Illumina MiSeq platform. There were no differences (P > 0.05) in Shannon and Chao 1 indexes between the challenges, diets, and phenotypes (NB vs. WB). However, there was a difference (P = 0.001) in the beta diversity of the samples between the challenged and nonchallenged groups. Relative bacterial abundance differed (false discovery rate, FDR < 0.05) between the challenge treatments, but there were no significant differences (FDR > 0.05) among the three diets or two phenotypes. Predicted energy metabolism, nucleotide metabolism, and amino acid and coenzyme biosynthesis activities only differed (q-value < 0.05) between challenged and nonchallenged groups. The cocci challenge altered the gut microbial composition on Butyricicoccus pullicaecorum, Sporobacter termitidis, and Subdoligranulum variabile, but the dietary antibiotic and probiotic treatments did not impact gut microbial composition. No strong association was found between WB myopathy and gut microbial composition in this study.},
}
@article {pmid35689995,
year = {2022},
author = {Gyawali, I and Zeng, Y and Zhou, J and Li, J and Wu, T and Shu, G and Jiang, Q and Zhu, C},
title = {Effect of novel Lactobacillus paracaesi microcapsule on growth performance, gut health and microbiome community of broiler chickens.},
journal = {Poultry science},
volume = {101},
number = {8},
pages = {101912},
doi = {10.1016/j.psj.2022.101912},
pmid = {35689995},
issn = {1525-3171},
abstract = {The beneficial action of probiotics is questioned time and again due to the loss of their survivability under gastrointestinal conditions, particularly gastric acid. In this experiment, a probiotic species was encapsulated to improve its delivery to the distal parts, and its effects on production performance, gut health, and microbial profile in broilers were investigated. A total of 240 Arbor acres (AA) broilers were randomly allotted into 3 treatments with 8 replicate pens per treatment and 10 broilers in each pen for 42 d. Dietary treatments were 1) basal feed without any additives (CON), 2) CON+15 ppm Virginiamycin (ANT), and 3) CON+500 ppm encapsulated Lactobacillus paracaesi (ELP). The result showed that the addition of ELP to the feed did not affect growth performance and carcass characteristics significantly. However, ELP increased the ratio of villus height to crypt depth (P < 0.05) and mRNA expression of ZO-1 (P < 0.05) relative to the CON or ANT group. Similarly, qPCR showed that dietary supplementation of ELP raised gene expression of the anti-inflammatory cytokine and tended to decrease proinflammatory cytokines resulting improve in immunity. Moreover, chicks fed with ELP had lower malondialdehyde (MDA) (P < 0.05) than CON and lower reactive oxygen species (ROS) (P < 0.05) level than ANT in serum. In contrast, the total antioxidant capacity (TAOC) level was tended to increase. The ammonia level of ileum and cecum chyme was decreased (P < 0.05) in the ELP group than CON while the level of propionic acid of cecal content was increased (P < 0.05). 16S rRNA sequencing revealed the dietary treatment modulated the diversity and composition of cecal microflora. At the phylum level, Bacteroidetes was enriched, and Proteobacteria was depleted in the ELP group. At the genus level, ELP increased Bacteroides (P < 0.05) compared to control. The results indicate that oral delivery of probiotics via microcapsule could impart beneficial effects on birds and be used as an alternative to antibiotics.},
}
@article {pmid35689993,
year = {2022},
author = {Wang, Y and Zhang, Y and Pan, T and Lin, H and Zhou, Y},
title = {Metabolic differences of the oral microbiome related to dental caries - A pilot study.},
journal = {Archives of oral biology},
volume = {141},
number = {},
pages = {105471},
doi = {10.1016/j.archoralbio.2022.105471},
pmid = {35689993},
issn = {1879-1506},
abstract = {OBJECTIVE: We aimed to investigate the composition and functions discrepancy of supragingival plaque associated with active deciduous teeth caries in mixed dentitions.<br><br>DESIGN: Thirty-three subjects with mixed dentition participated in this study. Children with deciduous teeth caries (dt ≥ 3) were recruited to the caries group, whereas children without deciduous teeth caries (dt = 0) were recruited to the caries-free group. Plaque were collected from deciduous teeth surface and permanent teeth surface respectively. A total of 66 samples of dental plaque were collected and conserved. Illumina 16S rRNA sequencing and diversity analysis were performed for microbiome. Untargeted liquid chromatograph-mass (LC-MS) and partial least squares discriminant analysis were performed for metabolome.<br><br>RESULTS: A dominant microbiome of 8 phyla and 22 genera were detected. The alpha diversity indices did not detect differences between the caries and caries-free groups (p > 0.05). Beta diversity analysis showed that the microbiota composition was similar between subgroups. Comparative analysis at genus level did not detect difference between caries and caries-free subgroups. The metabolomics analysis yielded 419 biochemical metabolites, 56 of which were related to caries status. Metabolites in glucose metabolism and byproducts of oxidative stress were identified as related to dental caries in mixed dentition. Dominant bacteria are positively correlated with metabolites, such as Streptococcus and organic acids.<br><br>CONCLUSIONS: The upgrade of glucose metabolism and oxidative stress was observed in caries status. Functions discrepancy of oral microbiome may be more pronounced than the composition of oral microbiome with active dental caries in mixed dentitions.},
}
@article {pmid35689685,
year = {2022},
author = {Mills, JG and Selway, CA and Thomas, T and Weyrich, LS and Lowe, AJ},
title = {Schoolyard Biodiversity Determines Short-Term Recovery of Disturbed Skin Microbiota in Children.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {35689685},
issn = {1432-184X},
abstract = {Creating biodiverse urban habitat has been proposed, with growing empirical support, as an intervention for increasing human microbial diversity and reducing associated diseases. However, ecological understanding of urban biodiversity interventions on human skin microbiota remains limited. Here, we experimentally test the hypotheses that disturbed skin microbiota recover better in outdoor schoolyard environments and that greater biodiversity provides a greater response. Repeating the experiment three times, we disturbed skin microbiota of fifty-seven healthy 10-to-11-year-old students with a skin swab (i.e., cleaning), then exposed them to one school environment-either a 'classroom' (n = 20), 'sports field' (n = 14), or biodiverse 'forest' (n = 23)-for 45 min. Another skin swab followed the exposure to compare 'before' and 'after' microbial communities. After 45 min, the disturbance immediately followed by outdoor exposure, especially the 'forest', had an enriching and diversifying effect on skin microbiota, while 'classroom' exposure homogenised inter-personal variability. Each effect compounded over consecutive days indicating longer-term exposure outcomes. The experimental disturbance also reduced the core skin microbiota, and only outdoor environments were able to replenish lost species richness to core membership (n species > 50% prevalent). Overall, we find that environmental setting, especially including biodiversity, is important in human microbiota recovery periods and that the outdoors provide resilience to skin communities. This work also has implications for the inclusion of short periods of outside or forest exposure in school scheduling. Future investigations of the health impacts of permanent urban biodiversity interventions are needed.},
}
@article {pmid35689660,
year = {2022},
author = {Chen, X and Sun, B and Li, L and Sun, Z and Zhu, X and Zhong, X and Xu, Y},
title = {The oral microbiome analysis reveals the similarities and differences between periodontitis and Crohn's disease-associated periodontitis.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnac054},
pmid = {35689660},
issn = {1574-6968},
abstract = {Patients with Crohn's disease (CD) have higher incidences of oral diseases such as dental caries and periodontitis than healthy people. Studies indicate that the interaction between gut and oral microbiota is an important factor. To compare the composition and diversity of the oral microbiome in periodontitis and CD-associated periodontitis, subgingival plaque and saliva samples from patients with these diseases were collected for 16S rRNA gene sequencing analyses. In CD-associated periodontitis, the subgingival plaque had greater microbial diversity than saliva. Subgingival plaque had decreased abundances of Firmicutes, Streptococcus, and Haemophilus and increased abundances of Bacteroidetes, Actinomyces, Treponema_2, Capnocytophaga, and Porphyromonas relative to saliva. The microbial composition in subgingival plaque was similar between the two diseases. Both red complex (Porphyromonas, Tannerella, and Treponema) and orange complex (Fusobacteria) bacteria were abundant in periodontitis subgingival plaque, while orange complex bacteria (Prevotella_2 and Prevotella) were abundant in CD-associated periodontitis subgingival plaque. Pocket depth was significantly positively correlated with multiple periodontal pathogens, including Porphyromonas, Tannerella, and Treponema. This study reveals the similarities and differences in the oral microbiome between periodontitis and CD-associated periodontitis, which provides a foundation to further explore the associations between CD and periodontitis.},
}
@article {pmid35689551,
year = {2022},
author = {Taati Moghadam, M and Amirmozafari, N and Mojtahedi, A and Bakhshayesh, B and Shariati, A and Masjedian Jazi, F},
title = {Association of perturbation of oral bacterial with incident of Alzheimer's disease: A pilot study.},
journal = {Journal of clinical laboratory analysis},
volume = {},
number = {},
pages = {e24483},
doi = {10.1002/jcla.24483},
pmid = {35689551},
issn = {1098-2825},
abstract = {OBJECTIVE: This case-control study was designed to compare the composition of the predominant oral bacterial microbiome in Alzheimer's disease (AD) and control group.<br><br>SUBJECT: A total of 30 adult participants (15 AD and 15 healthy individuals) were entered in this study. The composition of oral bacterial microbiome was examined by quantitative real-time polymerase chain reaction (qPCR) using bacterial 16S rDNA gene. The levels of systemic inflammatory cytokines in both groups were assessed using enzyme-linked immunosorbent assays (ELISA).<br><br>RESULTS: The loads of Porphyromonas gingivalis, Fusobacterium nucleatum, and Prevotella intermedia were significantly more abundant in the AD compared to the control group (p < 0.05). Although Aggregatibacter actinomycetemcomitans and Streptococcus mutans were relatively frequent in the AD group, no significance difference was observed in their copy number between two groups. Although the concentrations of IL-1, IL-6, and TNF-α were higher in the AD group, there was a significant difference in their levels between the two groups (p < 0.05). Finally, there was a significant relationship between increased number of pathogenic bacteria in oral microbiome and higher concentration of cytokines in patient's blood.<br><br>CONCLUSION: Our knowledge of oral microbiome and its exact association with AD is rather limited; our study showed a significant association between changes in oral microbiome bacteria, increased inflammatory cytokines, and AD.},
}
@article {pmid35689543,
year = {2022},
author = {Rong, T and Zhu, P and Zhou, Y and Li, Q and Wan, Z and Li, R and Ruojun, W},
title = {Altered skin fungal and bacterial community compositions in tinea capitis.},
journal = {Mycoses},
volume = {},
number = {},
pages = {},
doi = {10.1111/myc.13480},
pmid = {35689543},
issn = {1439-0507},
abstract = {BACKGROUND: Tinea capitis is an infection of the scalp and hair shaft caused by dermatophytes that predominantly occurs in children. Skin fungal infections have been found to be associated with alterations in the overall bacterial and fungal communities. However, the scalp microbiome in tinea capitis have not been fully investigated.<br><br>OBJECTIVES: To investigate and compare the scalp bacterial and fungal microbiomes between children with tinea capitis and healthy children and between children and adults.<br><br>METHODS: Skin samples were collected from the scalp. Bacterial and fungal community compositions were analyzed by amplification sequencing of the V3-V4 of 16S rDNA and ITS1-5F, respectively.<br><br>RESULTS: The predominant fungi detected using amplicon sequencing were consistent with the culture- or real-time PCR-positive pathogens in most samples. Children with tinea capitis had lower fungal and higher bacterial Shannon diversity than healthy children. A higher relative abundance of pathogenic fungi and significant alterations in the bacterial community in the lesional sites of tinea capitis than healthy scalps. Compared with adults, healthy children were characterized by higher Shannon diversities with significantly lower relative abundances of Malassezia and Cutibacterium and higher relative abundances of Candida and Streptococcus.<br><br>CONCLUSIONS: We demonstrated that tinea capitis was characterized by significant alterations in both fungal and bacterial communities and amplicon sequencing could be a complementary method for pathogen identification.},
}
@article {pmid35689294,
year = {2022},
author = {Fricke, WF and Ravel, J},
title = {More data needed on neonatal microbiome seeding.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {88},
pmid = {35689294},
issn = {2049-2618},
}
@article {pmid35689274,
year = {2022},
author = {Judkins, TC and Oula, ML and Sims, SM and Langkamp-Henken, B},
title = {The effect of a probiotic on gastrointestinal symptoms due to menstruation in healthy adult women on oral contraceptives: randomized, double-blind, placebo-controlled trial protocol.},
journal = {Trials},
volume = {23},
number = {1},
pages = {481},
pmid = {35689274},
issn = {1745-6215},
support = {FLA-FOS-005636//Lallemand Health Solutions/ ; },
abstract = {INTRODUCTION: For many women, uncomfortable and stressful symptoms accompany the menstrual cycle each month, sometimes in a debilitating manner. Previous studies have reported that gastrointestinal symptoms in healthy women significantly differ by the day of the menstrual cycle, but few studies have assessed interventions intended to minimize these symptoms. Probiotics supplements have been shown to attenuate gastrointestinal symptom severity as well as self-reported feelings of stress in various populations. This study evaluates the effect of a probiotic on abdominal pain and gastrointestinal symptoms in healthy women who take an oral contraceptive, have regular menses, and typically experience these symptoms during menstruation with the primary aim being change in abdominal pain intensity related to the menstrual cycle with probiotic versus placebo supplementation.<br><br>METHODS AND ANALYSIS: In this randomized, double-blind, placebo-controlled parallel study, participants will receive either a probiotic or placebo supplement. Participants will begin answering questionnaires approximately 7 days before the start of menstruation (i.e., active bleeding), and 3 days later, they will begin consuming the study supplement for 8 weeks. The questionnaires administered will collect data about abdominal pain severity (primary outcome) and duration related to the menstrual cycle, digestive health, dietary intake, stress, and digestion-associated quality-of-life. A subgroup of women will provide weekly vaginal swabs and stool samples to examine the effect of the probiotic supplement on microbiota composition and diversity for exploratory purposes. Two-sided tests using a linear model and a type I error rate of α = 0.05 will be employed to test all hypotheses. Continuous variables will be presented as means with standard errors and categorical variables, as counts or proportions.<br><br>ETHICS AND DISSEMINATION: This study was reviewed and approved by the University of Florida Institutional Review Board 01. Written informed consent will be obtained from all participants prior to any study activities. Study findings will be disseminated at scientific conferences and publication in the trial registry or in a peer-reviewed journal. Any protocol amendments will be reported in the final manuscript of this study.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov NCT04457401 . Registered prospectively on 07 July 2020. The trial was completed in December of 2021.<br><br>PROTOCOL VERSION: V4.0 (11-04-2020) TRIAL STATUS: Currently recruiting. Recruitment began in November 2020 and extend until December 2021.},
}
@article {pmid35689257,
year = {2022},
author = {Irani, H and Khodami, B and Abiri, B and Saidpour, A},
title = {Effect of time restricted feeding on anthropometric measures, eating behavior, stress, and brain-derived neurotrophic factor (BDNF) and lipopolysaccharide-binding protein (LBP) levels in women with overweight/obesity and food addiction: a study protocol for a randomized clinical trial.},
journal = {Trials},
volume = {23},
number = {1},
pages = {482},
pmid = {35689257},
issn = {1745-6215},
abstract = {BACKGROUND: Food addiction is one of the behavioral factors that play an important role in the pathogenesis of obesity. Much evidence is available suggesting intestinal microbiomes can play a role in eating behavior, body composition, and BDNF levels, and they can be modified by time-restricted feeding (TRF). So, this study will aim to evaluate the effect of TRF on anthropometric measures, eating behavior, stress, and serum BDNF and LBP levels in women with overweight/obesity and food addiction.<br><br>METHODS: We will carry out a randomized clinical trial for 8 weeks to evaluate the effect of a TRF on anthropometric measures, eating behavior, stress level, serum BDNF and LBP levels in women with overweight/obesity and food addiction.<br><br>DISCUSSION: Given the effect of BDNF on regulating eating behavior and body weight and the effect of dietary restrictions on BDNF and the gut microbiome, the TRF diet could possibly be a new way to successfully manage weight through modifying BDNF in people with eating disorders, including food addiction.<br><br>TRIAL REGISTRATION: Iranian Registry of Clinical Trials IRCT20131228015968N7 . Registered on 25 October 2020.},
}
@article {pmid35689136,
year = {2022},
author = {Vafaei, S and Taheri, H and Hajimomeni, Y and Fakhre Yaseri, A and Abolhasani Zadeh, F},
title = {The role of NLRP3 inflammasome in colorectal cancer: potential therapeutic target.},
journal = {Clinical &amp; translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico},
volume = {},
number = {},
pages = {},
pmid = {35689136},
issn = {1699-3055},
abstract = {All phases of carcinogenesis are affected by inflammation. Activation of the inflammasome is a crucial signaling mechanism that leads to acute and chronic inflammation. When specific nucleotide-binding domains, leucine-rich repeat-containing proteins (NLRs) are activated, inflammasomes are formed. The NLRP3 is one of the NLR family members with the most functional characterization. NLRP3 can modulate the immune systems, apoptosis, growth, and/or the gut microbiome to impact cancer development. Colorectal cancer (CRC) is one of the most common cancers, and it begins as a tissue overgrowth on the internal part of the rectum or colon. In vivo and in vitro studies showed that the NLRP3 inflammasome has a role in CRC development due to its broad activity in shaping immune responses. Here, onwards, we focus on the NLRP3 inflammasome role in CRC development, as well as the therapeutic prospective of modifying NLRP3 inflammasome in the context of anti-cancer therapy.},
}
@article {pmid35689007,
year = {2022},
author = {Abdelbary, MMH and Kuppe, C and Michael, SS and Krüger, T and Floege, J and Conrads, G},
title = {Impact of sucroferric oxyhydroxide on the oral and intestinal microbiome in hemodialysis patients.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {9614},
pmid = {35689007},
issn = {2045-2322},
support = {TPL107//Vifor Pharma/ ; TPL107//Vifor Pharma/ ; TPL107//Vifor Pharma/ ; },
abstract = {Hyperphosphatemia is a consequence of chronic kidney disease associated with mineral/bone impairment, increased cardiovascular events and mortality. Therapeutically, most dialysis patients have to take phosphate binders. Here, we investigated effects of the Fe(3+)-based phosphate binder sucroferric oxyhydroxide (SFOH) on the oral and gastrointestinal microbiome of 11 hemodialysis patients. Saliva, dental plaque and stool were collected at baseline, one and four weeks of SFOH intake and subjected to 16S rRNA gene (V3-V4 region) directed Illumina MiSeq-based analysis. Total Fe, Fe(2+) and Fe(3+) were determined in stool and saliva. Overall, the microbiome did not change significantly. However, some patient-, sample- and taxon-specific differences were noted, which allowed patients to be divided into those with a shift in their microbiome (6/11) and those without a shift (5/11). Total Fe and Fe(2+) were highest after one week of SFOH, particularly in patients who exhibited a shift in microbiome composition. Eight bacterial taxa showed significant unidirectional changes during treatment. In-depth microbiome analysis revealed that taxa that significantly benefited from iron plethora had no iron-binding siderophores or alternatives, which was in contrast to taxa that significantly declined under iron plethora. Patients with microbiome-shift were significantly younger and had higher serum phosphate concentrations. In conclusion, this study sheds light on the impact of iron on the microbiome of hemodialysis patients.},
}
@article {pmid35688919,
year = {2022},
author = {Thomas, CM and Desmond-Le Quéméner, E and Gribaldo, S and Borrel, G},
title = {Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3358},
pmid = {35688919},
issn = {2041-1723},
support = {ANR-19-CE02-0005-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {Archaea are common constituents of the gut microbiome of humans, ruminants, and termites but little is known about their diversity and abundance in other animals. Here, we analyse sequencing and quantification data of archaeal and bacterial 16S rRNA genes from 250 species of animals covering a large taxonomic spectrum. We detect the presence of archaea in 175 animal species belonging to invertebrates, fish, amphibians, birds, reptiles and mammals. We identify five dominant gut lineages, corresponding to Methanobrevibacter, Methanosphaera, Methanocorpusculum, Methanimicrococcus and "Ca. Methanomethylophilaceae". Some archaeal clades, notably within Methanobrevibacter, are associated to certain hosts, suggesting specific adaptations. The non-methanogenic lineage Nitrososphaeraceae (Thaumarchaeota) is frequently present in animal samples, although at low abundance, but may have also adapted to the gut environment. Host phylogeny, diet type, fibre content, and intestinal tract physiology are major drivers of the diversity and abundance of the archaeome in mammals. The overall abundance of archaea is more influenced by these factors than that of bacteria. Methanogens reducing methyl-compounds with H2 can represent an important fraction of the overall methanogens in many animals. Together with CO2-reducing methanogens, they are influenced by diet and composition of gut bacteria. Our results provide key elements toward our understanding of the ecology of archaea in the gut, an emerging and important field of investigation.},
}
@article {pmid35688912,
year = {2022},
author = {Penno, C and Motherway, MO and Fu, Y and Sharma, V and Crispie, F and Cotter, PD and Houeix, B and Joshi, L and Bottacini, F and O'Dwyer, A and Loughran, G and Atkins, JF and van Sinderen, D},
title = {Maximum depth sequencing reveals an ON/OFF replication slippage switch and apparent in vivo selection for bifidobacterial pilus expression.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {9576},
pmid = {35688912},
issn = {2045-2322},
support = {PDTM/20011/9/HRBI_/Health Research Board/Ireland ; IRCLA/2019/74//Irish Research Council/ ; IRCLA/2019/74//Irish Research Council/ ; SFI/12/RC/2273-P1/SFI_/Science Foundation Ireland/Ireland ; },
abstract = {The human gut microbiome, of which the genus Bifidobacterium is a prevalent and abundant member, is thought to sustain and enhance human health. Several surface-exposed structures, including so-called sortase-dependent pili, represent important bifidobacterial gut colonization factors. Here we show that expression of two sortase-dependent pilus clusters of the prototype Bifidobacterium breve UCC2003 depends on replication slippage at an intragenic G-tract, equivalents of which are present in various members of the Bifidobacterium genus. The nature and extent of this slippage is modulated by the host environment. Involvement of such sortase-dependent pilus clusters in microbe-host interactions, including bacterial attachment to the gut epithelial cells, has been shown previously and is corroborated here for one case. Using a Maximum Depth Sequencing strategy aimed at excluding PCR and sequencing errors introduced by DNA polymerase reagents, specific G-tract sequences in B. breve UCC2003 reveal a range of G-tract lengths whose plasticity within the population is functionally utilized. Interestingly, replication slippage is shown to be modulated under in vivo conditions in a murine model. This in vivo modulation causes an enrichment of a G-tract length which appears to allow biosynthesis of these sortase-dependent pili. This work provides the first example of productive replication slippage influenced by in vivo conditions. It highlights the potential for microdiversity generation in "beneficial" gut commensals.},
}
@article {pmid35688739,
year = {2022},
author = {Tricarico, JM and de Haas, Y and Hristov, AN and Kebreab, E and Kurt, T and Mitloehner, F and Pitta, D},
title = {Symposium review: Development of a funding program to support research on enteric methane mitigation from ruminants.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2021-21397},
pmid = {35688739},
issn = {1525-3198},
abstract = {Enteric methane is a major source of greenhouse gas emissions from milk production systems. Two organizations based in the United States, the Foundation for Food and Agriculture Research and the Dairy Research Institute, have developed a collaborative program to align resources and fund projects to identify, develop, and validate new and existing mitigation options for enteric methane emissions from dairy and beef cattle. This collaborative program is called the Greener Cattle Initiative. The program will develop requests for proposals and award grants on projects that address challenges within, but not limited, to the following research areas: dairy and beef cattle nutrition, rumen microbiome, dairy and beef cattle genetics, sensing and data technology for enteric methane measurement and prediction, and socioeconomic analysis of enteric methane mitigation practices. The program is structured as a consortium with closed participation and a flat governance collaboration model. The Greener Cattle Initiative program will continue incorporating participants from the food and agriculture industry, commodity groups, and nonprofit organizations who share common objectives and contribute in-kind and matching funds to the program, up to a total of 10 organizations. Research findings will be communicated broadly, after a waiting period for exclusive access to program participants, to create shared knowledge on enteric methane mitigation. The Greener Cattle Initiative is expected to award up to $5 million in research grant funding in a 5-year period, which will contribute to advancing the voluntary greenhouse gas reduction goals established by both the United States and global dairy sectors.},
}
@article {pmid35688483,
year = {2022},
author = {Hu, Y and Amir, A and Huang, X and Li, Y and Huang, S and Wolfe, E and Weiss, S and Knight, R and Xu, ZZ},
title = {Diurnal and eating-associated microbial patterns revealed via high-frequency saliva sampling.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.276482.121},
pmid = {35688483},
issn = {1549-5469},
abstract = {The oral microbiome is linked to oral and systemic health, but its fluctuation under frequent daily activities remains elusive. Here, we sampled saliva at 10- to 60-min intervals to track the high-resolution microbiome dynamics during the course of human activities. This dense time series data showed that eating activity markedly perturbed the salivary microbiota, with tongue-specific Campylobacter concisus and Oribacterium sinus and dental plaque-specific Lautropia mirabilis, Rothia aeria, and Neisseria oralis increased after every meal in a temporal order. The observation was reproducible in multiple subjects and across an 11-mo period. The microbiome composition showed significant diurnal oscillation patterns at different taxonomy levels with Prevotella/Alloprevotella increased at night and Bergeyella HMT 206/Haemophilus slowly increased during the daytime. We also identified microbial co-occurring patterns in saliva that are associated with the intricate biogeography of the oral microbiome. Microbial source tracking analysis showed that the contributions of distinct oral niches to the salivary microbiome were dynamically affected by daily activities, reflecting the role of saliva in exchanging microbes with other oral sites. Collectively, our study provides insights into the temporal microbiome variation in saliva and highlights the need to consider daily activities and diurnal factors in design of oral microbiome studies.},
}
@article {pmid35688340,
year = {2022},
author = {Caputi, V and Bastiaanssen, TFS and Peterson, V and Sajjad, J and Simons, LP and Murphy, A and Stanton, C and McNamarad, B and Shorten, GD and Cryan, JF and O'Mahony, SM},
title = {Sex, Pain, and the Microbiome: The Relationship between Baseline Gut Microbiota Composition, Gender and Somatic Pain in Healthy Individuals.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2022.06.002},
pmid = {35688340},
issn = {1090-2139},
abstract = {BACKGROUND AND AIM: Relative to men, women present with pain conditions more commonly. Although consistent differences exist between men and women in terms of physiological pain sensitivity, the underlying mechanisms are incompletely understood and yet could inform the development of effective sex specific treatments for pain. The gut microbiota can modulate nervous system functioning, including pain signaling pathways. We hypothesized that the gut microbiota and critical components of the gut-brain axis might influence electrical pain thresholds. Further, we hypothesized that sex, menstrual cycle, and hormonal contraceptive use might account for inter-sex differences in pain perception.<br><br>METHODS: Healthy, non-obese males (N=15) and females (N=16), (nine of whom were using hormonal contraceptives), were recruited. Male subjects were invited to undergo testing once, whereas females were invited three times across the menstrual cycle, based on self-reported early follicular (EF), late follicular (LF), or mid-luteal (ML) phase. On test days, electrical stimulation on the right ankle was performed; salivary cortisol levels were measured in the morning; levels of lipopolysaccharide-binding protein (LBP), soluble CD14 (sCD14), pro-inflammatory cytokines were assessed in plasma, and microbiota composition and short-chain fatty acids (SCFAs) levels were determined in fecal samples.<br><br>RESULTS: We observed that the pain tolerance threshold/pain sensation threshold (PTT/PST) ratio was significantly lesser in women than men, but not PST or PTT alone. Further, hormonal contraceptive use was associated with increased LBP levels (LF &amp; ML phase), whilst sCD14 levels or inflammatory cytokines were not affected. Interestingly, in women, hormonal contraceptive use was associated with an increase in the relative abundance of Erysipelatoclostridium, and the relative abundances of certain bacterial genera correlated positively with pain sensation thresholds (Prevotella and Megasphera) during the LF phase and cortisol awakening response (Anaerofustis) during the ML phase. In comparison with men, women displayed overall stronger associations between i) SCFAs data, ii) cortisol data, iii) inflammatory cytokines and PTT and PST.<br><br>DISCUSSION: and conclusion. Our findings support the hypothesis that the gut microbiota may be one of the factors determining the physiological inter-sex differences in pain perception. Further research is needed to investigate the molecular mechanisms by which specific sex hormones and gut microbes modulate pain signaling pathways, but this study highlights the possibilities for innovative individual targeted therapies for pain management.},
}
@article {pmid35688268,
year = {2022},
author = {Zhang, KK and Liu, JL and Chen, LJ and Li, JH and Yang, JZ and Xu, LL and Chen, YK and Zhang, QY and Li, XW and Liu, Y and Zhao, D and Xie, XL and Wang, Q},
title = {Gut microbiota mediates methamphetamine-induced hepatic inflammation via the impairment of bile acid homeostasis.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {113208},
doi = {10.1016/j.fct.2022.113208},
pmid = {35688268},
issn = {1873-6351},
abstract = {Methamphetamine (Meth), an addictive psychostimulant of abuse worldwide, has been a common cause of acute toxic hepatitis in adults. Gut microbiota has emerged as a modulator of host immunity via metabolic pathways. However, the microbial mechanism of Meth-induced hepatic inflammation and effective therapeutic strategies remain unknown. Here, mice were intraperitoneally (i.p.) injected with Meth to induce hepatotoxicity. Cecal microbiome and bile acids (BAs) composition were analysed after Meth administration. Fecal microbiota transplantation (FMT) technology was utilized to investigate the role of microbiota. Additionally, the protective effects of obeticholic acid (OCA), an agonist of farnesoid X receptor (FXR), were evaluated. Results indicated that Meth administration induced hepatic cholestasis, dysfunction and aroused hepatic inflammation by stimulating the TLR4/MyD88/NF-κB pathway in mice. Meanwhile, Meth disturbed the cecal microbiome and impaired the homeostasis of BAs. Interestingly, FMT from Meth administered mice resulted in serum and hepatic BA accumulation and transferred similar phenotypic changes into the healthy recipient mice. Finally, OCA normalized Meth-induced BA accumulation in both serum and the liver, and effectively protected against Meth-induced hepatic dysfunction and inflammation by suppressing the TLR4/MyD88/NF-κB pathway. This study established the importance of microbial mechanism and its inhibition as a potential therapeutic target to treat Meth-related hepatotoxicity.},
}
@article {pmid35688245,
year = {2022},
author = {Lu, X and Zhang, JX and Zhang, L and Wu, D and Tian, J and Yu, LJ and He, L and Zhong, S and Du, H and Deng, DF and Ding, YZ and Wen, H and Jiang, M},
title = {Negative impacts of chronic dietary exposure to polyethylene microplastics on growth, gut microbiota, liver metabolism and gene expressions in genetically improved farmed tilapia (Oreochromis niloticus).},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {156571},
doi = {10.1016/j.scitotenv.2022.156571},
pmid = {35688245},
issn = {1879-1026},
abstract = {Microplastics (MPs) pollution has been recognized as a threat to sustainable fisheries due to the concerns of MPs contamination in fish feed production and susceptibility to ingestion of MPs from the aquaculture environment. Here, we report a comprehensive investigation about the impacts of dietary exposure to polyethylene microplastics (PE-MPs) for 9 weeks on growth performance, gut microbiota, liver metabolism, and gene expressions in brain and liver of the genetically improved farmed tilapia (GIFT, Oreochromis niloticus). Dietary exposure to two kinds of PE-MPs with different median size (27 μm and 63 μm, respectively) concentration-dependently decreased weight gain (WG), while increased feed conversion ratio (FCR) and hepatosomatic index (HSI) of the tilapia. Dietary administration of PE-MPs also significantly reduced the activities of intestinal protease and amylase. PE-MPs particles of the larger size groups (63 μm) were mainly detected in feces, but those of the smaller ones (27 μm) tended to be accumulated in intestine. PE-MPs ingestion altered the gut microbiota composition, and Fusobacteria, Verrucomicrobia and Firmicutes were the overrepresented bacterial taxa. Metabolomic assays of liver samples in fish fed the diets containing 8 % of 27 μm and 63 μm PE-MPs revealed the particle size-specific variations in composition of differential metabolites, and pathways such as amino acid and glycerophospholipid metabolism were affected by dietary PE-MPs exposure. Gene expressions of brain and liver samples were analyzed by RNA-seq. Photoperiodism and circadian rhythm were the representative biological processes enriched for the differentially expressed genes (DEGs) identified from the brain. Citrate cycle (TCA cycle) was the most enriched pathway revealed by a joint transcriptomic and metabolic pathway analysis for the liver, followed by propanoate and pyruvate metabolism. Furthermore, an integration analysis of the gut microbiome and liver transcriptome data identified significant associations between several pathogenic bacteria taxa and immune pathways. Our data systematically cataloged the adverse impacts of chronic exposure to PE-MPs on physiology and metabolism of GIFT tilapia.},
}
@article {pmid35687750,
year = {2022},
author = {Qian, L and Ouyang, H and Gordils-Valentin, L and Hong, J and Jayaraman, A and Zhu, X},
title = {Identification of Gut Bacterial Enzymes for Keto-Reductive Metabolism of Xenobiotics.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.2c00312},
pmid = {35687750},
issn = {1554-8937},
abstract = {Human gastrointestinal microbiota are known for the keto-reductive metabolism of small-molecule pharmaceuticals; however, the responsible enzymes remain poorly understood. Through in vitro biochemical assays, we report the identification of enzymes encoded in the genome of Clostridium bolteae that can reduce the ketone groups of nabumetone, hydrocortisone, and tacrolimus. The homologues to a newly identified enzyme (i.e., DesE) are potentially widely distributed in the gut microbiome. The selected enzymes display different levels of activities against additional chemicals such as two dietary compounds (i.e., raspberry ketone and zingerone), chemotherapeutic drug doxorubicin, and its aglycone metabolite doxorubicinone. Thus, our results expand the repertoire of enzymes that can reduce the ketone groups in small molecules and could serve as the basis for future personalized medicine approaches.},
}
@article {pmid35687695,
year = {2022},
author = {Sanidad, KZ and Amir, M and Ananthanarayanan, A and Singaraju, A and Shiland, NB and Hong, HS and Kamada, N and Inohara, N and Núñez, G and Zeng, MY},
title = {Maternal gut microbiome-induced IgG regulates neonatal gut microbiome and immunity.},
journal = {Science immunology},
volume = {7},
number = {72},
pages = {eabh3816},
doi = {10.1126/sciimmunol.abh3816},
pmid = {35687695},
issn = {2470-9468},
abstract = {The gut microbiome elicits antigen-specific immunoglobulin G (IgG) at steady state that cross-reacts to pathogens to confer protection against systemic infection. The role of gut microbiome-specific IgG antibodies in the development of the gut microbiome and immunity against enteric pathogens in early life, however, remains largely undefined. In this study, we show that gut microbiome-induced maternal IgG is transferred to the neonatal intestine through maternal milk via the neonatal Fc receptor and directly inhibits Citrobacter rodentium colonization and attachment to the mucosa. Enhanced neonatal immunity against oral C. rodentium infection was observed after maternal immunization with a gut microbiome-derived IgG antigen, outer membrane protein A, or induction of IgG-inducing gut bacteria. Furthermore, by generating a gene-targeted mouse model with complete IgG deficiency, we demonstrate that IgG knockout neonates are more susceptible to C. rodentium infection and exhibit alterations of the gut microbiome that promote differentiation of interleukin-17A-producing γδ T cells in the intestine, which persist into adulthood and contribute to increased disease severity in a dextran sulfate sodium-induced mouse model of colitis. Together, our studies have defined a critical role for maternal gut microbiome-specific IgG antibodies in promoting immunity against enteric pathogens and shaping the development of the gut microbiome and immune cells in early life.},
}
@article {pmid35687396,
year = {2022},
author = {Hines, IS and Smith, SA and Kuhn, DD and Stevens, AM},
title = {Development of a Controlled Laboratory-scale Inoculation System to Study Vibrio parahaemolyticus-oyster Interactions.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnac055},
pmid = {35687396},
issn = {1574-6968},
abstract = {Prevalence of seafood-borne gastroenteritis caused by the human pathogen Vibrio parahaemolyticus is increasing globally despite current preventative measures. The United States Centers for Disease Control have designated V. parahaemolyticus as a reportable emerging human pathogen. The Eastern oyster (Crassostrea virginica) is a natural reservoir of the bacterium in marine environments, but little is actually known regarding interactions between oysters and V. parahaemolyticus. Therefore, a laboratory-scale Biosafety Level-2 (BSL2) inoculation system was developed wherein Chesapeake Bay region oysters harvested during summer or winter months, were exposed to the clinical RIMD2210633 strain carrying a chloramphenicol-selective marker (VP RIMDmC). Homogenized whole oyster tissues were spread on selective and differential agar medium to measure viable VP RIMDmC levels. Endogenous Vibrio spp. cell numbers were significantly reduced followed chloramphenicol treatment and this likely contributed to higher VP RIMDmC oyster-associated levels, especially using winter-harvested animals. Summer-harvested oysters had significantly higher existing Vibrio levels and a lower level of artificial oyster-associated VP RIMDmC. Thus, the pre-existing microbiome appears to afford some protection from an external V. parahaemolyticus challenge. Overall, this system successfully enabled controlled manipulation of parameters influencing V. parahaemolyticus-oyster interactions and will be useful in safely testing additional pertinent environmental variables and potential mitigation strategies.},
}
@article {pmid35687318,
year = {2022},
author = {Sridhar, R and Dittmar, K and Williams, HM},
title = {USING SURFACE WASHING TO REMOVE THE ENVIRONMENTAL COMPONENT FROM FLEA MICROBIOME ANALYSIS.},
journal = {The Journal of parasitology},
volume = {108},
number = {3},
pages = {245-253},
doi = {10.1645/21-60},
pmid = {35687318},
issn = {1937-2345},
abstract = {Microbial metabarcoding is a common method to study the biology of blood-feeding arthropods and identify patterns of potential pathogen transmission. Before DNA extraction, specimens are often surface washed to remove environmental contaminants. While surface washing is common, its effects on microbial diversity remain unclear. We characterized the microbiome of the flea species Ceratophyllus idius, an avian ectoparasite, and a potential vector of pathogens, using high-throughput 16S rRNA sequencing. Half of the nests from which fleas were collected were subjected to an environmental manipulation in which nesting materials were periodically replaced. In a crossed study design we surface washed half of the flea samples from each environmental condition to produce 4 experimental conditions. Environmental manipulations resulted in significant differences in the diversity and structure of the flea microbiome, but these differences were unapparent when specimens were surface washed. Furthermore, differential abundance testing of the experimental groups revealed that surface washing predominantly affected the abundance of bacterial groups that are characterized as environmental contaminants. These findings suggest that environmental changes primarily affect the surface microbiome of arthropods and that surface washing is a useful tool to reduce the footprint of the external microbiome on analysis.},
}
@article {pmid35687206,
year = {2022},
author = {Adenaike, AS and Akpan, U and Awopejo, OO and Oloye, OS and Alli-Balogun, AO and Agbaje, M and Ikeobi, CON},
title = {Characterization of the cecal microbiome composition of Nigerian indigenous chickens.},
journal = {Tropical animal health and production},
volume = {54},
number = {4},
pages = {211},
pmid = {35687206},
issn = {1573-7438},
abstract = {Poultry cecum microbes are dynamic and complex. They play important roles in disease prevention, detoxification of harmful substances, nutrient processing, and ingestion harvesting. It may be possible to increase poultry productivity by better understanding and controlling the microbial population. We analyzed the composition and function of Nigerian hens' cecal microbiota using high-throughput sequencing methods. Using high-throughput sequencing of the 16S rRNA genes (V1-V9) hypervariable regions, the cecal microbiota of three Nigerian indigenous chicken genotypes (Naked neck, Frizzle, and Normal feather) was described and compared. A total of two phyla were represented among the three genotypes (Firmicutes and Proteobacteria). Microbiological diversity was found in the community, with naked neck having the most evenness, followed by normal feather, which had the least. There were a lot of similarities between the naked neck and frizzle feather chicken groups when it came to genetic diversity between them. For example, the bacterial cecal microbiota of the naked neck chickens was more diverse, with a higher concentration of motility proteins, two-component systems, bacterial secretion systems, and the formation and breakdown of secondary metabolites. More understanding on gut microbiota roles and interactions will help Nigerian poultry farmers improve their methods and give valuable data for the study of bacteria in the chicken gut.},
}
@article {pmid35687002,
year = {2022},
author = {Sterling, JJ and Sakihara, TS and Brannock, PM and Pearson, ZG and Maclaine, KD and Santos, SR and Havird, JC},
title = {Primary microbial succession in the anchialine ecosystem.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icac087},
pmid = {35687002},
issn = {1557-7023},
abstract = {When new land is created, initial microbial colonization lays the foundation for further ecological succession of plant and animal communities. Primary microbial succession of new aquatic habitats formed during volcanic activity has received little attention. The anchialine ecosystem, which includes coastal ponds in young lava flows, offers an opportunity to examine this process. Here, we characterized microbial communities of anchialine habitats in Hawaii that were created during volcanic eruptions in 2018. Benthic samples from three habitats were collected ∼2 years after their formation and at later time points spanning ∼1 year. Sequence profiling (16S and 18S) of prokaryotic and eukaryotic communities was used to test whether communities were similar to those from older, established anchialine habitats, and if community structure changed over time. Results show that microbial communities from the new habitats were unlike any from established anchialine microbial communities, having higher proportions of Planctomycetota and Chloroflexi but lower proportions of green algae. Each new habitat also harbored its own unique community relative to other habitats. While community composition in each habitat underwent statistically significant changes over time, they remained distinctive from established anchialine habitats. New habitats also had highly elevated temperatures compared to other habitats. These results suggest idiosyncratic microbial consortia form during early succession of Hawaiian anchialine habitats. Future monitoring will reveal whether the early communities described here remain stable after temperatures decline and macro-organisms become more abundant, or if microbial communities will continue to change and eventually resemble those of established habitats. This work is a key first step in examining primary volcanic succession in aquatic habitats and suggests young anchialine habitats may warrant special conservation status.},
}
@article {pmid35687001,
year = {2022},
author = {Forsman, AM and Savage, AE and Hoenig, BD and Gaither, MR},
title = {DNA metabarcoding across disciplines: sequencing our way to greater understanding across scales of biological organization.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icac090},
pmid = {35687001},
issn = {1557-7023},
abstract = {DNA metabarcoding describes the use of targeted DNA (i.e., amplicon) sequencing to identify community constituents from a complex sample containing genetic material from multiple organisms, such as water, soil, gut contents, microbiomes, or biofilms. This molecular approach for characterizing mixed DNA samples relies on the development of "universal primers" that allow for effective amplification of target sequences across a broad range of taxa. Armed with optimized lab protocols and rigorous bioinformatics tools, DNA metabarcoding can produce a wealth of information about the hidden biodiversity of various sample types by probing for organisms' molecular footprints. DNA metabarcoding has received considerable popular press over the last few years because of gut microbiome studies in humans and beyond. However, there are many other applications that are continually integrating molecular biology with other fields of study to address questions that have previously been unanswerable, for both prokaryotic and eukaryotic targets. For example, we can now sample mostly-digested gut contents from virtually any organism to learn about ontogeny and foraging ecology. Water samples collected from different locations can be filtered to extract eDNA (i.e., environmental DNA), revealing the biodiversity of fishes and other taxa targeted by carefully selected primer sets. This universal primer metabarcoding approach has even been extended to looking at diverse gene families within single species, which is particularly useful for complex immune system genetics. The purpose of this SICB symposium was to bring together researchers using DNA metabarcoding approaches to (a) showcase the diversity of applications of this technique for addressing questions spanning ecology, evolution, and physiology, and (b) to spark connections among investigators from different fields that are utilizing similar approaches to facilitate optimization and standardization of metabarcoding methods and analyses. The resulting manuscripts from this symposium represent a great diversity of metabarcoding applications and taxonomic groups of interest.},
}
@article {pmid35686590,
year = {2022},
author = {Jiang, S and Nie, J and Chen, YX and Wang, XY and Chen, F},
title = {Structure and Composition of Candidate Phyla Radiation in Supragingival Plaque of Caries Patients.},
journal = {The Chinese journal of dental research : the official journal of the Scientific Section of the Chinese Stomatological Association (CSA)},
volume = {25},
number = {2},
pages = {107-118},
doi = {10.3290/j.cjdr.b3086339},
pmid = {35686590},
issn = {1867-5646},
abstract = {OBJECTIVE: To investigate the composition and abundance of candidate phyla radiation (CPR) in the oral cavity in caries patients and a healthy population.<br><br>METHODS: The raw macrogenomic sequencing data for a total of 88 subjects were downloaded from the National Centre for Biotechnology Sequence Read Archive (NCBI SRA) public database according to the public data usage specifications. Trimmomatic (Department for Metabolic Networks, Potsdam, Germany) and Bowtie 2 (University of Maryland, College Park, MD, USA) were used to quality control and dehost the host sequences. Species annotation was made using Kraken2 (Johns Hopkins University, Baltimore, MD, USA) and Bracken (Johns Hopkins University) based on the reference database. According to the results of the species annotation, the species-significant differences and species correlation of caries and healthy oral microbiota in species composition and microbiota diversity were analysed to study the distribution and abundance differences of CPR in the oral environment.<br><br>RESULTS: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria were the main components. The relative abundance of TM7 (Candidatus Saccharibacteria) and GN02 (Candidatus Gracilibacteria) of CPR is second only to the aforementioned five bacteria, indicating that CPR is an important part of the oral microbiota. TM7 and GN02 were common to both the caries patients and healthy patients and were detected in all samples, suggesting that CPR is the 'core microbiome'. There was a correlation between CPR and a variety of oral microbiota, among which the positive correlation with Capnocytophaga was the strongest, suggesting that Capnocytophaga might be the potential host bacteria of CPR.<br><br>CONCLUSION: CPR is an indispensable part of the oral microbiota. It is the 'core microflora' of the oral cavity and may play an important role in the stability and function of the oral microecological environment. Capnocytophaga may be the potential host bacteria of CPR.},
}
@article {pmid35686484,
year = {2022},
author = {Chen, Y and Rudolph, S and Longo, BN and Pace, F and Roh, T and Condruti, R and Gee, M and Watnick, P and Kaplan, DL},
title = {Bioengineered 3D tissue model of intestine epithelium with oxygen gradients to sustain human gut microbiome.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e2200447},
doi = {10.1002/adhm.202200447},
pmid = {35686484},
issn = {2192-2659},
abstract = {The human gut microbiome is crucial to host physiology and health. Therefore, stable in vitro coculture of primary human intestinal cells with a microbiome community is essential for understanding intestinal disease progression and revealing novel therapeutic targets. Here, we present a three-dimensional (3D) scaffold system to regenerate an in vitro human intestinal epithelium that recapitulates many functional characteristics of the in vivo small intestine. The epithelium, derived from human intestinal enteroids, contains mature intestinal epithelial cell types and possesses selectively permeable barrier functions. Importantly, by properly positioning the scaffolds cultured under normal atmospheric conditions, two physiologically relevant oxygen gradients, a proximal-to-distal oxygen gradient along the gastrointestinal (GI) tract and a radial oxygen gradient across the epithelium, were distinguished in the tissues when the lumens were faced up and down in cultures, respectively. Furthermore, the presence of the low oxygen gradients supported the coculture of intestinal epithelial cells along with a complex living commensal gut microbiome (including obligate anaerobes) to simulate temporal microbiome dynamics in the native human gut. This unique silk scaffold platform may enable the exploration of microbiota-related mechanisms of disease pathogenesis and host-pathogen dynamics in infectious diseases including the potential to explore the human microbiome-gut-brain axis and potential novel microbiome-based therapeutics. This article is protected by copyright. All rights reserved.},
}
@article {pmid35686183,
year = {2022},
author = {Guo, XJ and Xiong, YB and Jia, Y and Cui, XH and Wu, WZ and Tian, JS and Yang, H and Ren, Y},
title = {Altered Metabolomics in Bipolar Depression With Gastrointestinal Symptoms.},
journal = {Frontiers in psychiatry},
volume = {13},
number = {},
pages = {861285},
doi = {10.3389/fpsyt.2022.861285},
pmid = {35686183},
issn = {1664-0640},
abstract = {Objective: Although gastrointestinal (GI) symptoms are very common in patients with bipolar disorder (BD), Few studies have researched the pathomechanism behind these symptoms. In the present study, we aim at elucidate the pathomechanism of GI symptoms in BD through metabolomic analysis.<br><br>Method: BD patients were recruited from Shanxi Bethune Hospital that divided into two groups, each group assessed with the 24-item Hamilton Depression Rating Scale (HAMD-24) according to the presence or absence of GI symptoms. Healthy controls were recruited from the medical examination center of the same hospital. Differential metabolites were identified and further analyzed using Metabo Analyst 3.0 to identify associated metabolic pathways.<br><br>Results: There were significantly higher HAMD-24 scores in the GI symptoms group than that of non-GI symptoms group (p = 0.007). Based on metabolomic analysis results, we found that the common disturbances metabolic pathway of both two patients groups was ketone body metabolism, and the unique disturbances metabolic pathways of BD with GI symptoms were fatty acid biosynthesis and tyrosine metabolism, and these changes were independent of dietary habits.<br><br>Conclusion: BD patients with GI symptoms exhibited disturbances in fatty acid and tyrosine metabolism, perhaps suggesting that the GI symptoms in BD patients are related to disturbances of the gut microbiome. Both groups of patients jointly exhibit disturbances of ketone body metabolism, which may serve as a biomarker for the pathogenesis of BD patients.},
}
@article {pmid35685930,
year = {2022},
author = {Bziuk, N and Maccario, L and Sørensen, SJ and Schikora, A and Smalla, K},
title = {Barley Rhizosphere Microbiome Transplantation - A Strategy to Decrease Susceptibility of Barley Grown in Soils With Low Microbial Diversity to Powdery Mildew.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {830905},
doi = {10.3389/fmicb.2022.830905},
pmid = {35685930},
issn = {1664-302X},
abstract = {Beneficial bacteria in the rhizosphere are known to trigger faster and stronger plant immune responses to biotic and abiotic stressors. In the present study, we aimed to test the hypothesis that a rhizosphere microbiome transplant (RMT) may improve the immune response and reduce the disease rates of barley (Hordeum vulgare). This hypothesis was tested in a greenhouse system with the powdery mildew-causing fungus Blumeria graminis f. sp. hordei (Bgh). Detached rhizosphere microbiome from barley grown in a field soil was transplanted to barley seedlings grown in potting soil with reduced microbial diversity. Saline-treated plants served as control. At the three-leaf stage, barley was infected with Bgh. Decreased susceptibility to Bgh was observed for barley treated with the RMT as displayed by lower Bgh pustule counts in a detached leaf assay. A trend toward enhanced relative transcript abundances of the defense-related genes PR1b and PR17b was observed in leaves, 24 h after the Bgh challenge, when compared to the control. Moreover, 10 days after the Bgh challenge, the barley rhizosphere microbiome was harvested and analyzed by sequencing of 16S rRNA gene amplicons. The microbial community composition was significantly influenced by the RMT and displayed higher microbial diversity compared to the control. Furthermore, microbial beta-diversity and predicted functional profiles revealed a treatment-dependent clustering. Bacterial isolates from the RMT showed in vitro plant beneficial traits related to induced resistance. Our results showed that transplantation of a rhizosphere microbiome could be a sustainable strategy to improve the health of plants grown in potting soil with low microbial diversity under greenhouse conditions.},
}
@article {pmid35685929,
year = {2022},
author = {Seitz, TJ and Schütte, UME and Drown, DM},
title = {Unearthing Shifts in Microbial Communities Across a Soil Disturbance Gradient.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {781051},
doi = {10.3389/fmicb.2022.781051},
pmid = {35685929},
issn = {1664-302X},
abstract = {Permafrost, an important source of soil disturbance, is particularly vulnerable to climate change in Alaska where 85% of the land is underlained with discontinuous permafrost. Boreal forests, home to plants integral to subsistence diets of many Alaska Native communities, are not immune to the effects of climate change. Soil disturbance events, such as permafrost thaw, wildfires, and land use change can influence abiotic conditions, which can then affect active layer soil microbial communities. In a previous study, we found negative effects on boreal plants inoculated with microbes impacted by soil disturbance compared to plants inoculated with microbes from undisturbed soils. Here, we identify key shifts in microbial communities altered by soil disturbance using 16S rRNA gene sequencing and make connections between microbial community changes and previously observed plant growth. Additionally, we identify further community shifts in potential functional mechanisms using long read metagenomics. Across a soil disturbance gradient, microbial communities differ significantly based on the level of soil disturbance. Consistent with the earlier study, the family Acidobacteriaceae, which consists of known plant growth promoters, was abundant in undisturbed soil, but practically absent in most disturbed soil. In contrast, Comamonadaceae, a family with known agricultural pathogens, was overrepresented in most disturbed soil communities compared to undisturbed. Within our metagenomic data, we found that soil disturbance level is associated with differences in microbial community function, including mechanisms potentially involved in plant pathogenicity. These results indicate that a decrease in plant growth can be linked to changes in the microbial community and functional composition driven by soil disturbance and climate change. Together, these results build a genomic understanding of how shifting soil microbiomes may affect plant productivity and ecosystem health as the Arctic warms.},
}
@article {pmid35685890,
year = {2022},
author = {Lamichhane, S and Siljander, H and Salonen, M and Ruohtula, T and Virtanen, SM and Ilonen, J and Hyötyläinen, T and Knip, M and Orešič, M},
title = {Impact of Extensively Hydrolyzed Infant Formula on Circulating Lipids During Early Life.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {859627},
doi = {10.3389/fnut.2022.859627},
pmid = {35685890},
issn = {2296-861X},
abstract = {Background: Current evidence suggests that the composition of infant formula (IF) affects the gut microbiome, intestinal function, and immune responses during infancy. However, the impact of IF on circulating lipid profiles in infants is still poorly understood. The objectives of this study were to (1) investigate how extensively hydrolyzed IF impacts serum lipidome compared to conventional formula and (2) to associate changes in circulatory lipids with gastrointestinal biomarkers including intestinal permeability.<br><br>Methods: In a randomized, double-blind controlled nutritional intervention study (n = 73), we applied mass spectrometry-based lipidomics to analyze serum lipids in infants who were fed extensively hydrolyzed formula (HF) or conventional, regular formula (RF). Serum samples were collected at 3, 9, and 12 months of age. Child's growth (weight and length) and intestinal functional markers, including lactulose mannitol (LM) ratio, fecal calprotectin, and fecal beta-defensin, were also measured at given time points. At 3 months of age, stool samples were analyzed by shotgun metagenomics.<br><br>Results: Concentrations of sphingomyelins were higher in the HF group as compared to the RF group. Triacylglycerols (TGs) containing saturated and monounsaturated fatty acyl chains were found in higher levels in the HF group at 3 months, but downregulated at 9 and 12 months of age. LM ratio was lower in the HF group at 9 months of age. In the RF group, the LM ratio was positively associated with ether-linked lipids. Such an association was, however, not observed in the HF group.<br><br>Conclusion: Our study suggests that HF intervention changes the circulating lipidome, including those lipids previously found to be associated with progression to islet autoimmunity or overt T1D.<br><br>Clinical Trial Registration: [Clinicaltrials.gov], identifier [NCT01735123].},
}
@article {pmid35685788,
year = {2022},
author = {Tomita, S and Kusada, H and Kojima, N and Ishihara, S and Miyazaki, K and Tamaki, H and Kurita, R},
title = {Polymer-based chemical-nose systems for optical-pattern recognition of gut microbiota.},
journal = {Chemical science},
volume = {13},
number = {20},
pages = {5830-5837},
doi = {10.1039/d2sc00510g},
pmid = {35685788},
issn = {2041-6520},
abstract = {Gut-microbiota analysis has been recognized as crucial in health management and disease treatment. Metagenomics, a current standard examination method for the gut microbiome, is effective but requires both expertise and significant amounts of general resources. Here, we show highly accessible sensing systems based on the so-called chemical-nose strategy to transduce the characteristics of microbiota into fluorescence patterns. The fluorescence patterns, generated by twelve block copolymers with aggregation-induced emission (AIE) units, were analyzed using pattern-recognition algorithms, which identified 16 intestinal bacterial strains in a way that correlates with their genome-based taxonomic classification. Importantly, the chemical noses classified artificial models of obesity-associated gut microbiota, and further succeeded in detecting sleep disorder in mice through comparative analysis of normal and abnormal mouse gut microbiota. Our techniques thus allow analyzing complex bacterial samples far more quickly, simply, and inexpensively than common metagenome-based methods, which offers a powerful and complementary tool for the practical analysis of the gut microbiome.},
}
@article {pmid35685770,
year = {2022},
author = {Bowers, SJ and Summa, KC and Thompson, RS and González, A and Vargas, F and Olker, C and Jiang, P and Lowry, CA and Dorrestein, PC and Knight, R and Wright, KP and Fleshner, M and Turek, FW and Vitaterna, MH},
title = {A Prebiotic Diet Alters the Fecal Microbiome and Improves Sleep in Response to Sleep Disruption in Rats.},
journal = {Frontiers in neuroscience},
volume = {16},
number = {},
pages = {889211},
doi = {10.3389/fnins.2022.889211},
pmid = {35685770},
issn = {1662-4548},
abstract = {Sleep disruption is a challenging and exceedingly common physiological state that contributes to a wide range of biochemical and molecular perturbations and has been linked to numerous adverse health outcomes. Modern society exerts significant pressure on the sleep/wake cycle via myriad factors, including exposure to electric light, psychological stressors, technological interconnection, jet travel, shift work, and widespread use of sleep-affecting compounds. Interestingly, recent research has identified a link between the microbiome and the regulation of sleep, suggesting that interventions targeting the microbiome may offer unique therapeutic approaches to challenges posed by sleep disruption. In this study, we test the hypothesis that administration of a prebiotic diet containing galactooligosaccharides (GOS) and polydextrose (PDX) in adult male rats improves sleep in response to repeated sleep disruption and during recovery sleep. We found that animals fed the GOS/PDX prebiotic diet for 4 weeks exhibit increased non-rapid eye movement (NREM) and rapid eye movement (REM) sleep during 5 days of sleep disruption and increased total sleep time during 24 h of recovery from sleep disruption compared to animals fed a control diet, despite similar baseline sleep characteristics. Further, the GOS/PDX prebiotic diet led to significant changes in the fecal microbiome. Consistent with previous reports, the prebiotic diet increased the relative abundance of the species Parabacteroides distasonis, which positively correlated with sleep parameters during recovery sleep. Taken together, these findings suggest that the GOS/PDX prebiotic diet may offer an approach to improve resilience to the physiologic challenge of sleep disruption, in part through impacts on the microbiome.},
}
@article {pmid35685081,
year = {2022},
author = {Zhang, L and Ai, T and Xie, C and Xia, W and Zhang, Y and Liao, H and Jia, L and Fan, Y and Xu, J},
title = {Lower airway microbiome of children with recurrent wheezing: a clinical cohort study.},
journal = {Translational pediatrics},
volume = {11},
number = {5},
pages = {696-705},
doi = {10.21037/tp-22-165},
pmid = {35685081},
issn = {2224-4344},
abstract = {Background: Wheezing is one of the most common respiratory symptoms in childhood especially in infants. In recent years, the incidence of recurrent wheezing is on the rise worldwide. To investigate the lower airway microbiota in patients with recurrent wheezing and provide insights into clinical diagnosis and treatment.<br><br>Methods: This study initially enrolled 45 hospitalised children with recurrent wheezing symptoms awaiting complete fiberoptic bronchoscopy. Of these, 13 children with tracheobronchomalacia were excluded. The final population included 32 participants (group A). The control group comprised 23 children who inhaled a foreign body and were admitted to the hospital for fiberoptic bronchoscopy within 24 hours (group B). Deoxyribonucleic acid (DNA) was extracted from the bronchoalveolar lavage fluid (BALF) and amplified for the 16S ribosomal Ribonucleic Acid (rRNA) gene, and sequencing of the microbiome was performed using the Illumina Nova Seq 6000 system.<br><br>Results: There were significant differences in the gestational duration (P=0.0458), mode of delivery (P=0.0261), and allergy status (P=0.0000) between groups A and B, but they had similar richness (P=0.8574). There was also a marked difference in the diversity of flora composition between the two groups (P=0.0095). The three most common phyla of microbiota in the two groups were Proteobacteria, Firmicutes, and Bacteroidetes. Species with notably different phyla included Proteobacteria, Bacteroidota, Fusobacteriota, and Acidobacteriota. There was a significant enrichment in the of Proteobacteria and lower levels of Bacteroidota, Fusobacteriota, and Acidobacteriota in group A compared to that in group B.<br><br>Conclusions: Significant changes occur in the lower airway microbiota during recurrent wheezing in children. The discovery of beneficial airway bacteria may facilitate the prevention and treatment of recurrent wheezing or asthma in children.},
}
@article {pmid35684340,
year = {2022},
author = {Nandwana, V and Nandwana, NK and Das, Y and Saito, M and Panda, T and Das, S and Almaguel, F and Hosmane, NS and Das, BC},
title = {The Role of Microbiome in Brain Development and Neurodegenerative Diseases.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {11},
pages = {},
doi = {10.3390/molecules27113402},
pmid = {35684340},
issn = {1420-3049},
abstract = {Hundreds of billions of commensal microorganisms live in and on our bodies, most of which colonize the gut shortly after birth and stay there for the rest of our lives. In animal models, bidirectional communications between the central nervous system and gut microbiota (Gut-Brain Axis) have been extensively studied, and it is clear that changes in microbiota composition play a vital role in the pathogenesis of various neurodevelopmental and neurodegenerative disorders, such as Autism Spectrum Disorder, Alzheimer's disease, Parkinson's disease, Multiple Sclerosis, Amyotrophic Lateral Sclerosis, anxiety, stress, and so on. The makeup of the microbiome is impacted by a variety of factors, such as genetics, health status, method of delivery, environment, nutrition, and exercise, and the present understanding of the role of gut microbiota and its metabolites in the preservation of brain functioning and the development of the aforementioned neurological illnesses is summarized in this review article. Furthermore, we discuss current breakthroughs in the use of probiotics, prebiotics, and synbiotics to address neurological illnesses. Moreover, we also discussed the role of boron-based diet in memory, boron and microbiome relation, boron as anti-inflammatory agents, and boron in neurodegenerative diseases. In addition, in the coming years, boron reagents will play a significant role to improve dysbiosis and will open new areas for researchers.},
}
@article {pmid35684099,
year = {2022},
author = {Gold, MS and Quinn, PJ and Campbell, DE and Peake, J and Smart, J and Robinson, M and O'Sullivan, M and Vogt, JK and Pedersen, HK and Liu, X and Pazirandeh-Micol, E and Heine, RG},
title = {Effects of an Amino Acid-Based Formula Supplemented with Two Human Milk Oligosaccharides on Growth, Tolerability, Safety, and Gut Microbiome in Infants with Cow's Milk Protein Allergy.},
journal = {Nutrients},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/nu14112297},
pmid = {35684099},
issn = {2072-6643},
abstract = {This open-label, non-randomized, multicenter trial (Registration: NCT03661736) aimed to assess if an amino acid-based formula (AAF) supplemented with two human milk oligosaccharides (HMO) supports normal growth and is well tolerated in infants with a cow's milk protein allergy (CMPA). Term infants aged 1-8 months with moderate-to-severe CMPA were enrolled. The study formula was an AAF supplemented with 2'-fucosyllactose (2'-FL) and lacto-N-neotetraose (LNnT). Infants were fed the study formula for 4 months and were offered to remain on the formula until 12 months of age. Tolerance and safety were assessed throughout the trial. Out of 32 infants (mean age 18.6 weeks; 20 (62.5%) male), 29 completed the trial. During the 4-month principal study period, the mean weight-for-age Z score (WAZ) increased from -0.31 at the baseline to +0.28 at the 4-months' follow-up. Linear and head growth also progressed along the WHO child growth reference, with a similar small upward trend. The formula was well tolerated and had an excellent safety profile. When comparing the microbiome at the baseline to the subsequent visits, there was a significant on-treatment enrichment in HMO-utilizing bifidobacteria, which was associated with a significant increase in fecal short-chain fatty acids. In addition, we observed a significant reduction in the abundance of fecal Proteobacteria, suggesting that the HMO-supplemented study formula partially corrected the gut microbial dysbiosis in infants with CMPA.},
}
@article {pmid35683097,
year = {2022},
author = {Radziemska, M and Gusiatin, MZ and Cydzik-Kwiatkowska, A and Blazejczyk, A and Kumar, V and Kintl, A and Brtnicky, M},
title = {Effect of Biochar on Metal Distribution and Microbiome Dynamic of a Phytostabilized Metalloid-Contaminated Soil Following Freeze-Thaw Cycles.},
journal = {Materials (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/ma15113801},
pmid = {35683097},
issn = {1996-1944},
support = {2019/03/X/NZ9/01276//Polish National Science Centre/ ; },
abstract = {In the present paper the effectiveness of biochar-aided phytostabilization of metal/metalloid-contaminated soil under freezing-thawing conditions and using the metal tolerating test plant Lolium perenne L. is comprehensively studied. The vegetative experiment consisted of plants cultivated for over 52 days with no exposure to freezing-thawing in a glass greenhouse, followed by 64 days under freezing-thawing in a temperature-controlled apparatus and was carried out in initial soil derived from a post-industrial urban area, characterized by the higher total content of Zn, Pb, Cu, Cr, As and Hg than the limit values included in the classification provided by the Regulation of the Polish Ministry of Environment. According to the substance priority list published by the Toxic Substances and Disease Registry Agency, As, Pb, and Hg are also indicated as being among the top three most hazardous substances. The initial soil was modified by biochar obtained from willow chips. The freeze-thaw effect on the total content of metals/metalloids (metal(-loid)s) in plant materials (roots and above-ground parts) and in phytostabilized soils (non- and biochar-amended) as well as on metal(-loid) concentration distribution/redistribution between four BCR (community bureau of reference) fractions extracted from phytostabilized soils was determined. Based on metal(-loid)s redistribution in phytostabilized soils, their stability was evaluated using the reduced partition index (Ir). Special attention was paid to investigating soil microbial composition. In both cases, before and after freezing-thawing, biochar increased plant biomass, soil pH value, and metal(-loid)s accumulation in roots, and decreased metal(-loid)s accumulation in stems and total content in the soil, respectively, as compared to the corresponding non-amended series (before and after freezing-thawing, respectively). In particular, in the phytostabilized biochar-amended series after freezing-thawing, the recorded total content of Zn, Cu, Pb, and As in roots substantially increased as well as the Hg, Cu, Cr, and Zn in the soil was significantly reduced as compared to the corresponding non-amended series after freezing-thawing. Moreover, exposure to freezing-thawing itself caused redistribution of examined metal(-loid)s from mobile and/or potentially mobile into the most stable fraction, but this transformation was favored by biochar presence, especially for Cu, Pb, Cr, and Hg. While freezing-thawing greatly affected soil microbiome composition, biochar reduced the freeze-thaw adverse effect on bacterial diversity and helped preserve bacterial groups important for efficient soil nutrient conversion. In biochar-amended soil exposed to freezing-thawing, psychrotolerant and trace element-resistant genera such as Rhodococcus sp. or Williamsia sp. were most abundant.},
}
@article {pmid35682976,
year = {2022},
author = {Ludwig-Müller, J},
title = {What Can We Learn from -Omics Approaches to Understand Clubroot Disease?.},
journal = {International journal of molecular sciences},
volume = {23},
number = {11},
pages = {},
doi = {10.3390/ijms23116293},
pmid = {35682976},
issn = {1422-0067},
abstract = {Clubroot is one of the most economically significant diseases worldwide. As a result, many investigations focus on both curing the disease and in-depth molecular studies. Although the first transcriptome dataset for the clubroot disease describing the clubroot disease was published in 2006, many different pathogen-host plant combinations have only recently been investigated and published. Articles presenting -omics data and the clubroot pathogen Plasmodiophora brassicae as well as different host plants were analyzed to summarize the findings in the richness of these datasets. Although genome data for the protist have only recently become available, many effector candidates have been identified, but their functional characterization is incomplete. A better understanding of the life cycle is clearly required to comprehend its function. While only a few proteome studies and metabolome analyses were performed, the majority of studies used microarrays and RNAseq approaches to study transcriptomes. Metabolites, comprising chemical groups like hormones were generally studied in a more targeted manner. Furthermore, functional approaches based on such datasets have been carried out employing mutants, transgenic lines, or ecotypes/cultivars of either Arabidopsis thaliana or other economically important host plants of the Brassica family. This has led to new discoveries of potential genes involved in disease development or in (partial) resistance or tolerance to P. brassicae. The overall contribution of individual experimental setups to a larger picture will be discussed in this review.},
}
@article {pmid35682625,
year = {2022},
author = {Zaborowska, M and Wyszkowska, J and Borowik, A and Kucharski, J},
title = {Effect of Separate and Combined Toxicity of Bisphenol A and Zinc on the Soil Microbiome.},
journal = {International journal of molecular sciences},
volume = {23},
number = {11},
pages = {},
doi = {10.3390/ijms23115937},
pmid = {35682625},
issn = {1422-0067},
support = {30.610.006-110//University of Warmia and Mazury in Olsztyn, Faculty of Agriculture and Forestry, Department of Soil Science and Microbiology/ ; 010/RID/2018/19//Minister of Education and Science in the range of the program entitled &quot;Regional Initiative of Ex-cellence&quot; for the years 2019-2022/ ; },
abstract = {The research objective was established by taking into account common sources of soil contamination with bisphenol A (B) and zinc (Zn2+), as well as the scarcity of data on the effect of metabolic pathways involved in the degradation of organic compounds on the complexation of zinc in soil. Therefore, the aim of this study was to determine the spectrum of soil homeostasis disorders arising under the pressure of both the separate and combined toxicity of bisphenol A and Zn2+. With a broad pool of indicators, such as indices of the effect of xenobiotics (IFX), humic acid (IFH), plants (IFP), colony development (CD), ecophysiological diversity (EP), the Shannon-Weaver and the Simpson indices, as well as the index of soil biological fertility (BA21), the extent of disturbances was verified on the basis of enzymatic activity, microbiological activity, and structural diversity of the soil microbiome. A holistic character of the study was achieved, having determined the indicators of tolerance (IT) of Sorghum Moench (S) and Panicum virgatum (P), the ratio of the mass of their aerial parts to roots (PR), and the SPAD leaf greenness index. Bisphenol A not only failed to perform a complexing role towards Zn2+, but in combination with this heavy metal, had a particularly negative effect on the soil microbiome and enzymatic activity. The NGS analysis distinguished certain unique genera of bacteria in all objects, representing the phyla Actinobacteriota and Proteobacteria, as well as fungi classified as members of the phyla Ascomycota and Basidiomycota. Sorghum Moench (S) proved to be more sensitive to the xenobiotics than Panicum virgatum (P).},
}
@article {pmid35682588,
year = {2022},
author = {Gréau, L and Blaudez, D and Heintz, D and Zumsteg, J and Billet, D and Cébron, A},
title = {Response of Poplar and Associated Fungal Endophytic Communities to a PAH Contamination Gradient.},
journal = {International journal of molecular sciences},
volume = {23},
number = {11},
pages = {},
doi = {10.3390/ijms23115909},
pmid = {35682588},
issn = {1422-0067},
support = {ANR-19-CE34-0009//Agence Nationale de la Recherche/ ; },
abstract = {Microbial populations associated to poplar are well described in non-contaminated and metal-contaminated environments but more poorly in the context of polycyclic aromatic hydrocarbon (PAH) contamination. This study aimed to understand how a gradient of phenanthrene (PHE) contamination affects poplar growth and the fungal microbiome in both soil and plant endosphere (roots, stems and leaves). Plant growth and fitness parameters indicated that the growth of Populus canadensis was impaired when PHE concentration increased above 400 mg kg-1. Values of alpha-diversity indicators of fungal diversity and richness were not affected by the PHE gradient. The PHE contamination had a stronger impact on the fungal community composition in the soil and root compartments compared to that of the aboveground organs. Most of the indicator species whose relative abundance was correlated with PHE contamination decreased along the gradient indicating a toxic effect of PHE on these fungal OTUs (Operational Taxonomic Units). However, the relative abundance of some OTUs such as Cadophora, Alternaria and Aspergillus, potentially linked to PHE degradation or being plant-beneficial taxa, increased along the gradient. Finally, this study allowed a deeper understanding of the dual response of plant and fungal communities in the case of a soil PAH contamination gradient leading to new perspectives on fungal assisted phytoremediation.},
}
@article {pmid35682578,
year = {2022},
author = {Ustjanzew, A and Sencio, V and Trottein, F and Faber, J and Sandhoff, R and Paret, C},
title = {Interaction between Bacteria and the Immune System for Cancer Immunotherapy: The α-GalCer Alliance.},
journal = {International journal of molecular sciences},
volume = {23},
number = {11},
pages = {},
doi = {10.3390/ijms23115896},
pmid = {35682578},
issn = {1422-0067},
abstract = {Non-conventional T cells, such as γδ T and invariant natural killer T (iNKT) cells, are emerging players in fighting cancer. Alpha-galactosylceramide (α-GalCer) is used as an exogenous ligand to activate iNKT cells. Human cells don't have a direct pathway producing α-GalCer, which, however, can be produced by bacteria. We searched the literature for bacteria strains that are able to produce α-GalCer and used available sequencing data to analyze their presence in human tumor tissues and their association with survival. The modulatory effect of antibiotics on the concentration of α-GalCer was analyzed in mice. The human gut bacteria Bacteroides fragilis, Bacteroides vulgatus, and Prevotella copri produce α-GalCer structures that are able to activate iNKT cells. In mice, α-GalCer was depleted upon treatment with vancomycin. The three species were detected in colon adenocarcinoma (COAD) and rectum adenocarcinoma tissues, and Prevotella copri was also detected in bone tumors and glioblastoma tissues. Bacteroides vulgatus in COAD tissues correlated with better survival. In conclusion, α-GalCer-producing bacteria are part of the human gut microbiome and can infiltrate tumor tissues. These results suggest a new mechanism of interaction between bacteria and immune cells: α-GalCer produced by bacteria may activate non-conventional T cells in tumor tissues, where they can exert a direct or indirect anti-tumor activity.},
}
@article {pmid35682558,
year = {2022},
author = {Yang, J and Hamade, M and Wu, Q and Wang, Q and Axtell, R and Giri, S and Mao-Draayer, Y},
title = {Current and Future Biomarkers in Multiple Sclerosis.},
journal = {International journal of molecular sciences},
volume = {23},
number = {11},
pages = {},
doi = {10.3390/ijms23115877},
pmid = {35682558},
issn = {1422-0067},
support = {R01AI137047/NH/NIH HHS/United States ; R01EY027346/NH/NIH HHS/United States ; RG-1807-31964//National Multiple Sclerosis Society/ ; UM1-AI110557-05//National Institute of Allergy and Infectious Diseases/ ; UM1-AI144298-01//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {Multiple sclerosis (MS) is a debilitating autoimmune disorder. Currently, there is a lack of effective treatment for the progressive form of MS, partly due to insensitive readout for neurodegeneration. The recent development of sensitive assays for neurofilament light chain (NfL) has made it a potential new biomarker in predicting MS disease activity and progression, providing an additional readout in clinical trials. However, NfL is elevated in other neurodegenerative disorders besides MS, and, furthermore, it is also confounded by age, body mass index (BMI), and blood volume. Additionally, there is considerable overlap in the range of serum NfL (sNfL) levels compared to healthy controls. These confounders demonstrate the limitations of using solely NfL as a marker to monitor disease activity in MS patients. Other blood and cerebrospinal fluid (CSF) biomarkers of axonal damage, neuronal damage, glial dysfunction, demyelination, and inflammation have been studied as actionable biomarkers for MS and have provided insight into the pathology underlying the disease process of MS. However, these other biomarkers may be plagued with similar issues as NfL. Using biomarkers of a bioinformatic approach that includes cellular studies, micro-RNAs (miRNAs), extracellular vesicles (EVs), metabolomics, metabolites and the microbiome may prove to be useful in developing a more comprehensive panel that addresses the limitations of using a single biomarker. Therefore, more research with recent technological and statistical approaches is needed to identify novel and useful diagnostic and prognostic biomarker tools in MS.},
}
@article {pmid35682493,
year = {2022},
author = {Vergadi, E and Rouva, G and Angeli, M and Galanakis, E},
title = {Infectious Diseases Associated with Desert Dust Outbreaks: A Systematic Review.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {11},
pages = {},
doi = {10.3390/ijerph19116907},
pmid = {35682493},
issn = {1660-4601},
abstract = {BACKGROUND: Desert dust outbreaks and dust storms are the major source of particulate matter globally and pose a major threat to human health. We investigated the microorganisms transported with desert dust particles and evaluated their potential impact on human health.<br><br>METHODS: A systematic review of all reports on the association between non-anthropogenic desert dust pollution, dust microorganisms and human health is conducted.<br><br>RESULTS: In total, 51 articles were included in this review. The affected regions studied were Asia (32/51, 62.7%) followed by Europe (9/51, 17.6%), America (6/51, 11.8%), Africa (4/51, 7.8%) and Australia (1/51, 2.0%). The Sahara Desert was the most frequent source of dust, followed by Asian and American deserts. In 39/51 studies the dust-related microbiome was analyzed, while, in 12/51 reports, the association of desert dust with infectious disease outbreaks was examined. Pathogenic and opportunistic agents were isolated from dust in 24/39 (61.5%) and 29/39 (74.4%) of the studies, respectively. A significant association of dust events with infectious disease outbreaks was found in 10/12 (83.3%) reports. The infectious diseases that were mostly investigated with dust outbreaks were pneumonia, respiratory tract infections, COVID-19, pulmonary tuberculosis and coccidioidomycosis.<br><br>CONCLUSIONS: Desert dust outbreaks are vehicles of a significant number of pathogenic or opportunistic microorganisms and limited data indicate an association between dust events and infectious disease outbreaks. Further research is required to strengthen the correlation between dust events and infectious diseases and subsequently guide preventive public health measures.},
}
@article {pmid35682310,
year = {2022},
author = {Amro, B and Ramirez Aristondo, ME and Alsuwaidi, S and Almaamari, B and Hakim, Z and Tahlak, M and Wattiez, A and Koninckx, PR},
title = {New Understanding of Diagnosis, Treatment and Prevention of Endometriosis.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {11},
pages = {},
doi = {10.3390/ijerph19116725},
pmid = {35682310},
issn = {1660-4601},
abstract = {For 100 years, pelvic endometriosis has been considered to originate from the implantation of endometrial cells following retrograde menstruation or metaplasia. Since some observations, such as the clonal aspect, the biochemical variability of lesions and endometriosis in women without endometrium, the genetic-epigenetic (G-E) theory describes that endometriosis only begins after a series of cumulative G-E cellular changes. This explains that the endometriotic may originate from any pluripotent cell apart from the endometrium, that 'endometrium-like cells' can harbour important G-E differences, and that the risk is higher in predisposed women with more inherited incidents. A consequence is a high risk after puberty which decreases progressively thereafter. Considering a 10-year delay between initiation and performing a laparoscopy, this was observed in the United Arab Emirates, Belgium, France and USA. The subsequent growth varies with the G-E changes and the environment but is self-limiting probably because of the immunologic reaction and fibrosis. That each lesion has a different set of G-E incidents explains the variability of pain and the response to hormonal treatment. New lesions may develop, but recurrences after surgical excision are rare. The fibrosis around endometriosis belongs to the body and does not need to be removed. This suggests conservative excision or minimal bowel without safety margins and superficial treatment of ovarian endometriosis. This G-E concept also suggests prevention by decreasing oxidative stress from retrograde menstruation or the peritoneal microbiome. This suggests the prevention of vaginal infections and changes in the gastrointestinal microbiota through food intake and exercise. In conclusion, a higher risk of initiating endometriosis during adolescence was observed in UAE, France, Belgium and USA. This new understanding and the limited growth opens perspectives for earlier diagnosis and better treatment.},
}
@article {pmid35681899,
year = {2022},
author = {de Souza, OF and Vecchi, B and Gumina, E and Matté, F and Gazoni, FL and Hernandez-Velasco, X and Hall, JW and Stefanello, C and Layton, S},
title = {Development and Evaluation of a Commercial Direct-Fed Microbial (Zymospore®) on the Fecal Microbiome and Growth Performance of Broiler Chickens under Experimental Challenge Conditions.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/ani12111436},
pmid = {35681899},
issn = {2076-2615},
abstract = {Direct-fed microbials (DFM) are added to broiler chicken diets in order to promote the proliferation of beneficial intestinal bacterial populations, which may lead to gains in performance efficiency and, potentially, reduce the level of enteric pathogens in the broiler chickens. The selection and laboratory evaluation of Bacillus subtilis strains as well as the experimental trial results of a novel Bacillus-based commercial DFM product are described. Fifteen wild-type Bacillus subtilis strains were characterized and assayed for their enzyme production capability, spore resistance to pH, salinity, and temperature, and ability to inhibit the growth of E. coli and Salmonella spp. The final DFM formulation was evaluated and compared to an antibiotic growth promoter (AGPs) in two experimental trials. In Experiment 1, broilers were given a defined challenge of Eimeria spp. and Clostridium perfringens to induce intestinal dysbiosis. The optimal dose of the DFM was determined to be 0.3 kg/ton of feed. At this dose, the broilers fed the DFM performed as well as the Flavomycin®-fed broilers. Further, intestinal microbiome analysis indicates that the use of the DFM enhances bacterial diversity of the gut flora by day 5 of age, increasing levels of lactic acid bacteria (LAB) and Clostridiales by 25 days of age, which may enhance the digestion of feed and promote growth of the birds. In Experiment 2, the broilers were raised on recycled litter and given an undefined challenge orally to mimic commercial growth conditions. In this trial, the DFM performed as well as the bacitracin methylene disalicylate (BMD)-11%-fed birds. The results of the present studies suggest that this novel DFM, Zymospore®, improves the performance of broiler chickens under experimental challenge conditions as effective as an AGP, providing a safe and effective substitute to the poultry industry.},
}
@article {pmid35681824,
year = {2022},
author = {Hall, JA and Isaiah, A and McNett, ERL and Klopfenstein, JJ and Davis, TZ and Suchodolski, JS and Bobe, G},
title = {Supranutritional Selenium-Yeast Supplementation of Beef Cows during the Last Trimester of Pregnancy Results in Higher Whole-Blood Selenium Concentrations in Their Calves at Weaning, but Not Enough to Improve Nasal Microbial Diversity.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/ani12111360},
pmid = {35681824},
issn = {2076-2615},
support = {None//USDA FY18 Animal Health and Disease Program/ ; },
abstract = {We previously reported that feeding Se-biofortified alfalfa hay to weaned beef calves in a preconditioning program increases whole-blood Se (WB-Se) concentrations and nasal microbiome abundance and diversity during the preconditioning period, decreases morbidity and mortality during the feedlot period, and increases carcass weight and quality at slaughter. The objective of the current study was to see whether similar improvements can be achieved through Se supplementation of dams during various pregnancy trimesters. In a two-year experimental study, 80 Angus-cross cows received once-weekly Se-yeast boluses containing 105 mg of Se, during either the first (TR-1), second (TR-2), or third (TR-3) pregnancy trimester, or were not bolused (CTR). Whole-blood Se concentrations were higher from CTR, to TR-1, to TR-2, and to TR-3 in newborn calves (all p < 0.01). At weaning, only calves from TR-3 mothers had higher WB-Se concentrations compared with calves from CTR mothers (p = 0.02), and no significant differences in nasal microbiome abundance and diversity or nasal microbiota were observed. In the feedlot period, morbidity was low, and no differences were observed. At slaughter, no differences in carcass weight and quality were observed. In conclusion, Se supplementation of pregnant cows is effective for increasing WB-Se concentration of newborn calves, and the increase can be sustained until weaning for calves born to TR-3 dams. However, the increase in WB-Se concentrations is small and does not result in beneficial changes in the nasal microbiome. Thus, calves should be fed Se-biofortified forages again at weaning in a preconditioning program in order to diversify the nasal microbiome prior to entering the feedlot.},
}
@article {pmid35681493,
year = {2022},
author = {Das De, T and Sharma, P and Tevatiya, S and Chauhan, C and Kumari, S and Yadav, P and Singla, D and Srivastava, V and Rani, J and Hasija, Y and Pandey, KC and Kajla, M and Dixit, R},
title = {Bidirectional Microbiome-Gut-Brain-Axis Communication Influences Metabolic Switch-Associated Responses in the Mosquito Anopheles culicifacies.},
journal = {Cells},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/cells11111798},
pmid = {35681493},
issn = {2073-4409},
support = {Health-NIMR-2017-01-03/AP/db//Tata Trusts/ ; No.3/1/3/ICRMR-VFS/HRD/2/2016//Indian Council of Medical Research/ ; 3/1/3/PDF(18)/2018-HRD//Indian Council of Medical Research/ ; },
abstract = {The periodic ingestion of a protein-rich blood meal by adult female mosquitoes causes a drastic metabolic change in their innate physiological status, which is referred to as a 'metabolic switch'. While understanding the neural circuits for host-seeking is modestly attended, how the gut 'metabolic switch' modulates brain functions, and resilience to physiological homeostasis, remains unexplored. Here, through a comparative brain RNA-Seq study, we demonstrate that the protein-rich diet induces the expression of brain transcripts related to mitochondrial function and energy metabolism, possibly causing a shift in the brain's engagement to manage organismal homeostasis. A dynamic mRNA expression pattern of neuro-signaling and neuro-modulatory genes in both the gut and brain likely establishes an active gut-brain communication. The disruption of this communication through decapitation does not affect the modulation of the neuro-modulator receptor genes in the gut. In parallel, an unusual and paramount shift in the level of neurotransmitters (NTs), from the brain to the gut after blood feeding, further supports the idea of the gut's ability to serve as a 'second brain'. After blood-feeding, a moderate enrichment of the gut microbial population, and altered immunity in the gut of histamine receptor-silenced mosquitoes, provide initial evidence that the gut-microbiome plays a crucial role in gut-brain-axis communication. Finally, a comparative metagenomics evaluation of the gut microbiome highlighted that blood-feeding enriches the family members of the Morganellaceae and Pseudomonadaceae bacterial communities. The notable observation of a rapid proliferation of Pseudomonas bacterial sp. and tryptophan enrichment in the gut correlates with the suppression of appetite after blood-feeding. Additionally, altered NTs dynamics of naïve and aseptic mosquitoes provide further evidence that gut-endosymbionts are key modulators for the synthesis of major neuroactive molecules. Our data establish a new conceptual understanding of microbiome-gut-brain-axis communication in mosquitoes.},
}
@article {pmid35681429,
year = {2022},
author = {Uhlig, F and Hyland, NP},
title = {Making Sense of Quorum Sensing at the Intestinal Mucosal Interface.},
journal = {Cells},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/cells11111734},
pmid = {35681429},
issn = {2073-4409},
support = {Marie Skłodowska-Curie grant agreement No 754535//European Union/ ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; },
abstract = {The gut microbiome can produce metabolic products that exert diverse activities, including effects on the host. Short chain fatty acids and amino acid derivatives have been the focus of many studies, but given the high microbial density in the gastrointestinal tract, other bacterial products such as those released as part of quorum sensing are likely to play an important role for health and disease. In this review, we provide of an overview on quorum sensing (QS) in the gastrointestinal tract and summarise what is known regarding the role of QS molecules such as auto-inducing peptides (AIP) and acyl-homoserine lactones (AHL) from commensal, probiotic, and pathogenic bacteria in intestinal health and disease. QS regulates the expression of numerous genes including biofilm formation, bacteriocin and toxin secretion, and metabolism. QS has also been shown to play an important role in the bacteria-host interaction. We conclude that the mechanisms of action of QS at the intestinal neuro-immune interface need to be further investigated.},
}
@article {pmid35681291,
year = {2022},
author = {Li, J and Zou, C and Liu, Y},
title = {Amelioration of Ovalbumin-Induced Food Allergy in Mice by Targeted Rectal and Colonic Delivery of Cyanidin-3-O-Glucoside.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/foods11111542},
pmid = {35681291},
issn = {2304-8158},
support = {2019YFC1605003-3//National Key Research and Development Program of China/ ; ZR2020001//Jimei University Young Talent Program/ ; },
abstract = {Targeted rectal and colonic delivery is an effective strategy to exploit the biological functions of polyphenols. This work investigated the anti-food allergy (FA) activity of cyanidin-3-O-glucoside (C3G) delivered by enteric sodium alginate in vivo. The results showed that through targeted rectal and colonic delivery, the C3G showed better results in ameliorating clinical allergic symptoms, diarrhea, and serological indicators including ovalbumin-specific IgE, histamine, and mast cell protease-1. The C3G was more efficient in enhancing the intestinal epithelial barrier by up-regulating the tight junction protein expression and promoting secretory IgA and β-defensin secretion. The improved bioactivity in regulating T helper (Th)1/Th2 immune balance in the intestinal mucosa was also observed. Compared with the intestinal microbiota structure of the model group, targeted rectal and colonic delivery of C3G was able to bring the abundance of Bacteroidota and Firmicutes close to the levels found in normal mice. Furthermore, there was an evident increase in beneficial bacteria in the intestinal flora, such as Lactobacillus and Odoribacter, and a decrease in pathogenic bacteria like Helicobacter and Turicibacter. Therefore, the anti-FA activity of C3G could be increased via targeted rectal and colonic delivery, while the mechanism might be attributed to the regulation of intestinal microecological homeostasis.},
}
@article {pmid35681289,
year = {2022},
author = {Yang, Y and Zhou, Z and Liu, Y and Xu, X and Xu, Y and Zhou, W and Chen, S and Mao, J},
title = {Non-Alcoholic Components in Huangjiu as Potential Factors Regulating the Intestinal Barrier and Gut Microbiota in Mouse Model of Alcoholic Liver Injury.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/foods11111537},
pmid = {35681289},
issn = {2304-8158},
support = {22138004//National Natural Science Foundation of China/ ; 32001828//National Natural Science Foundation of China/ ; },
abstract = {Different alcoholic beverages and drinking patterns might exert divergent impacts on alcoholic liver disease (ALD) progression. Whether the abundant non-alcoholic components (NAC) in fermented wine could alleviate ethanol (EtOH)-induced adverse influences on the liver remains unknown. Hence, the chronic ALD mouse model was established to compare the effects of Huangjiu (a typical fermented wine) and EtOH feeding on the liver, intestinal barrier, gut microbiota, and intestinal short-chain fatty acids (SCFAs) content. Although Huangjiu intake led to slight hepatic steatosis, it mitigated oxidative stress, inflammation, and intestinal damage relative to EtOH intake. In comparison with EtOH feeding, Huangjiu significantly improved the intestinal barrier integrity and reduced hepatic lipopolysaccharide levels by up-regulating the expression of intestinal tight junction proteins (ZO-1 and occludin) and antimicrobial activity peptides (Reg3β and Reg3γ). The administration of Huangjiu NAC partially restored alcohol-induced gut microbiota dysbiosis via recovering the abundance of Lactobacillus, Faecalibaculum, and Akkermansia. Moreover, mice receiving Huangjiu showed higher SCFAs levels (such as acetic acid and butyric acid) than those receiving EtOH. Huangjiu consumption resulted in lower hepatotoxicity than pure EtOH, at the same alcohol dose. The NAC in Huangjiu might attenuate the progression of ALD by regulating intestinal barrier function and microbiota-meditated gut ecology.},
}
@article {pmid35681245,
year = {2022},
author = {Li, M and Hong, L and Ye, W and Wang, Z and Shen, H},
title = {Phyllosphere bacterial and fungal communities vary with host species identity, plant traits and seasonality in a subtropical forest.},
journal = {Environmental microbiome},
volume = {17},
number = {1},
pages = {29},
pmid = {35681245},
issn = {2524-6372},
support = {GML2019ZD0408//Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; GML2019ZD0408//Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 31370446//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Phyllosphere microbes play important roles in host plant performance and fitness. Recent studies have suggested that tropical and temperate forests harbor diverse phyllosphere bacterial and fungal communities and their assembly is driven by host species identity and plant traits. However, no study has yet examined how seasonality (e.g. dry vs. wet seasons) influences phyllosphere microbial community assembly in natural forests. In addition, in subtropical forests characterized as the transitional zonal vegetation type from tropical to temperate forests, how tree phyllosphere microbial communities are assembled remains unknown. In this study, we quantified bacterial and fungal community structure and diversity on the leaves of 45 tree species with varying phylogenetic identities and importance values within a 20-ha lower subtropical evergreen broad-leaved forest plot in dry and wet seasons. We explored if and how the microbial community assembly varies with host species identity, plant traits and seasonality.<br><br>RESULTS: Phyllosphere microbial communities in the subtropical forest are more abundant and diverse than those in tropical and temperate forests, and the tree species share a "core microbiome" in either bacteria or fungi. Variations in phyllosphere bacterial and fungal community assembly are explained more by host species identity than by seasonality. There is a strong clustering of the phyllosphere microbial assemblage amongst trees by seasonality, and the seasonality effects are more pronounced on bacterial than fungal community assembly. Host traits have different effects on community compositions and diversities of both bacteria and fungi, and among them calcium concentration and importance value are the most powerful explaining variables for bacteria and fungi, respectively. There are significant evolutionary associations between host species and phyllosphere microbiome.<br><br>CONCLUSIONS: Our results suggest that subtropical tree phyllosphere microbial communities vary with host species identity, plant traits and seasonality. Host species identity, compared to seasonality, has greater effects on phyllosphere microbial community assembly, and such effects differ between bacterial and fungal communities. These findings advance our understanding of the patterns and drivers of phyllosphere microbial community assembly in zonal forests at a global scale.},
}
@article {pmid35681218,
year = {2022},
author = {Dawkins, JJ and Allegretti, JR and Gibson, TE and McClure, E and Delaney, M and Bry, L and Gerber, GK},
title = {Gut metabolites predict Clostridioides difficile recurrence.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {87},
pmid = {35681218},
issn = {2049-2618},
support = {R01 GM130777/GM/NIGMS NIH HHS/United States ; R35GM143056/GM/NIGMS NIH HHS/United States ; President's Scholar Award//Brigham Research Institute/ ; Junior Faculty Development Award//American College of Gastroenterology/ ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R21AI154075//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {BACKGROUND: Clostridioides difficile infection (CDI) is the most common hospital acquired infection in the USA, with recurrence rates > 15%. Although primary CDI has been extensively linked to gut microbial dysbiosis, less is known about the factors that promote or mitigate recurrence. Moreover, previous studies have not shown that microbial abundances in the gut measured by 16S rRNA amplicon sequencing alone can accurately predict CDI recurrence.<br><br>RESULTS: We conducted a prospective, longitudinal study of 53 non-immunocompromised participants with primary CDI. Stool sample collection began pre-CDI antibiotic treatment at the time of diagnosis, and continued up to 8 weeks post-antibiotic treatment, with weekly or twice weekly collections. Samples were analyzed using (1) 16S rRNA amplicon sequencing, (2) liquid chromatography/mass-spectrometry metabolomics measuring 1387 annotated metabolites, and (3) short-chain fatty acid profiling. The amplicon sequencing data showed significantly delayed recovery of microbial diversity in recurrent participants, and depletion of key anaerobic taxa at multiple time-points, including Clostridium cluster XIVa and IV taxa. The metabolomic data also showed delayed recovery in recurrent participants, and moreover mapped to pathways suggesting distinct functional abnormalities in the microbiome or host, such as decreased microbial deconjugation activity, lowered levels of endocannabinoids, and elevated markers of host cell damage. Further, using predictive statistical/machine learning models, we demonstrated that the metabolomic data, but not the other data sources, can accurately predict future recurrence at 1 week (AUC 0.77 [0.71, 0.86; 95% interval]) and 2 weeks (AUC 0.77 [0.69, 0.85; 95% interval]) post-treatment for primary CDI.<br><br>CONCLUSIONS: The prospective, longitudinal, and multi-omic nature of our CDI recurrence study allowed us to uncover previously unrecognized dynamics in the microbiome and host presaging recurrence, and, in particular, to elucidate changes in the understudied gut metabolome. Moreover, we demonstrated that a small set of metabolites can accurately predict future recurrence. Our findings have implications for development of diagnostic tests and treatments that could ultimately short-circuit the cycle of CDI recurrence, by providing candidate metabolic biomarkers for diagnostics development, as well as offering insights into the complex microbial and metabolic alterations that are protective or permissive for recurrence. Video Abstract.},
}
@article {pmid35681072,
year = {2022},
author = {Ferchiou, S and Caza, F and Villemur, R and Betoulle, S and St-Pierre, Y},
title = {Species- and site-specific circulating bacterial DNA in Subantarctic sentinel mussels Aulacomya atra and Mytilus platensis.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {9547},
pmid = {35681072},
issn = {2045-2322},
support = {RGPIN-2019-06607//National Sciences and Engineering Council of Canada/ ; RGPIN-2019-06607//National Sciences and Engineering Council of Canada/ ; RGPIN-2019-06607//National Sciences and Engineering Council of Canada/ ; RGPIN-2019-06607//National Sciences and Engineering Council of Canada/ ; },
abstract = {Impacts of climate changes are particularly severe in polar regions where warmer temperatures and reductions in sea-ice covers threaten the ecological integrity of marine coastal ecosystems. Because of their wide distribution and their ecological importance, mussels are currently used as sentinel organisms in monitoring programs of coastal ecosystems around the world. In the present study, we exploited the concept of liquid biopsy combined to a logistically friendly sampling method to study the hemolymphatic bacterial microbiome in two mussel species (Aulacomya atra and Mytilus platensis) in Kerguelen Islands, a remote Subantarctic volcanic archipelago. We found that the circulating microbiome signatures of both species differ significantly even though their share the same mussel beds. We also found that the microbiome differs significantly between sampling sites, often correlating with the particularity of the ecosystem. Predictive models also revealed that both species have distinct functional microbiota, and that the circulating microbiome of Aulacomya atra was more sensitive to changes induced by acute thermal stress when compared to Mytilus platensis. Taken together, our study suggests that defining circulating microbiome is a useful tool to assess the health status of marine ecosystems and to better understand the interactions between the sentinel species and their habitat.},
}
@article {pmid35680985,
year = {2022},
author = {Liu, C and Ng, SK and Ding, Y and Lin, Y and Liu, W and Wong, SH and Sung, JJ and Yu, J},
title = {Meta-analysis of mucosal microbiota reveals universal microbial signatures and dysbiosis in gastric carcinogenesis.},
journal = {Oncogene},
volume = {},
number = {},
pages = {},
pmid = {35680985},
issn = {1476-5594},
abstract = {The consistency of the associations between gastric mucosal microbiome and gastric cancer across studies remained unexamined. We aimed to identify universal microbial signatures in gastric carcinogenesis through a meta-analysis of gastric microbiome from multiple studies. Compositional and ecological profiles of gastric microbes across stages of gastric carcinogenesis were significantly altered. Meta-analysis revealed that opportunistic pathobionts Fusobacterium, Parvimonas, Veillonella, Prevotella and Peptostreptococcus were enriched in GC, while commensals Bifidobacterium, Bacillus and Blautia were depleted in comparison to SG. The co-occurring correlation strengths of GC-enriched bacteria were increased along disease progression while those of GC-depleted bacteria were decreased. Eight bacterial taxa, including Veillonella, Dialister, Granulicatella, Herbaspirillum, Comamonas, Chryseobacterium, Shewanella and Helicobacter, were newly identified by this study as universal biomarkers for robustly discriminating GC from SG, with an area under the curve (AUC) of 0.85. Moreover, H. pylori-positive samples exhibited reduced microbial diversity, altered microbiota community and weaker interactions among gastric microbes. Our meta-analysis demonstrated comprehensive and generalizable gastric mucosa microbial features associated with histological stages of gastric carcinogenesis, including GC associated bacteria, diagnostic biomarkers, bacterial network alteration and H. pylori influence.},
}
@article {pmid35680890,
year = {2022},
author = {Horn, KJ and Schopper, MA and Drigot, ZG and Clark, SE},
title = {Airway Prevotella promote TLR2-dependent neutrophil activation and rapid clearance of Streptococcus pneumoniae from the lung.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {3321},
pmid = {35680890},
issn = {2041-1723},
support = {K22AI143922//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; Research Program Grant//American Thoracic Society (American Thoracic Society, Inc.)/ ; Innovation Award//American Lung Association (Lung Association)/ ; Webb-Waring Biomedical Research Award//Boettcher Foundation/ ; },
abstract = {This study investigates how specific members of the lung microbiome influence the early immune response to infection. Prevotella species are a major component of the endogenous airway microbiota. Increased abundance of Prevotella melaninogenica correlates with reduced infection with the bacterial pathogen Streptococcus pneumoniae, indicating a potentially beneficial role. Here, we show that P. melaninogenica enhances protection against S. pneumoniae, resulting in rapid pathogen clearance from the lung and improved survival in a mouse lung co-infection model. This response requires recognition of P. melaninogenica lipoproteins by toll-like receptor (TLR)2, the induction of TNFα, and neutrophils, as the loss of any of these factors abrogates Prevotella-induced protection. Improved clearance of S. pneumoniae is associated with increased serine protease-mediated killing by lung neutrophils and restraint of P. melaninogenica-induced inflammation by IL-10 in co-infected mice. Together, these findings highlight innate immune priming by airway Prevotella as an important protective feature in the respiratory tract.},
}
@article {pmid35680712,
year = {2022},
author = {López-Bucio, J and Esparza-Reynoso, S and Pelagio-Flores, R},
title = {Nitrogen availability determines plant growth promotion and the induction of root branching by the probiotic fungus Trichoderma atroviride in Arabidopsis seedlings.},
journal = {Archives of microbiology},
volume = {204},
number = {7},
pages = {380},
pmid = {35680712},
issn = {1432-072X},
support = {A1-S-34768//Consejo Nacional de Ciencia y Tecnología/ ; },
abstract = {Plant growth-promoting fungi are integral components of the root microbiome that help the host resist biotic and abiotic stress while improving nutrient acquisition. Trichoderma atroviride is a common inhabitant of the rhizosphere, which establishes a perdurable symbiosis with plants through the emission of volatiles, diffusible compounds, and robust colonization. Currently, little is known on how the environment influences the Trichoderma-plant interaction. In this report, we assessed plant growth and root architectural reconfiguration of Arabidopsis seedlings grown in physical contact with T. atroviride under contrasting nitrate and ammonium availability. The shoot and root biomass accumulation and lateral root formation triggered by the fungus required high nitrogen supplements and involved nitrate reduction via AtNIA1 and NIA2. Ammonium supplementation did not restore biomass production boosted by T. atroviride in nia1nia2 double mutant, but instead fungal inoculation increased nitric oxide accumulation in Arabidopsis primary root tips depending upon nitrate supplements. N deprived seedlings were largely resistant to the effects of nitric oxide donor SNP triggering lateral root formation. T. atroviride enhanced expression of CHL1:GUS in root tips, particularly under high N supplements and required an intact CHL1 nitrate transporter to promote lateral root formation in Arabidopsis seedlings. These data imply that the developmental programs strengthened by Trichoderma and the underlying growth promotion in plants are dependent upon adequate nitrate nutrition and may involve nitric oxide as a second messenger.},
}
@article {pmid35680554,
year = {2022},
author = {Kuhl, LP and Marostica, PJC and Macedo, AJ and Kuhl, G and Siebert, M and Manica, D and Sekine, L and Schweiger, C},
title = {High microbiome variability in pediatric tracheostomy cannulas in patients with similar clinical characteristics.},
journal = {Brazilian journal of otorhinolaryngology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bjorl.2022.05.001},
pmid = {35680554},
issn = {1808-8686},
abstract = {OBJECTIVES: To evaluate the bacterial microbiome found in tracheostomy cannulas of a group of children diagnosed with glossoptosis secondary to Robin Sequence (RS), and its clinical implications.<br><br>METHODS: Pediatric patients were enrolled in the study at the time of the cannula change in the hospital. During this procedure, the removed cannula was collected and stored for amplicon sequencing of 16s rRNA. DNA extraction was performed using DNeasy PowerBiofilm Kit (QIAGEN® ‒ Cat nº 24000-50) while sequencing was performed with the S5 (Ion S5™ System, Thermo Fisher Scientific), following Brazilian Microbiome Project (BMP) protocol.<br><br>RESULTS: All 12 patients included in the study were using tracheostomy uncuffed cannulas of the same brand, had tracheostomy performed for over 1-year and had used the removed cannula for approximately 3-months. Most abundant genera found were Aggregatibacter, Pseudomonas, Haemophilus, Neisseria, Staphylococcus, Fusobacterium, Moraxella, Streptococcus, Alloiococcus, and Capnocytophaga. Individual microbiome of each individual was highly variable, not correlating to any particular clinical characteristic.<br><br>CONCLUSION: The microbiome of tracheostomy cannulas is highly variable, even among patients with similar clinical characteristics, making it challenging to determine a standard for normality.},
}
@article {pmid35680131,
year = {2022},
author = {Kim, HJ and Kim, JH and Han, S and Kim, W},
title = {Compositional alteration of the nasal microbiome and Staphylococcus aureus-characterized dysbiosis in the nasal mucosa of patients with allergic rhinitis.},
journal = {Clinical and experimental otorhinolaryngology},
volume = {},
number = {},
pages = {},
doi = {10.21053/ceo.2021.01928},
pmid = {35680131},
issn = {1976-8710},
abstract = {Objectives: Host-microbial commensalism can shape the innate immune responses in the nasal mucosa, and the microbial characteristics of the nasal mucus directly impact the mechanisms of initial allergic responses in the nasal epithelium. We sought to determine alterations of the microbial composition in the nasal mucus of patients with allergic rhinitis (AR) and to elucidate the interplay between dysbiosis of the nasal microbiome and allergic inflammation.<br><br>Methods: A total of 364,923 high-quality bacterial 16S ribosomal RNA-encoding gene sequence reads from 104 samples from the middle turbinate mucosa of healthy participants and patients with AR was obtained and analyzed using the Quantitative Insights into Microbial Ecology pipeline.<br><br>Results: We analyzed the microbiota in samples of nasal mucus from patients with AR (n = 42) and clinically healthy participants (n = 30). Proteobacteria (Ralstonia genus) and Actinobacteria (Propionibacterium genus) phyla were predominant in the nasal mucus of healthy subjects, whereas the Firmicutes (Staphylococcus genus) phylum was significantly abundant in the nasal mucus of patients with AR. Especially, Ralstonia genus were significantly dominant in the clinically healthy subjects. Additional pyrosequencing data from 32 subjects (healthy participants: N=15, AR patients: N=17) revealed a greater abundance of Staphylococcus epidermidis, Corynebacterium accolens, and Nocardia coeliaca, accounting for 41.55% of mapped sequences in the nasal mucus of healthy participants. The dysbiosis of nasal microbiome was more pronounced and Staphylococcus aureus exhibited the greatest abundance (37.69%) in the presence of microbial distribution in the nasal mucus of patients with AR depending on the positive response to house dust mites and patient age and height.<br><br>Conclusion: This study revealed alterations in the nasal microbiome that occur in the nasal mucus of patients with AR at the levels of microbial genera and species. S. aureus-dominant dysbiosis was distinctive in the nasal mucus of patients with AR, suggesting a role of host-microbial commensalism in allergic inflammation.},
}
@article {pmid35680095,
year = {2022},
author = {Rehner, J and Schmartz, GP and Groeger, L and Dastbaz, J and Ludwig, N and Hannig, M and Rupf, S and Seitz, B and Flockerzi, E and Berger, T and Reichert, MC and Krawczyk, M and Meese, E and Herr, C and Bals, R and Becker, SL and Keller, A and Müller, R and , },
title = {Systematic cross-biospecimen evaluation of DNA extraction kits for long- and short-read multi-metagenomic sequencing studies.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.gpb.2022.05.006},
pmid = {35680095},
issn = {2210-3244},
abstract = {High-quality DNA extraction is a crucial step in metagenomic studies. Bias by different isolation kits impairs the comparison across data sets. A trending topic is, however, the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases. We thus collected bile, stool, saliva, plaque, sputum, and conjunctival swab samples and performed DNA extraction with three commercial kits. For each combination of specimen type and DNA extraction, 20 GB metagenomic data were generated using short-read sequencing. While profiles of the specimen type showed close proximity to each other, we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kit. No kit outperformed all selected kits on every specimen. We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit. Depending on the specimen, our data indicate that over 10 GB of sequencing data are required to achieve sufficient resolution, but DNA-based identification was superior to identification by mass spectrometry. Finally, long-read nanopore sequencing confirmed the results (correlation coefficient > 0.98). Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.},
}
@article {pmid35679932,
year = {2022},
author = {Li, S and Ondon, BS and Ho, SH and Jiang, J and Li, F},
title = {Antibiotic resistant bacteria and genes in wastewater treatment plants: From occurrence to treatment strategies.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {156544},
doi = {10.1016/j.scitotenv.2022.156544},
pmid = {35679932},
issn = {1879-1026},
abstract = {This study aims to discuss the following: (1) occurrence and proliferation of antibiotic resistance in wastewater treatment plants (WWTPs); (2) factors influencing antibiotic resistance bacteria and genes in WWTPs; (3) tools to assess antibiotic resistance in WWTPs; (4) environmental contamination of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from WWTPs; (5) effects of ARB and ARGs from WWTPs on human health; and (6) treatment strategies. In general, resistant and multi-resistant bacteria, including Enterobacteriaceae, Pseudomonas aeruginosa, and Escherichia coli, exist in various processes of WWTPs. The existence of ARB and ARGs results from the high concentration of antibiotics in wastewater, which promote selective pressures on the local bacteria present in WWTPs. Thus, improving wastewater treatment technology and avoiding the misuse of antibiotics is critical to overcoming the threat of proliferation of ARBs and ARGs. Numerous factors can affect the development of ARB and ARGs in WWTPs. Abiotic factors can affect the bacterial community dynamics, thereby, affecting the applicability of ARB during the wastewater treatment process. Furthermore, the organic loads and other nutrients influence bacterial survival and growth. Specifically, molecular methods for the rapid characterization and detection of ARBs or their genes comprise DNA sequencing, real-time PCR, simple and multiplex PCR, and hybridization-based technologies, including micro- and macro-arrays. The reuse of effluent from WWTPs for irrigation is an efficient method to overcome water scarcity. However, there are also some potential environmental risks associated with this practice, such as increase in the levels of antibiotic resistance in the soil microbiome. Human mortality rates may significantly increase, as ARB can lead to resistance among several types of antibiotics or longer treatment times. Some treatment technologies, such as anaerobic and aerobic treatment, coagulation, membrane bioreactors, and disinfection processes, are considered potential techniques to restrict antibiotic resistance in the environment.},
}
@article {pmid35679824,
year = {2022},
author = {Parida, S and Drewes, JL},
title = {Unwanted passengers: Microbes hitchiking in breast cancer metastases.},
journal = {Cell host &amp; microbe},
volume = {30},
number = {6},
pages = {875-877},
doi = {10.1016/j.chom.2022.05.010},
pmid = {35679824},
issn = {1934-6069},
abstract = {In a recent Cell paper, Fu et al. bridge descriptive cancer microbiome research with mechanistic and functional insight. With savvy use of antibiotics, the authors demonstrate divergent roles of the gut and intratumoral microbiome in breast tumor growth and metastasis, providing potentially actionable tools for better breast cancer management.},
}
@article {pmid35679823,
year = {2022},
author = {Armet, AM and Deehan, EC and O'Sullivan, AF and Mota, JF and Field, CJ and Prado, CM and Lucey, AJ and Walter, J},
title = {Rethinking healthy eating in light of the gut microbiome.},
journal = {Cell host &amp; microbe},
volume = {30},
number = {6},
pages = {764-785},
doi = {10.1016/j.chom.2022.04.016},
pmid = {35679823},
issn = {1934-6069},
abstract = {Given the worldwide epidemic of diet-related chronic diseases, evidence-based dietary recommendations are fundamentally important for health promotion. Despite the importance of the human gut microbiota for the physiological effects of diet and chronic disease etiology, national dietary guidelines around the world are just beginning to capitalize on scientific breakthroughs in the microbiome field. In this review, we discuss contemporary nutritional recommendations from a microbiome science perspective, focusing on mechanistic evidence that established host-microbe interactions as mediators of the physiological effects of diet. We apply this knowledge to inform discussions of nutrition controversies, advance innovative dietary strategies, and propose an experimental framework that integrates the microbiome into nutrition research. The congruence of key paradigms in the nutrition and microbiome disciplines validates current recommendations in dietary guidelines, and the systematic incorporation of microbiome science into nutrition research has the potential to further improve and innovate healthy eating.},
}
@article {pmid35679822,
year = {2022},
author = {Schmidt, TM},
title = {Stitching together a healthy gut microbiome with fiber.},
journal = {Cell host &amp; microbe},
volume = {30},
number = {6},
pages = {762-763},
doi = {10.1016/j.chom.2022.05.007},
pmid = {35679822},
issn = {1934-6069},
abstract = {Inter-individual variability in the gut microbiome confounds efforts to understand host responses to dietary fiber. In this issue of Cell Host &amp; Microbe, Lancaster et al. report individual and generalized host and microbiome responses in an interventional study of fiber supplements, motivating consideration of an alternative classification of fiber.},
}
@article {pmid35679819,
year = {2022},
author = {Brown, EM},
title = {Fatty liver? Microbiome sphingolipids to the rescue.},
journal = {Cell host &amp; microbe},
volume = {30},
number = {6},
pages = {755-757},
doi = {10.1016/j.chom.2022.05.008},
pmid = {35679819},
issn = {1934-6069},
abstract = {In this issue of Cell Host &amp; Microbe, Le et al. discover that addition of exogenous Bacteroides sphingolipids can reverse lipid accumulation in the liver in a mouse model of hepatic steatosis. An elegant labeling strategy also revealed a unique microbially produced sphingolipid that was able to transit to the liver.},
}
@article {pmid35679804,
year = {2022},
author = {Rangel, LI and Bolton, MD},
title = {The unsung roles of microbial secondary metabolite effectors in the plant disease cacophony.},
journal = {Current opinion in plant biology},
volume = {68},
number = {},
pages = {102233},
doi = {10.1016/j.pbi.2022.102233},
pmid = {35679804},
issn = {1879-0356},
abstract = {Plants counter disease with an array of responses to styme pathogen ingress. In contrast to this cacophony, plant pathogens orchestrate a finely tuned repertoire of virulence mechanisms in their attempt to cause disease. One such example is the production of secondary metabolite effectors (SMEs). Despite many attempts to functionally categorize SMEs, their many roles in plant disease have proven they march to the beat of their producer's drum. Some lesser studied features of SMEs in plant disease include self-resistance (SR) and manipulation of the microbiome to enhance pathogen virulence. SR can be accomplished in three general compositions, with the first being the transport of the SME to a benign location; the second being modification of the SME so it cannot harm the producer; and the third being metabolic regulation of the SME or the producer homolog of the SME target. SMEs may also play an interlude prior to disease by shaping the plant microbial community, allowing producers to better establish themselves. Taken together, SMEs are integral players in the phytopathology canon.},
}
@article {pmid35679795,
year = {2022},
author = {Sun, Q and Yang, H and Liu, M and Ren, S and Zhao, H and Ming, T and Tang, S and Tao, Q and Chen, L and Zeng, S and Duan, DD and Xu, H},
title = {Berberine suppresses colorectal cancer by regulation of Hedgehog signaling pathway activity and gut microbiota.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {103},
number = {},
pages = {154227},
doi = {10.1016/j.phymed.2022.154227},
pmid = {35679795},
issn = {1618-095X},
abstract = {BACKGROUND: A growing body of evidence reveals that dysregulation of Hedgehog signaling pathway and dysbiosis of gut microbiota are associated with the pathogenesis of colorectal cancer (CRC). Berberine, a botanical benzylisoquinoline alkaloid, possesses powerful activities against various malignancies including CRC, with the underlying mechanisms to be illuminated.<br><br>PURPOSE: The present study investigated the potencies of berberine on CRC and deciphered the action mechanisms in the context of Hedgehog signaling cascade and gut microbiota.<br><br>METHODS: The effects of berberine on the malignant phenotype, apoptosis, cell cycle and Hedgehog signaling of CRC cells were examined in vitro. In azoxymethane/dextran sulfate sodium-caused mouse CRC, the efficacies of berberine on the carcinogenesis, pathological profile, apoptosis, cell cycle and Hedgehog signaling were determined in vivo. Also, the influences of berberine on gut microbiota in CRC mice were assessed by high-throughput DNA sequencing analysis of 16S ribosomal RNA of fecal microbiome in CRC mice.<br><br>RESULTS: In the present study, berberine was found to dampen the proliferation, migration, invasion and colony formation of CRC cells, without toxicity to normal colonic cells. Additionally, berberine induced apoptosis and arrested cell cycle at G0/G1 phase in CRC cells, accompanied by reduced Hedgehog signaling pathway activity in vitro. In mouse CRC, berberine suppressed tumor growth, ameliorated pathological manifestations, and potentially induced the apoptosis and cell cycle arrest of CRC, with lowered Hedgehog signaling cascade in vivo. Additionally, berberine decreased β-diversity of gut microbiota in CRC mice, without influence on α-diversity. Berberine also enriched probiotic microbes and depleted pathogenic microbes, and modulated the functionality of gut microbiota in CRC mice.<br><br>CONCLUSIONS: Overall, berberine may suppress colorectal cancer, orchestrated by down-regulation of Hedgehog signaling pathway activity and modulation of gut microbiota.},
}
@article {pmid35679413,
year = {2022},
author = {Olm, MR and Dahan, D and Carter, MM and Merrill, BD and Yu, FB and Jain, S and Meng, X and Tripathi, S and Wastyk, H and Neff, N and Holmes, S and Sonnenburg, ED and Jha, AR and Sonnenburg, JL},
title = {Robust variation in infant gut microbiome assembly across a spectrum of lifestyles.},
journal = {Science (New York, N.Y.)},
volume = {376},
number = {6598},
pages = {1220-1223},
doi = {10.1126/science.abj2972},
pmid = {35679413},
issn = {1095-9203},
abstract = {Infant microbiome assembly has been intensely studied in infants from industrialized nations, but little is known about this process in nonindustrialized populations. We deeply sequenced infant stool samples from the Hadza hunter-gatherers of Tanzania and analyzed them in a global meta-analysis. Infant microbiomes develop along lifestyle-associated trajectories, with more than 20% of genomes detected in the Hadza infant gut representing novel species. Industrialized infants-even those who are breastfed-have microbiomes characterized by a paucity of Bifidobacterium infantis and gene cassettes involved in human milk utilization. Strains within lifestyle-associated taxonomic groups are shared between mother-infant dyads, consistent with early life inheritance of lifestyle-shaped microbiomes. The population-specific differences in infant microbiome composition and function underscore the importance of studying microbiomes from people outside of wealthy, industrialized nations.},
}
@article {pmid35679092,
year = {2022},
author = {Greene, LK and Andriambeloson, JB and Rasoanaivo, HA and Yoder, AD and Blanco, MB},
title = {Variation in gut microbiome structure across the annual hibernation cycle in a wild primate.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiac070},
pmid = {35679092},
issn = {1574-6941},
abstract = {The gut microbiome can mediate host metabolism, including facilitating energy-saving strategies like hibernation. The dwarf lemurs of Madagascar (Cheirogaleus spp.) are the only obligate hibernators among primates. They also hibernate in the sub-tropics, and unlike temperate hibernators, fatten by converting fruit sugars to lipid deposits, torpor at relatively warm temperatures, and forage for a generalized diet after emergence. Despite these ecological differences, we might expect hibernation to shape the gut microbiome in similar ways across mammals. We therefore compare gut microbiome profiles, determined by amplicon sequencing of rectal swabs, in wild furry-eared dwarf lemurs (C. crossleyi) during fattening, hibernation, and after emergence. The dwarf lemurs exhibited reduced gut microbial diversity during fattening, intermediate diversity and increased community homogenization during hibernation, and greatest diversity after emergence. The Mycoplasma genus was enriched during fattening, whereas the Aerococcaceae and Actinomycetaceae families, and not Akkermansia, bloomed during hibernation. As expected, the dwarf lemurs showed seasonal reconfigurations of the gut microbiome; however, the patterns of microbial diversity diverged from temperate hibernators, and better resembled the shifts associated with dietary fruits and sugars in primates and model organisms. Our results thus highlight the potential for dwarf lemurs for probing microbiome-mediated metabolism in primates under contrasting conditions.},
}
@article {pmid35678705,
year = {2022},
author = {Sun, J and Prabhu, A and Aroney, STN and Rinke, C},
title = {Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials.},
journal = {Microbial genomics},
volume = {8},
number = {6},
pages = {},
doi = {10.1099/mgen.0.000842},
pmid = {35678705},
issn = {2057-5858},
abstract = {Plastics are inexpensive and widely used organic polymers, but their high durability hinders biodegradation. Polystyrene, including extruded polystyrene (also known as styrofoam), is among the most commonly produced plastics worldwide and is recalcitrant to microbial degradation. In this study, we assessed changes in the gut microbiome of superworms (Zophobas morio) reared on bran, polystyrene or under starvation conditions over a 3 weeks period. Superworms on all diets were able to complete their life cycle to pupae and imago, although superworms reared on polystyrene had minimal weight gains, resulting in lower pupation rates compared to bran reared worms. The change in microbial gut communities from baseline differed considerably between diet groups, with polystyrene and starvation groups characterized by a loss of microbial diversity and the presence of opportunistic pathogens. Inferred microbial functions enriched in the polystyrene group included transposon movements, membrane restructuring and adaptations to oxidative stress. We detected several encoded enzymes with reported polystyrene and styrene degradation abilities, supporting previous reports of polystyrene-degrading bacteria in the superworm gut. By recovering metagenome-assembled genomes (MAGs) we linked phylogeny and functions and identified genera including Pseudomonas, Rhodococcus and Corynebacterium that possess genes associated with polystyrene degradation. In conclusion, our results provide the first metagenomic insights into the metabolic pathways used by the gut microbiome of superworms to degrade polystyrene. Our results also confirm that superworms can survive on polystyrene feed, but this diet has considerable negative impacts on host gut microbiome diversity and health.},
}
@article {pmid35678665,
year = {2022},
author = {Mohamed, A and Asa, SL and McCormick, T and Al-Shakhshir, H and Dasari, A and Mauricio, R and Salem, I and Ocuin, LM and Bajor, D and Lee, RT and Selfridge, JE and Kardan, A and Lee, Z and Avril, N and Kopp, S and Winter, JM and Hardacre, JM and Ammori, JB and Ghannoum, MA},
title = {The Role of the Microbiome in Gastroentero-Pancreatic Neuroendocrine Neoplasms (GEP-NENs).},
journal = {Current issues in molecular biology},
volume = {44},
number = {5},
pages = {2015-2028},
doi = {10.3390/cimb44050136},
pmid = {35678665},
issn = {1467-3045},
abstract = {Gut microbiome balance plays a key role in human health and maintains gut barrier integrity. Dysbiosis, referring to impaired gut microbiome, is linked to a variety of diseases, including cancers, through modulation of the inflammatory process. Most studies concentrated on adenocarcinoma of different sites with very limited information on gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs). In this study, we have analyzed the gut microbiome (both fungal and bacterial communities) in patients with metastatic GEP-NENs. Fecal samples were collected and compared with matched healthy control samples using logistic regression distances utilizing R package MatchIt (version 4.2.0, Daniel E. Ho, Stanford, CA, USA). We examined differences in microbiome profiles between GEP-NENs and control samples using small subunit (SSU) rRNA (16S), ITS1, ITS4 genomic regions for their ability to accurately characterize bacterial and fungal communities. We correlated the results with different behavioral and dietary habits, and tumor features including differentiation, grade, primary site, and therapeutic response. All tests are two-sided and p-values ≤ 0.05 were considered statistically significant. Gut samples of 34 patients (12 males, 22 females, median age 64 years) with metastatic GEP-NENs (22 small bowel, 10 pancreatic, 1 gall bladder, and 1 unknown primary) were analyzed. Twenty-nine patients had well differentiated GEP-neuroendocrine tumors (GEP-NETs), (G1 = 14, G2 = 12, G3 = 3) and five patients had poorly differentiated GEP-neuroendocrine carcinomas (GEP-NECs). Patients with GEP-NENs had significantly decreased bacterial species and increased fungi (notably Candida species, Ascomycota, and species belonging to saccharomycetes) compared to controls. Patients with GEP-NECs had significantly enriched populations of specific bacteria and fungi (such as Enterobacter hormaechei, Bacteroides fragilis and Trichosporon asahii) compared to those with GEP-NETs (p = 0.048, 0.0022 and 0.034, respectively). In addition, higher grade GEP-NETs were associated with significantly higher Bacteroides fragilis (p = 0.022), and Eggerthella lenta (p = 0.00018) species compared to lower grade tumors. There were substantial differences associated with dietary habits and therapeutic responses. This is the first study to analyze the role of the microbiome environment in patients with GEP-NENs. There were significant differences between GEP-NETs and GEP-NECs, supporting the role of the gut microbiome in the pathogenesis of these two distinct entities.},
}
@article {pmid35678589,
year = {2022},
author = {Higgins, SA and Mann, M and Heck, M},
title = {Strain tracking of 'Candidatus Liberibacter asiaticus', citrus greening disease pathogen, enabled by high-resolution microbiome analysis of the Asian citrus psyllid.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-02-22-0067-R},
pmid = {35678589},
issn = {0031-949X},
abstract = {The Asian citrus psyllid, Diaphorina citri, is an invasive insect and a vector of 'Candidatus Liberibacter asiaticus' (CLas), a bacterium whose growth in Citrus species results in huanglongbing (HLB), also known as citrus greening disease. Methods to enrich and sequence CLas from D. citri often rely on biased genome amplification and nevertheless contain significant quantities of host DNA. To overcome these hurdles, we developed a simple pre-treatment DNase and filtration (hereafter PDF) protocol to remove host DNA and directly sequence CLas and the complete, primarily uncultivable, microbiome from D. citri adults. The PDF protocol yielded CLas abundances upwards of 60% and facilitated direct measurement of CLas and endosymbiont replication rates in psyllids. The PDF protocol confirmed our strains derived from a progenitor Florida CLas strain and accumulated 156 genetic variants, underscoring the utility of this data for bacterial strain tracking. CLas genetic polymorphisms arising in lab-reared psyllid populations included prophage encoding regions with key functions in CLas pathogenesis, putative antibiotic resistance loci, and a single secreted effector. These variants suggest laboratory propagation of CLas may result in different phenotypic trajectories among laboratories, and may confound CLas physiology or therapeutic design and evaluation if these differences remain undocumented. Finally, we obtained genetic signatures affiliated with Citrus nuclear and organellar genomes, entomopathogenic fungal mitochondria, and commensal bacteria from laboratory-reared and field-collected D. citri adults. Hence, the PDF protocol can directly inform agricultural management strategies related to bacterial strain tracking, insect microbiome surveillance, and antibiotic resistance screening.},
}
@article {pmid35678568,
year = {2022},
author = {Korenblum, E and Massalha, H and Aharoni, A},
title = {Plant-microbe interactions in the rhizosphere via a circular metabolic economy.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koac163},
pmid = {35678568},
issn = {1532-298X},
abstract = {Chemical exchange often serves as the first step in plant-microbe interactions and exchanges of various signals, nutrients, and metabolites continue throughout the interaction. Here, we highlight the role of metabolite exchanges and metabolic crosstalk in the microbiome-root-shoot-environment nexus. Roots secret a diverse set of metabolites; this assortment of root exudates, including secondary metabolites such as benzoxazinoids, coumarins, flavonoids, indolic compounds, and terpenes, shapes the rhizosphere microbiome. In turn, the rhizosphere microbiome affects plant growth and defense. These inter-kingdom chemical interactions are based on a metabolic circular economy, a seemingly wasteless system in which rhizosphere members exchange (i.e. consume, reuse, and redesign) metabolites. This review also describes the recently discovered phenomenon 'Systemically Induced Root Exudation of Metabolites' in which the rhizosphere microbiome governs plant metabolism by inducing systemic responses that shift the metabolic profiles of root exudates. Metabolic exchange in the rhizosphere is based on chemical gradients that form specific microhabitats for microbial colonization and we describe recently developed high-resolution methods to study chemical interactions in the rhizosphere. Finally, we propose an action plan to advance the metabolic circular economy in the rhizosphere for sustainable solutions to the cumulative degradation of soil health in agricultural lands.},
}
@article {pmid35678528,
year = {2022},
author = {Drewes, JL and Chen, J and Markham, NO and Knippel, RJ and Domingue, JC and Tam, AJ and Chan, JL and Kim, L and McMann, M and Stevens, C and Dejea, CM and Tomkovich, S and Michel, J and White, JR and Mohammad, F and Campodonico, VL and Heiser, CN and Wu, X and Wu, S and Ding, H and Simner, P and Carroll, K and Shrubsole, MJ and Anders, RA and Walk, ST and Jobin, C and Wan, F and Coffey, RJ and Housseau, F and Lau, KS and Sears, CL},
title = {Human colon cancer-derived Clostridioides difficile strains drive colonic tumorigenesis in mice.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {},
doi = {10.1158/2159-8290.CD-21-1273},
pmid = {35678528},
issn = {2159-8290},
abstract = {Defining the complex role of the microbiome in colorectal cancer (CRC) and the discovery of novel, pro-tumorigenic microbes are areas of active investigation. In the present study, culturing and reassociation experiments revealed that toxigenic strains of Clostridioides difficile drove the tumorigenic phenotype of a subset of CRC patient-derived mucosal slurries in germ-free ApcMin/+ mice. Tumorigenesis was dependent on the C. difficile toxin TcdB and was associated with induction of Wnt signaling, reactive oxygen species, and pro-tumorigenic mucosal immune responses marked by infiltration of activated myeloid cells and interleukin-17 (IL-17)-producing lymphoid and innate lymphoid cell subsets. These findings suggest that chronic colonization with toxigenic C. difficile is a potential driver of CRC in patients.},
}
@article {pmid35678287,
year = {2022},
author = {Hou, Y and Tan, T and Guo, Z and Ji, Y and Hu, J and Zhang, Y},
title = {Gram-selective antibacterial peptide hydrogels.},
journal = {Biomaterials science},
volume = {},
number = {},
pages = {},
doi = {10.1039/d2bm00558a},
pmid = {35678287},
issn = {2047-4849},
abstract = {The human microbiome plays fundamental roles in human health and disease. However, widely used broad-spectrum antibiotics severely disrupt human-related microbial communities, eventually leading to resistant bacteria, posing a growing threat to global medical health. Antimicrobial peptides (AMPs) are promising antimicrobial agents that barely cause bacterial resistance. Excellent broad-spectrum antimicrobial activities have been achieved using hydrogels self-assembled from AMPs, but there is still a lack of AMP hydrogels that can target Gram-positive and Gram-negative bacteria. Herein, several hydrogels self-assembled from AMPs, termed IK1, IK3, and IK4, were designed and synthesized. In vitro antibacterial results indicated that the IK1 and IK4 hydrogels specifically targeted Gram-positive and Gram-negative bacteria, respectively, while the IK3 hydrogel targeted both Gram-positive and Gram-negative bacteria. The desired broad-spectrum or Gram-selective AMP hydrogels are believed to be obtained through the rational design of the hydrophilicity, hydrophobicity, and charge properties of the peptide molecules. Good in vivo Gram-selective antibacterial properties and the ability to promote wound healing have been demonstrated via treating mouse wound models with these AMP hydrogels. We believe that these Gram-selective AMP hydrogels could potentially have important applications in treating common recurring infections.},
}
@article {pmid35678078,
year = {2022},
author = {Xiao, W and Ma, ZS},
title = {Influences of Helicobacter pylori infection on diversity, heterogeneity, and composition of human gastric microbiomes across stages of gastric cancer development.},
journal = {Helicobacter},
volume = {},
number = {},
pages = {e12899},
doi = {10.1111/hel.12899},
pmid = {35678078},
issn = {1523-5378},
abstract = {BACKGROUND: About a half of the world's population is infected with Helicobacter pylori (H. pylori), but only 1%-3% of them develop gastric cancer. As a primary risk factor for gastric cancer, the relationship between H. pylori infection and gastric microbiome has been a focus in recent years.<br><br>MATERIALS AND METHODS: We reanalyze 11 human gastric microbiome datasets with or without H. pylori, covering the healthy control (HC) and four disease stages (chronic gastritis (CG), atrophic gastritis (AG), intestinal metaplasia (IM), and gastric cancer (GC)) of gastric cancer development to quantitatively compare the influences of the H. pylori infection and disease stages on the diversity, heterogeneity, and composition of gastric microbiome. Four medical ecology approaches including (i) diversity analysis with Hill numbers, (ii) heterogeneity analysis with Taylor's power law extensions (TPLE), (iii) diversity scaling analysis with diversity-area relationship (DAR) model, and (iv) shared species analysis were applied to fulfill the data reanalysis.<br><br>RESULTS: (i) The influences of H. pylori infection on the species diversity, spatial heterogeneity, and potential diversity of gastric microbiome seem to be more prevalent than the influences of disease stages during gastric cancer development. (ii) The influences of H. pyloriinfection on diversity, heterogeneity, and composition of gastric microbiomes in HC, CG, IM, and GC stages appear more prevalent than those in AG stage.<br><br>CONCLUSION: Our study confirmed the impact of H. pylori infection on human gastric microbiomes: The influences of H. pylori infection on the diversity, heterogeneity, and composition of gastric microbiomes appear to be disease-stage dependent.},
}
@article {pmid35677910,
year = {2022},
author = {Yi, X and Cha, M},
title = {Gut Dysbiosis Has the Potential to Reduce the Sexual Attractiveness of Mouse Female.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {916766},
doi = {10.3389/fmicb.2022.916766},
pmid = {35677910},
issn = {1664-302X},
abstract = {Increasing evidence has shown that the gut microbiome has significant effects on mate preferences of insects; however, whether gut microbiota composition affects sexual attractiveness and mate preference in mammals remains largely unknown. Here, we showed that antibiotic treatment significantly restructured the gut microbiota composition of both mouse males and females. Males, regardless of antibiotic treatment, exhibited a higher propensity to interact with the control females than the antibiotic-treated females. The data clearly showed that gut microbiota dysbiosis reduced the sexual attractiveness of females to males, implying that commensal gut microbiota influences female attractiveness to males. The reduced sexual attractiveness of the antibiotic-treated females may be beneficial to discriminating males by avoiding disorders of immunity and sociability in offspring that acquire maternal gut microbiota via vertical transmission. We suggest further work should be oriented to increase our understanding of the interactions between gut microbiota dysbiosis, sexual selection, and mate choice of wild animals at the population level.},
}
@article {pmid35677897,
year = {2022},
author = {Altayb, HN and Chaieb, K and Baothman, O and Alzahrani, FA and Zamzami, MA and Almugadam, BS},
title = {Study of oral microbiota diversity among groups of families originally from different countries.},
journal = {Saudi journal of biological sciences},
volume = {29},
number = {7},
pages = {103317},
doi = {10.1016/j.sjbs.2022.103317},
pmid = {35677897},
issn = {1319-562X},
abstract = {The diversity of oral microbiota is affected by diets habits, gender, age, ethnic group, and environment. The acquisition of oral microbiota and the role of family on oral microbiota development is poorly understood. This study aims to characterize and compare the oral bacterial microbiota among families using 16S rRNA gene sequencing. This work was conducted in Jeddah city from 2020 to 2021, in which four families composed of 20 members of different ethnicity and lifestyle were recruited. After the collection of saliva samples, the DNA was extracted and processed for 16S rRNA gene metagenomics sequencing. Among 378 OUTs generated, 39 (10.3%) were unique in group A, 13 (3.4%) unique in group B, and 11 (2.9%) were unique in groups C and D. We observed a significant variation at the level of top abundance phylum (14), families (23), genera (24), and species (22) of bacteria among family members. Within family groups, different bacterial species were reported to be more dominant among certain family members than the other; Prevotella melaninogenica, Prevotella histicola and Haemophilus parainfluenzae, Veillonella atypica, Porphyromonas pasteri and Haemophilus pittmaniae were more dominant in parents of some families than the other family member. In summary, this study highlights the precise and perceptible association of oral microbial between family members. Our findings documented the clustering of certain bacterial species in family groups, supporting the role of community in the development of oral microbiota.},
}
@article {pmid35677657,
year = {2022},
author = {Wu, TT and Xiao, J and Manning, S and Saraithong, P and Pattanaporn, K and Paster, BJ and Chen, T and Vasani, S and Gilbert, C and Zeng, Y and Li, Y},
title = {Multimodal Data Integration Reveals Mode of Delivery and Snack Consumption Outrank Salivary Microbiome in Association With Caries Outcome in Thai Children.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {881899},
doi = {10.3389/fcimb.2022.881899},
pmid = {35677657},
issn = {2235-2988},
abstract = {Early childhood caries (ECC) is not only the most common chronic childhood disease but also disproportionately affects underserved populations. Of those, children living in Thailand have been found to have high rates of ECC and severe ECC. Frequently, the cause of ECC is blamed on a handful of cariogenic organisms, such as Streptococcus mutans and Streptococcus sobrinus. However, ECC is a multifactorial disease that results from an ecological shift in the oral cavity from a neutral pH (~7.5) to an acidic pH (<5.5) environment influenced by the host individual's biological, socio-behavioral, and lifestyle factors. Currently, there is a lack of understanding of how risk factors at various levels influence the oral health of children at risk. We applied a statistical machine learning approach for multimodal data integration (parallel and hierarchical) to identify caries-related multiplatform factors in a large cohort of mother-child dyads living in Chiang Mai, Thailand (N=177). Whole saliva (1 mL) was collected from each individual for DNA extraction and 16S rRNA sequencing. A set of maternal and early childhood factors were included in the data analysis. Significantly, vaginal delivery, preterm birth, and frequent sugary snacking were found to increase the risk for ECC. The salivary microbial diversity was significantly different in children with ECC or without ECC. Results of linear discriminant analysis effect size (LEfSe) analysis of the microbial community demonstrated that S. mutans, Prevotella histicola, and Leptotrichia hongkongensis were significantly enriched in ECC children. Whereas Fusobacterium periodonticum was less abundant among caries-free children, suggesting its potential to be a candidate biomarker for good oral health. Based on the multimodal data integration and statistical machine learning models, the study revealed that the mode of delivery and snack consumption outrank salivary microbiome in predicting ECC in Thai children. The biological and behavioral factors may play significant roles in the microbial pathobiology of ECC and warrant further investigation.},
}
@article {pmid35677549,
year = {2022},
author = {Ried, K and Travica, N and Paye, Y and Sali, A},
title = {Effects of a Probiotic Formulation on Seasonal Allergic Rhinitis in Adults-A Randomized Double-Blind Placebo-Controlled Trial: The Probiotics for Hay Fever Trial.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {887978},
doi = {10.3389/fnut.2022.887978},
pmid = {35677549},
issn = {2296-861X},
abstract = {Background: Seasonal-allergic-rhinitis (hay fever) affects approximately 4.6 million (20%) Australians each year. Hay fever manifests as runny/blocked nose and often itchy/sore/swollen eyes, with symptoms greatly impacting the quality of life. Rescue medications such as antihistamines are often needed to restore function, but they may trigger some other unwanted side effects. Probiotics have shown promise to reduce hay fever symptoms.<br><br>Objective: In this randomized double-blind placebo-controlled 12-week trial, we aimed to assess the tolerability and efficacy of the probiotic formula "NC-Seasonal-Biotic" on symptoms, quality-of-life, and immunological and microbial factors.<br><br>Methods: Adults, who had previously suffered from hay fever symptoms, were screened for eligibility and randomly allocated to probiotic or placebo trial powder. Treatment effectiveness was assessed by questionnaires, daily total-nasal-symptom-score, and weekly rhinoconjunctivitis quality-of-life questionnaire. Secondary outcome measures included immunological parameters such as T-cell immunity (Th1/Th2 ratio) and the stool-microbiome analysis. Tolerability was assessed weekly by the gastrointestinal symptom scale.<br><br>Results: Recruitment and follow-up were challenging around the 2020/2021 hay fever season in Melbourne, Australia, due to the harsh COVID-19 restrictions and extended lockdowns. Out of the 82 adults enrolled in this study, 75% participated (n = 60), and half (n = 40) completed the 10-12-week intervention period. In the intention-to-treat analysis, no significant differences in hay fever symptoms were apparent between the groups, while quality-of-life trended toward greater improvement in the active group. Intention-to-treat analysis was confounded due to a third of all participants not completing the full 10-12-week-intervention period. Subgroup analyses of the participants (n = 40) completing the full 10-12-week study period revealed a significantly greater reduction in symptoms in the active group compared with the placebo group, including runny nose (p = 0.04) and itchy eyes (p = 0.01). Furthermore, the active group reported significant improvements in the quality-of-life, including more functionality during the day (p = 0.05), better sleep (p = 0.005), less fatigue (p = 0.04), less thirst (p = 0.007), and less irritability (p = 0.007). Immunological parameters, measured by T-helper cell ratio (Th1/Th2), improved significantly in the active group compared with the placebo group. Most microbial changes were not statistically different between the groups. The trial powder was generally well tolerated.<br><br>Conclusion: Our study suggests the probiotic formula "NC-Seasonal-Biotic," taken for 10-12 weeks, as effective in reducing hay fever symptoms, such as runny nose and itchy eyes, and improved the quality-of-life and immunological parameters while being well tolerated.<br><br>Clinical Trial Registration: [www.ClinicalTrials.gov], identifier [ACTRN126200 01078943].},
}
@article {pmid35677336,
year = {2022},
author = {Jalodia, R and Antoine, D and Braniff, RG and Dutta, RK and Ramakrishnan, S and Roy, S},
title = {Opioid-Use, COVID-19 Infection, and Their Neurological Implications.},
journal = {Frontiers in neurology},
volume = {13},
number = {},
pages = {884216},
doi = {10.3389/fneur.2022.884216},
pmid = {35677336},
issn = {1664-2295},
abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an imminent threat to human health and public safety. ACE2 and transmembrane serine protease 2 proteins on host cells provide the viral entry point to SARS-CoV-2. Although SARS-CoV-2 mainly infects the respiratory system, there have been reports of viral neurotropism and central nervous system injury as indicated by plasma biomarkers, including neurofilament light chain protein and glial fibrillary acidic protein. Even with a small proportion of infections leading to neurological manifestation, the overall number remains high. Common neurological manifestations of SARS-CoV-2 infection include anosmia, ageusia, encephalopathy, and stroke, which are not restricted to only the most severe infection cases. Opioids and opioid antagonists bind to the ACE2 receptor and thereby have been hypothesized to have therapeutic potential in treating COVID-19. However, in the case of other neurotropic viral infections such as human immunodeficiency virus (HIV), opioid use has been established to exacerbate HIV-mediated central nervous system pathogenesis. An analysis of electronic health record data from more than 73 million patients shows that people with Substance Use Disorders are at higher risk of contracting COVID-19 and suffer worse consequences then non-users. Our in-vivo and in-vitro unpublished studies show that morphine treatment causes increased expression of ACE2 in murine lung and brain tissue as early as 24 h post treatment. At the same time, we also observed morphine and lipopolysaccharides treatment lead to a synergistic increase in ACE2 expression in the microglial cell line, SIM-A9. This data suggests that opioid treatment may potentially increase neurotropism of SARS-CoV-2 infection. We have previously shown that opioids induce gut microbial dysbiosis. Similarly, gut microbiome alterations have been reported with SARS-CoV-2 infection and may play a role in predicting COVID-19 disease severity. However, there are no studies thus far linking opioid-mediated dysbiosis with the severity of neuron-specific COVID-19 infection.},
}
@article {pmid35677160,
year = {2022},
author = {Zhong, G and Wei, W and Liao, W and Wang, R and Peng, Y and Zhou, Y and Huang, X and Xian, S and Peng, S and Zhang, Z and Feng, S and Liu, Y and Hong, H and Xia, Y and Yan, Y and Liu, Q and Liu, Z},
title = {Tumor Microbiome in Nasopharyngeal Carcinoma and Its Association With Prognosis.},
journal = {Frontiers in oncology},
volume = {12},
number = {},
pages = {859721},
doi = {10.3389/fonc.2022.859721},
pmid = {35677160},
issn = {2234-943X},
abstract = {Introduction: Previous studies have reported a close relationship between cancer and microbes, particularly gut and tumor microbiota; however, the presence of tumor microbiome in nasopharyngeal carcinoma (NPC) and its role in the prognosis of NPC remain unclear.<br><br>Methods: We collected 64 samples including tissues from 50 patients with NPC (NPC group) and 14 patients with chronic nasopharyngitis (control group) receiver operating characteristics and we applied 16S ribosome RNA gene sequencing of all samples to assess microbiome profiles and immunohistochemistry to detect tumor microbiome in NPC.<br><br>Results: Patients in the control group harbored higher species diversity than those in the NPC group; however, the beta diversity was more distinct in the NPC group. In total, three genera with statistically significant differences between the two groups were identified. The area under the receiver operating characteristics (ROC) curve (AUC) was calculated using the relative abundance of these three significant genera, and a value of 0.842 was achieved. Furthermore, Turicibacter was confirmed as a potentially independent prognostic factor for NPC patients, and the progression-free survival (PFS) was markedly prolonged in patients with a low relative abundance of Turicibacter compared to patients with a high relative abundance of this genus (cutoff: 0.0046, hazard ratio: 5.10, 95% confidence interval: 2.04-12.77, p = 0.004).<br><br>Conclusions: The present study provided strong evidence of a correlation between tumor microbiome and NPC; the tumor microbiome may be considered a biomarker for early NPC diagnosis. Turicibacter potentially served as a independently prognostic indicator for NPC patients.},
}
@article {pmid35677094,
year = {2022},
author = {Liu, WC and Huang, MY and Balasubramanian, B and Jha, R},
title = {Heat Stress Affects Jejunal Immunity of Yellow-Feathered Broilers and Is Potentially Mediated by the Microbiome.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {913696},
doi = {10.3389/fphys.2022.913696},
pmid = {35677094},
issn = {1664-042X},
abstract = {In the perspective of the global climate change leading to increasing temperature, heat stress (HS) has become a severe issue in broiler production, including the indigenous yellow-feathered broilers. The present study aimed to investigate the effects of HS on jejunal immune response, microbiota structure and their correlation in yellow-feathered broilers. A total of forty female broilers (56-days-old) were randomly and equally divided into normal treatment group (NT group, 21.3 ± 1.2°C, 24 h/day) and HS group (32.5 ± 1.4°C, 8 h/day) with five replicates of each for 4 weeks feeding trial. The results showed that HS exposure increased the contents of TNF-α, IL-1β, and IL-6 in jejunal mucosa (p < 0.05). The HS exposure up-regulated the relative fold changes of NF-κB, TNF-α, IL-1β, and IL-6 (p < 0.01) while down-regulated the relative fold change of IFN-γ in jejunal mucosa (p < 0.05). Meanwhile, HS had no significant impacts on alpha diversity of jejunal microbiota such as Simpson, Chao1 richness estimator (Chao 1), abundance-based coverage estimators (ACE), and Shannon index (p > 0.10). Broilers exposed to HS reduced the jejunal microbial species number at the class and order level (p < 0.05). Moreover, HS decreased the relative abundance of Ruminococcus, Bdellovibrio, and Serratia at the genus level in jejunum (p < 0.05). At the phylum level, four species of bacteria (Bacteroidetes, Cyanobacteria, Thermi, and TM7) were significantly associated with immune-related genes expression (p < 0.05). At the genus level, ten species of bacteria were significantly correlated with the expression of immune-related genes (p < 0.05), including Caulobacteraceae, Actinomyces, Ruminococcaceae, Thermus, Bdellovibrio, Clostridiales, Sediminibacterium, Bacteroides, Sphingomonadales and Ruminococcus. In particular, the microbial with significantly different abundances, Ruminococcus and Bdellovibrio, were negatively associated with pro-inflammatory cytokines expression (p < 0.05). These findings demonstrated that HS exposure promoted the production of pro-inflammatory cytokines in yellow-feathered broilers' jejunum. The detrimental effects of HS on jejunal immune response might be related to dysbiosis, especially the reduced levels of Ruminococcus and Bdellovibrio.},
}
@article {pmid35677075,
year = {2022},
author = {Lai, P and Nguyen, L and Okin, D and Drew, D and Battista, V and Jesudasen, S and Kuntz, T and Bhosle, A and Thompson, K and Reinicke, T and Lo, CH and Woo, J and Caraballo, A and Berra, L and Vieira, J and Huang, CY and Adhikari, UD and Kim, M and Sui, HY and Magicheva-Gupta, M and McIver, L and Goldberg, M and Kwon, D and Huttenhower, C and Chan, A},
title = {Metagenomic assessment of gut microbial communities and risk of severe COVID-19.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-1717624/v1},
pmid = {35677075},
abstract = {The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure. We profiled 127 hospitalized patients with COVID-19 (n=79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites. 48 species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID", suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with predicting whether stool was obtained from patients with severe vs. moderate COVID-19. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease. Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to validate these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.},
}
@article {pmid35677024,
year = {2022},
author = {Zenobia, C and Darveau, RP},
title = {Does Oral Endotoxin Contribute to Systemic Inflammation?.},
journal = {Frontiers in oral health},
volume = {3},
number = {},
pages = {911420},
doi = {10.3389/froh.2022.911420},
pmid = {35677024},
issn = {2673-4842},
abstract = {The oral microbiome, with a unique emphasis on Porphyromonas gingivalis has been associated with a constellation of inflammatory diseases such as cardiovascular disease, rheumatoid arthritis, Alzheimer's disease, type II diabetes, and non-alcoholic associated fatty liver disease. Periodontal disease has also been shown to induce "leaky gut" leading to metabolic endotoxemia. Several recent studies investigating the habitants of the blood microbiome have found the majority of species appear to be derived from oral and skin bacterial communities in otherwise healthy individuals. Many of the same pathologies associated with perturbations of oral health, such as cardiovascular disease, show alterations to the composition of the blood microbiome as well as circulating neutrophil phenotypes. Gingival inflammation is associated with activated blood neutrophil phenotypes that can exacerbate a distal inflammatory insult which may explain the connection between oral and systemic inflammatory conditions. While in the oral cavity, neutrophils encounter oral microbes that are adept in manipulating neutrophil activity which can re-enter the vasculature thereafter. Endotoxin from oral microbes can differ significantly depending on bacterial community and state of oral health to alter cellular LPS tolerance mechanisms which may contribute to the primed neutrophil phenotype seen in periodontitis and provide a mechanism by which the oral-microbes can affect systemic health outcomes. This review synthesizes the studies between inflammatory diseases and oral health with emphasis on microbiome and corresponding lipopolysaccharides in immune tolerance and activation.},
}
@article {pmid35676509,
year = {2022},
author = {Gharechahi, J and Sarikhan, S and Han, JL and Ding, XZ and Salekdeh, GH},
title = {Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates.},
journal = {NPJ biofilms and microbiomes},
volume = {8},
number = {1},
pages = {46},
pmid = {35676509},
issn = {2055-5008},
support = {2021-YWF-ZX-02//CSC | Chinese Government Scholarship/ ; },
abstract = {Rumen microbiota facilitates nutrition through digestion of recalcitrant lignocellulosic substrates into energy-accessible nutrients and essential metabolites. Despite the high similarity in rumen microbiome structure, there might be distinct functional capabilities that enable different ruminant species to thrive on various lignocellulosic substrates as feed. Here, we applied genome-centric metagenomics to explore phylogenetic diversity, lignocellulose-degrading potential and fermentation metabolism of biofilm-forming microbiota colonizing 11 different plant substrates in the camel rumen. Diversity analysis revealed significant variations in the community of rumen microbiota colonizing different substrates in accordance with their varied physicochemical properties. Metagenome reconstruction recovered genome sequences of 590 bacterial isolates and one archaeal lineage belonging to 20 microbial phyla. A comparison to publicly available reference genomes and rumen metagenome-assembled genomes revealed that most isolates belonged to new species with no well-characterized representatives. We found that certain low abundant taxa, including members of Verrucomicrobiota, Planctomycetota and Fibrobacterota, possessed a disproportionately large number of carbohydrate active enzymes per Mb of genome, implying their high metabolic potential to contribute to the rumen function. In conclusion, we provided a detailed picture of the diversity and functional significance of rumen microbiota colonizing feeds of varying lignocellulose composition in the camel rumen. A detailed analysis of 591 metagenome-assembled genomes revealed a network of interconnected microbiota and highlighted the key roles of certain taxonomic clades in rumen function, including those with minimal genomes (e.g., Patescibacteria). The existence of a diverse array of gene clusters encoding for secondary metabolites unveiled the specific functions of these biomolecules in shaping community structure of rumen microbiota.},
}
@article {pmid35676397,
year = {2022},
author = {Nuzhat, S and Palit, P and Mahfuz, M and Islam, MR and Hasan, SMT and Islam, MM and Sarker, SA and Kyle, DJ and Flannery, RL and Vinjamuri, A and Lebrilla, CB and Ahmed, T},
title = {Association of human milk oligosaccharides and nutritional status of young infants among Bangladeshi mother-infant dyads.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {9456},
pmid = {35676397},
issn = {2045-2322},
support = {OPP1179599//Bill and Melinda Gates Foundation/ ; OPP1179599//Bill and Melinda Gates Foundation/ ; OPP1179599//Bill and Melinda Gates Foundation/ ; OPP1179599//Bill and Melinda Gates Foundation/ ; OPP1179599//Bill and Melinda Gates Foundation/ ; OPP1179599//Bill and Melinda Gates Foundation/ ; OPP1179599//Bill and Melinda Gates Foundation/ ; OPP1179599//Bill and Melinda Gates Foundation/ ; OPP1179599//Bill and Melinda Gates Foundation/ ; OPP1179599//Bill and Melinda Gates Foundation/ ; OPP1179599//Bill and Melinda Gates Foundation/ ; OPP1179599//Bill and Melinda Gates Foundation/ ; },
abstract = {Human milk oligosaccharides (HMOs) support the development of a healthy gut microbiome and the growth of infants. We aimed to determine the association of different HMOs with severe acute malnutrition (SAM) among Bangladeshi young infants. This study was nested within a single-blind, randomized, pilot clinical trial (NCT0366657). A total of 45 breastmilk samples from mothers of < 6 months old infants who had SAM (n = 26) or were non-malnourished (n = 19) and were analyzed for constituent HMOs. Of the infants with SAM, 14 (53.85%) had secretor mothers, and 11 (57.89%) of the non-malnourished infants had secretor mothers. A one-unit increase in the relative abundance of sialylated HMOs was associated with higher odds of SAM in age and sex adjusted model (aOR = 2.00, 90% CI 1.30, 3.06), in age, sex, and secretor status adjusted model (aOR = 1.96, 90% CI 1.29, 2.98), and also in age and sex adjusted model among non-secretor mothers (aOR = 2.86, 90% CI 1.07, 7.62). In adjusted models, there was no evidence of a statistically significant association between SAM and fucosylated or undecorated HMOs. Our study demonstrates that a higher relative abundance of sialylated HMOs in mothers' breastmilk may have a negative impact on young infants' nutritional status.},
}
@article {pmid35676021,
year = {2022},
author = {Stevens Brentjens, L and Habets, D and Den Hartog, J and Al-Nasiry, S and Wieten, L and Morré, S and Van Montfoort, A and Romano, A and van Golde, R},
title = {Endometrial factors in the implantation failure spectrum: protocol of a MUltidisciplinary observational cohort study in women with Repeated Implantation failure and recurrent Miscarriage (MURIM Study).},
journal = {BMJ open},
volume = {12},
number = {6},
pages = {e056714},
doi = {10.1136/bmjopen-2021-056714},
pmid = {35676021},
issn = {2044-6055},
abstract = {INTRODUCTION: Women with repeated implantation failure (RIF) and unexplained recurrent miscarriage (RM) are proposed to be at opposite ends of the implantation spectrum, with RM representing an overly receptive endometrium (implantation of genetically aberrant or poor-quality embryos) versus RIF representing an overly selective endometrium (no implantation even with good quality embryos). In both cases, often no explanation for reproductive failure can be found and although promising add-on treatments have been introduced, therapeutic options are frequently limited to supportive care. Both RM and RIF are multifactorial and research indicates that the interplay between steroidogenesis, uterine natural killer (uNK) cells and the microbiome determine the capacity of the endometrium to be a biosensor for invading embryos. Our objective is to elucidate whether there is a difference in endometrial receptivity parameters (ie, steroid metabolism, uNK cells and the microbiome) between women aged 18-38 years with reproductive failure (RIF and RM), and fertile controls.<br><br>METHODS AND ANALYSIS: Single-centre, observational cohort study. Endometrial biopsies, vaginal swabs and peripheral blood will be collected during the window of implantation and menstrual blood in the subsequent menstruation. The study parameters are the steroid profile (steroid levels and mRNA levels, protein expression and activity of steroid enzymes) in endometrial tissue and peripheral blood, as well as the activating or inhibitory phenotype of uNK cells based on receptor expression in menstrual blood and endometrial tissue and determination of the vaginal and endometrial microbiome using the inter spacer bacterial profiling technique.<br><br>ETHICS AND DISSEMINATION: The protocol is approved by the local medical ethical review committee at the Maastricht University Medical Centre. Findings from this study will be shared with the academic and medical community and the patient organisations to optimise and individualise medical care of patients with implantation failure and miscarriages.<br><br>TRIAL REGISTRATION NUMBER: NTR7571, registered 28 February 2019.},
}
@article {pmid35676015,
year = {2022},
author = {Shoji, F and Yamashita, T and Kinoshita, F and Takamori, S and Fujishita, T and Toyozawa, R and Ito, K and Yamazaki, K and Nakashima, N and Okamoto, T},
title = {Artificial intelligence-derived gut microbiome as a predictive biomarker for therapeutic response to immunotherapy in lung cancer: protocol for a multicentre, prospective, observational study.},
journal = {BMJ open},
volume = {12},
number = {6},
pages = {e061674},
doi = {10.1136/bmjopen-2022-061674},
pmid = {35676015},
issn = {2044-6055},
abstract = {INTRODUCTION: Immunotherapy is the fourth leading therapy for lung cancer following surgery, chemotherapy and radiotherapy. Recently, several studies have reported about the potential association between the gut microbiome and therapeutic response to immunotherapy. Nevertheless, the specific composition of the gut microbiome or combination of gut microbes that truly predict the efficacy of immunotherapy is not definitive.<br><br>METHODS AND ANALYSIS: The present multicentre, prospective, observational study aims to discover the specific composition of the gut microbiome or combination of gut microbes predicting the therapeutic response to immunotherapy in lung cancer using artificial intelligence. The main inclusion criteria are as follows: (1) pathologically or cytologically confirmed metastatic or postoperative recurrent lung cancer including non-small cell lung cancer and small cell lung cancer; (2) age≥20 years at the time of informed consent; (3) planned treatment with immunotherapy including combination therapy and monotherapy, as the first-line immunotherapy; and (4) ability to provide faecal samples. In total, 400 patients will be enrolled prospectively. Enrolment will begin in 2021, and the final analyses will be completed by 2024.<br><br>ETHICS AND DISSEMINATION: The study protocol was approved by the institutional review board of each participating centre in 2021 (Kyushu Cancer Center, IRB approved No. 2021-13, 8 June 2021 and Kyushu Medical Center, IRB approved No. 21-076, 31 August 2021). Study results will be disseminated through peer-reviewed journals and national and international conferences.<br><br>TRIAL REGISTRATION NUMBER: UMIN000046428.},
}
@article {pmid35675542,
year = {2022},
author = {Peters, BA and Lin, J and Qi, Q and Usyk, M and Isasi, CR and Mossavar-Rahmani, Y and Derby, CA and Santoro, N and Perreira, KM and Daviglus, ML and Kominiarek, MA and Cai, J and Knight, R and Burk, RD and Kaplan, RC},
title = {Menopause Is Associated with an Altered Gut Microbiome and Estrobolome, with Implications for Adverse Ca