@article {pmid33242664,
year = {2020},
author = {Ghadimi, D and de Vrese, M and Ebsen, M and Röcken, C and Olaf Frahm, S and Zahlten, J and Fölster-Holst, R and Heller, KJ and Bockelmann, W},
title = {Study on the additive protective effect of PGLYRP3 and Bifidobacterium adolescentis Reuter 1963 on severity of DSS-induced colitis in Pglyrp3 knockout (Pglyrp3 -/-) and wild-type (WT) mice.},
journal = {Immunobiology},
volume = {226},
number = {1},
pages = {152028},
doi = {10.1016/j.imbio.2020.152028},
pmid = {33242664},
issn = {1878-3279},
abstract = {BACKGROUND AND AIMS: Pglyrp3 is a bactericidal innate immunity protein known to sustain the habitual gut microbiome and protect against experimental colitis. Intestinal inflammation and metaflammation are commonly associated with a marked reduction of commensal bifidobacteria. Whether Pglyrp3 and bifidobacteria interact synergistically or additively to alleviate metaflammation is unknown. We investigated the extent to which Pglyrp3 and bifidobacteria regulate metaflammation and gut bacterial dysbiosis in DSS-induced mouse models of intestinal inflammation.

MATERIAL & METHODS: 8-10 weeks old male mice were used. In both WT and Pglyrp3 -/- experiments, the mice were randomly divided into three groups of 16 mice per group: (1) a control group receiving sterile tap water, (2) an experimental group receiving sterile tap water supplemented with only 5% DSS, and (3) an experimental group receiving sterile tap water supplemented with 5% DSS and 1 × 109 CFU/ml of Bifidobacterium adolescentis (B.a.) for 7 days. Wild-type (WT) littermates of the respective gene (i.e. Pglyrp3) were used as controls throughout the study. Clinical signs of general health and inflammation were monitored daily. Faecal pellet samples were analysed by qRT-PCR for microbial composition. Histology of relevant organs was carried out on day 8. Metabolic parameters and liver inflammation were determined in serum samples.

RESULTS: Intestinal inflammation in mice of group 2 were significantly increased compared to those of control group 1. There was a significant difference in mean scores for inflammation severity between DSS-treated WT and DSS-treated Pglyrp3 -/- mice. Buildup of key serum metabolic markers (cholesterol, triglyceride and glucose) was set off by colonic inflammation. qRT-PCR quantification showed that DSS significantly decreased the Clostridium coccoides and Bifidobacterium cell counts while increasing those of Bacteroides group in both WT and Pglyrp3 -/- mice. These manifestations of DSS-induced dysbiosis were significantly attenuated by feeding B.a. Both the local and systemic ill-being of the mice alleviated when they received B.a.

DISCUSSION: This study shows that Pglyrp3 facilitates recognition of bifidobacterial cell wall-derived peptidoglycan, thus leading additively to a reduction of metaflammation through an increase in the number of bifidobacteria, which were able to mitigate intestinal immunopathology in the context of Pglyrp3 blockade.},
}

@article {pmid33242652,
year = {2020},
author = {Sun, N and Hu, H and Wang, F and Li, L and Zhu, W and Shen, Y and Xiu, J and Xu, Q},
title = {Antibiotic-induced microbiome depletion in adult mice disrupts blood-brain barrier and facilitates brain infiltration of monocytes after bone-marrow transplantation.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2020.11.032},
pmid = {33242652},
issn = {1090-2139},
abstract = {The crosstalk between intestinal bacteria and the central nervous system, so called "the gut-brain axis", is critically important for maintaining brain homeostasis and function. This study aimed to investigate the integrity of the blood-brain barrier (BBB) and migration of bone marrow (BM)-derived cells to the brain parenchyma after intestinal microbiota depletion in adult mice. Gut microbiota dysbiosis was induced with 5 non-absorbable antibiotics in drinking water in mice that had received bone marrow transplantation (BMT) from green fluorescent protein (GFP) transgenic mice. Antibiotic-induced microbiome depletion reduced expression of tight-junction proteins of the brain blood vessels and increased BBB permeability. Fecal microbiota transplantation of antibiotics treated mice with pathogen-free gut microbiota decreased BBB permeability and up-regulated the expression of tight junction proteins. The BM-derived GFP+ cells were observed to infiltrate specific brain regions, including the nucleus accumbens (NAc), the septal nucleus (SPT) and the hippocampus (CA3). The infiltrated cells acquired a ramified microglia-like morphology and Iba1, a microglia marker, was expressed in all GFP+ cells, whereas they were negative for the astrocyte marker GFAP. Furthermore, treatment with CCR2 antagonist (RS102895) suppressed the recruitment of BM-derived monocytes to the brain. We report for the first time the migration of BM-derived monocytes to the brain regions involved in regulating emotional behaviors after depletion of intestinal microbiota in BMT background mice. However, mechanisms responsible for the migration and functions of the microglia-like infiltrated cells in the brain need further investigation. These findings indicate that monocyte recruitment to the brain in response to gut microbiota dysbiosis may represent a novel cellular mechanism that contributes to the development of brain disorders.},
}

@article {pmid33242642,
year = {2020},
author = {Neilands, J and Kinnby, B},
title = {Porphyromonas gingivalis initiates coagulation and secretes polyphosphates - A mechanism for sustaining chronic inflammation?.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {104648},
doi = {10.1016/j.micpath.2020.104648},
pmid = {33242642},
issn = {1096-1208},
abstract = {BACKGROUND: Periodontitis is a chronic inflammation resulting in destruction of tooth-supporting bone. Chronic inflammation is characterized by extravascular fibrin deposition. Fibrin is central to destruction of bone; monocytes bind to fibrin and form osteoclasts, thus providing a link between coagulation and the tissue destructive processes in periodontitis. The oral microbiome is essential to oral health. However, local ecological changes, such as increased biofilm formation, result in a dysbiotic microbiome characterized by an increase of protease-producing species e.g. Porphyromonas gingivalis. Proteases initiate inflammation and may cleave coagulation factors. Polyphosphates (polyP) may also provide bacteria with procoagulant properties similar to platelet-released polyP. P. gingivalis has also been found in remote locations related to vascular pathology and Alzheimer's disease.

OBJECTIVES: The aim of this study was to investigate procoagulant activity of ten different species of oral bacteria present in oral health and disease as well as presence of polyP and fibrin formation in planktonic and biofilm cells.

METHODS: Oral bacteria were studied for protease production and procoagulant activity. The presence of polyP and formation of fibrin was observed using confocal microscopy.

RESULTS: P. gingivalis showed strong protease activity and was the only species exerting procoagulant activity. Confocal microscopy showed polyP intracellularly in planktonic bacteria and extracellularly after biofilm formation. Fibrin formation emanated from planktonic bacteria and from both bacteria and polyP in biofilm cultures.

CONCLUSIONS: The procoagulant activity of P. gingivalis could explain its role in chronic inflammation, locally in oral tissues as well as in remote locations.},
}

@article {pmid33242602,
year = {2020},
author = {van den Bosch, MHJ},
title = {Osteoarthritis year in review 2020: biology.},
journal = {Osteoarthritis and cartilage},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joca.2020.10.006},
pmid = {33242602},
issn = {1522-9653},
abstract = {This year in review about osteoarthritis biology highlights a selection of articles published between the 2019 and 2020 Osteoarthritis Research Society International (OARSI) World Congress meetings, within the field of osteoarthritis biology. Highlights were selected from PubMed searches covering osteoarthritis (OA) cartilage, subchondral bone, synovium and aging. Subsequently, a personal selection was based on new and emerging themes together with common research topics that were studied by multiple groups. Themes discussed include novel insights into the inflammatory changes during OA, with a number of noteworthy publications concerning the role of macrophages in healthy and osteoarthritic joints. Next, the application of mesenchymal stem cells as OA-dampening therapy is discussed, including possible ways to improve their efficacy by pre-treatment. Other significant themes including treatment of OA with metformin, enhancing autophagy to alleviate OA and the involvement of the gastro-intestinal microbiome in development of OA symptoms and structural damage are discussed. An effort was made to connect the seemingly distant topics from which the overarching conclusion can be drawn that over the last year promising breakthroughs have been achieved in further understanding the biology of OA development and that new therapeutic possibilities have been explored.},
}

@article {pmid33242487,
year = {2020},
author = {Claudia, S and Marta, C and Laia, NM and Đorđe, T and Joan, P and Jordi, T and Bayona, JM and Benjamin, P},
title = {Antibiotic and antibiotic-resistant gene loads in swine slurries and their digestates: implications for their use as fertilizers in agriculture.},
journal = {Environmental research},
volume = {},
number = {},
pages = {110513},
doi = {10.1016/j.envres.2020.110513},
pmid = {33242487},
issn = {1096-0953},
abstract = {The spread of antibiotic resistance in bacteria is a matter of global concern, and the identification of possible sources of the associated genetic elements (antibiotic resistance genes -ARGs-, components of the horizontal gene transfer mechanism), is becoming an urgent need. While the transmission of ARGs in medical settings have been adequately characterized, ARG propagation in agroecosystems remains insufficiently studied. Particularly crucial is the determination of potential risks associated to the use of swine slurries and related products as component of organic fertilizers, an increasingly used farming practice. We determined ARGs and antibiotic loads analyzed from swine slurries and digestates from eight farms from Catalonia (NE Spain), and compared the results with their microbiome composition. Both ARGs and antibiotic were conspicuous in farm organic wastes, and the levels of some antibiotics exceeded currently accepted minimum inhibitory concentrations. Particularly, the presence of high loads of fluoroquinolones was directly correlated to the prevalence of the related qnrS1 ARG in the slurry. We also found evidence that ARG loads were directly correlated to the prevalence of determined bacterial taxa (Actinobacteria, Proteobacteria, Spirochaeta), a parameter that could be potentially modulated by the processing of the raw slurry prior to their use as fertilizer.},
}

@article {pmid33242416,
year = {2020},
author = {Afshinnekoo, E and Scott, RT and MacKay, MJ and Pariset, E and Cekanaviciute, E and Barker, R and Gilroy, S and Hassane, D and Smith, SM and Zwart, SR and Nelman-Gonzalez, M and Crucian, BE and Ponomarev, SA and Orlov, OI and Shiba, D and Muratani, M and Yamamoto, M and Richards, SE and Vaishampayan, PA and Meydan, C and Foox, J and Myrrhe, J and Istasse, E and Singh, N and Venkateswaran, K and Keune, JA and Ray, HE and Basner, M and Miller, J and Vitaterna, MH and Taylor, DM and Wallace, D and Rubins, K and Bailey, SM and Grabham, P and Costes, SV and Mason, CE and Beheshti, A},
title = {Fundamental Biological Features of Spaceflight: Advancing the Field to Enable Deep-Space Exploration.},
journal = {Cell},
volume = {183},
number = {5},
pages = {1162-1184},
doi = {10.1016/j.cell.2020.10.050},
pmid = {33242416},
issn = {1097-4172},
abstract = {Research on astronaut health and model organisms have revealed six features of spaceflight biology that guide our current understanding of fundamental molecular changes that occur during space travel. The features include oxidative stress, DNA damage, mitochondrial dysregulation, epigenetic changes (including gene regulation), telomere length alterations, and microbiome shifts. Here we review the known hazards of human spaceflight, how spaceflight affects living systems through these six fundamental features, and the associated health risks of space exploration. We also discuss the essential issues related to the health and safety of astronauts involved in future missions, especially planned long-duration and Martian missions.},
}

@article {pmid33241674,
year = {2020},
author = {Henig, I and Yehudai-Ofir, D and Zuckerman, T},
title = {The clinical role of the gut microbiome and fecal microbiota transplantation in allogeneic stem cell transplantation.},
journal = {Haematologica},
volume = {Online ahead of print},
number = {},
pages = {},
doi = {10.3324/haematol.2020.247395},
pmid = {33241674},
issn = {1592-8721},
abstract = {Outcomes of allogeneic hematopoietic stem cell transplantation (allo- HSCT) have improved in the recent decade; however, infections and graft-versus-host disease remain two leading complications significantly contributing to early transplant-related mortality. In past years, the human intestinal microbial composition (microbiota) has been found to be associated with various disease states, including cancer, response to cancer immunotherapy and to modulate the gut innate and adaptive immune response. In the setting of allo-HSCT, the intestinal microbiota diversity and composition appear to have an impact on infection risk, mortality and overall survival. Microbial metabolites have been shown to contribute to the health and integrity of intestinal epithelial cells during inflammation, thus mitigating graft-versus-host disease in animal models. While the cause-andeffect relationship between the intestinal microbiota and transplant-associated complications has not yet been fully elucidated, the above findings have already resulted in the implementation of various interventions aiming to restore the intestinal microbiota diversity and composition. Among others, these interventions include the administration of fecal microbiota transplantation. The present review, based on published data, is intended to define the role of the latter approach in the setting of allo-HSCT.},
}

@article {pmid33241010,
year = {2020},
author = {Liu, J and Luo, M and Zhang, Y and Cao, G and Wang, S},
title = {Association of high-risk human papillomavirus infection duration and cervical lesions with vaginal microbiota composition.},
journal = {Annals of translational medicine},
volume = {8},
number = {18},
pages = {1161},
doi = {10.21037/atm-20-5832},
pmid = {33241010},
issn = {2305-5839},
abstract = {Background: Cervical cancer is reportedly caused by the synergistic effects of persistent high-risk human papillomavirus (HPV) infection. Cervical microbiota represent a unique and dynamically changing microecological system that is directly exposed to the vagina. The relationship between HPV and the composition of the cervical microbiome has long been a primary focus of research.

Methods: To determine the specific differential florae throughout the process of cervical cancer development, in the present study, 16S rRNA sequencing was combined with KEGG pathway enrichment analysis to analyse five groups of cervical scraping samples with increasing durations of HPV infection and cervical intraepithelial neoplasia pathological classification.

Results: The findings revealed that decreasing levels of probiotics, including Shuttleworthia, Prevotella, Lactobacillus, and Sneathia, and increasing levels of pathogenic bacteria, including Dispar, Streptococcus, and Faecalibacterium prausnitzii, could be the direct result of early HPV infection. Other pathogenic bacteria, such as Bifidobacteriaceae, might represent key factors in cancer progression. Additionally, KEGG pathway enrichment analysis indicated that HPV infection directly inhibits multiple pathways, including those of sporulation, porphyrin and chlorophyll metabolism, arginine and proline metabolism, isoquinoline alkaloid biosynthesis, and ansamycin biosynthesis, which may lead to the development of early symptoms of cervical cancer. Biomarkers were predicted based on operational taxonomic unit (OTU) abundance data, and OTU851726 and OTU715913 were undoubtedly the best potential indicators of cervical cancer.

Conclusions: The findings of the present study could assist with the development of a guideline for screening new clinical drugs for cervical cancer.},
}

@article {pmid33240966,
year = {2020},
author = {Stockler, RM and Higgins, KV and Hallowell, H and Groover, ES and Hiltbold, EM and Newcomer, BW and Walz, PH},
title = {In vivo Microbiome Profiling of the Luminal and Mucosal Surface of the Duodenum Using a Cannulated Yearling Bovine Model.},
journal = {Frontiers in veterinary science},
volume = {7},
number = {},
pages = {601874},
doi = {10.3389/fvets.2020.601874},
pmid = {33240966},
issn = {2297-1769},
abstract = {The gut microbiome provides important metabolic functions for the host animal. Bacterial dysbiosis as a result of bacterial, viral, and parasitic gastrointestinal infections can adversely affect the metabolism, productivity, and overall health. The objective of this study is to characterize the commensal microbiome present in the lumen and the mucosal surface of the duodenum of cattle, as we hypothesize that due to metabolic processes and or host proprieties, there are differences in the natural microbiota present in the mucosal surface and luminal contents of the bovine duodenum. Duodenal lumen contents and mucosal biopsies were collected from six dairy crossbred yearling steers. A flexible video-endoscope was used to harvest biopsy samples via a T shaped intestinal cannula. In order to assess as much environmental and individual steer microbiota variation as possible, each animal was sampled three times over a 6 week period. The DNA was extracted from the samples and submitted for16S rRNA gene Ion Torrent PGM bacterial sequencing. A detailed descriptive analysis from phylum to genus taxonomic level was reported. Differences in the microbiome population between two different sites within the duodenum were successfully characterized. A great and significant microbiota diversity was found between the luminal and mucosal biopsy At the phylum taxonomic level, Firmicutes, and Bacteroidetes composed over 80% of the microbiome. Further analysis at lower taxonomic levels, class, family, and genus, showed distinct diversity and distribution of the microbiome. Characterizing the gastrointestinal microbiome in vivo is imperative. The novelty of this study is the use of live cattle undergoing customary husbandry allowing real-time analysis of the duodenum microbiome contributing to the literature with respect to the bovine duodenum microbiome.},
}

@article {pmid33240722,
year = {2020},
author = {Shaik, L and Kashyap, R and Thotamgari, SR and Singh, R and Khanna, S},
title = {Gut-Brain Axis and its Neuro-Psychiatric Effects: A Narrative Review.},
journal = {Cureus},
volume = {12},
number = {10},
pages = {e11131},
doi = {10.7759/cureus.11131},
pmid = {33240722},
issn = {2168-8184},
abstract = {The gut microbiota regulates the function and health of the human gut. Preliminary evidence suggests its impact on multiple human systems including the nervous and immune systems. A major area of research has been the directional relationship between intestinal microbiota and the central nervous system (CNS), called the microbiota-gut-brain axis. It is hypothesized that the intestinal microbiota affects brain activity and behavior via endocrine, neural, and immune pathways. An alteration in the composition of the gut microbiome has been linked to a variety of neurodevelopmental and neurodegenerative disorders. The connection between gut microbiome and several CNS disorders indicates that the focus of research in the future should be on the bacterial and biochemical targets. Through this review, we outline the established knowledge regarding the gut microbiome and gut-brain axis. In addition to gut microbiome in neurological and psychiatry diseases, we have briefly discussed microbial metabolites affecting the blood-brain barrier (BBB), immune dysregulation, modification of autonomic sensorimotor connections, and hypothalamus-pituitary-adrenal axis.},
}

@article {pmid33240577,
year = {2020},
author = {Patin, NV and Brown, E and Chebli, G and Garfield, C and Kubanek, J and Stewart, FJ},
title = {Microbial and chemical dynamics of a toxic dinoflagellate bloom.},
journal = {PeerJ},
volume = {8},
number = {},
pages = {e9493},
doi = {10.7717/peerj.9493},
pmid = {33240577},
issn = {2167-8359},
abstract = {Harmful Algal Blooms (HABs) exert considerable ecological and economic damage and are becoming increasingly frequent worldwide. However, the biological factors underlying HABs remain uncertain. Relationships between algae and bacteria may contribute to bloom formation, strength, and duration. We investigated the microbial communities and metabolomes associated with a HAB of the toxic dinoflagellate Karenia brevis off the west coast of Florida in June 2018. Microbial communities and intracellular metabolite pools differed based on both bacterial lifestyle and bloom level, suggesting a complex role for blooms in reshaping microbial processes. Network analysis identified K. brevis as an ecological hub in the planktonic ecosystem, with significant connections to diverse microbial taxa. These included four flavobacteria and one sequence variant unidentified past the domain level, suggesting uncharacterized diversity in phytoplankton-associated microbial communities. Additionally, intracellular metabolomic analyses associated high K. brevis levels with higher levels of aromatic compounds and lipids. These findings reveal water column microbial and chemical characteristics with potentially important implications for understanding HAB onset and duration.},
}

@article {pmid33240394,
year = {2020},
author = {Qiu, X and Zhao, X and Cui, X and Mao, X and Tang, N and Jiao, C and Wang, D and Zhang, Y and Ye, Z and Zhang, H},
title = {Characterization of fungal and bacterial dysbiosis in young adult Chinese patients with Crohn's disease.},
journal = {Therapeutic advances in gastroenterology},
volume = {13},
number = {},
pages = {1756284820971202},
doi = {10.1177/1756284820971202},
pmid = {33240394},
issn = {1756-283X},
abstract = {Intestinal microbiota dysbiosis has been described in inflammatory bowel disease (IBD), but data from China are limited. In this study, we performed molecular analysis of the fecal microbial community from 20 healthy Chinese subjects and 25 patients with Crohn's disease (CD), and evaluated associations with bacterial and fungal compositions. Decreased richness and diversity of bacterial composition was observed in the CD group compared with healthy (H) subjects. Significant structural differences in bacterial (but not fungal) composition among healthy controls and CD patients were found. A reduction in Firmicutes and Actinobacteria abundance, and overrepresentation of Proteobacteria were observed in the CD patients compared with the H group. The Escherichia-Shigella genus was overrepresented in the CD group, whereas Faecalibacterium, Gemmiger, Bifidobacterium, Romboutsia, Ruminococcus, Roseburia, and Fusicatenibacter abundance were decreased in the CD group compared with H subjects. Differences in fungal microbiota between the H and CD groups were observed at the genus rather than at the phylum level. The Candida genus was overrepresented in the CD (active disease) group compared with the H group, whereas no difference between CD (remission) and H groups was observed. Aspergillus, unclassified_Sordariomycetes, and Penicillium genera had greater representation in the H subjects compared with the CD group. Bacterial and fungal intra- and inter-kingdom correlations were observed between the H and CD groups. Therefore, fecal bacterial and fungal microbiome communities differed considerably between H and CD patients, and between Chinese and Western populations. The role of gut microbiota in homeostasis and in gastrointestinal disorders should be investigated further.},
}

@article {pmid33240345,
year = {2019},
author = {Lavigne, SE},
title = {The oral microbiome and precision medicine: A peek into the future of periodontal diagnostics.},
journal = {Canadian journal of dental hygiene : CJDH = Journal canadien de l'hygiene dentaire : JCHD},
volume = {53},
number = {2},
pages = {83-85},
pmid = {33240345},
issn = {1712-171X},
}

@article {pmid33240336,
year = {2020},
author = {Srivastava, D and Baksi, KD and Kuntal, BK and Mande, SS},
title = {Corrigendum: "EviMass": A Literature Evidence-Based Miner for Human Microbial Associations.},
journal = {Frontiers in genetics},
volume = {11},
number = {},
pages = {614051},
doi = {10.3389/fgene.2020.614051},
pmid = {33240336},
issn = {1664-8021},
abstract = {[This corrects the article DOI: 10.3389/fgene.2019.00849.].},
}

@article {pmid33240281,
year = {2020},
author = {Lei, V and Petty, AJ and Atwater, AR and Wolfe, SA and MacLeod, AS},
title = {Skin Viral Infections: Host Antiviral Innate Immunity and Viral Immune Evasion.},
journal = {Frontiers in immunology},
volume = {11},
number = {},
pages = {593901},
doi = {10.3389/fimmu.2020.593901},
pmid = {33240281},
issn = {1664-3224},
abstract = {The skin is an active immune organ that functions as the first and largest site of defense to the outside environment. Serving as the primary interface between host and pathogen, the skin's early immune responses to viral invaders often determine the course and severity of infection. We review the current literature pertaining to the mechanisms of cutaneous viral invasion for classical skin-tropic, oncogenic, and vector-borne skin viruses. We discuss the skin's evolved mechanisms for innate immune viral defense against these invading pathogens, as well as unique strategies utilized by the viruses to escape immune detection. We additionally explore the roles that demographic and environmental factors, such as age, biological sex, and the cutaneous microbiome, play in altering the host immune response to viral threats.},
}

@article {pmid33240253,
year = {2020},
author = {Oberpaul, M and Zumkeller, CM and Culver, T and Spohn, M and Mihajlovic, S and Leis, B and Glaeser, SP and Plarre, R and McMahon, DP and Hammann, P and Schäberle, TF and Glaeser, J and Vilcinskas, A},
title = {High-Throughput Cultivation for the Selective Isolation of Acidobacteria From Termite Nests.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {597628},
doi = {10.3389/fmicb.2020.597628},
pmid = {33240253},
issn = {1664-302X},
abstract = {Microbial communities in the immediate environment of socialized invertebrates can help to suppress pathogens, in part by synthesizing bioactive natural products. Here we characterized the core microbiomes of three termite species (genus Coptotermes) and their nest material to gain more insight into the diversity of termite-associated bacteria. Sampling a healthy termite colony over time implicated a consolidated and highly stable microbiome, pointing toward the fact that beneficial bacterial phyla play a major role in termite fitness. In contrast, there was a significant shift in the composition of the core microbiome in one nest during a fungal infection, affecting the abundance of well-characterized Streptomyces species (phylum Actinobacteria) as well as less-studied bacterial phyla such as Acidobacteria. High-throughput cultivation in microplates was implemented to isolate and identify these less-studied bacterial phylogenetic group. Amplicon sequencing confirmed that our method maintained the bacterial diversity of the environmental samples, enabling the isolation of novel Acidobacteriaceae and expanding the list of cultivated species to include two strains that may define new species within the genera Terracidiphilus and Acidobacterium.},
}

@article {pmid33240248,
year = {2020},
author = {Zhang, QQ and Liu, ZH and Liu, LL and Hu, G and Lei, GL and Wang, Y and Cao, Y and Wu, W and Zhang, L and Liao, QP},
title = {Prebiotic Maltose Gel Can Promote the Vaginal Microbiota From BV-Related Bacteria Dominant to Lactobacillus in Rhesus Macaque.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {594065},
doi = {10.3389/fmicb.2020.594065},
pmid = {33240248},
issn = {1664-302X},
abstract = {The high incidence of bacterial vaginosis recurrence is common after treatment with an antibiotic agent and suggests the need for new treatments to prevent this. We conducted a randomized trial to evaluate the ability of maltose gel to treat bacterial vaginosis. Eighteen female rhesus macaques were randomly assigned, in a 2:1 ratio, to receive maltose gel or placebo gel by syringe to the fornix of the vagina for five consecutive days. We used 16S rRNA sequencing data from 70 swab samples of vaginal secretions in two groups in total on days 0, 3, and 5 after medication initiation and days 3 and 5 after medication withdrawal for the study of microbiome composition. We found that, in the placebo control group, there was no significant change in the composition and abundance of vaginal microbiota during the follow-up period. In the maltose gel test group, the abundance of Lactobacillus in the vagina microbiota increased gradually with the prolongation of the treatment time on Days 3 and 5 (ANOVA p = 6.99e-5 < 0.01) but began to decrease after the withdrawal of maltose gel, which was different from that of the control group. Correspondingly, the diversity and abundance of BV-related bacteria, Fusobacterium, Parvimonas, Mobiluncus, Campylobacter, Prevotella, and Sneathia, decreased on Day 0 to Day 5 of medication and increased after drug withdrawal in the maltose gel test group. The study confirms that maltose gel can facilitate the proliferation of Lactobacillus and promote the transition of the vaginal microbiota from BV-related bacteria dominant to Lactobacillus dominant in the rhesus macaque.},
}

@article {pmid33240240,
year = {2020},
author = {Sela, R and Laviad-Shitrit, S and Halpern, M},
title = {Changes in Microbiota Composition Along the Metamorphosis Developmental Stages of Chironomus transvaalensis.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {586678},
doi = {10.3389/fmicb.2020.586678},
pmid = {33240240},
issn = {1664-302X},
abstract = {Chironomids (Diptera; Chironomidae), also known as non-biting midges, are one of the most abundant insects in freshwater habitats. Our aim was to understand whether the metamorphosis developmental stages affect the endogenous microbiota composition of Chironomus transvaalensis. Toward our objective, we analyzed the endogenous microbiota composition of C. transvaalensis' four life stages: egg masses, larvae, pupae, and adults. Significant differences were found between the microbiota compositions of the different developmental stages of this Chironomus species. We observed a decline in bacterial diversity as the insect evolved from egg mass to adult, while the highest richness was observed in the pupal stage. Although there were significant differences between the microbiota compositions of each life stage, a bacterial core, which included 27 Amplicon Sequence Variants (ASVs), was found in all the developmental life stages (in ≥75% of samples). Chironomids are natural reservoirs of Vibrio cholerae and Aeromonas species, and the Vibrio and Aeromonas ASVs were part of the core bacteria. The presence of the ompW gene, which is specific to V. cholerae, confirmed the presence of this species in all the chironomid's life stages. Thus, the results provide important insights about the host-microbe interactions in chironomids with a specific understanding of chironomids-Vibrio-Aeromonas-microbiota interactions.},
}

@article {pmid33240227,
year = {2020},
author = {Mhatre, S and Wood, JM and Sielaff, AC and Mora, M and Duller, S and Singh, NK and Karouia, F and Moissl-Eichinger, C and Venkateswaran, K},
title = {Assessing the Risk of Transfer of Microorganisms at the International Space Station Due to Cargo Delivery by Commercial Resupply Vehicles.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {566412},
doi = {10.3389/fmicb.2020.566412},
pmid = {33240227},
issn = {1664-302X},
abstract = {Background: With increasing numbers of interplanetary missions, there is a need to establish robust protocols to ensure the protection of extraterrestrial planets being visited from contamination by terrestrial life forms. The current study is the first report comparing the commercial resupply vehicle (CRV) microbiome with the International Space Station (ISS) microbiome to understand the risks of contamination, thus serving as a model system for future planetary missions.

Results: Samples obtained from the internal surfaces and ground support equipment of three CRV missions were subjected to various molecular techniques for microbial diversity analysis. In total, 25 samples were collected with eight defined locations from each CRV mission prior to launch. In general, the internal surfaces of vehicles were clean, with an order of magnitude fewer microbes compared to ground support equipment. The first CRV mission had a larger microbial population than subsequent CRV missions, which were clean as compared to the initial CRV locations sampled. Cultivation assays showed the presence of Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes and members of Ascomycota and Basidiomycota. As expected, shotgun metagenome analyses revealed the presence of more microbial taxa compared to cultivation-based assays. The internal locations of the CRV microbiome reportedly showed the presence of microorganisms capable of tolerating ultraviolet radiation (e.g., Bacillus firmus) and clustered separately from the ISS microbiome.

Conclusions: The metagenome sequence comparison of the CRV microbiome with the ISS microbiome revealed significant differences showing that CRV microbiomes were a negligible part of the ISS environmental microbiome. These findings suggest that the maintenance protocols in cleaning CRV surfaces are highly effective in controlling the contaminating microbial population during cargo transfer to the ISS via the CRV route.},
}

@article {pmid33240225,
year = {2020},
author = {Albright, MBN and Johansen, R and Thompson, J and Lopez, D and Gallegos-Graves, V and Kroeger, ME and Runde, A and Mueller, RC and Washburne, A and Munsky, B and Yoshida, T and Dunbar, J},
title = {Soil Bacterial and Fungal Richness Forecast Patterns of Early Pine Litter Decomposition.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {542220},
doi = {10.3389/fmicb.2020.542220},
pmid = {33240225},
issn = {1664-302X},
abstract = {Discovering widespread microbial processes that drive unexpected variation in carbon cycling may improve modeling and management of soil carbon (Prescott, 2010; Wieder et al., 2015a, 2018). A first step is to identify community features linked to carbon cycle variation. We addressed this challenge using an epidemiological approach with 206 soil communities decomposing Ponderosa pine litter in 618 microcosms. Carbon flow from litter decomposition was measured over a 6-week incubation. Cumulative CO2 from microbial respiration varied two-fold among microcosms and dissolved organic carbon (DOC) from litter decomposition varied five-fold, demonstrating large functional variation despite constant environmental conditions where strong selection is expected. To investigate microbial features driving DOC concentration, two microbial community cohorts were delineated as "high" and "low" DOC. For each cohort, communities from the original soils and from the final microcosm communities after the 6-week incubation with litter were taxonomically profiled. A logistic model including total biomass, fungal richness, and bacterial richness measured in the original soils or in the final microcosm communities predicted the DOC cohort with 72 (P < 0.05) and 80 (P < 0.001) percent accuracy, respectively. The strongest predictors of the DOC cohort were biomass and either fungal richness (in the original soils) or bacterial richness (in the final microcosm communities). Successful forecasting of functional patterns after lengthy community succession in a new environment reveals strong historical contingencies. Forecasting future community function is a key advance beyond correlation of functional variance with end-state community features. The importance of taxon richness-the same feature linked to carbon fate in gut microbiome studies-underscores the need for increased understanding of biotic mechanisms that can shape richness in microbial communities independent of physicochemical conditions.},
}

@article {pmid33240224,
year = {2020},
author = {Doster, E and Thomas, KM and Weinroth, MD and Parker, JK and Crone, KK and Arthur, TM and Schmidt, JW and Wheeler, TL and Belk, KE and Morley, PS},
title = {Metagenomic Characterization of the Microbiome and Resistome of Retail Ground Beef Products.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {541972},
doi = {10.3389/fmicb.2020.541972},
pmid = {33240224},
issn = {1664-302X},
abstract = {Ground beef can be a reservoir for a variety of bacteria, including spoilage organisms, and pathogenic foodborne bacteria. These bacteria can exhibit antimicrobial resistance (AMR) which is a public health concern if resistance in pathogens leads to treatment failure in humans. Culture-dependent techniques are commonly used to study individual bacterial species, but these techniques are unable to describe the whole community of microbial species (microbiome) and the profile of AMR genes they carry (resistome), which is critical for getting a holistic perspective of AMR. The objective of this study was to characterize the microbiome and resistome of retail ground beef products labeled as coming from conventional or raised without antibiotics (RWA) production systems. Sixteen ground beef products were purchased from 6 retail grocery outlets in Fort Collins, CO, half of which were labeled as produced from cattle raised conventionally and half of products were from RWA production. Total DNA was extracted and isolated from each sample and subjected to 16S rRNA amplicon sequencing for microbiome characterization and target-enriched shotgun sequencing to characterize the resistome. Differences in the microbiome and resistome of RWA and conventional ground beef were analyzed using the R programming software. Our results suggest that the resistome and microbiome of retail ground beef products with RWA packaging labels do not differ from products that do not carry claims regarding antimicrobial drug exposures during cattle production. The resistome predominantly consisted of tetracycline resistance making up more than 90% of reads mapped to resistance gene accessions in our samples. Firmicutes and Proteobacteria predominated in the microbiome of all samples (69.6% and 29.0%, respectively), but Proteobacteria composed a higher proportion in ground beef from conventionally raised cattle. In addition, our results suggest that product management, such as packaging type, could exert a stronger influence on the microbiome than the resistome in consumer-ready products. Metagenomic analyses of ground beef is a promising tool to investigate community-wide shifts in retail ground beef. Importantly, however, results from metagenomic sequencing must be carefully considered in parallel with traditional methods to better characterize the risk of AMR in retail products.},
}

@article {pmid33240001,
year = {2020},
author = {Łoś-Rycharska, E and Gołębiewski, M and Grzybowski, T and Rogalla-Ładniak, U and Krogulska, A},
title = {The microbiome and its impact on food allergy and atopic dermatitis in children.},
journal = {Postepy dermatologii i alergologii},
volume = {37},
number = {5},
pages = {641-650},
doi = {10.5114/ada.2019.90120},
pmid = {33240001},
issn = {1642-395X},
abstract = {Food allergy (FA) affects 4-10% of children, especially children with atopic dermatitis (AD). During infancy the gut microbiome may determine both the course of FA and tolerance to food allergens. Analogically, the skin microbiome changes in the course of AD. Most studies have associated FA with a lower abundance and diversity of Lactobacillales and Clostridiales, but greater numbers of Enterobacterales, while AD in children has been associated with lower numbers of Staphylococcus epidermidis and S. hominis but an abundance of S. aureus and Streptococcus species. An understanding of the impact of the microbiome on the clinical course of FA and AD may allow for the development of new models of allergy treatment and prevention.},
}

@article {pmid33239817,
year = {2020},
author = {Conroy, G and Crew, B and Tay, A},
title = {Clusters of Excellence: the new 'brains trusts' of German science.},
journal = {Nature},
volume = {587},
number = {7835},
pages = {S116-S117},
doi = {10.1038/d41586-020-03322-0},
pmid = {33239817},
issn = {1476-4687},
}

@article {pmid33239787,
year = {2020},
author = {Gola, A and Dorrington, MG and Speranza, E and Sala, C and Shih, RM and Radtke, AJ and Wong, HS and Baptista, AP and Hernandez, JM and Castellani, G and Fraser, IDC and Germain, RN},
title = {Commensal-driven immune zonation of the liver promotes host defence.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-020-2977-2},
pmid = {33239787},
issn = {1476-4687},
abstract = {The liver connects the intestinal portal vasculature with the general circulation, using a diverse array of immune cells to protect from pathogens that translocate from the gut1. In liver lobules, blood flows from portal triads that are situated in periportal lobular regions to the central vein via a polarized sinusoidal network. Despite this asymmetry, resident immune cells in the liver are considered to be broadly dispersed across the lobule. This differs from lymphoid organs, in which immune cells adopt spatially biased positions to promote effective host defence2,3. Here we used quantitative multiplex imaging, genetic perturbations, transcriptomics, infection-based assays and mathematical modelling to reassess the relationship between the localization of immune cells in the liver and host protection. We found that myeloid and lymphoid resident immune cells concentrate around periportal regions. This asymmetric localization was not developmentally controlled, but resulted from sustained MYD88-dependent signalling induced by commensal bacteria in liver sinusoidal endothelial cells, which in turn regulated the composition of the pericellular matrix involved in the formation of chemokine gradients. In vivo experiments and modelling showed that this immune spatial polarization was more efficient than a uniform distribution in protecting against systemic bacterial dissemination. Together, these data reveal that liver sinusoidal endothelial cells sense the microbiome, actively orchestrating the localization of immune cells, to optimize host defence.},
}

@article {pmid33239489,
year = {2020},
author = {Ka, Y and Ogura, T and Tomiyama, K and Ueno, M and Nozu, R and Tsuruzono, N and Nozawa, Y and Hamano, M and Takakura, A and Takahashi, R},
title = {Creation of an experimental rearing environment for microbiome animal research using an individually ventilated cage system and bioBUBBLE enclosure.},
journal = {Experimental animals},
volume = {},
number = {},
pages = {},
doi = {10.1538/expanim.20-0129},
pmid = {33239489},
issn = {1881-7122},
abstract = {To avoid microbial contamination risk, vinyl film isolators are generally used in animal microbiome experiments involving germ-free (GF) mice and/or gnotobiotic (GB) mice. However, it can take several months to gain expertise in operating the isolator competently. Furthermore, sterilization and sterility testing, which are essential for isolator preparation, can take more than 20 days. Hence, we built an experimental rearing environment that combines an individual ventilation cage system and a bioBUBBLE clean room enclosure to easily set up an experimental animal microbiome environment for animal facilities. In this work, a three-step evaluation was conducted. First, we examined whether GF mice can be maintained in this rearing environment without bacterial contamination. Next, we examined whether GF and GB mice can be maintained without cross-contamination in one individual ventilation cage rack. Finally, we tested whether GF mice can be maintained in a biological safety cabinet controlled by negative pressure. In our series of experiments, no microbial contamination occurred over more than 3 months. These results indicated that our rearing system that combines the individual ventilation cage and bioBUBBLE systems can be used not only for experiments with GF mice but also for Biosafety Level 2 experiments that handle bacteria. Our system can mitigate various disadvantages of using vinyl film isolators. In conclusion, we established an experimental method with improved working time and efficiency compared with those of the previous vinyl isolator method.},
}

@article {pmid33239459,
year = {2020},
author = {Takashima, M and Manabe, RI and Ohkuma, M},
title = {Draft Genome Sequence of Oleaginous Yeast Saitozyma sp. Strain JCM 24511, Isolated from Soil on Iriomote Island, Okinawa, Japan.},
journal = {Microbiology resource announcements},
volume = {9},
number = {48},
pages = {},
pmid = {33239459},
issn = {2576-098X},
abstract = {Here, we report draft genome sequence of oleaginous yeast strain Saitozyma sp. JCM 24511, which is phylogenetically closely related to Saitozyma podzolica These data will have implications not only for the study of the oleaginous activities of yeasts but also for the study of the plant-microorganism microbiome.},
}

@article {pmid33239396,
year = {2020},
author = {Baker, JL and Morton, JT and Dinis, M and Alvarez, R and Tran, NC and Knight, R and Edlund, A},
title = {Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.265645.120},
pmid = {33239396},
issn = {1549-5469},
abstract = {Dental caries, the most common chronic infectious disease worldwide, has a complex etiology involving the interplay of microbial and host factors that are not completely understood. In this study, the oral microbiome, and 38 host cytokines and chemokines, were analyzed across 23 children with caries and 24 children with healthy dentition. De novo assembly of metagenomic sequencing obtained 527 metagenome-assembled genomes (MAGs), representing 150 bacterial species. 42 of these species had no genomes in public repositories, therefore representing novel taxa. These new genomes greatly expanded the known pangenomes of many oral clades, including the enigmatic Saccharibacteria clades G3 and G6, which had distinct functional repertoires compared to other oral Saccharibacteria. Saccharibacteria are understood to be obligate epibionts, which are dependent on host bacteria. This data suggests that the various Saccharibacteria clades may rely on their hosts for highly distinct metabolic requirements, which would have significant evolutionary and ecological implications. Across the study group, Rothia, Neisseria, and Haemophilus spp were associated with good dental health, while Prevotella spp., Streptococcus mutans, and Human herpesvirus 4 (Epstein-barr virus/EBV) were more prevalent in children with caries. Finally, ten of the host immunological markers were significantly elevated in the caries group, and co-occurrence analysis provided an atlas of potential relationships between microbes and host immunological molecules. Overall, this study illustrated the oral microbiome at an unprecedented resolution, and contributed several leads for further study that will increase the understanding of caries pathogenesis and guide therapeutic development.},
}

@article {pmid33239339,
year = {2020},
author = {Ianiro, G and Gasbarrini, A and Cammarota, G},
title = {Autologous faecal microbiota transplantation for type 1 diabetes: a potential mindshift in therapeutic microbiome manipulation?.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2020-323252},
pmid = {33239339},
issn = {1468-3288},
}

@article {pmid33238618,
year = {2020},
author = {Zhang, X and Zhao, A and Sandhu, AK and Edirisinghe, I and Burton-Freeman, BM},
title = {Functional Deficits in Gut Microbiome of Young and Middle-Aged Adults with Prediabetes Apparent in Metabolizing Bioactive (Poly)phenols.},
journal = {Nutrients},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/nu12113595},
pmid = {33238618},
issn = {2072-6643},
support = {N/A//National Processed Raspberry Council/ ; },
abstract = {BACKGROUND: Gut microbiota metabolize select dietary (poly)phenols to absorbable metabolites that exert biological effects important in metabolic health. Microbiota composition associated with health/disease status may affect its functional capacity to yield bioactive metabolites from dietary sources. Therefore, this study assessed gut microbiome composition and its related functional capacity to metabolize fruit (poly)phenols in individuals with prediabetes and insulin resistance (PreDM-IR, n = 26) compared to a metabolically healthy Reference group (n = 10).

METHODS: Shotgun sequencing was used to characterize gut microbiome composition. Targeted quantitative metabolomic analyses of plasma and urine collected over 24 h were used to assess microbial-derived metabolites in response to a (poly)phenol-rich raspberry test drink.

RESULTS: PreDM-IR compared to the Reference group: (1) enriched Blautia obeum and Blautia wexlerae and depleted Bacteroides dorei and Coprococcus eutactus. Akkermansia muciniphila and Bacteroides spp. were depleted in the lean PreDM-IR subset; and (2) impaired microbial catabolism of select (poly)phenols resulting in lower 3,8-dihydroxy-urolithin (urolithin A), phenyl-γ-valerolactones and various phenolic acids concentrations (p < 0.05). Controlling for obesity revealed relationships with microbial species that may serve as metagenomic markers of diabetes development and therapeutic targets.

CONCLUSIONS: Data provide insight from multi-omics approaches to advance knowledge at the diet-gut-disease nexus serving as a platform for devising dietary strategies to improve metabolic health.},
}

@article {pmid33237770,
year = {2020},
author = {Gao, H and Song, R and Li, Y and Zhang, W and Wan, Z and Wang, Y and Zhang, H and Han, S},
title = {Effects of Oat Fiber Intervention on Cognitive Behavior in LDLR-/- Mice Modeling Atherosclerosis by Targeting the Microbiome-Gut-Brain Axis.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.0c05677},
pmid = {33237770},
issn = {1520-5118},
abstract = {It is known that cardiovascular disease can result in cognitive impairment. However, whether oat fiber improves cognitive behavior through a cardiovascular-related mechanism remains unclear. The present work was aimed to elucidate the potential of oat fiber on cognitive behavior by targeting the neuroinflammation signal and microbiome-gut-brain axis in a mouse model of atherosclerosis. Male low-density lipoprotein receptor knock-out (LDLR-/-) mice were treated with a high fat/cholesterol diet without or with 0.8% oat fiber for 14 weeks. Behavioral tests indicated that LDLR-/- mice exhibited a significant cognitive impairment; however, oat fiber can improve cognitive behavior by reducing latency to the platform and increasing the number of crossing and swimming distance in the target quadrant. Oat fiber can inhibit Aβ plaque processing in both the cortex and hippocampus via decreasing the relative protein expression of GFAP and IBα1. Notably, oat fiber inhibited the nod-like receptor family pyrin domain-containing 3 inflammasome activation and blocked the toll-like receptor 4 signal pathway in both the cortex and hippocampus, accompanied by a reduction of circulating serum lipopolysaccharide. In addition, oat fiber raised the expressions of short-chain fatty acid (SCFA) receptors and tight junction proteins (zonula occludens-1 and occludin) and improved intestinal microbiota diversity via increasing the contents of gut metabolites SCFAs. In summary, the present study provided experimental evidence that dietary oat fiber retarded the progression of cognitive impairment in a mouse model of atherosclerosis. Mechanistically, the neuroprotective potential was related to oat fiber and its metabolites SCFAs on the diversity and abundance of gut microbiota that produced anti-inflammatory metabolites, leading to repressed neuroinflammation and reduced gut permeability through the microbiome-gut-brain axis.},
}

@article {pmid33237651,
year = {2020},
author = {Von Schoen-Angerer, T and Tierny, EM and Wildhaber, J and Tarr, P and Huber, BM},
title = {[Strategies to reduce antibiotic use with the help of complementary and integrative medicine].},
journal = {Revue medicale suisse},
volume = {16},
number = {716},
pages = {2301-2305},
pmid = {33237651},
issn = {1660-9379},
abstract = {Limiting antibiotic use is urgent due to increasing antibiotic resistance and the long-term implications of a disturbed microbiome. Data on antibiotic use of physicians integrating conventional and complementary medicine show that a significant reduction of antibiotic use in primary care is possible. In the setting of non-complicated infections in out-patient medicine, open dialogue with the patient, recognizing the importance of fever and reducing antipyretic use are general measures that can help reduce patients' concerns, and increase their trust in a well-functioning immune system and a treatment approach without antibiotics. Accumulating evidence suggests that complementary medicine strategies are useful in the management of common infections without antibiotics.},
}

@article {pmid33236934,
year = {2020},
author = {Robinson, JM and Cando-Dumancela, C and Liddicoat, C and Weinstein, P and Cameron, R and Breed, MF},
title = {Vertical Stratification in Urban Green Space Aerobiomes.},
journal = {Environmental health perspectives},
volume = {128},
number = {11},
pages = {117008},
doi = {10.1289/EHP7807},
pmid = {33236934},
issn = {1552-9924},
abstract = {BACKGROUND: Exposure to a diverse environmental microbiome is thought to play an important role in "educating" the immune system and facilitating competitive exclusion of pathogens to maintain human health. Vegetation and soil are key sources of airborne microbiota--the aerobiome. A limited number of studies have attempted to characterize the dynamics of near surface green space aerobiomes, and no studies to date have investigated these dynamics from a vertical perspective. Vertical stratification in the aerobiome could have important implications for public health and for the design, engineering, and management of urban green spaces.

OBJECTIVES: The primary objectives of this study were to: a) assess whether significant vertical stratification in bacterial species richness and evenness (alpha diversity) of the aerobiome occurred in a parkland habitat in Adelaide, South Australia; b) assess whether significant compositional differences (beta diversity) between sampling heights occurred; and c) to preliminarily assess whether there were significant altitudinal differences in potentially pathogenic and beneficial bacterial taxa.

METHODS: We combined an innovative columnar sampling method at soil level, 0.0, 0.5, 1.0, and 2.0 m , using passive petri dish sampling to collect airborne bacteria. We used a geographic information system (GIS) to select study sites, and we used high-throughput sequencing of the bacterial 16S rRNA gene to assess whether significant vertical stratification of the aerobiome occurred.

RESULTS: Our results provide evidence of vertical stratification in both alpha and beta (compositional) diversity of airborne bacterial communities, with diversity decreasing roughly with height. We also found significant vertical stratification in potentially pathogenic and beneficial bacterial taxa.

DISCUSSION: Although additional research is needed, our preliminary findings point to potentially different exposure attributes that may be contingent on human height and activity type. Our results lay the foundations for further research into the vertical characteristics of urban green space aerobiomes and their implications for public health and urban planning. https://doi.org/10.1289/EHP7807.},
}

@article {pmid33236419,
year = {2020},
author = {Montecchiani, V and Fanos, V},
title = {Human microbiome and allergy.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {31 Suppl 26},
number = {},
pages = {5-7},
doi = {10.1111/pai.13360},
pmid = {33236419},
issn = {1399-3038},
abstract = {Human microbiome contributes to critical functions that impact health and disease. It influences the development of the immune system, and the pathogenesis of immunological disorders included allergy. While it is easy to understand how airway microbiome, influencing local inflammation and immune activity, could contribute to shaping asthma phenotype, it is not so obvious to understand the influence by the gut microbiome, but there is growing evidence about it. The increase of allergic disorders in western countries led to investigate the role environment is playing and how it may change our microbiome and immune system, with the hope of finding new preventive approaches for allergy.},
}

@article {pmid33236315,
year = {2020},
author = {Hasan, A and Hasan, LK and Schnabl, B and Greytak, M and Yadlapati, R},
title = {Microbiome of the Aerodigestive Tract in Health and Esophageal Disease.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10620-020-06720-6},
pmid = {33236315},
issn = {1573-2568},
support = {120515/DK/NIDDK NIH HHS/United States ; },
abstract = {The diverse human gut microbiome is comprised of approximately 40 trillion microorganisms representing up to 1000 different bacterial species. The human microbiome plays a critical role in gut epithelial health and disease susceptibility. While the interaction between gut microbiome and gastrointestinal pathology is increasingly understood, less is known about the interaction between the microbiome and the aerodigestive tract. This review of the microbiome of the aerodigestive tract in health, and alterations in microbiome across esophageal pathologies highlights important findings and areas for future research. First, microbiome profiles are distinct along the aerodigestive tract, spanning the oral cavity to the stomach. In patients with reflux-related disease such as gastro-esophageal reflux disease, Barrett's esophagus, and esophageal adenocarcinoma, investigators have observed an overall increase in gram negative bacteria in the esophageal microbiome compared to healthy individuals. However, whether differences in microbiome promote disease development, or if these shifts are a consequence of disease remains unknown. Interestingly, use of proton pump inhibitor therapy is also associated with shifts in the microbiome, with distinct shifts and patterns along the aerodigestive tract. The relationship between the human gut microbiome and esophageal pathology is a ripe area for investigation, and further understanding of these pathways may promote development of novel targets in prevention and therapy for esophageal diseases.},
}

@article {pmid33236213,
year = {2020},
author = {Vasconcellos, RLF and Romagnoli, EM and Taketani, RG and Santos, SN and Zucchi, TD and Melo, IS},
title = {Impact of Inoculation with Pseudomonas aestus CMAA 1215T on the Non-target Resident Bacterial Community in a Saline Rhizosphere Soil.},
journal = {Current microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00284-020-02285-9},
pmid = {33236213},
issn = {1432-0991},
support = {2012/16623-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {Plant growth reduction caused by osmotic stress, pathogens, and nutrient scarcity can be overcome by inoculation with plant growth-promoting rhizobacteria (PGPR). Knowing the effects of PGPR on the microbial community beyond those on plant growth can bring new options of soil microbiota management. The present study aimed to investigate the effect of inoculation with the newly described Pseudomonas aestus CMAA 1215T [a 1-aminocyclopropane-1-carboxylate (ACC) deaminase and glycine-betaine producer] on the rhizosphere bacterial community of Zea mays in natural (non-salinized) and saline soil. The bacterial community structure was assessed by sequencing the V6-V7 16S ribosomal RNA using the Ion Personal Genome Machine™. The non-metric multidimensional scaling (NMDS) of the OTU profile (ANOSIM P < 0.01) distinguishes all the treatments (with and without inoculation under saline and natural soils). Inoculated samples shared 1234 OTUs with non-inoculated soil. The most abundant classes in all samples were Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Acidobacteriia, Bacteroidia, Thermoleophilia, Verrucomicrobiae, Ktenodobacteria, and Bacilli. The inoculation, on the other hand, caused an increase in the abundance of the genera Bacillus, Bryobacter, Bradyrhizobium, "Candidatus Xiphinematobacter", and "Candidatus Udaeobacter" independent of soil salinization. "Candidatus Udaeobacter" has the largest Mean Decrease in Gini Values with higher abundance on inoculated salted soil. In addition, Pseudomonas inoculation reduced the abundance of Gammaproteobacteria and Phycisphaerae. Understanding how inoculation modifies the bacterial community is essential to manage the rhizospheric microbiome to create a multi-inoculant approach and to understand its effects on ecological function.},
}

@article {pmid33236030,
year = {2020},
author = {Marotz, C and Belda-Ferre, P and Ali, F and Das, P and Huang, S and Cantrel, K and Jiang, L and Martino, C and Diner, R and Rahman, G and McDonald, D and Armstrong, G and Kodera, S and Donato, S and Ecklu-Mensah, G and Gottel, N and Salas Garcia, M and Chiang, L and Salido, RA and Shaffer, JP and Bryant, M and Sanders, K and Humphrey, G and Ackermann, G and Haiminen, N and Beck, KL and Kim, HC and Carrieri, AP and Parida, L and Vazquez-Baeza, Y and Torriani, FJ and Knight, R and Gilbert, J and Sweeney, D and Allard, SM},
title = {Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2020.11.19.20234229},
pmid = {33236030},
abstract = {Synergistic effects of bacteria on viral stability and transmission are widely documented but remain unclear in the context of SARS-CoV-2. We collected 972 samples from hospitalized ICU patients with coronavirus disease 2019 (COVID-19), their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and contextualized the massive microbial diversity in this dataset in a meta-analysis of over 20,000 samples. Sixteen percent of surfaces from COVID-19 patient rooms were positive, with the highest prevalence in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples increasingly resembled the patient microbiome throughout their stay, SARS-CoV-2 was less frequently detected there (11%). Despite surface contamination in almost all patient rooms, no health care workers providing COVID-19 patient care contracted the disease. SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity across human and surface samples, and higher biomass in floor samples. 16S microbial community profiles allowed for high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia was highly predictive of SARS-CoV-2 across sample types, and had higher prevalence in positive surface and human samples, even when comparing to samples from patients in another intensive care unit prior to the COVID-19 pandemic. These results suggest that bacterial communities contribute to viral prevalence both in the host and hospital environment.},
}

@article {pmid33235447,
year = {2020},
author = {Hua, JL and Hu, WP and Zuo, YH and Zhang, J},
title = {Prevention of Acute Exacerbation in Subjects with Moderate-to-very Severe COPD by Modulating Lower Respiratory Microbiome: Protocol of a Prospective, Multicenter, Randomized Controlled Trial.},
journal = {International journal of chronic obstructive pulmonary disease},
volume = {15},
number = {},
pages = {2985-2990},
doi = {10.2147/COPD.S274005},
pmid = {33235447},
issn = {1178-2005},
abstract = {Background: COPD is a global respiratory disease that has produced a worldwide health care burden. Acute exacerbation of COPD (AECOPD) is the leading cause of death in patients with COPD and accounts for the majority of expenditure of COPD management. The colonization of potential pathogenic bacteria in the lower respiratory tract is an important cause of the acute exacerbation especially in patients with moderate and severe COPD. Some clinical studies have shown the potential of oral probiotics, aerosol-inhaled amikacin and combined vaccination to prevent AECOPD.

Methods and Analysis: We hypothesize that patients with stable COPD will benefit from aerosol-inhaled amikacin, oral probiotics or combined vaccination in terms of preventing acute exacerbation of COPD, slowing the progression of the disease and improving their quality of life. The trial aimsto investigate the efficacy and safety of the above interventions to decolonize bacteria in the lower respiratory tract and prevent acute exacerbation of COPD. In the study, 144 patients with stable phase of moderate-to-very severe COPD will be recruited and randomized into aerosol-inhaled amikacin group, oral probiotics group, combined vaccination group and the control group at a 1:1:1:1 ratio. The primary outcome is time to the first COPD exacerbation. Other endpoints include colonization of potential pathogenic bacteria in induced sputum, microbiome in induced sputum, pulmonary function and symptoms of patients, inflammation level and adverse events, serious adverse events, and death.},
}

@article {pmid33235223,
year = {2020},
author = {Sagar, NM and Duboc, H and Kay, GL and Alam, MT and Wicaksono, AN and Covington, JA and Quince, C and Kokkorou, M and Svolos, V and Palmieri, LJ and Gerasimidis, K and Walters, JRF and Arasaradnam, RP},
title = {The pathophysiology of bile acid diarrhoea: differences in the colonic microbiome, metabolome and bile acids.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {20436},
doi = {10.1038/s41598-020-77374-7},
pmid = {33235223},
issn = {2045-2322},
abstract = {Bile acid diarrhoea (BAD) is a common disorder resulting from increased loss of bile acids (BAs), overlapping irritable bowel syndrome with diarrhoea (IBS-D). The gut microbiota metabolises primary BAs to secondary BAs, with differing impacts on metabolism and homeostasis. The aim of this study was to profile the microbiome, metabolic products and bile acids in BAD. Patients with BAD diagnosed by SeHCAT testing, were compared with other IBS-D patients, and healthy controls. Faecal 16S ribosomal RNA gene analysis was undertaken. Faecal short chain fatty acid (SCFA) and urinary volatile organic compounds (VOCs) were measured. BAs were quantified in serum and faeces. Faecal bacterial diversity was significantly reduced in patients with BAD. Several taxa were enriched compared to IBS-D. SCFA amounts differed in BAD, controls and IBS-D, with significantly more propionate in BAD. Separation of VOC profiles was evident, but the greatest discrimination was between IBS-D and controls. Unconjugated and primary BA in serum and faeces were significantly higher in BAD. The faecal percentage primary BA was inversely related to SeHCAT. BAD produces dysbiosis, with metabolite differences, including VOC, SCFA and primary BAs when compared to IBS-D. These findings provide new mechanistic insights into the pathophysiology of BAD.},
}

@article {pmid33235036,
year = {2020},
author = {Becker, SL and Manson, JE},
title = {Menopause, the gut microbiome, and weight gain: correlation or causation?.},
journal = {Menopause (New York, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/GME.0000000000001702},
pmid = {33235036},
issn = {1530-0374},
abstract = {The gut microbiome is a key regulator of metabolism and influences the metabolism of estrogens, however, the microbiome's role in the changes in body composition and metabolic risk factors experienced by menopausal women remains largely unexplored. Menopause has been shown to alter the gut microbiome, and rodent studies suggest that microbiome changes postovariectomy are associated with increased adiposity, decreased metabolic rate, and insulin resistance, changes attenuated by estrogen administration. Given these data, a deeper understanding of the gut microbiome's relationship to menopause-induced changes in body composition and metabolism is warranted and may offer opportunity for novel therapeutic interventions.The microbiome is central to both systemic and estrogen metabolism, and is altered by the menopausal transition, suggesting an important role of the microbiome in the increased metabolic risk faced by menopausal women. Although additional research is needed to establish a causal link, the interrelationship between menopause and the gut microbiome may represent a new frontier to address menopause-related metabolic risk.},
}

@article {pmid33234298,
year = {2020},
author = {Rowe, M and Veerus, L and Trosvik, P and Buckling, A and Pizzari, T},
title = {The Reproductive Microbiome: An Emerging Driver of Sexual Selection, Sexual Conflict, Mating Systems, and Reproductive Isolation: (Trends in Ecology and Evolution 35, 220-234, 2020).},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2020.10.015},
pmid = {33234298},
issn = {1872-8383},
}

@article {pmid33234272,
year = {2020},
author = {Langholtz, M and Davison, BH and Jager, HI and Eaton, L and Baskaran, LM and Davis, M and Brandt, CC},
title = {Increased nitrogen use efficiency in crop production can provide economic and environmental benefits.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {143602},
doi = {10.1016/j.scitotenv.2020.143602},
pmid = {33234272},
issn = {1879-1026},
abstract = {Potential economic and environmental benefits of increasing nitrogen-use efficiency (NUE) are widely recognized but scarcely quantified. This study quantifies the effects of increased NUE on 1) the national agricultural economy using a simulation model of US agriculture and 2) regional water quality effects using a biogeochemical model for the Arkansas-White-Red river basin. National economic effects are reported for NUE improvement scenarios of 10%, 20%, 50%, and 100%, whereas regional water quality effects are estimated for a 20% NUE improvement scenario in the Arkansas-White-Red river basin. Simulating a 20% increase in NUE in row crops is shown to reduce N requirements by 1.4 million tonnes y-1 and increase farmer net profits by 1.6% ($743 million) per year by 2026 over the baseline simulation for the same period. For each 10% increase in NUE, annual farm revenues for commodity crops increased over the baseline by approximately $350 million per year by 2026. Changes in crop prices and land-use relative to the baseline were less than 2%. This suggests a net benefit even though fertilizer cost savings can result in increased cultivation of land, i.e., 'Jevon's paradox'. Results from the biogeochemical model of the Arkansas-White-Red river basin suggest that a 20% increase in NUE corresponds to a 5.72% reduction in nitrate loadings to freshwaters, with higher reductions in agricultural watersheds. The value of these reductions was estimated as $43 ha-1, for a total of $15.3 to 136.7 million yr-1 in avoided water treatment costs. After estimating the social value of increased NUE, we conclude with a discussion of potential strategies to increase efficiency and the research needed to achieve this goal. These include perennialization of the agricultural landscape, genetic crop improvement, targeted fertilizer application, and manipulation of the plant-root microbiome.},
}

@article {pmid33233565,
year = {2020},
author = {Estrada-Peña, A and Cabezas-Cruz, A and Obregón, D},
title = {Behind Taxonomic Variability: The Functional Redundancy in the Tick Microbiome.},
journal = {Microorganisms},
volume = {8},
number = {11},
pages = {},
doi = {10.3390/microorganisms8111829},
pmid = {33233565},
issn = {2076-2607},
abstract = {The taxonomic composition and diversity of tick midgut microbiota have been extensively studied in different species of the genera Rhipicephalus, Ixodes, Amblyomma, Haemaphysalis, Hyalomma, Dermacentor, Argas and Ornithodoros, while the functional significance of bacterial diversity has been proportionally less explored. In this study, we used previously published 16S amplicon sequence data sets from three Ixodes scapularis cohorts, two of uninfected nymphs, and one of larvae experimentally infected with Borrelia burgdorferi, to test the functional redundancy of the tick microbiome. We predicted the metabolic profiling of each sample using the state-of-the-art metagenomics tool PICRUSt2. The results showed that the microbiomes of all I. scapularis samples share only 80 taxa (24.6%, total 324), while out of the 342 metabolic pathways predicted, 82.7%, were shared by all the ticks. Borrelia-infected larvae lack 15.4% of pathways found in the microbiome of uninfected nymphs. Taxa contribution analysis showed that the functional microbiome of uninfected ticks was highly redundant, with, in some cases, up to 198 bacterial taxa contributing to a single pathway. However, Borrelia-infected larvae had a smaller redundancy with 6.7% of pathways provided by more than 100 genera, while 15.7-19.2% of pathways were provided by more than 100 genera in the two cohorts of uninfected ticks. In addition, we compared the functional profiles of three microbial communities from each data set, identified through a network-based approach, and we observed functional similarity between them. Based on the functional redundancy and functional similarity of the microbiome of ticks in different developmental stages and infection status, we concluded that the tick gut microbiota is a self-regulating community of very diverse bacteria contributing to a defined set of metabolic pathways and functions with yet unexplored relevance for tick fitness and/or bacterial community stability. We propose a change of focus in which the tick microbiome must be analyzed in all dimensions, highlighting their functional traits, instead of the conventional taxonomic profiling.},
}

@article {pmid33233349,
year = {2020},
author = {Santiago-Rodriguez, TM and Garoutte, A and Adams, E and Nasser, W and Ross, MC and La Reau, A and Henseler, Z and Ward, T and Knights, D and Petrosino, JF and Hollister, EB},
title = {Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method.},
journal = {Genes},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/genes11111380},
pmid = {33233349},
issn = {2073-4425},
abstract = {Sequencing of the 16S rRNA gene (16S) has long been a go-to method for microbiome characterization due to its accessibility and lower cost compared to shotgun metagenomic sequencing (SMS). However, 16S sequencing rarely provides species-level resolution and cannot provide direct assessment of other taxa (e.g., viruses and fungi) or functional gene content. Shallow shotgun metagenomic sequencing (SSMS) has emerged as an approach to bridge the gap between 16S sequencing and deep metagenomic sequencing. SSMS is cost-competitive with 16S sequencing, while also providing species-level resolution and functional gene content insights. In the present study, we evaluated the effects of sequencing depth on marker gene-mapping- and alignment-based annotation of bacteria in healthy human stool samples. The number of identified taxa decreased with lower sequencing depths, particularly with the marker gene-mapping-based approach. Other annotations, including viruses and pathways, also showed a depth-dependent effect on feature recovery. These results refine the understanding of the suitability and shortcomings of SSMS, as well as annotation tools for metagenomic analyses in human stool samples. Results may also translate to other sample types and may open the opportunity to explore the effect of sequencing depth and annotation method.},
}

@article {pmid33232877,
year = {2020},
author = {Yan, X and He, M and Zheng, J and Zhu, T and Zou, Z and Tang, B and Yu, Y and Mai, B},
title = {Tris (1,3-dichloro-2-propyl) phosphate exposure disrupts the gut microbiome and its associated metabolites in mice.},
journal = {Environment international},
volume = {146},
number = {},
pages = {106256},
doi = {10.1016/j.envint.2020.106256},
pmid = {33232877},
issn = {1873-6750},
abstract = {BACKGROUND: Tris (1,3-dichloro-2-propyl) phosphate (TDCIPP) has been frequently detected in environmental media and biological samples. However, knowledge of its adverse health consequences is limited, and its impacts on the human gut microbiota, which play a key role in health and disease, remain unexplored.

OBJECTIVES: To better evaluate the potential risk of TDCIPP exposure in human health, we investigated the effects of TDCIPP on gut microbiome and gut metabolites in C57BL/6 mice.

METHODS: We applied an integrated analytical approach by combing 16S rRNA gene sequencing, metagenomic sequencing and 1H NMR metabolomics analysis in fecal samples collected from mouse with TDCIPP exposure as well as those from controls.

RESULTS: Both 16S rRNA sequencing and metagenome sequencing showed that TDCIPP exposure significantly changed the gut microbiome, with a remarkable increased Firmicutes at the expense of Bacteroidetes after exposure. Perturbed gut metabolic profiles in the treated group were also observed and closely related with altered gut microbiome. Gene functional annotation analysis further suggested perturbed gut metabolites could be directly caused by altered gut microbiome.

CONCLUSION: TDCIPP exposure has great influence on the gut ecosystem as reflected by perturbation of microbiome community structure, microbial species, gut microbe associated gene expression and gut metabolites, which may contribute to the progression of certain uncharacterized gut microbiota related host diseases. Our findings provide novel insights into adverse effects of TDCIPP exposure on human health.},
}

@article {pmid33232664,
year = {2020},
author = {Reese, AT and Phillips, SR and Owens, LA and Venable, EM and Langergraber, KE and Machanda, ZP and Mitani, JC and Muller, MN and Watts, DP and Wrangham, RW and Goldberg, TL and Emery Thompson, M and Carmody, RN},
title = {Age Patterning in Wild Chimpanzee Gut Microbiota Diversity Reveals Differences from Humans in Early Life.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2020.10.075},
pmid = {33232664},
issn = {1879-0445},
abstract = {Survival in primates is facilitated by commensal gut microbes that ferment otherwise indigestible plant matter, resist colonization by pathogens, and train the developing immune system.1,2 However, humans are unique among primates in that we consume highly digestible foods, wean early, mature slowly, and exhibit high lifelong investments in maintenance.3-6 These adaptations suggest that lifetime trajectories of human-microbial relationships could differ from those of our closest living relatives. Here, we profile the gut microbiota of 166 wild chimpanzees aged 8 months to 67 years in the Kibale National Park, Uganda and compare the patterns of gut microbial maturation to those previously observed in humans. We found that chimpanzee gut microbial alpha-diversity, composition, density, interindividual variation, and within-individual change over time varied significantly with age. Notably, gut microbial signatures in infants <2 years old were distinct across all five metrics. Infant chimpanzee guts were enriched in some of the same taxa prevalent in infant humans (e.g., Bifidobacterium, Streptococcus, and Bacteroides), and chimpanzee gut microbial communities, like those of humans, exhibited higher interindividual variation in infancy versus later in life. However, in direct contrast to human infants, chimpanzee infants harbored surprisingly high-diversity rather than low-diversity gut bacterial communities compared with older conspecifics. These data indicate differential trajectories of gut microbiota development in humans and chimpanzees that are consistent with interspecific differences in lactation, diet, and immune function. Probing the phenotypic consequences of differential early-life gut microbial diversity in chimpanzees and other primates will illuminate the life history impacts of the hominid-microbiome partnership.},
}

@article {pmid33232475,
year = {2020},
author = {Ilett, EE and Jørgensen, M and Noguera-Julian, M and Nørgaard, JC and Daugaard, G and Helleberg, M and Paredes, R and Murray, DD and Lundgren, J and MacPherson, C and Reekie, J and Sengeløv, H},
title = {Associations of the gut microbiome and clinical factors with acute GVHD in allogeneic HSCT recipients.},
journal = {Blood advances},
volume = {4},
number = {22},
pages = {5797-5809},
doi = {10.1182/bloodadvances.2020002677},
pmid = {33232475},
issn = {2473-9537},
abstract = {Acute graft-versus-host disease (aGVHD) is a leading cause of transplantation-related mortality after allogeneic hematopoietic stem cell transplantation (aHSCT). 16S ribosomal RNA (16S rRNA) gene-based studies have reported that lower gut bacterial diversity and the relative abundance of certain bacteria after aHSCT are associated with aGVHD. Using shotgun metagenomic sequencing and a large cohort, we aimed to confirm and extend these observations. Adult aHSCT recipients with stool samples collected from day -30 to day 100 relative to aHSCT were included. One sample was selected per patient per period (pre-aHSCT (day -30 to day 0), early post-aHSCT (day 1 to day 28), and late post-aHSCT (day 29 to day 100)), resulting in 150 aHSCT recipients and 259 samples. Microbial and clinical factors were tested for differences between time periods and an association with subsequent aGVHD. Patients showed a decline in gut bacterial diversity posttransplant, with several patients developing a dominance of Enterococcus. A total of 36 recipients developed aGVHD at a median of 34 days (interquartile range, 26-50 days) post-aHSCT. Lower microbial gene richness (P = .02), a lower abundance of the genus Blautia (P = .05), and a lower abundance of Akkermansia muciniphila (P = .01) early post-aHSCT was observed in those who developed aGVHD. Myeloablative conditioning was associated with aGVHD along with a reduction in gene richness and abundance of Blautia and A muciniphila. These results confirm low diversity and Blautia being associated with aGVHD. Crucially, we add that pretransplant conditioning is associated with changes in gut microbiota. Investigations are warranted to determine the interplay of gut microbiota and conditioning in the development of aGVHD.},
}

@article {pmid33232449,
year = {2020},
author = {Lyles, JK and Oli, M},
title = {The Student-Centered Classroom: The New Gut Feeling.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaa191},
pmid = {33232449},
issn = {1574-6968},
abstract = {A student-centered, interactive course-based undergraduate research experience (CURE) was implemented in a microbiology course in order to provide an authentic research experience and to stimulate student interest and improve understanding of fermentation, probiotics, the human microbiome, and related topics. Students were immersed in the scientific process as they used fundamental techniques to investigate the probiotic composition of a fermented milk beverage, kefir-an unknown question with no predetermined outcomes. In order to assess the benefits and effect of this learning experience on the students, pre- and post-study surveys were administered using Qualtrics. Post-study, 93% of participants agreed that fermented foods are beneficial to human health (compared to 52% pre-study), and notably, 100% of participants indicated that they plan to apply this material in both their personal and professional lives and would suggest consuming probiotics or fermented products to alleviate gastrointestinal issues. As evidenced by demographic data, this CURE is suitable for implementation at both large and small institutions with diverse student populations. Collectively, these data indicate that this collaborative, discovery-based learning experience is a powerful educational tool, encouraging students to make real-life connections between microbiology, medicine, and their own health.},
}

@article {pmid33231850,
year = {2020},
author = {Buness, CW and Johnson, KM and Ali, AH and Alrabadi, L and Lindor, KD and Miloh, T and Cox, KL},
title = {Successful response of primary sclerosing cholangitis and associated ulcerative colitis to oral vancomycin may depend on brand and personalized dose: report in an adolescent.},
journal = {Clinical journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12328-020-01296-0},
pmid = {33231850},
issn = {1865-7265},
abstract = {Primary sclerosing cholangitis (PSC) is a rare, progressive liver disease characterized by cholestasis and bile duct fibrosis that has no accepted therapy known to delay or arrest its progression. We report a 23-year-old female patient who at age 14 was diagnosed with moderate pancolonic ulcerative colitis (UC) and at age 15 with small-duct PSC unresponsive to conventional therapy. The patient began single drug therapy with the antibiotic oral vancomycin (OVT) and achieved normalization of liver enzymes and resolution of UC symptoms with colonic mucosal healing. These improvements have persisted over 8 years. There has been no colon dysplasia, liver fibrosis or failure, bile duct stricture, or cancer. Of note, the patient's response was dependent on the brand of oral vancomycin capsule, as well as dose. This raised the questions of possible differences in bioequivalence of different commercial versions of the drug and whether this factor might play into the variability of efficacy seen in published trials. Evidence suggests that oral vancomycin both alters the intestinal microbiome and has immunomodulatory effects. Its striking effectiveness in this and other patients supports further investigation in randomized trials, with careful attention to its bioavailability profile in the gut.},
}

@article {pmid33231591,
year = {2020},
author = {Xu, Y and Curtasu, MV and Bendiks, Z and Marco, ML and P Nørskov, N and Knudsen, KEB and Hedemann, MS and Lærke, HN},
title = {Effects of dietary fibre and protein content on intestinal fibre degradation, short-chain fatty acid and microbiota composition in a high-fat fructose-rich diet induced obese Göttingen Minipig model.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d0fo02252g},
pmid = {33231591},
issn = {2042-650X},
abstract = {Obesity-related metabolic syndrome has been linked with gut microbiome dysbiosis while dietary fibre (DF) and protein can modify the gut microbial ecosystem and metabolism. After 20-weeks of high-fat fructose-rich diet feeding for the development of obesity, forty-three 30-week old Göttingen Minipigs (31 ± 4.0 kg body weight) were allocated to one of the four diets with low or high DF and protein contents in a two by two factorial design and digesta were collected from the intestinal segments of minipigs after 8 weeks at libitum feeding. High DF content increased (P < 0.001) while high protein content decreased (P = 0.004) the content of non-starch polysaccharides (NSP) in all intestinal segments. Arabinoxylan (AX) as proportion of NSP was higher with high DF (P < 0.001) but decreased from the distal small intestine to the mid colon (P < 0.001). High DF increased the relative abundance of Blautia, Faecalibacterium and Peptococcus in the caecum, the mid colon and faeces, reduced the intestinal concentrations of total short-chain fatty acids (SCFA) (P = 0.020) and acetate (P = 0.011) but slightly increased butyrate pools in the large intestine (P ≤ 0.050) compared to low DF. High protein increased the SCFA (P = 0.026) and propionate (P = 0.044) concentrations in the gut. High DF induced a lower increase in the BCFA concentration and proportion throughout the colon (P < 0.001). The butyrate concentrations in plasma from the jugular vein were increased with high DF diets (P = 0.031), whereas the propionate concentrations were increased (P < 0.001) and succinate were decreased (P = 0.001) with high protein diets compared with low protein diets. In conclusion, AX in the high DF diets was continuously degraded up to the mid-colon, associated with enriched butyrate-producing bacteria and slightly improved butyrate production, while protein fermentation was attenuated by high DF and high protein did not show prebiotic effects in this obese minipig model.},
}

@article {pmid33231332,
year = {2020},
author = {Stothart, MR and Greuel, RJ and Gavriliuc, S and Henry, A and Wilson, AJ and McLoughlin, PD and Poissant, J},
title = {Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.15747},
pmid = {33231332},
issn = {1365-294X},
abstract = {Studies of microbiome variation in wildlife often emphasize host physiology and diet as proximate selective pressures acting on host-associated microbiota. In contrast, microbial dispersal and ecological drift are more rarely considered. Using amplicon sequencing, we characterized the bacterial microbiome of adult female (n = 86) Sable Island horses (Nova Scotia, Canada) as part of a detailed individual-based study of this feral population. Using data on sampling date, horse location, age, parental status, and local habitat variables, we contrasted the ability of spatiotemporal, life history, and environmental factors to explain microbiome diversity among Sable Island horses. We extended inferences made from these analyses with both phylogeny-informed and phylogeny-independent null modeling approaches to identify deviations from stochastic expectations. Phylogeny-informed diversity measures were correlated with spatial and local habitat variables, but null modelling results suggested that heterogeneity in ecological drift, rather than differential selective pressures acting on the microbiome, was responsible for these correlations. Conversely, phylogeny-independent diversity measures were best explained by host spatial and social structure, suggesting that taxonomic composition of the microbiome was shaped most strongly by bacterial dispersal. Parental status was important but correlated with measures of β-dispersion rather than β-diversity (mares without foals had lower alpha diversity and more variable microbiomes than mares with foals). Our results suggest that between host microbiome variation within the Sable Island horse population is driven more strongly by bacterial dispersal and ecological drift than by differential selective pressures. These results emphasize the need to consider alternative ecological processes in the study of microbiomes.},
}

@article {pmid33230597,
year = {2020},
author = {Hidalgo, KJ and Saito, T and Silva, RS and Delforno, TP and Duarte, ICS and de Oliveira, VM and Okada, DY},
title = {Microbiome taxonomic and functional profiles of two domestic sewage treatment systems.},
journal = {Biodegradation},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10532-020-09921-y},
pmid = {33230597},
issn = {1572-9729},
support = {401720/2016-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Anaerobic systems for domestic sewage treatment, like septic tanks and anaerobic filters, are used in developing countries due to favorable economic and functional features. The anaerobic filter is used for the treatment of the septic tank effluent, to improve the COD removal efficiency of the system. The microbial composition and diversity of the microbiome from two wastewater treatment systems (factory and rural school) were compared through 16S rRNA gene sequencing using MiSeq 2 × 250 bp Illumina sequencing platform. Additionally, 16S rRNA data were used to predict the functional profile of the microbial communities using PICRUSt2. Results indicated that hydrogenotrophic methanogens, like Methanobacterium, were found in higher abundance in both systems compared to acetotrophic methanogens belonging to Methanosaeta genus. Also, important syntrophic microorganisms (Smithella, Syntrophus, Syntrophobacter) were found in the factory and rural school wastewater treatment systems. Microbial communities were also compared between stages (septic tank and anaerobic filter) of each wastewater treatment stage, revealing that, in the case of the rural school, both microbial communities were quite similar most likely due to hydraulic short-circuit issues. Meanwhile, in the factory, microbial communities from the septic tank and anaerobic filter were different. The school system showed lower COD removal rates (2-30%), which were probably related to a higher abundance of Firmicutes members in addition to the hydraulic short-circuit and low abundance of Chloroflexi members. On the other hand, the fiberglass factory presented higher COD removal rates (60-83%), harboring phyla reported as the core microbiome of anaerobic digesters (Bacteroidetes, Chloroflexi, and Proteobacteria phyla). The knowledge of the structure and composition of wastewater treatment systems may provide support for the improvement of the pollutant removal in anaerobic process.},
}

@article {pmid33230497,
year = {2020},
author = {Calder, PC},
title = {Nutrition, immunity and COVID-19.},
journal = {BMJ nutrition, prevention & health},
volume = {3},
number = {1},
pages = {74-92},
doi = {10.1136/bmjnph-2020-000085},
pmid = {33230497},
issn = {2516-5542},
abstract = {The immune system protects the host from pathogenic organisms (bacteria, viruses, fungi, parasites). To deal with this array of threats, the immune system has evolved to include a myriad of specialised cell types, communicating molecules and functional responses. The immune system is always active, carrying out surveillance, but its activity is enhanced if an individual becomes infected. This heightened activity is accompanied by an increased rate of metabolism, requiring energy sources, substrates for biosynthesis and regulatory molecules, which are all ultimately derived from the diet. A number of vitamins (A, B6, B12, folate, C, D and E) and trace elements (zinc, copper, selenium, iron) have been demonstrated to have key roles in supporting the human immune system and reducing risk of infections. Other essential nutrients including other vitamins and trace elements, amino acids and fatty acids are also important. Each of the nutrients named above has roles in supporting antibacterial and antiviral defence, but zinc and selenium seem to be particularly important for the latter. It would seem prudent for individuals to consume sufficient amounts of essential nutrients to support their immune system to help them deal with pathogens should they become infected. The gut microbiota plays a role in educating and regulating the immune system. Gut dysbiosis is a feature of disease including many infectious diseases and has been described in COVID-19. Dietary approaches to achieve a healthy microbiota can also benefit the immune system. Severe infection of the respiratory epithelium can lead to acute respiratory distress syndrome (ARDS), characterised by excessive and damaging host inflammation, termed a cytokine storm. This is seen in cases of severe COVID-19. There is evidence from ARDS in other settings that the cytokine storm can be controlled by n-3 fatty acids, possibly through their metabolism to specialised pro-resolving mediators.},
}

@article {pmid33230338,
year = {2020},
author = {Trivedi, P and Leach, JE and Tringe, SG and Sa, T and Singh, BK},
title = {Author Correction: Plant-microbiome interactions: from community assembly to plant health.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41579-020-00490-8},
pmid = {33230338},
issn = {1740-1534},
abstract = {A Correction to this paper has been published: https://doi.org/10.1038/s41579-020-00490-8.},
}

@article {pmid33230198,
year = {2020},
author = {Milani, GP and Silano, M and Mazzocchi, A and Bettocchi, S and De Cosmi, V and Agostoni, C},
title = {Personalized nutrition approach in pediatrics: a narrative review.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41390-020-01291-8},
pmid = {33230198},
issn = {1530-0447},
abstract = {Dietary habits represent the main determinant of health. Although extensive research has been conducted to modify unhealthy dietary behaviors across the lifespan, obesity and obesity-associated comorbidities are increasingly observed worldwide. Individually tailored interventions are nowadays considered a promising frontier for nutritional research. In this narrative review, the technologies of importance in a pediatric clinical setting are discussed. The first determinant of the dietary balance is represented by energy intakes matching individual needs. Most emerging studies highlight the opportunity to reconsider the widely used prediction equations of resting energy expenditure. Artificial Neural Network approaches may help to disentangle the role of single contributors to energy expenditure. Artificial intelligence is also useful in the prediction of the glycemic response, based on the individual microbiome. Other factors further concurring to define individually tailored nutritional needs are metabolomics and nutrigenomic. Since most available data come from studies in adult groups, new efforts should now be addressed to integrate all these aspects to develop comprehensive and-above all-effective interventions for children. IMPACT: Personalized dietary advice, specific to individuals, should be more effective in the prevention of chronic diseases than general recommendations about diet. Artificial Neural Networks algorithms are technologies of importance in a pediatric setting that may help practitioners to provide personalized nutrition. Other approaches to personalized nutrition, while promising in adults and for basic research, are still far from practical application in pediatrics.},
}

@article {pmid33229197,
year = {2020},
author = {Li, K and Hao, Z and Du, J and Gao, Y and Yang, S and Zhou, Y},
title = {Bacteroides thetaiotaomicron relieves colon inflammation by activating aryl hydrocarbon receptor and modulating CD4+T cell homeostasis.},
journal = {International immunopharmacology},
volume = {},
number = {},
pages = {107183},
doi = {10.1016/j.intimp.2020.107183},
pmid = {33229197},
issn = {1878-1705},
abstract = {Inflammatory bowel disease (IBD) is a form of nonspecific chronic intestinal inflammation associated with gut microbiome dysbiosis. Modulating the composition of the intestinal flora may be a viable means of alleviating such inflammatory pathology. Bacteroides thetaiotaomicron (B. thetaiotaomicron) is a symbiotic intestinal microbe that has been associated with IBD, although the mechanistic basis for this association remains to be clarified. In this present study, we determined that B. thetaiotaomicron can alleviate colonic inflammation through mechanisms associated with the modulation of tryptophan metabolism and T cell subsets within inflamed intestinal tissues. Specifically, we found that B. thetaiotaomicron promotes the preferential differentiation of anti-inflammatory Treg/Th2 cells while suppressing the relative differentiation of pro-inflammatory Th1/Th17 cells, thereby decreasing inflammation within the colon. At a molecular level, B. thetaiotaomicron treatment was linked to altered CpG methylation within the Foxp3 promoter that was associated with enhanced Treg cell functionality. In a murine dextran sulfate sodium (DSS) colitis model system, B. thetaiotaomicron increased the levels of the aryl hydrocarbon receptor (AHR) ligands indole metabolites-indole acetic acid (IAA) and indole propionic acid (IPA), thereby increasing AHR activation that is related to changes of transcription factor expression profiles within T cells. In summary, our data suggest that B. thetaiotaomicron can activate AHR and modulate CD4+ T cell differentiation profiles in a murine DSS colitis model system, suggesting that this bacterium may be of therapeutic relevance for the treatment of IBD.},
}

@article {pmid33229098,
year = {2020},
author = {Duan, Y and Xiong, D and Wang, Y and Zhang, Z and Li, H and Dong, H and Zhang, J},
title = {Toxicological effects of microplastics in Litopenaeus vannamei as indicated by an integrated microbiome, proteomic and metabolomic approach.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {143311},
doi = {10.1016/j.scitotenv.2020.143311},
pmid = {33229098},
issn = {1879-1026},
abstract = {Microplastics (MPs) are a hazardous pollutant of world concern that threaten aquatic organisms and ecosystems. In this study, we chose the worldwide-distributed shrimp Litopenaeus vannamei as a model and investigated the toxicological effects of five types of MPs on L. vannamei using several omics approaches. After 14 days of exposure to MPs, obvious intestinal microbiota variation was observed, such as increased abundances of Bacteroidetes and Proteobacteria and a decreased abundance of Firmicutes. Specifically, MPs induced several putative opportunistic pathogens and reduced lactic acid- and short-chain fatty acid-producing bacteria. Alternatively, MPs altered haemolymph proteome profiles, but the five types of MPs had different effects on the enriched pathways and the expression of immune-related proteins. Furthermore, MPs also caused haemolymph metabolite variation, especially in amino acid and alpha-linolenic acid metabolism, and 28 differential metabolites were altered in the five MP-treated groups. Changes in intestinal bacteria were correlated with the haemolymph proteins and metabolites of the shrimp. Overall, these results reveal the toxicological effects of MPs on the intestinal microbiota and the host's immunity and metabolism in shrimp.},
}

@article {pmid33228781,
year = {2020},
author = {Nené, NR and Barrett, J and Jones, A and Evans, I and Reisel, D and Timms, JF and Paprotka, T and Leimbach, A and Franchi, D and Colombo, N and Bjørge, L and Zikan, M and Cibula, D and Widschwendter, M},
title = {DNA methylation signatures to predict the cervicovaginal microbiome status.},
journal = {Clinical epigenetics},
volume = {12},
number = {1},
pages = {180},
doi = {10.1186/s13148-020-00966-7},
pmid = {33228781},
issn = {1868-7083},
support = {634570//Horizon 2020 Framework Programme/ ; 742432//H2020 European Research Council/ ; },
abstract = {BACKGROUND: The composition of the microbiome plays an important role in human health and disease. Whether there is a direct association between the cervicovaginal microbiome and the host's epigenome is largely unexplored.

RESULTS: Here we analyzed a total of 448 cervicovaginal smear samples and studied both the DNA methylome of the host and the microbiome using the Illumina EPIC array and next-generation sequencing, respectively. We found that those CpGs that are hypo-methylated in samples with non-lactobacilli (O-type) dominating communities are strongly associated with gastrointestinal differentiation and that a signature consisting of 819 CpGs was able to discriminate lactobacilli-dominating (L-type) from O-type samples with an area under the receiver operator characteristic curve (AUC) of 0.84 (95% CI = 0.77-0.90) in an independent validation set. The performance found in samples with more than 50% epithelial cells was further improved (AUC 0.87) and in women younger than 50 years of age was even higher (AUC 0.91). In a subset of 96 women, the buccal but not the blood cell DNA showed the same trend as the cervicovaginal samples in discriminating women with L- from O-type cervicovaginal communities.

CONCLUSIONS: These findings strongly support the view that the epithelial epigenome plays an essential role in hosting specific microbial communities.},
}

@article {pmid33228670,
year = {2020},
author = {Yue, YC and Yang, BY and Lu, J and Zhang, SW and Liu, L and Nassar, K and Xu, XX and Pang, XY and Lv, JP},
title = {Metabolite secretions of Lactobacillus plantarum YYC-3 may inhibit colon cancer cell metastasis by suppressing the VEGF-MMP2/9 signaling pathway.},
journal = {Microbial cell factories},
volume = {19},
number = {1},
pages = {213},
doi = {10.1186/s12934-020-01466-2},
pmid = {33228670},
issn = {1475-2859},
support = {31871833//National Natural Science Foundation of China/ ; 2017YFC1600903//National Key R&D Program of China/ ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is a major clinical challenge, and the gut microbiome plays important roles in the occurrence and metastasis of CRC. Lactobacillus and their metabolites are thought to be able to suppress the growth of CRC cells. However, the antimetastatic mechanism of Lactobacillus or their metabolites toward CRC cells is not clear. Therefore, the aim of this study was to assess the inhibitory mechanism of cell-free supernatants (CFSs) of L. rhamnosus GG, L. casei M3, and L. plantarum YYC-3 on metastasis of CRC cells.

RESULTS: YYC-3 CFS showed the highest inhibitory effect on CRC cell growth, invasion and migration, and inhibited MMP2, MMP9, and VEGFA gene and protein expression, and protein secretion. Furthermore, it suppressed the activities of MMPs by gelatin zymography. Moreover, the effective compounds in these CFSs were analyzed by Q Exactive Focus liquid chromatography-mass spectrometry.

CONCLUSIONS: Our results showed that metabolite secretions of YYC-3 may inhibited cell metastasis by downregulating the VEGF/MMPs signaling pathway. These data suggest that treatment of CRC cells with metabolites from L. plantarum YYC-3 may reduce colon cancer metastasis.},
}

@article {pmid33228639,
year = {2020},
author = {Liu, C and Ponsero, AJ and Armstrong, DG and Lipsky, BA and Hurwitz, BL},
title = {The dynamic wound microbiome.},
journal = {BMC medicine},
volume = {18},
number = {1},
pages = {358},
doi = {10.1186/s12916-020-01820-6},
pmid = {33228639},
issn = {1741-7015},
abstract = {BACKGROUND: Diabetic foot ulcers (DFUs) account for the majority of all limb amputations and hospitalizations due to diabetes complications. With 30 million cases of diabetes in the USA and 500,000 new diagnoses each year, DFUs are a growing health problem. Diabetes patients with limb amputations have high postoperative mortality, a high rate of secondary amputation, prolonged inpatient hospital stays, and a high incidence of re-hospitalization. DFU-associated amputations constitute a significant burden on healthcare resources that cost more than 10 billion dollars per year. Currently, there is no way to identify wounds that will heal versus those that will become severely infected and require amputation.

MAIN BODY: Accurate identification of causative pathogens in diabetic foot ulcers is a critical component of effective treatment. Compared to traditional culture-based methods, advanced sequencing technologies provide more comprehensive and unbiased profiling on wound microbiome with a higher taxonomic resolution, as well as functional annotation such as virulence and antibiotic resistance. In this review, we summarize the latest developments in defining the microbiology of diabetic foot ulcers that have been unveiled by sequencing technologies and discuss both the future promises and current limitations of these approaches. In particular, we highlight the temporal patterns and system dynamics in the diabetic foot microbiome monitored and measured during wound progression and medical intervention, and explore the feasibility of molecular diagnostics in clinics.

CONCLUSION: Molecular tests conducted during weekly office visits to clean and examine DFUs would allow clinicians to offer personalized treatment and antibiotic therapy. Personalized wound management could reduce healthcare costs, improve quality of life for patients, and recoup lost productivity that is important not only to the patient, but also to healthcare payers and providers. These efforts could also improve antibiotic stewardship and control the rise of "superbugs" vital to global health.},
}

@article {pmid33228152,
year = {2020},
author = {Kirchner, S and Lei, V and MacLeod, AS},
title = {The Cutaneous Wound Innate Immunological Microenvironment.},
journal = {International journal of molecular sciences},
volume = {21},
number = {22},
pages = {},
doi = {10.3390/ijms21228748},
pmid = {33228152},
issn = {1422-0067},
support = {R01AI139207/GF/NIH HHS/United States ; Physician Strong-Start Award//Duke University/ ; },
abstract = {The skin represents the first line of defense and innate immune protection against pathogens. Skin normally provides a physical barrier to prevent infection by pathogens; however, wounds, microinjuries, and minor barrier impediments can present open avenues for invasion through the skin. Accordingly, wound repair and protection from invading pathogens are essential processes in successful skin barrier regeneration. To repair and protect wounds, skin promotes the development of a specific and complex immunological microenvironment within and surrounding the disrupted tissue. This immune microenvironment includes both innate and adaptive processes, including immune cell recruitment to the wound and secretion of extracellular factors that can act directly to promote wound closure and wound antimicrobial defense. Recent work has shown that this immune microenvironment also varies according to the specific context of the wound: the microbiome, neuroimmune signaling, environmental effects, and age play roles in altering the innate immune response to wounding. This review will focus on the role of these factors in shaping the cutaneous microenvironment and how this ultimately impacts the immune response to wounding.},
}

@article {pmid33228099,
year = {2020},
author = {Kang, M and Choe, D and Kim, K and Cho, BK and Cho, S},
title = {Synthetic Biology Approaches in The Development of Engineered Therapeutic Microbes.},
journal = {International journal of molecular sciences},
volume = {21},
number = {22},
pages = {},
doi = {10.3390/ijms21228744},
pmid = {33228099},
issn = {1422-0067},
support = {2018M3A9H3024759//National Research Foundation of Korea/ ; 2018M3A9F3079664//National Research Foundation of Korea/ ; 2018R1A1A3A04079196//National Research Foundation of Korea/ ; },
abstract = {Since the intimate relationship between microbes and human health has been uncovered, microbes have been in the spotlight as therapeutic targets for several diseases. Microbes contribute to a wide range of diseases, such as gastrointestinal disorders, diabetes and cancer. However, as host-microbiome interactions have not been fully elucidated, treatments such as probiotic administration and fecal transplantations that are used to modulate the microbial community often cause nonspecific results with serious safety concerns. As an alternative, synthetic biology can be used to rewire microbial networks such that the microbes can function as therapeutic agents. Genetic sensors can be transformed to detect biomarkers associated with disease occurrence and progression. Moreover, microbes can be reprogrammed to produce various therapeutic molecules from the host and bacterial proteins, such as cytokines, enzymes and signaling molecules, in response to a disturbed physiological state of the host. These therapeutic treatment systems are composed of several genetic parts, either identified in bacterial endogenous regulation systems or developed through synthetic design. Such genetic components are connected to form complex genetic logic circuits for sophisticated therapy. In this review, we discussed the synthetic biology strategies that can be used to construct engineered therapeutic microbes for improved microbiome-based treatment.},
}

@article {pmid33228011,
year = {2020},
author = {Cano-Ortiz, A and Laborda-Illanes, A and Plaza-Andrades, I and Membrillo Del Pozo, A and Villarrubia Cuadrado, A and Rodríguez Calvo de Mora, M and Leiva-Gea, I and Sanchez-Alcoholado, L and Queipo-Ortuño, MI},
title = {Connection between the Gut Microbiome, Systemic Inflammation, Gut Permeability and FOXP3 Expression in Patients with Primary Sjögren's Syndrome.},
journal = {International journal of molecular sciences},
volume = {21},
number = {22},
pages = {},
doi = {10.3390/ijms21228733},
pmid = {33228011},
issn = {1422-0067},
support = {CPI13/00003//Miguel Servet Type II" program, ISCIII, Spain/ ; C-0030-2018//"Nicolas Monardes" research program of the Consejería de Salud (C-0030-2018, Junta de Andalucía, Spain/ ; PE-0106-2019//Predoctoral grant from Consejería de Salud y Familia, Andalucia, Spain/ ; FI19-00112//predoctoral grant PFIS-ISCIII, Madrid, Spain/ ; },
abstract = {The aims of this study were to explore intestinal microbial composition and functionality in primary Sjögren's syndrome (pSS) and to relate these findings to inflammation, permeability and the transcription factor Forkhead box protein P3 (FOXP3) gene expression in peripheral blood. The study included 19 pSS patients and 19 healthy controls matched for age, sex, and body mass index. Fecal bacterial DNA was extracted and analyzed by 16S rRNA sequencing using an Ion S5 platform followed by a bioinformatics analysis using Quantitative Insights into Microbial Ecology (QIIME II) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Our data suggest that the gut microbiota of pSS patients differs at both the taxonomic and functional levels with respect to healthy controls. The gut microbiota profile of our pSS patients was characterized by a lower diversity and richness and with Bacteroidetes dominating at the phylum level. The pSS patients had less beneficial or commensal butyrate-producing bacteria and a higher proportion of opportunistic pathogens with proinflammatory activity, which may impair intestinal barrier function and therefore contribute to inflammatory processes associated with pSS by increasing the production of proinflammatory cytokines and decreasing the release of the anti-inflammatory cytokine IL-10 and the peripheral FOXP3 mRNA expression, implicated in the development and function of regulatory T cells (Treg) cells. Further studies are needed to better understand the real impact of dysbiosis on the course of pSS and to conceive preventive or therapeutic strategies to counteract microbiome-driven inflammation.},
}

@article {pmid33228000,
year = {2020},
author = {Li, J and Chang, S and Guo, H and Ji, Y and Jiang, H and Ruan, L and Du, M},
title = {Altered Salivary Microbiome in the Early Stage of HIV Infections among Young Chinese Men Who Have Sex with Men (MSM).},
journal = {Pathogens (Basel, Switzerland)},
volume = {9},
number = {11},
pages = {},
doi = {10.3390/pathogens9110960},
pmid = {33228000},
issn = {2076-0817},
support = {81771084//National Natural Science Foundation of China/ ; },
abstract = {Human immunodeficiency virus (HIV) infections are spiking in Chinese young men who have sex with men (MSM). To explore alterations in the salivary microbiome and its correlation with demographic characteristics, CD4+ T cell count and viral load (VL) in HIV infections, samples of unstimulated whole saliva were analyzed by 16S rRNA gene sequencing using the Illumina MiSeq platform in 20 HIV newly infected patients before the initiation of antiretroviral therapy (ART) and at three and six months after, and in 20 age- and gender-paired healthy Chinese people. The results showed that the alpha diversity of salivary microbiota in HIV infections did not show differences from the healthy controls, but was reduced after six months under ART treatment. Comparative analysis revealed that Streptococcus was enriched in HIV-infected individuals, while Neisseria was enriched in the healthy control group. After effective ART, the salivary microbiota composition was not completely restored, although some microbiota recovered. In addition, we found Provotella_7, Neisseria and Haemophilus were correlated negatively with CD4+ T cell count, while Neisseria was correlated positively with VL. We conclude that HIV infections experience a dysbiosis of the salivary microbiome. The salivary microbiome test could be a substitute for the blood tests in the diagnosis and prognosis of diseases.},
}

@article {pmid33227982,
year = {2020},
author = {Vernocchi, P and Gili, T and Conte, F and Del Chierico, F and Conta, G and Miccheli, A and Botticelli, A and Paci, P and Caldarelli, G and Nuti, M and Marchetti, P and Putignani, L},
title = {Network Analysis of Gut Microbiome and Metabolome to Discover Microbiota-Linked Biomarkers in Patients Affected by Non-Small Cell Lung Cancer.},
journal = {International journal of molecular sciences},
volume = {21},
number = {22},
pages = {},
doi = {10.3390/ijms21228730},
pmid = {33227982},
issn = {1422-0067},
abstract = {Several studies in recent times have linked gut microbiome (GM) diversity to the pathogenesis of cancer and its role in disease progression through immune response, inflammation and metabolism modulation. This study focused on the use of network analysis and weighted gene co-expression network analysis (WGCNA) to identify the biological interaction between the gut ecosystem and its metabolites that could impact the immunotherapy response in non-small cell lung cancer (NSCLC) patients undergoing second-line treatment with anti-PD1. Metabolomic data were merged with operational taxonomic units (OTUs) from 16S RNA-targeted metagenomics and classified by chemometric models. The traits considered for the analyses were: (i) condition: disease or control (CTRLs), and (ii) treatment: responder (R) or non-responder (NR). Network analysis indicated that indole and its derivatives, aldehydes and alcohols could play a signaling role in GM functionality. WGCNA generated, instead, strong correlations between short-chain fatty acids (SCFAs) and a healthy GM. Furthermore, commensal bacteria such as Akkermansia muciniphila, Rikenellaceae, Bacteroides, Peptostreptococcaceae, Mogibacteriaceae and Clostridiaceae were found to be more abundant in CTRLs than in NSCLC patients. Our preliminary study demonstrates that the discovery of microbiota-linked biomarkers could provide an indication on the road towards personalized management of NSCLC patients.},
}

@article {pmid33227973,
year = {2020},
author = {Yeh, CF and Chen, YH and Liu, SF and Kao, HL and Wu, MS and Yang, KC and Wu, WK},
title = {Mutual Interplay of Host Immune System and Gut Microbiota in the Immunopathology of Atherosclerosis.},
journal = {International journal of molecular sciences},
volume = {21},
number = {22},
pages = {},
doi = {10.3390/ijms21228729},
pmid = {33227973},
issn = {1422-0067},
abstract = {Inflammation is the key for the initiation and progression of atherosclerosis. Accumulating evidence has revealed that an altered gut microbiome (dysbiosis) triggers both local and systemic inflammation to cause chronic inflammatory diseases, including atherosclerosis. There have been some microbiome-relevant pro-inflammatory mechanisms proposed to link the relationships between dysbiosis and atherosclerosis such as gut permeability disruption, trigger of innate immunity from lipopolysaccharide (LPS), and generation of proatherogenic metabolites, such as trimethylamine N-oxide (TMAO). Meanwhile, immune responses, such as inflammasome activation and cytokine production, could reshape both composition and function of the microbiota. In fact, the immune system delicately modulates the interplay between microbiota and atherogenesis. Recent clinical trials have suggested the potential of immunomodulation as a treatment strategy of atherosclerosis. Here in this review, we present current knowledge regarding to the roles of microbiota in contributing atherosclerotic pathogenesis and highlight translational perspectives by discussing the mutual interplay between microbiota and immune system on atherogenesis.},
}

@article {pmid33227782,
year = {2020},
author = {Castanheira, CP and Sallas, ML and Nunes, RAL and Lorenzi, NPC and Termini, L},
title = {Microbiome and Cervical Cancer.},
journal = {Pathobiology : journal of immunopathology, molecular and cellular biology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1159/000511477},
pmid = {33227782},
issn = {1423-0291},
abstract = {Persistent infection with some types of mucosal human papillomavirus (HPV) is the etiological factor for the development of cervical cancer and its precursor lesions. Besides, several cofactors are known to play a role in cervical disease onset and progression either by favoring or by preventing HPV infection and persistence. The microbiome of a healthy female genital tract is characterized by the presence of 1 or few varieties of lactobacilli. However, high-throughput studies addressing the bacterial diversity and abundance in the female genital tract have shown that several factors, including hormonal levels, hygiene habits, and sexually transmitted diseases may disrupt the natural balance, favoring the outgrowth of some groups of bacteria, which in turn may favor some pathological states. Recently, the vaginal microbiome has emerged as a new variable that could greatly influence the natural history of HPV infections and their clinical impact. In this context, changes in the vaginal microbiome have been detected in women infected with HPV and women with HPV-associated lesions and cancer. However, the role of specific bacteria groups in the development/progression or prevention/regression of HPV-associated pathologies is not well understood. In this review we summarize the current knowledge concerning changes in vaginal microbiome and cervical disease. We discuss the potential functional interplay between specific bacterial groups and HPV infection outcomes.},
}

@article {pmid33227713,
year = {2020},
author = {Wang, Y and Shao, T and Wang, J and Huang, X and Deng, X and Cao, Y and Zhou, M and Zhao, C},
title = {An update on potential biomarkers for diagnosing diabetic foot ulcer at early stage.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {133},
number = {},
pages = {110991},
doi = {10.1016/j.biopha.2020.110991},
pmid = {33227713},
issn = {1950-6007},
abstract = {As one of major chronic complications of diabetes, diabetic foot ulcer (DFU) is the main cause of disability and death. The clinical diagnosis and prognosis of DFU is inadequate. For clinicians, if the risk stratification of DFU can be obtained earlier in diabetic patients, the hospitalization, disability and mortality rate will be reduced. In addition to the inflammatory biomarkers that have been widely concerned and used, e.g., procalcitonin, pentraxin-3, C-reactive protein (CRP), interleukins (ILs), and tumor necrosis factor-α (TNF-α), etc., a more comprehensive prediction of the risk and severity of DFU is needed to reflect new biomarkers for therapeutic intervention effects. Along with the development of systems biology technology, genomics, proteomics, metabolomics and microbiome have been used in the studies on DFU for better understanding of the disease. In this review, new biomarkers that are expected to assist in the accurate diagnosis and risk stratification of DFU will be discussed and summarized in detail.},
}

@article {pmid33227667,
year = {2020},
author = {Bijnens, K and Thijs, S and Leynen, N and Stevens, V and McAmmond, B and Van Hamme, J and Vangronsveld, J and Artois, T and Smeets, K},
title = {Differential effect of silver nanoparticles on the microbiome of adult and developing planaria.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {230},
number = {},
pages = {105672},
doi = {10.1016/j.aquatox.2020.105672},
pmid = {33227667},
issn = {1879-1514},
abstract = {Silver nanoparticles (AgNPs) are widely incorporated in household, consumer and medical products. Their unintentional release via wastewaters raises concerns on their environmental impact, particularly for aquatic organisms and their associated bacterial communities. It is known that the microbiome plays an important role in its host's health and physiology, e.g. by producing essential nutrients and providing protection against pathogens. A thorough understanding of the effects of AgNPs on bacterial communities and on their interactions with the host is crucial to fully assess AgNP toxicity on aquatic organisms. Our results indicate that the microbiome of the invertebrate Schmidtea mediterranea, a freshwater planarian, is affected by AgNP exposure at the tested 10 μg/ml concentration. Using targeted amplification of the bacterial 16S rRNA gene V3-V4 region, two independent experiments on the microbiomes of adult worms revealed a consistent decrease in Betaproteobacteriales after AgNP exposure, mainly attributed to a decrease in Curvibacter and Undibacterium. Although developing tissues and organisms are known to be more sensitive to toxic compounds, three independent experiments in regenerating worms showed a less pronounced effect of AgNP exposure on the microbiome, possibly because underlying bacterial community changes during development mask the AgNP induced effect. The presence of a polyvinyl-pyrrolidone (PVP) coating did not significantly alter the outcome of the experiments compared to those with uncoated particles. The observed variation between the different experiments underlines the highly variable nature of microbiomes and emphasises the need to repeat microbiome experiments, within and between physiological states of the animal.},
}

@article {pmid33227623,
year = {2020},
author = {Araujo, DV and Watson, GA and Oliva, M and Heirali, A and Coburn, B and Spreafico, A and Siu, LL},
title = {Bugs as drugs: The role of microbiome in cancer focusing on immunotherapeutics.},
journal = {Cancer treatment reviews},
volume = {92},
number = {},
pages = {102125},
doi = {10.1016/j.ctrv.2020.102125},
pmid = {33227623},
issn = {1532-1967},
abstract = {The human microbiome comprising microorganisms, their collective genomes and metabolic products has gained tremendous research interest in oncology, as multiple cohorts and case studies have demonstrated discernible interpatient differences in this ecosystem based on clinical variables including disease type, stage, diet, antibiotic usage, cancer treatments, therapeutic responses and toxicities. The modulation of the gut microbiome is the subject of many ongoing preclinical and clinical investigations, through the manipulation of diet, as well as the use of prebiotics, probiotics, specific antibiotics, fecal microbial transplantation, microbial consortia and stool substitutes. Standardization and quality control are needed to maximize the information being generated in this growing field, ranging from technical assays to measure microbiome composition, to methodological aspects in the analysis and reporting of results. Proof-of-mechanism and proof-of-concept clinical trials with appropriate controls are needed to confirm or refute the feasibility, safety and ultimately the clinical utility of human microbiome modulation in cancer patients.},
}

@article {pmid33227575,
year = {2020},
author = {McKenzie, ND and Hong, H and Ahmad, S and Holloway, RW},
title = {The gut microbiome and cancer immunotherapeutics: A review of emerging data and implications for future gynecologic cancer research.},
journal = {Critical reviews in oncology/hematology},
volume = {157},
number = {},
pages = {103165},
doi = {10.1016/j.critrevonc.2020.103165},
pmid = {33227575},
issn = {1879-0461},
abstract = {Investigation of the gynecologic tract microbial milieu has revealed potential new biomarkers. Simultaneously, immunotherapeutics are establishing their place in the treatment of gynecologic malignancies. The interplay between the microbiome, the tumor micro-environment and response to therapy is a burgeoning area of interest. There is evidence to support that microbes, through their genetic make-up, gene products, and metabolites affect human physiology, metabolism, immunity, disease susceptibility, response to pharmacotherapy, and the severity of disease-related side effects. Specifically, the richness and diversity of the gut microbiome appears to affect carcinogenesis, response to immunotherapy, and modulate severity of immune-mediated adverse effects. These effects have best been described in other tumor types and these have shown compelling results. This review summarizes the current understanding and scope of the interplay between the human microbiome, host factors, cancer, and response to treatments. These findings support further exploring whether these associations exist for gynecologic malignancies.},
}

@article {pmid33226731,
year = {2020},
author = {Diaz, PI},
title = {Subgingival fungi, Archaea, and viruses under the omics loupe.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.12352},
pmid = {33226731},
issn = {1600-0757},
abstract = {The microbial communities that inhabit the gingival crevice are responsible for the pathological processes that affect the periodontium. The changes in composition and function of subgingival bacteria as disease develops have been extensively studied. Subgingival communities, however, also contain fungi, Archaea, and viruses, which could contribute to the dysbiotic processes associated with periodontal diseases. High-throughput DNA sequencing has facilitated a better understanding of the mycobiome, archaeome, and virome. However, the number of studies available on the nonbacterial components of the subgingival microbiome remains limited in comparison with publications focusing on bacteria. Difficulties in characterizing fungal, archaeal, and viral populations arise from the small portion of the total metagenome mass they occupy and lack of comprehensive reference genome databases. In addition, specialized approaches potentially introducing bias are required to enrich for viral particles, while harsh methods of cell lysis are needed to recover nuclei acids from certain fungi. While the characterization of the subgingival diversity of fungi, Archaea and viruses is incomplete, emerging evidence suggests that they could contribute in different ways to subgingival dysbiosis. Certain fungi, such as Candida albicans are suggested to facilitate colonization of bacterial pathogens. Methanogenic Archaea are associated with periodontitis severity and are thought to partner synergistically with bacterial fermenters, while viruses may affect immune responses or shape microbial communities in ways incompletely understood. This review describes the manner in which omics approaches have improved our understanding of the diversity of fungi, Archaea, and viruses within subgingival communities. Further characterization of these understudied components of the subgingival microbiome is required, together with mechanistic studies to unravel their ecological role and potential contributions to dysbiosis.},
}

@article {pmid33226714,
year = {2020},
author = {Kumar, PS and Dabdoub, SM and Ganesan, SM},
title = {Probing periodontal microbial dark matter using metataxonomics and metagenomics.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.12349},
pmid = {33226714},
issn = {1600-0757},
abstract = {Our view of the periodontal microbial community has been shaped by a century or more of cultivation-based and microscopic investigations. While these studies firmly established the infection-mediated etiology of periodontal diseases, it was apparent from the very early days that periodontal microbiology suffered from what Staley and Konopka described as the "great plate count anomaly", in that these culturable bacteria were only a minor part of what was visible under the microscope. For nearly a century, much effort has been devoted to finding the right tools to investigate this uncultivated majority, also known as "microbial dark matter". The discovery that DNA was an effective tool to "see" microbial dark matter was a significant breakthrough in environmental microbiology, and oral microbiologists were among the earliest to capitalize on these advances. By identifying the order in which nucleotides are arranged in a stretch of DNA (DNA sequencing) and creating a repository of these sequences, sequence databases were created. Computational tools that used probability-driven analysis of these sequences enabled the discovery of new and unsuspected species and ascribed novel functions to these species. This review will trace the development of DNA sequencing as a quantitative, open-ended, comprehensive approach to characterize microbial communities in their native environments, and explore how this technology has shifted traditional dogmas on how the oral microbiome promotes health and its role in disease causation and perpetuation.},
}

@article {pmid33226710,
year = {2020},
author = {Weyrich, LS},
title = {The evolutionary history of the human oral microbiota and its implications for modern health.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.12353},
pmid = {33226710},
issn = {1600-0757},
abstract = {Numerous biological and cultural factors influence the microbial communities (microbiota) that inhabit the human mouth, including diet, environment, hygiene, physiology, health status, genetics, and lifestyle. As oral microbiota can underpin oral and systemic diseases, tracing the evolutionary history of oral microbiota and the factors that shape its origins will unlock information to mitigate disease today. Despite this, the origins of many oral microbes remain unknown, and the key factors in the past that shaped our oral microbiota are only now emerging. High throughput DNA sequencing of oral microbiota using ancient DNA and comparative anthropological methodologies has been employed to investigate oral microbiota origins, revealing a complex, rich history. Here, I review the current literature on the factors that shaped and guided oral microbiota evolution, both in Europe and globally. In Europe, oral microbiota evolution was shaped by interactions with Neandertals, the adaptation of farming, widespread integration of industrialization, and postindustrial lifestyles that emerged after World War II. Globally, evidence for a multitude of different oral microbiota histories is emerging, likely supporting dissimilarities in modern oral health across discrete human populations. I highlight how these evolutionary changes are linked to the development of modern oral diseases and discuss the remaining factors that need to be addressed to improve this embryonic field of research. I argue that understanding the evolutionary history of our oral microbiota is necessary to identify new treatment and prevention options to improve oral and systemic health in the future.},
}

@article {pmid33226703,
year = {2020},
author = {Bostanci, N and Grant, M and Bao, K and Silbereisen, A and Hetrodt, F and Manoil, D and Belibasakis, GN},
title = {Metaproteome and metabolome of oral microbial communities.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.12351},
pmid = {33226703},
issn = {1600-0757},
support = {//Karolinska Institutet Strategic Funds/ ; //Swedish Research Council/ ; //Janggen-Pöhn Foundation/ ; },
abstract = {The emergence of high-throughput technologies for the comprehensive measurement of biomolecules, also referred to as "omics" technologies, has helped us gather "big data" and characterize microbial communities. In this article, we focus on metaproteomic and metabolomic approaches that support hypothesis-driven investigations on various oral biologic samples. Proteomics reveals the working units of the oral milieu and metabolomics unveils the reactions taking place; and so these complementary techniques can unravel the functionality and underlying regulatory processes within various oral microbial communities. Current knowledge of the proteomic interplay and metabolic interactions of microorganisms within oral biofilm and salivary microbiome communities is presented and discussed, from both clinical and basic research perspectives. Communities indicative of, or from, health, caries, periodontal diseases, and endodontic lesions are represented. Challenges, future prospects, and examples of best practice are given.},
}

@article {pmid33226702,
year = {2020},
author = {Zaura, E and Pappalardo, VY and Buijs, MJ and Volgenant, CMC and Brandt, BW},
title = {Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.12359},
pmid = {33226702},
issn = {1600-0757},
abstract = {With this review, we aim to increase the quality standards for clinical studies with microbiome as an output parameter. We critically address the existing body of evidence for good quality practices in oral microbiome studies based on 16S rRNA gene amplicon sequencing. First, we discuss the usefulness of microbiome profile analyses. Is a microbiome study actually the best approach for answering the research question? This is followed by addressing the criteria for the most appropriate study design, sample size, and the necessary data (study metadata) that should be collected. Next, we evaluate the available evidence for best practices in sample collection, transport, storage, and DNA isolation. Finally, an overview of possible sequencing options (eg, 16S rRNA gene hypervariable regions, sequencing platforms), processing and data interpretation approaches, as well as requirements for meaningful data storage, sharing, and reporting are provided.},
}

@article {pmid33226700,
year = {2020},
author = {Buduneli, N},
title = {Environmental factors and periodontal microbiome.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.12355},
pmid = {33226700},
issn = {1600-0757},
abstract = {Periodontal diseases are chronic inflammatory, multifactorial diseases where the major triggering factors for disease onset are bacteria and their toxins, but the major part of tissue destruction occurs as a result of host response towards the periodontal microbiome. Periodontal microbiome consists of a wide range of microorganisms including obligate and facultative anaerobes. In health, there is a dynamic balance between the host, environment, and the microbiome. Environmental factors, mainly tobacco smoking and psychological stress, disrupt the symbiotic relationship. Tobacco smoke and its components alter the bacterial surface and functions such as growth. Psychological stressors and stress hormones may affect the outcome of an infection by changing the virulence factors and/or host response. This review aims to provide currently available data on the effects of the major environmental factors on the periodontal microbiome.},
}

@article {pmid33226695,
year = {2020},
author = {Feres, M and Retamal-Valdes, B and Gonçalves, C and Cristina Figueiredo, L and Teles, F},
title = {Did Omics change periodontal therapy?.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.12358},
pmid = {33226695},
issn = {1600-0757},
abstract = {The starting point for defining effective treatment protocols is a clear understanding of the etiology and pathogenesis of a condition. In periodontal diseases, this understanding has been hindered by a number of factors, such as the difficulty in differentiating primary pathogens from nonpathogens in complex biofilm structures. The introduction of DNA sequencing technologies, including taxonomic and functional analyses, has allowed the oral microbiome to be investigated in much greater breadth and depth. This article aims to compile the results of studies, using next-generation sequencing techniques to evaluate the periodontal microbiome, in an attempt to determine how far the knowledge provided by these studies has brought us in terms of influencing the way we treat periodontitis. The taxonomic data provided, to date, by published association and elimination studies using next-generation sequencing confirm previous knowledge on the role of classic periodontal pathogens in the pathobiology of disease and include new species/genera. Conversely, species and genera already considered as host-compatible and others less explored were associated with periodontal health as their levels were elevated in healthy individuals and increased after therapy. Functional and transcriptomic analyses also demonstrated that periodontal biofilms are taxonomically diverse, functionally congruent, and highly cooperative. Very few interventional studies to date have examined the effects of treatment on the periodontal microbiome, and such studies are heterogeneous in terms of design, sample size, sampling method, treatment provided, and duration of follow-up. Hence, it is still difficult to draw meaningful conclusions from them. Thus, although OMICS knowledge has not yet changed the way we treat patients in daily practice, the information provided by these studies opens new avenues for future research in this field. As new pathogens and beneficial species become identified, future randomized clinical trials could monitor these species/genera more comprehensively. In addition, the metatranscriptomic data, although still embryonic, suggest that the interplay between the host and the oral microbiome may be our best opportunity to implement personalized periodontal treatments. Therapeutic schemes targeting particular bacterial protein products in subjects with specific genetic profiles, for example, may be the futuristic view of enhanced periodontal therapy.},
}

@article {pmid33226693,
year = {2020},
author = {Teles, F and Wang, Y and Hajishengallis, G and Hasturk, H and Marchesan, JT},
title = {Impact of systemic factors in shaping the periodontal microbiome.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.12356},
pmid = {33226693},
issn = {1600-0757},
abstract = {Since 2010, next-generation sequencing platforms have laid the foundation to an exciting phase of discovery in oral microbiology as it relates to oral and systemic health and disease. Next-generation sequencing has allowed large-scale oral microbial surveys, based on informative marker genes, such as 16S ribosomal RNA, community gene inventories (metagenomics), and functional analyses (metatranscriptomics), to be undertaken. More specifically, the availability of next-generation sequencing has also paved the way for studying, in greater depth and breadth, the effect of systemic factors on the periodontal microbiome. It was natural to investigate systemic diseases, such as diabetes, in such studies, along with systemic conditions or states, , pregnancy, menopause, stress, rheumatoid arthritis, and systemic lupus erythematosus. In addition, in recent years, the relevance of systemic "variables" (ie, factors that are not necessarily diseases or conditions, but may modulate the periodontal microbiome) has been explored in detail. These include ethnicity and genetics. In the present manuscript, we describe and elaborate on the new and confirmatory findings unveiled by next-generation sequencing as it pertains to systemic factors that may shape the periodontal microbiome. We also explore the systemic and mechanistic basis for such modulation and highlight the importance of those relationships in the management and treatment of patients.},
}

@article {pmid33226688,
year = {2020},
author = {Duran-Pinedo, AE},
title = {Metatranscriptomic analyses of the oral microbiome.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.12350},
pmid = {33226688},
issn = {1600-0757},
support = {/DE/NIDCR NIH HHS/United States ; 2R01DE021553/NH/NIH HHS/United States ; },
abstract = {Although the composition of the oral human microbiome is now well studied, regulation of genes within oral microbial communities remains mostly uncharacterized. Current concepts of periodontal disease and caries highlight the importance of oral biofilms and their role as etiological agents of those diseases. Currently, there is increased interest in exploring and characterizing changes in the composition and gene-expression profiles of oral microbial communities. These efforts aim to identify changes in functional activities that could explain the transition from health to disease and the reason for the chronicity of those infections. It is now clear that the functions of distinct species within the subgingival microbiota are intimately intertwined with the rest of the microbial community. This point highlights the relevance of examining the expression profile of specific species within the subgingival microbiota in the case of periodontal disease or caries lesions, in the context of the other members of the biofilm in vivo. Metatranscriptomic analysis of the oral community is the starting point for identifying environmental signals that modulate the shift in metabolism of the community from commensal to dysbiotic. These studies give a snapshot of the expression patterns of microbial communities and also allow us to determine triggers to diseases. For example, in the case of caries, studies have unveiled a potential new pathway of sugar metabolism, namely the use of sorbitol as an additional source of carbon by Streptococcus mutans; and in the case of periodontal disease, high levels of extracellular potassium could be a signal of disease. Longitudinal studies are needed to identify the real markers of the initial stages of caries and periodontal disease. More information on the gene-expression profiles of the host, along with the patterns from the microbiome, will lead to a clearer understanding of the modulation of health and disease. This review presents a summary of these initial studies, which have opened the door to a new understanding of the dynamics of the oral community during the dysbiotic process in the oral cavity.},
}

@article {pmid33226670,
year = {2020},
author = {Kumar, PS},
title = {Microbiomics: Were we all wrong before?.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.12373},
pmid = {33226670},
issn = {1600-0757},
abstract = {Periodontal microbiology has historically been based on an "us against them" paradigm, one that focuses mainly on identifying microbes and viruses that cause disease. However, such a bottom-up approach limits our appreciation of the incredible diversity of this ecosystem and the essential ways in which microbial interactions contribute to health and homeostasis of the subgingival niche. Microbiomics-the science of collectively characterizing and quantifying molecules responsible for the structure, function, and dynamics of a microbial community-has enabled us to study these communities in their natural habitat, thereby revolutionizing our knowledge of host-associated microbes and reconceptualizing our definition of "human." When this systems-biology approach is combined with ecologic principles, it explicates the complex relationship that exist between microbiota and between them and us, the human. In this volume of Periodontology 2000, a group of 12 female scientists take the lead in investigating how metagenomics, genomics, metatranscriptomics, proteomics, metaproteomics, and metabolomics have achieved the following: (a) widened our view of the periodontal microbiome; (b) expanded our understanding of the evolution of the human oral microbiome; (c) shone a light on not just bacteria, but also other prokaryotic and eukaryotic members of the community; (d) elucidated the effects of anthropogenic behavior and systemic diseases on shaping these communities; and (e) influenced traditional patterns of periodontal therapeutics.},
}

@article {pmid33226601,
year = {2021},
author = {Cait, A and Messing, M and Cait, J and Canals Hernaez, D and McNagny, KM},
title = {Antibiotic Treatment in an Animal Model of Inflammatory Lung Disease.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2223},
number = {},
pages = {281-293},
doi = {10.1007/978-1-0716-1001-5_19},
pmid = {33226601},
issn = {1940-6029},
abstract = {Allergic disease is on the rise and yet the underlying cause and risk factors are not fully understood. While lifesaving in many circumstances, the use of antibiotics and the subsequent disruption of the microbiome are positively correlated with the development of allergies. Here, we describe the use of the antibiotic vancomycin in combination with the papain-induced mouse model of allergic disease that allows for the assessment of microbiome perturbations and the impact on allergy development.},
}

@article {pmid33226501,
year = {2020},
author = {Filippelli, M and dell'Omo, R and Amoruso, A and Paiano, I and Pane, M and Napolitano, P and Bartollino, S and Costagliola, C},
title = {Intestinal microbiome: a new target for chalaziosis treatment in children?.},
journal = {European journal of pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00431-020-03880-5},
pmid = {33226501},
issn = {1432-1076},
abstract = {Intestinal dysbiosis (changes in the gut commensal microbiome) is related to several ophthalmic diseases. The aim of this study was to verify whether oral specific probiotics can alter the clinical course of chalaziosis and its recurrence. A prospective comparative pilot study involving 26 children suffering from chalaziosis was conducted. Children were randomly divided into two groups. The first group received medical treatment (lid hygiene, warm compression and dexamethasone/tobramycin ointment for at least 20 days), and the second group received medical treatment plus a daily supplementation of oral probiotics (≥ 1 × 10^9 live cells of Streptococcus thermophilus ST10 (DSM 25246), ≥ 1 × 10^9 live cells of Lactococcus lactis LCC02 (DSM 29536) and ≥ 1 × 10^9 live cells of Lactobacillus delbrueckii subsp. bulgaricus (DSM 16606) with maltodextrin as the bulking agent (Probiotical S.p.A., Novara, Italy). All patients were evaluated at 2-week intervals for 3 months. If the lesion had not disappeared or decreased in size to 1 mm or less in diameter at the time of subsequent visits, the same procedure was repeated for another 3-month cycle. There was a significant difference in the time taken for complete resolution of the chalazion between the two groups in favour of the children receiving the probiotics. The treatment was not associated with any significant complications in either group. Trial registration: The trial was registered at clinical trials.gov under NCT04322500 on 25/03/2020 ("retrospectively registered").Conclusions: Modification of the intestinal microbiome with specific probiotics can alter the clinical course of chalaziosis in children by re-establishing intestinal and immune homeostasis. Probiotic supplementation can increase the effectiveness of traditional therapies by prompting the complete resolution of chalaziosis in a shorter amount of time, in an easy and feasible way. What is Known: • The intestinal microbiome plays a crucial role in several inflammatory diseases of the eye and is considered a therapeutic target. • Probiotics play a role in the prevention and treatment of different conditions in children. What is New: • In children probiotic supplementation is safe and effective. • Probiotic supplementation reduced the time required for complete resolution of the chalazion.},
}

@article {pmid33226500,
year = {2020},
author = {Walther, C and Zumbülte, S and Faerber, CM and Wierichs, RJ and Meyer-Lueckel, H and Conrads, G and Henne, K and Esteves-Oliveira, M},
title = {Analysis of relative bacterial activity and lactate dehydrogenase gene expression of caries-associated bacteria in a site-specific natural biofilm: an ex vivo study.},
journal = {Clinical oral investigations},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00784-020-03691-w},
pmid = {33226500},
issn = {1436-3771},
support = {(#39/17)//Medizinische Fakultät, RWTH Aachen University (DE)/ ; },
abstract = {OBJECTIVES: Detecting bacterial activity is considered a promising approach to monitor shifts from symbiosis to dysbiosis in oral microbiome. The present study aimed at investigating both the relative bacterial activity and the lactate dehydrogenase (ldh) gene expression of caries-associated bacteria in a site-specific natural biofilm.

MATERIAL AND METHODS: Sixty subjects (age, mean ± SE: 30.1 ± 1.4) were allocated to two groups: caries-free subjects (CF) or caries-active subjects (CA). CF presented one sound surface (CFS, n = 30). CA presented two donor sites: a cavitated caries lesion (CAC, n = 30) and a sound reference surface (CAS, n = 30). Real-time quantitative PCR (q-PCR) on species or genus level and total bacteria was performed targeting the 16S gene, the 16S rRNA, the ldh gene, and the ldh mRNA (increasing 16S ribosomal RNA copy numbers can function as an indicator of increased energy metabolism). As the 16S rRNA abundance represents the number of ribosomes, while the 16S gene abundance represents the number of genomes, the quotient of the relative abundances functions as a measure for the relative bacterial activity (%).

RESULTS: Both lactobacilli and S. mutans showed the highest relative bacterial activity in CAC ((mean ± SE) 218 ± 60% and 61 ± 16%, respectively) and the lowest values for both sound reference surfaces (69 ± 48%; 8 ± 3%). Significant differences were found between CAC and CAS as well as between CAC and CFS for both lactobacilli and S. mutans (p < 0.05). The ldh gene expression of lactobacilli and S. mutans only showed moderate values in CAC (1.90E+03 ± 2.11E+03; 2.08E+04 ± 4.44E+04 transcripts/μl) and CFS (2.04E+03 ± 2.74E+03; 8.16E+03 ± 6.64E+03 transcripts/μl); consequently no significant differences were detected.

Caries-associated bacteria (lactobacilli and S. mutans) showed the highest relative bacterial activity in plaque of cavitated lesions, the lowest in sound surfaces, allowing the detection of a significant activity shift in health and disease for caries-active patients. However, no significant differences in ldh gene expression could be determined.},
}

@article {pmid33225985,
year = {2020},
author = {Huang, H and Ren, Z and Gao, X and Hu, X and Zhou, Y and Jiang, J and Lu, H and Yin, S and Ji, J and Zhou, L and Zheng, S},
title = {Integrated analysis of microbiome and host transcriptome reveals correlations between gut microbiota and clinical outcomes in HBV-related hepatocellular carcinoma.},
journal = {Genome medicine},
volume = {12},
number = {1},
pages = {102},
doi = {10.1186/s13073-020-00796-5},
pmid = {33225985},
issn = {1756-994X},
support = {81721091//Innovative Research Groups of National Natural Science Foundation of China/ ; 2019-I2M-5-030/2019RU019//Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences/ ; 2017ZX100203205//National S&T Major Project of China/ ; 2018ZX10301201-008//National S&T Major Project of China/ ; LGF18C100001//Zhejiang Provincial Public Welfare Technology Research Program/ ; 2016C04003//Zhejiang International Science and Technology Cooperation Project/ ; 2018YFC2000501//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: The gut-liver axis plays a pivotal role in the pathogenesis of hepatocellular carcinoma (HCC). However, the correlations between the gut microbiome and the liver tumor transcriptome in patients with HCC and the impact of the gut microbiota on clinical outcome are less well-understood.

METHODS: Fecal samples collected from HBV-related HCC patients (n = 113) and healthy volunteers (n = 100) were subjected to 16S rRNA sequencing of the microbiome. After a rigorous selection process, 32 paired tumor and adjacent non-tumor liver tissues from the HCC group were subjected to next-generation sequencing (NGS) RNA-seq. The datasets were analyzed individually and integrated with clinical characteristics for combined analysis using bioinformatics approaches. We further verified the potential of the gut microbiota to predict clinical outcome by a random forest model and a support vector machine model.

RESULTS: We found that Bacteroides, Lachnospiracea incertae sedis, and Clostridium XIVa were enriched in HCC patients with a high tumor burden. By integrating the microbiome and transcriptome, we identified 31 robust associations between the above three genera and well-characterized genes, indicating possible mechanistic relationships in tumor immune microenvironment. Clinical characteristics and database analysis suggested that serum bile acids may be important communication mediators between these three genera and the host transcriptome. Finally, among these three genera, six important microbial markers associated with tumor immune microenvironment or bile acid metabolism showed the potential to predict clinical outcome (AUC = 81%).

CONCLUSIONS: This study revealed that changes in tumor immune microenvironment caused by the gut microbiota via serum bile acids may be important factors associated with tumor burden and adverse clinical outcome. Gut microbes can be used as biomarkers of clinical features and outcomes, and the microbe-associated transcripts of host tumors can partly explain how gut microbiota promotes HCC pathogenesis.},
}

@article {pmid33225966,
year = {2020},
author = {Huang, L and Xu, C and Yang, W and Yu, R},
title = {A machine learning framework to determine geolocations from metagenomic profiling.},
journal = {Biology direct},
volume = {15},
number = {1},
pages = {27},
doi = {10.1186/s13062-020-00278-z},
pmid = {33225966},
issn = {1745-6150},
abstract = {BACKGROUND: Studies on metagenomic data of environmental microbial samples found that microbial communities seem to be geolocation-specific, and the microbiome abundance profile can be a differentiating feature to identify samples' geolocations. In this paper, we present a machine learning framework to determine the geolocations from metagenomics profiling of microbial samples.

RESULTS: Our method was applied to the multi-source microbiome data from MetaSUB (The Metagenomics and Metadesign of Subways and Urban Biomes) International Consortium for the CAMDA 2019 Metagenomic Forensics Challenge (the Challenge). The goal of the Challenge is to predict the geographical origins of mystery samples by constructing microbiome fingerprints.First, we extracted features from metagenomic abundance profiles. We then randomly split the training data into training and validation sets and trained the prediction models on the training set. Prediction performance was evaluated on the validation set. By using logistic regression with L2 normalization, the prediction accuracy of the model reaches 86%, averaged over 100 random splits of training and validation datasets.The testing data consists of samples from cities that do not occur in the training data. To predict the "mystery" cities that are not sampled before for the testing data, we first defined biological coordinates for sampled cities based on the similarity of microbial samples from them. Then we performed affine transform on the map such that the distance between cities measures their biological difference rather than geographical distance. After that, we derived the probabilities of a given testing sample from unsampled cities based on its predicted probabilities on sampled cities using Kriging interpolation. Results show that this method can successfully assign high probabilities to the true cities-of-origin of testing samples.

CONCLUSION: Our framework shows good performance in predicting the geographic origin of metagenomic samples for cities where training data are available. Furthermore, we demonstrate the potential of the proposed method to predict metagenomic samples' geolocations for samples from locations that are not in the training dataset.},
}

@article {pmid33225893,
year = {2020},
author = {Negroni, MA and Segers, FHID and Vogelweith, F and Foitzik, S},
title = {Immune challenge reduces gut microbial diversity and triggers fertility-dependent gene expression changes in a social insect.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {816},
doi = {10.1186/s12864-020-07191-9},
pmid = {33225893},
issn = {1471-2164},
support = {FO 298/19-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: The gut microbiome can influence life history traits associated with host fitness such as fecundity and longevity. In most organisms, these two life history traits are traded-off, while they are positively linked in social insects. In ants, highly fecund queens can live for decades, while their non-reproducing workers exhibit much shorter lifespans. Yet, when fertility is induced in workers by death or removal of the queen, worker lifespan can increase. It is unclear how this positive link between fecundity and longevity is achieved and what role the gut microbiome and the immune system play in this. To gain insights into the molecular regulation of lifespan in social insects, we investigated fat body gene expression and gut microbiome composition in workers of the ant Temnothorax rugatulus in response to an experimental induction of fertility and an immune challenge.

RESULTS: Fertile workers upregulated several molecular repair mechanisms, which could explain their extended lifespan. The immune challenge altered the expression of several thousand genes in the fat body, including many immune genes, and, interestingly, this transcriptomic response depended on worker fertility. For example, only fertile, immune-challenged workers upregulated genes involved in the synthesis of alpha-ketoglutarate, an immune system regulator, which extends the lifespan in Caenorhabditis elegans by down-regulating the TOR pathway and reducing oxidant production. Additionally, we observed a dramatic loss in bacterial diversity in the guts of the ants within a day of the immune challenge. Yet, bacterial density did not change, so that the gut microbiomes of many immune challenged workers consisted of only a single or a few bacterial strains. Moreover, the expression of immune genes was linked to the gut microbiome composition, suggesting that the ant host can regulate the microbiome in its gut.

CONCLUSIONS: Immune system flare-ups can have negative consequence on gut microbiome diversity, pointing to a previously underrated cost of immunity. Moreover, our results provide important insights into shifts in the molecular regulation of fertility and longevity associated with insect sociality.},
}

@article {pmid33225662,
year = {2020},
author = {Durrani, M and Nazli, R and Fatima, S and Abubakr, M},
title = {Impact Of Feeding Practice On Diversity Pattern Of The Gut Microbiome In Infants.},
journal = {Journal of Ayub Medical College, Abbottabad : JAMC},
volume = {32},
number = {4},
pages = {551-557},
pmid = {33225662},
issn = {1819-2718},
abstract = {BACKGROUND: The microbiome which is developed at the time of infancy remains predominant and influences the health in childhood and then throughout life through moderating different gut metabolic activities This study was designed to look for the impact of feeding practices on the diversity of gut microbiota in infants in a Pakistani cohort.

METHODS: A cross sectional study was carried out in 46 healthy infants [23breast-fed (BF) and 23 formula-fed (FF)], aged 0-4 months, enrolled from different centers and localities in Peshawar. Infants were screened to exclude any pathological or physiological condition that can vary the gut microbial flora such as gut surgeries and the use of antibiotics. Their stool samples were collected. DNA was extracted and subjected to next generation sequencing.

RESULTS: The results revealed that phylum Firmicutes was dominant in formula-fed infants (FF=25.4±22.7, BF=4.58±5.21), p=0.001. Similarly, Bacilli, Streptococcaceae, and Streptococcus were significantly higher in formula-fed infants. On the other hand, Selenomonadales and Streptococcus_salivarius were significantly higher in breast-fed infants with a p-value of 0.037 and 0.029 respectively when compared with formula fed infants.

CONCLUSIONS: The primary colonizer of the infant's gut is phylum Firmicutes, followed by Bacilli, Streptococcaceae, and Streptococcus in formula-fed infants and Selenomonadales and Streptococcus_salivarius in breast-fed infants.},
}

@article {pmid33225561,
year = {2020},
author = {Garcias-Bonet, N and Eguíluz, VM and Díaz-Rúa, R and Duarte, CM},
title = {Host-association as major driver of microbiome structure and composition in Red Sea seagrass ecosystems.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15334},
pmid = {33225561},
issn = {1462-2920},
abstract = {The role of the microbiome in sustaining seagrasses has recently been highlighted. However, our understanding of the seagrass microbiome lacks behind that of other organisms. Here, we analyze the endophytic and total bacterial communities of leaves, rhizomes, and roots of six Red Sea seagrass species and their sediments. The structure of seagrass bacterial communities revealed that the 1% most abundant OTUs accounted for 87.9 and 74.8 % of the total numbers of reads in sediment and plant tissue samples, respectively. We found taxonomically distinct bacterial communities in vegetated and bare sediments. Yet, our results suggest that lifestyle (i.e. free-living or host-association) is the main driver of bacterial community composition. Seagrass bacterial communities were tissue- and species-specific and differed from those of surrounding sediments. We identified OTUs belonging to genera related to N and S cycles in roots, and members of Actinobacteria, Bacteroidetes, and Firmicutes phyla as particularly enriched in root endosphere. The finding of highly similar OTUs in well-defined sub-clusters by network analysis suggests the co-occurrence of highly connected key members within Red Sea seagrass bacterial communities. These results provide key information towards the understanding of the role of microorganisms in seagrass ecosystem functioning framed under the seagrass holobiont concept. This article is protected by copyright. All rights reserved.},
}

@article {pmid33225533,
year = {2020},
author = {Bollmann-Giolai, A and Giolai, M and Heavens, D and Macaulay, I and Malone, J and Clark, MD},
title = {A low-cost pipeline for soil microbiome profiling.},
journal = {MicrobiologyOpen},
volume = {},
number = {},
pages = {e1133},
doi = {10.1002/mbo3.1133},
pmid = {33225533},
issn = {2045-8827},
support = {BBS/E/J/000PR9797/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //John Innes Foundation/ ; //Natural History Museum/ ; },
abstract = {Common bottlenecks in environmental and crop microbiome studies are the consumable and personnel costs necessary for genomic DNA extraction and sequencing library construction. This is harder for challenging environmental samples such as soil, which is rich in Polymerase Chain Reaction (PCR) inhibitors. To address this, we have established a low-cost genomic DNA extraction method for soil samples. We also present an Illumina-compatible 16S and ITS rRNA gene amplicon library preparation workflow that uses common laboratory equipment. We evaluated the performance of our genomic DNA extraction method against two leading commercial soil genomic DNA kits (MoBio PowerSoil® and MP Biomedicals™ FastDNA™ SPIN) and a recently published non-commercial extraction method by Zou et al. (PLoS Biology, 15, e2003916, 2017). Our benchmarking experiment used four different soil types (coniferous, broad-leafed, and mixed forest plus a standardized cereal crop compost mix) assessing the quality and quantity of the extracted genomic DNA by analyzing sequence variants of 16S V4 and ITS rRNA amplicons. We found that our genomic DNA extraction method compares well to both commercially available genomic DNA extraction kits in DNA quality and quantity. The MoBio PowerSoil® kit, which relies on silica column-based DNA extraction with extensive washing, delivered the cleanest genomic DNA, for example, best A260:A280 and A260:A230 absorbance ratios. The MP Biomedicals™ FastDNA™ SPIN kit, which uses a large amount of binding material, yielded the most genomic DNA. Our method fits between the two commercial kits, producing both good yields and clean genomic DNA with fragment sizes of approximately 10 kb. Comparative analysis of detected amplicon sequence variants shows that our method correlates well with the two commercial kits. Here, we present a low-cost genomic DNA extraction method for soil samples that can be coupled to an Illumina-compatible simple two-step amplicon library construction workflow for 16S V4 and ITS marker genes. Our method delivers high-quality genomic DNA at a fraction of the cost of commercial kits and enables cost-effective, large-scale amplicon sequencing projects. Notably, our extracted gDNA molecules are long enough to be suitable for downstream techniques such as full gene sequencing or even metagenomics shotgun approaches using long reads (PacBio or Nanopore), 10x Genomics linked reads, and Dovetail genomics.},
}

@article {pmid33225399,
year = {2020},
author = {Xu, H and Ma, C and Zhao, F and Chen, P and Liu, Y and Sun, Z and Cui, L and Kwok, LY and Zhang, H},
title = {Adjunctive treatment with probiotics partially alleviates symptoms and reduces inflammation in patients with irritable bowel syndrome.},
journal = {European journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00394-020-02437-4},
pmid = {33225399},
issn = {1436-6215},
support = {31720103911//National Natural Science Foundation of China/ ; },
abstract = {PURPOSE: Irritable bowel syndrome (IBS) is a functional bowel disorder. This study aimed to assess the effect of a probiotic product (containing Lactobacillus casei Zhang, Lactobacillus plantarum P-8, and Bifdobacterium animalis subsp. lactis V9) as an adjunct to a routine regimen in IBS management.

METHODS: Forty-five patients with IBS were randomized into the probiotic (n = 24) and control (n = 21) groups, receiving the routine regimen with or without probiotics for 28 days, respectively. Serum and fecal samples were collected and analyzed.

RESULTS: The IBS-symptom severity score (P < 0.01), serum levels of IL-6 (P < 0.01) and TNF-α (P < 0.001) were significantly lower in the probiotic group than the control group at day 28. The probiotic adjunctive treatment resulted in significant decreases in some bacterial genera that worsen IBS, such as Bacteroides (P < 0.01), Escherichia (P < 0.05), and Citrobacter (P < 0.05), significant decreases were also observed in some beneficial genera in the control group, including Bifidobacterium (P < 0.05), Eubacterium (P < 0.05), Dorea (P < 0.01), and Butyricicoccus (P < 0.05). Furthermore, significant correlations were found between some monitored parameters and compositional changes in the fecal microbiota, suggesting that the clinical improvement of IBS was likely associated with gut microbiota modulation. The enterotype analysis revealed that the initial fecal microbiota composition could influence clinical outcomes.

CONCLUSIONS: The adjunctive use of probiotics with a routine regimen showed additional clinical effectiveness compared to the routine regimen alone in managing IBS. A pretreatment gut microbiome analysis might help tailor a personalized probiotic regimen to optimize treatment effects.},
}

@article {pmid33225342,
year = {2020},
author = {Wilson, N and Zhao, N and Zhan, X and Koh, H and Fu, W and Chen, J and Li, H and Wu, MC and Plantinga, AM},
title = {MiRKAT: kernel machine regression-based global association tests for the microbiome.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaa951},
pmid = {33225342},
issn = {1367-4811},
abstract = {SUMMARY: Distance-based tests of microbiome beta diversity are an integral part of many microbiome analyses. MiRKAT enables distance-based association testing with a wide variety of outcome types, including continuous, binary, censored time-to-event, multivariate, correlated and high-dimensional outcomes. Omnibus tests allow simultaneous consideration of multiple distance and dissimilarity measures, providing higher power across a range of simulation scenarios. Two measures of effect size, a modified R-squared coefficient and a kernel RV coefficient, are incorporated to allow comparison of effect sizes across multiple kernels.

MiRKAT is available on CRAN as an R package.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid33224990,
year = {2020},
author = {Zhao, X and Zhang, Y and Guo, R and Yu, W and Zhang, F and Wu, F and Shang, J},
title = {The Alteration in Composition and Function of Gut Microbiome in Patients with Type 2 Diabetes.},
journal = {Journal of diabetes research},
volume = {2020},
number = {},
pages = {8842651},
doi = {10.1155/2020/8842651},
pmid = {33224990},
issn = {2314-6753},
abstract = {Background: Diabetes mellitus (DM) has become one of the most common chronic metabolic diseases worldwide. Due to the increasing prevalence and various complications, diabetes brings about a huge financial burden to DM patients. Nowadays, more and more studies reveal the relationship between diseases and gut microbial community. We aimed to explore the alteration in composition and function of the gut microbiome in T2DM patients.

Methods: A total of 137 patients with diabetes and 179 age- and gender-matched healthy controls selected from the healthy people sample center in the First Affiliated Hospital of Zhengzhou University were divided into the DM group and the Con group, respectively. We collected their venous blood for laboratory tests and stool samples for 16S rRNA sequencing. The comparison between the two groups including both composition and function of the gut microbiome is presented.

Results: We found that the α-diversity of bacterial taxa in the DM group had an evident decrease compared to that in the Con group. At the phylum level, the DM group had an obvious decrease of Bacteroidetes and a marked increase of Proteobacteria, Actinobacteria, and Verrucomicrobia. At the genus level, Bacteroides and Prevotella decreased the most while Escherichia-Shigella, Lachnospiraceae_incertae_sedis, Subdoligranulum, Enterococcus, and Klebsiella had different degrees of expansion in the DM group. The ROC based on 246 optimum OTUs had very high test efficiency with an AUC of 92.25% in the training set and 90.48% in the test set. As for prediction of metabolic function, the gut microbiome of DM patients was predicted to be more active in environmental information processing and human diseases but less in metabolism.

Conclusion: We observed alteration of composition and function of the gut microbiome in the DM group. These changes may provide a new treatment strategy for DM patients and new research targets.},
}

@article {pmid33224899,
year = {2020},
author = {Hu, Y and Xie, H and Gao, M and Huang, P and Zhou, H and Ma, Y and Zhou, M and Liang, J and Yang, J and Lv, Z},
title = {Dynamic of Composition and Diversity of Gut Microbiota in Triatoma rubrofasciata in Different Developmental Stages and Environmental Conditions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {10},
number = {},
pages = {587708},
doi = {10.3389/fcimb.2020.587708},
pmid = {33224899},
issn = {2235-2988},
abstract = {Triatoma rubrofasciata (T. rubrofasciata), one kind of triatomine insects, is the vector of Trypanosoma cruzi (T. cruzi), which lead to American trypanosomiasis. Although the gut microbiome may play an essential role in the development and susceptibility of triatomine, there is limited research on the gut microbiota of T. rubrofasciata. To elucidate the effect of the vector's developmental stages and environmental conditions on the gut microbiome, we employed 16S rRNA gene sequencing to profile the gut bacterial community diversity and composition of T. rubrofasciata. Significant shifts were observed in the overall gut microbe diversity and composition across the development of T. rubrofasciata and specific bacteria were detected in different stages. Serratia and Burkholderia-Caballeronia-Paraburkholderia were dominant in the 1st nymphal stage, while the abundance of Staphylococcus was low in the 1st nymphal stage. Oceanicaulis were undetectable in the adult stage and Odoribacter peaked in the 2nd nymphal stage. Moreover, Staphylococcus was correlated negatively with Serratia. Likewise, the total gut microbiota diversity and composition of T. rubrofasciata differentiated significantly by environmental conditions. The ingestion of a bloodmeal increased alpha diversity of gut bacterial communities, and Staphylococcus was more abundant in laboratory-reared bugs whereas Enterococcus enriched in wild-caught bugs. Furthermore, Pantoea was negatively correlated with Staphylococcus, and positively related to Bacillus only. The phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) algorithm showed obvious metagenomic functional differences by environmental conditions, and Chagas disease relevant pathway was enriched in wild-caught T. rubrofasciata.},
}

@article {pmid33224717,
year = {2019},
author = {Yin, R and Kuo, HC and Hudlikar, R and Sargsyan, D and Li, S and Wang, L and Wu, R and Kong, AN},
title = {Gut microbiota, dietary phytochemicals and benefits to human health.},
journal = {Current pharmacology reports},
volume = {5},
number = {},
pages = {332-344},
doi = {10.1007/s40495-019-00196-3},
pmid = {33224717},
issn = {2198-641X},
abstract = {Purpose of the review: In this review, we discuss the roles of the gut microbiota, dietary phytochemicals in improving human health. Recent studies have reported that the human gut microbiota can be altered by dietary phytochemicals including phenolics, carotenoids, and dietary fibers. In addition, both pathogenic and nonpathogenic bacteria show regulatory effects with phytochemicals, suggesting potential synergistic effects in the improvement of human gut health and prevention of chronic diseases.

Recent findings: Numerous studies have been conducted on gut microbial alterations induced by phytochemicals, such as phenolics and carotenoids. Butyrate, a short-chain fatty acid produced via bacterial fermentation in the colon, also shows a significantly beneficial effect in the maintenance of gut microbial homeostasis. However, the molecular mechanisms underlying the effects of diets and the interactions of the gut microorganisms remain poorly understood. The gut microbiome profile changes have been observed in chronic inflammation-induced diseases including colitis, Crohn's disease, immune dysfunction, colon cancer, obesity and diabetes. The anti-inflammatory effects of dietary phytochemicals against these diseases may be partially mediated by regulation of microbial profiles. Latest advances in biomedical technology such as the next-generation sequencing (NGS), and continuous cost reduction associated with these technologies, enabled researchers to perform ever-increasing number of large-scale, high-throughput computational analyses to elucidate the potential mechanism of phytochemical-microbiome interactions.

Summary: Information obtained from these studies may provide valuable insights to guide future clinical research for the development of therapeutics, botanicals and drug efficacy testing, many of which will be discussed in this review.},
}

@article {pmid33224157,
year = {2020},
author = {Wille, L and Messmer, MM and Bodenhausen, N and Studer, B and Hohmann, P},
title = {Heritable Variation in Pea for Resistance Against a Root Rot Complex and Its Characterization by Amplicon Sequencing.},
journal = {Frontiers in plant science},
volume = {11},
number = {},
pages = {542153},
doi = {10.3389/fpls.2020.542153},
pmid = {33224157},
issn = {1664-462X},
abstract = {Soil-borne pathogens cause severe root rot of pea (Pisum sativum L.) and are a major constraint to pea cultivation worldwide. Resistance against individual pathogen species is often ineffective in the field where multiple pathogens form a pea root rot complex (PRRC) and conjointly infect pea plants. On the other hand, various beneficial plant-microbe interactions are known that offer opportunities to strengthen plant health. To account for the whole rhizosphere microbiome in the assessment of root rot resistance in pea, an infested soil-based resistance screening assay was established. The infested soil originated from a field that showed severe pea root rot in the past. Initially, amplicon sequencing was employed to characterize the fungal microbiome of diseased pea roots grown in the infested soil. The amplicon sequencing evidenced a diverse fungal community in the roots including pea pathogens Fusarium oxysporum, F. solani, Didymella sp., and Rhizoctonia solani and antagonists such as Clonostachys rosea and several mycorrhizal species. The screening system allowed for a reproducible assessment of disease parameters among 261 pea cultivars, breeding lines, and landraces grown for 21 days under controlled conditions. A sterile soil control treatment was used to calculate relative shoot and root biomass in order to compare growth performance of pea lines with highly different growth morphologies. Broad sense heritability was calculated from linear mixed model estimated variance components for all traits. Emergence on the infested soil showed high (H2 = 0.89), root rot index (H2 = 0.43), and relative shoot dry weight (H2 = 0.51) medium heritability. The resistance screening allowed for a reproducible distinction between PRRC susceptible and resistant pea lines. The combined assessment of root rot index and relative shoot dry weight allowed to identify resistant (low root rot index) and tolerant pea lines (low relative shoot dry weight at moderate to high root rot index). We conclude that relative shoot dry weight is a valuable trait to select disease tolerant pea lines. Subsequently, the resistance ranking was verified in an on-farm experiment with a subset of pea lines. We found a significant correlation (rs = 0.73, p = 0.03) between the controlled conditions and the resistance ranking in a field with high PRRC infestation. The screening system allows to predict PRRC resistance for a given field site and offers a tool for selection at the seedling stage in breeding nurseries. Using the complexity of the infested field soil, the screening system provides opportunities to study plant resistance in the light of diverse plant-microbe interactions occurring in the rhizosphere.},
}

@article {pmid33223831,
year = {2020},
author = {Sanborn, V and Azcarate-Peril, MA and Updegraff, J and Manderino, L and Gunstad, J},
title = {Randomized Clinical Trial Examining the Impact of Lactobacillus rhamnosus GG Probiotic Supplementation on Cognitive Functioning in Middle-aged and Older Adults.},
journal = {Neuropsychiatric disease and treatment},
volume = {16},
number = {},
pages = {2765-2777},
doi = {10.2147/NDT.S270035},
pmid = {33223831},
issn = {1176-6328},
abstract = {Purpose: The gut microbiome has been linked to cognitive function and appears to worsen with aging. Probiotic supplementation has been found to improve the health of the gut microbiome. As such, it is possible that probiotic supplementation may protect the aging brain. The current study examined the cognitive benefits of probiotic supplementation (Lactobacillus rhamnosus GG) in healthy middle-aged and older adults.

Materials and Methods: The study was a double-blind, placebo-controlled, randomized clinical trial. Two hundred community-dwelling adults aged 52-75 were enrolled (mean age=64.3, SD=5.52). A three-month intervention involved daily consumption of probiotic or placebo. Independent sample t-tests, chi-squared tests, and repeated measure ANOVAs compared groups and examined changes over time. Primary outcome was change in NIH Toolbox Total Cognition Score from baseline to follow-up.

Results: A total of 145 participants were examined in primary analyses (probiotic=77, placebo=68) and excluded persons due to discontinuation, low adherence, missing data, or outlier values. Established criteria (ie ≥1 subtest t-scores ≤35; n=19, n=23) were used to operationally define cognitive impairment. Repeated measures ANOVAs revealed that persons with cognitive impairment who consumed probiotics exhibited a greater total cognition score improvement than persons with cognitive impairment in the placebo group and cognitively intact persons in probiotic or placebo groups.

Conclusion: Lactobacillus rhamnosus GG probiotic supplementation was associated with improved cognitive performance in middle-aged and older adults with cognitive impairment. Probiotic supplementation may be a novel method for protecting cognitive health in aging.},
}

@article {pmid33222612,
year = {2020},
author = {Wang, X and Liu, H and Li, Y and Huang, S and Zhang, L and Cao, C and Baker, PN and Tong, C and Zheng, P and Qi, H},
title = {Altered gut bacterial and metabolic signatures and their interaction in gestational diabetes mellitus.},
journal = {Gut microbes},
volume = {12},
number = {1},
pages = {1-13},
doi = {10.1080/19490976.2020.1840765},
pmid = {33222612},
issn = {1949-0984},
abstract = {Emerging evidence indicates that the gut microbiome can modulate metabolic homeostasis, and thus may influence the development of gestational diabetes mellitus (GDM). However, whether and how the gut microbiome and its correlated metabolites change in GDM is uncertain. Herein we compare the gut microbial compositions, and fecal and urine metabolomes, of 59 patients with GDM versus 48 pregnant healthy controls (HCs). We showed that the microbial and metabolic signatures of GDM patients were significantly different from those of HCs. Compared to HCs, the GDM subjects were characterized by enriched bacterial operational taxonomic units (OTUs) of the family Lachnospiraceae, and depleted OTUs of the families Enterobacteriaceae and Ruminococcaceae. Some altered gut microbes were significantly correlated with glucose values and fetal ultrasonography indexes. Moreover, we identified four fecal and 15 urine metabolites that discriminate GDM from HC. These differential metabolites are mainly involved in carbohydrate and amino acid metabolism. Significantly, co-occurrence network analysis revealed that Lachnospiraceae and Enterobacteriaceae bacterial OTUs formed strong co-occurring relationships with metabolites involved in carbohydrate and amino acid metabolism, suggesting that disturbed gut microbiome may mediate GDM. Furthermore, we identified a novel combinatorial marker panel that could distinguish GDM from HC subjects with high accuracy. Together our findings demonstrate that altered microbial composition and metabolic function may be relevant to the pathogenesis and pathophysiology of GDM.},
}

@article {pmid33222377,
year = {2020},
author = {Cai, W and Long, F and Wang, Y and Liu, H and Guo, K},
title = {Enhancement of microbiome management by machine learning for biological wastewater treatment.},
journal = {Microbial biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-7915.13707},
pmid = {33222377},
issn = {1751-7915},
support = {2020M673414//China Postdoctoral Science Foundation/ ; 21828802//National Natural Science Foundation of China/ ; 21878242//National Natural Science Foundation of China/ ; 22008194//National Natural Science Foundation of China/ ; },
abstract = {Here, we propose to develop microbiome-based machine learning models to predict the response of biological wastewater treatment systems to environmental or operational disturbances or to design specific microbiomes to achieve a desired system function. These machine learning models can be used to enhance the stability of microbiome-based biological systems and warn against the failure of these systems.},
}

@article {pmid33222307,
year = {2020},
author = {Majak, P and Molińska, K and Latek, M and Rychlik, B and Wachulec, M and Błauż, A and Budniok, A and Gruchała, M and Lach, J and Sobalska-Kwapis, M and Baranowska, M and Królikowska, K and Strapagiel, D and Majak, J and Chech, D and Pałczyński, C and Kuna, P},
title = {Upper-airway dysbiosis related to frequent sweets consumption increases the risk of asthma in children with chronic rhinosinusitis.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1111/pai.13417},
pmid = {33222307},
issn = {1399-3038},
abstract = {BACKGROUND: Innate immunity response to local dysbiosis seems to be one of the most important immunological backgrounds of chronic rhinosinusitis (CRS) and concomitant asthma. We aimed to assess clinical determinants of upper-airway dysbiosis and its effect on nasal inflammatory profile and asthma risk in young children with CRS.

METHODS: We recruited one hundred thirty-three children, aged 4-8 years with doctor-diagnosed CRS with or without asthma. The following procedures were performed in all participants: face-to-face standardized Sinus and Nasal Quality of Life questionnaire, skin prick test, taste perception testing, nasopharynx swab, and sampling of the nasal mucosa. Upper-airway dysbiosis was defined separately by asthma specific microbiome composition and reduced biodiversity. Multivariate methods were used to define the risk factors of asthma and upper-airway dysbiosis and their specific inflammatory profile of nasal mucosa.

RESULTS: The asthma-specific upper-airway microbiome composition reflected by the decreased ratio of Patescibacteria/Actinobacteria independently of atopy increased the risk of asthma (OR:8.32; 95%CI:2.93-23.6). This asthma-specific microbiome composition was associated with ≥7/week sweets consumption (OR:2.64; 95%C:1.11-6.28), reduced biodiversity (OR:3.83; 95%CI:1.65-8.87), the presence of Staphylococcus strains in the nasopharynx (OR:4.25; 95%CI:1.12-16.1), and lower expression of beta-defensin 2, IL-5, IL-13 in the nasal mucosa. The reduced biodiversity was associated with frequent antibiotic use and with a higher nasal expression of IL-17 and T1R3 (sweet taste receptor). In asthmatic children reduced sweet taste perception was observed.

CONCLUSIONS: Specific upper-airway dysbiosis related to frequent sweets consumption, frequent antibiotics courses, and altered nasal immune function increases the risk of asthma in young children with CRS.},
}

@article {pmid33222287,
year = {2020},
author = {Stewart, HL and Pitta, D and Indugu, N and Vecchiarelli, B and Hennessy, ML and Engiles, JB and Southwood, LL},
title = {Changes in the faecal bacterial microbiota during hospitalisation of horses with colic and the effect of different causes of colic.},
journal = {Equine veterinary journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/evj.13389},
pmid = {33222287},
issn = {2042-3306},
abstract = {BACKGROUND: Previous studies have identified alterations in the faecal microbiota of horses with colic; however, further work is needed to interpret these findings.

OBJECTIVES: To compare the faecal microbiota of horses presenting for colic at hospital admission, day 1 and day 3/discharge and with different colic duration and lesion locations.

STUDY DESIGN: Prospective observational clinical study.

METHODS: Faecal samples were collected from 17 colic cases at hospital admission, on day 1 and on day 3 post admission or at the time of hospital discharge if prior to 72 hours. Faecal samples were extracted for genomic DNA, PCR-amplified, sequenced, and analysed using QIIME. Species richness and Shannon diversity (alpha diversity) were estimated. The extent of the relationship between bacterial communities (beta diversity) was quantified using pairwise UniFrac distances, visualised using principal coordinate analysis (PCoA), and statistically analysed using PERMANOVA. The relative abundance of bacterial populations at the different time points and in different types of colic was compared using ANCOM.

RESULTS: There was a decrease in species richness from admission to day 3/hospital discharge (P < 0.05) and a lower species richness (P = 0.005) and Shannon diversity (P = 0.02) in horses with colic ≥60h compared to <60h. Based on PCoA and PERMANOVA, there was a significant difference in bacterial community composition for horses with different colic duration (P = 0.001) and lesion location (P = 0.006). Several differences in bacterial phyla and genera were observed at different time points and with different types of colic.

MAIN LIMITATIONS: Relatively low numbers and a diverse population of horses.

CONCLUSIONS: The microbiota changes from hospital admission to day 3/discharge in horses with colic and horses with colic ≥60h and large colon lesions have a distinct bacterial population compared to horses with colic <60h and small intestinal lesions.},
}