Viewport Size Code:
Login | Create New Account


About | Classical Genetics | Timelines | What's New | What's Hot

About | Classical Genetics | Timelines | What's New | What's Hot


Bibliography Options Menu

Hide Abstracts   |   Hide Additional Links
Long bibliographies are displayed in blocks of 100 citations at a time. At the end of each block there is an option to load the next block.

Bibliography on: Microbiome

The Electronic Scholarly Publishing Project: Providing world-wide, free access to classic scientific papers and other scholarly materials, since 1993.


ESP: PubMed Auto Bibliography 25 Oct 2021 at 01:48 Created: 


It has long been known that every multicellular organism coexists with large prokaryotic ecosystems — microbiomes — that completely cover its surfaces, external and internal. Recent studies have shown that these associated microbiomes are not mere contamination, but instead have profound effects upon the function and fitness of the multicellular organism. We now know that all MCEs are actually functional composites, holobionts, composed of more prokaryotic cells than eukaryotic cells and expressing more prokaryotic genes than eukaryotic genes. A full understanding of the biology of "individual" eukaryotes will now depend on an understanding of their associated microbiomes.

Created with PubMed® Query: microbiome[tiab] NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2021-10-22

Liu W, Fang X, Zhou Y, et al (2021)

Machine learning-based investigation of the relationship between gut microbiome and obesity status.

Microbes and infection pii:S1286-4579(21)00114-3 [Epub ahead of print].

Gut microbiota is believed to play a crucial role in obesity. However, the consistent findings among published studies regarding microbiome-obesity interaction are relatively rare, and one of the underlying causes could be the limited sample size of cohort studies. In order to identify gut microbiota changes between normal-weight individuals and obese individuals, fecal samples along with phenotype information from 2262 Chinese individuals were collected and analyzed. Compared with normal-weight individuals, the obese individuals exhibit lower diversity of species and higher diversity of metabolic pathways. In addition, various machine learning models were employed to quantify the relationship between obesity status and Body mass index (BMI) values, of which support vector machine model achieves best performance with 0.716 classification accuracy and 0.485 R2 score. In addition to two well-established obesity-associated species, three species that have potential to be obesity-related biomarkers, including Bacteroides caccae, Odoribacter splanchnicus and Roseburia hominis were identified. Further analyses of functional pathways also reveal some enriched pathways in obese individuals. Collectively, our data demonstrates tight relationship between obesity and gut microbiota in a large-scale Chinese population. These findings may provide potential targets for the prevention and treatment of obesity.

RevDate: 2021-10-22

Han L, Chen L, Li D, et al (2021)

Influence of polyethylene terephthalate microplastic and biochar co-existence on paddy soil bacterial community structure and greenhouse gas emission.

Environmental pollution (Barking, Essex : 1987) pii:S0269-7491(21)01968-0 [Epub ahead of print].

Microplastic (MP) contamination is ubiquitous in agricultural soils. As a cost-effective soil amendment, biochar (BC) often coincides with MP exposure. However, little research has been conducted regarding the independent and combined effects of MPs and BC on the soil microbiome and N2O/CH4 emissions. Therefore, in this study, polyethylene terephthalate (PET) and wheat straw-derived BC were used, respectively, as a representative MP and BC during an entire rice growth period. The high-throughput sequencing results showed that PET alone lowered bacterial diversity by 26.7%, while PET and BC co-existence did not induce apparent change. The relative abundances of some microbes (e.g., Cyanobacteria, Verrucomicrobia, and Bacteroidetes) that are associated with C and N cycling were changed at the phylum and class levels by all the treatments. In comparison with the control, the treatment of BC, PET, and their co-existence reduced the cumulative CH4 emissions by 50%, 53%, and 61%, respectively. The higher mitigation by BC + PET may be the result of higher soil Eh and a consequently lower methanogenesis functional gene mcrA abundance in the treated soils. In addition, BC and PET alone, as well as their combined treatment, increased the abundance of nitrification genes, enhancing the soil nitrification process. However, the relative contribution of the nitrification process to N2O emission was possibly lower than that of denitrification, in which the N2O reductase gene nosZ was found to be the primary gene regulating N2O emissions. BC alone increased nosZ abundance by 42.3%, thereby showing the potential in suppressing N2O emission. In contrast, when BC was co-added with PET, the nosZ abundance lowered possibly because of increased soil aeration, and thus its cumulative N2O emission was 38% higher than the BC treatment. Overall, these results demonstrated that BC and PET function differently in soil ecosystems when they coexisted.

RevDate: 2021-10-22

Suhadolnik MLS, Costa PS, Paiva MC, et al (2021)

Spatiotemporal dynamics of the resistome and virulome of riverine microbiomes disturbed by a mining mud tsunami.

The Science of the total environment pii:S0048-9697(21)06014-9 [Epub ahead of print].

Aquatic ecosystems are highly vulnerable to anthropogenic activities. However, it remains unclear how the microbiome responds to press disturbance events in these ecosystems. We examined the impact of the world's largest mining disaster (Brazil, 2015) on sediment microbiomes in two disturbed rivers compared to an undisturbed river during 390 days post-disturbance. The diversity and structure of the virulome and microbiome, and of antibiotic and metal resistomes, consistently differed between the disturbed and undisturbed rivers, particularly at day 7 post-disturbance. 684 different ARGs were predicted, 38% were exclusive to the disturbed rivers. Critical antibiotic resistance genes (ARGs), e.g., mcr and ereA2, were significantly more common in the disturbed microbiomes. 401 different ARGs were associated with mobile genetic elements (MGEs), 95% occurred in the disturbed rivers. While plasmids were the most common MGEs with a broad spectrum of ARGs, spanning 16 antibiotic classes, integrative conjugative elements (ICEs) and integrons disseminated ARGs associated with aminoglycoside and tetracycline, and aminoglycoside and beta-lactam, respectively. A significant increase in the relative abundance of class 1 integrons, ICEs, and pathogens was identified at day 7 in the disturbed microbiomes, 72-, 14- and 3- fold higher, respectively, compared with the undisturbed river. Mobile ARGs associated with ESKAPEE group pathogens, while metal resistance genes and virulence factor genes in nonpathogenic hosts predominated in all microbiomes. Network analysis showed highly interconnected ARGs in the disturbed communities, including genes targeting antibiotics of last resort. Interactions between copper and beta-lactam/aminoglycoside/macrolide resistance genes, mostly mobile and critical, were also uncovered. We conclude that the mud tsunami resulted in resistome expansion, enrichment of pathogens, and increases in promiscuous and mobile ARGs. From a One Health perspective, mining companies need to move toward more environmentally friendly and socially responsible mining practices to reduce risks associated with pathogens and critical and mobile ARGs.

RevDate: 2021-10-22

Debnath N, Kumar R, Kumar A, et al (2021)

Gut-microbiota derived bioactive metabolites and their functions in host physiology.

Biotechnology & genetic engineering reviews [Epub ahead of print].

Every individual harbours a complex, diverse and mutualistic microbial flora in their intestine and over the time it became an integral part of the body, affecting a plethora of activities of the host. Interaction between host and gut-microbiota affects several aspects of host physiology. Gut-microbiota affects host metabolism by fermenting unabsorbed/undigested carbohydrates in the large intestine. Not only the metabolic functions, any disturbances in the composition of the gut-microbiota during first 2-3 years of life may impact on the brain development and later affects cognition and behaviour. Thus, gut-dysbiosis causes certain serious pathological conditions in the host including metabolic disorders, inflammatory bowel disease and mood alterations, etc. Microbial-metabolites in recent times have emerged as key mediators and are responsible for microbiota induced beneficial effects on host. This review provides an overview of the mechanism of microbial-metabolite production, their respective physiological functions and the impact of gut-microbiome in health and diseases. Metabolites from dietary fibres, aromatic amino acids such as tryptophan, primary bile acids and others are the potential substances and link microbiota to host physiology. Many of these metabolites act as signalling molecules to a number of cells types and also help in the secretion of hormones. Moreover, interaction of microbiota derived metabolites with their host, immunity boosting mechanisms, protection against pathogens and modulation of metabolism is also highlighted here. Understanding all these functional attributes of metabolites produced from gut-microbiota may lead to the opening of a new avenue for preventing and developing potent therapies against several diseases.

RevDate: 2021-10-22

Howard EJ, Lam TKT, FA Duca (2021)

The Gut Microbiome: Connecting Diet, Glucose Homeostasis, and Disease.

Annual review of medicine [Epub ahead of print].

Type 2 diabetes rates continue to rise unabated, underscoring the need to better understand the etiology and potential therapeutic options available for this disease. The gut microbiome plays a role in glucose homeostasis, and diabetes is associated with alterations in the gut microbiome. Given that consumption of a Western diet is associated with increased metabolic disease, and that a Western diet alters the gut microbiome, it is plausible that changes in the gut microbiota mediate the dysregulation in glucose homeostasis. In this review, we highlight a few of the most significant mechanisms by which the gut microbiome can influence glucose regulation, including changes in gut permeability, gut-brain signaling, and production of bacteria-derived metabolites like short-chain fatty acids and bile acids. A better understanding of these pathways could lead to the development of novel therapeutics to target the gut microbiome in order to restore glucose homeostasis in metabolic disease. Expected final online publication date for the Annual Review of Medicine, Volume 73 is January 2022. Please see for revised estimates.

RevDate: 2021-10-22

Schlender J, Behrens F, McParland V, et al (2021)

Bacterial metabolites and cardiovascular risk in children with chronic kidney disease.

Molecular and cellular pediatrics, 8(1):17.

Cardiovascular complications are the major cause of the marked morbidity and mortality associated with chronic kidney disease (CKD). The classical cardiovascular risk factors such as diabetes and hypertension undoubtedly play a role in the development of cardiovascular disease (CVD) in adult CKD patients; however, CVD is just as prominent in children with CKD who do not have these risk factors. Hence, the CKD-specific pathophysiology of CVD remains incompletely understood. In light of this, studying children with CKD presents a unique opportunity to analyze CKD-associated mechanisms of CVD more specifically and could help to unveil novel therapeutic targets.Here, we comprehensively review the interaction of the human gut microbiome and the microbial metabolism of nutrients with host immunity and cardiovascular end-organ damage. The human gut microbiome is evolutionary conditioned and modified throughout life by endogenous factors as well as environmental factors. Chronic diseases, such as CKD, cause significant disruption to the composition and function of the gut microbiome and lead to disease-associated dysbiosis. This dysbiosis and the accompanying loss of biochemical homeostasis in the epithelial cells of the colon can be the result of poor diet (e.g., low-fiber intake), medications, and underlying disease. As a result of dysbiosis, bacteria promoting proteolytic fermentation increase and those for saccharolytic fermentation decrease and the integrity of the gut barrier is perturbed (leaky gut). These changes disrupt local metabolite homeostasis in the gut and decrease productions of the beneficial short-chain fatty acids (SCFAs). Moreover, the enhanced proteolytic fermentation generates unhealthy levels of microbially derived toxic metabolites, which further accumulate in the systemic circulation as a consequence of impaired kidney function. We describe possible mechanisms involved in the increased systemic inflammation in CKD that is associated with the combined effect of SCFA deficiency and accumulation of uremic toxins. In the future, a more comprehensive and mechanistic understanding of the gut-kidney-heart interaction, mediated largely by immune dysregulation and inflammation, might allow us to target the gut microbiome more specifically in order to attenuate CKD-associated comorbidities.

RevDate: 2021-10-22

Biassoni R, Di Marco E, Squillario M, et al (2021)

Pathways and microbiome modifications related to surgery and enterocolitis in Hirschsprung disease.

Pediatric surgery international [Epub ahead of print].

BACKGROUND: Hirschsprung disease (HSCR) is a congenital anomaly of the enteric nervous system. Abnormal microbiome composition was reported in HSCR patients. In this study, we addressed and analyzed microbiome modifications with relation tosurgery and HSCR associated enterocolitis (HAEC).

METHODS: The faecal microbiome of 31 HSCR patients (overall 64 samples) was analyzed. HAEC was diagnosed and classified according to a combination of Pastor's and Elhalabi's criteria. Stool samples were analyzed by 16S sequencing (7 out of 9 polymorphic regions). Compositional and relative abundance profiles, as well as the functional potentials of the microbial community, were analyzed with the marker gene sequencing profiles using PICRUSt.

RESULTS: The relative abundance of Bacteroidetes showed a severe decrease with slow recovery after surgery. Conversely, Proteobacteria transiently increased their abundance. Noteworthy, a strong linkage has been found between Proteobacteria descendants and HAEC occurrences. The inferred functional analysis indicated that virulence factors and fimbriae or pili might be associated with HAEC.

CONCLUSIONS: Our study, addressing microbiome dynamics, demonstrated relevant changes after surgical manipulation. Alpha-diversity analyses indicated that surgery deeply affects microbiome composition. Proteobacteria and Enterobacteriaceae seem to play a pivotal role in HAEC occurrences. Several virulence factors, such as fimbriae or pili, might explain the HAEC-predisposing potential of selected microbiomes. These results suggest some innovative therapeutic approaches that deserve to be tested in appropriate clinical trials.

RevDate: 2021-10-22

Pärnänen KMM, Hultman J, Markkanen M, et al (2021)

Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load.

The American journal of clinical nutrition pii:6408461 [Epub ahead of print].

BACKGROUND: Infants are at a high risk of acquiring fatal infections, and their treatment relies on functioning antibiotics. Antibiotic resistance genes (ARGs) are present in high numbers in antibiotic-naive infants' gut microbiomes, and infant mortality caused by resistant infections is high. The role of antibiotics in shaping the infant resistome has been studied, but there is limited knowledge on other factors which affect the antibiotic resistance burden of the infant gut.

OBJECTIVES: Our objectives were to determine the impact of early exposure to formula on the ARG load in neonates and infants born either pre- or full-term. Our hypotheses were that diet causes a selective pressure that influences the microbial community of the infant gut, and formula exposure would increase the abundance of taxa that carry ARGs.

DESIGN: Cross-sectionally sampled gut metagenomes of 46 neonates were used to build a generalized linear model to determine the impact of diet on ARG loads in neonates. The model was cross-validated using neonate metagenomes gathered from public databases using our custom statistical pipeline for cross-validation.

RESULTS: Formula-fed neonates had higher relative abundances of opportunistic pathogens such as Staphylococcus aureus, Staphylococcus epidermidis, Klebsiella pneumoniae, Klebsiella oxytoca, and Clostridioides difficile. The relative abundance of ARGs carried by gut bacteria was 69% higher in the formula receiving group (fold change 1.69, (95% CI 1.12, 2.55), P = 0.013, n = 180) compared to exclusively human milk-fed infants. The formula-fed infants also had significantly less typical infant bacteria such as bifidobacteria that have potential health benefits.

CONCLUSIONS: The novel finding that formula exposure is correlated with a higher neonatal ARG burden lays the foundation that clinicians should consider feeding mode in addition to antibiotic use during the first months of life to minimize the proliferation of antibiotic-resistant gut bacteria in infants.Clinical trial registry number: The Institutional Review Board of Pennsylvania State University, USA (IRB #35925) approved the study.

RevDate: 2021-10-22

Rico JE, Sandri EC, Sarmiento AC, et al (2021)

Modulation of Plasma and Milk Sphingolipids in Dairy Cows Fed High-Starch Diets.

Metabolites, 11(10): pii:metabo11100711.

Bovine milk is a significant source of sphingolipids, dietary compounds that can exert anti-inflammatory actions, and which can modulate the host's microbiome. Because sphingolipid synthesis can be modified by diet, we hypothesized that dietary conditions which reduced FFA availability may result in reduced sphingolipid synthesis. Twelve ruminally cannulated cows (120 ± 52 DIM; 35.5 ± 8.9 kg of milk/d; mean ± SD) were randomly assigned to treatment in a crossover design with 21-d periods. Treatments were (1) High starch (HS), (2) Control. The HS diet contained 29% starch, 24% NDF, and 2.8% fatty acids (FA), whereas the Control diet contained 20% starch, 31% NDF, and 2.3% FA. Plasma and milk samples were obtained on d 21 of each period and sphingolipids were quantified using targeted metabolomics. Univariate and multivariate analyses of generalized log-transformed and Pareto-scaled data included ANOVA (fixed effects of treatment) and discriminant analysis. The lipidomics analysis detected 71 sphingolipids across plasma and milk fat, including sphinganines (n = 3), dihydro-ceramides (n = 8), ceramides (Cer; n = 15), sphingomyelins (SM; n = 17), and glycosylated ceramides (n = 28). Followed by Cer, SM were the most abundant sphingolipids detected in milk and plasma, with a preponderance of 16:0-, 23:0-, and 24:0-carbon sidechains. Although no effects of HS diets were observed on plasma sphingolipids, we detected consistent reductions in the concentrations of several milk Cer (e.g., 22:0- and 24:0-Cer) and SM (17:0- and 23:0-SM) in response to HS. Discriminant analysis revealed distinct metabolite separation of HS and Control groups, with several Cer and SM being distinctively predictive of dietary treatment. We conclude that HS diets can reduce the secretion of milk Cer and SM, even in the absence of changes in circulating sphingolipids.

RevDate: 2021-10-22

Li J, Xu R, Zong L, et al (2021)

Dynamic Evolution and Correlation between Metabolites and Microorganisms during Manufacturing Process and Storage of Fu Brick Tea.

Metabolites, 11(10): pii:metabo11100703.

Fu brick tea (FBT) is one of the major brands of dark tea. Microbial fermentation is considered the key step in the development of the special characteristics of FBT. The systemic corelationship of the microbiome and metabolomics during manufacture of Fu brick tea is not fully understood. In this study, we comprehensively explored the microbiome and metabolite dynamic evolution during the FBT manufacturing processes, and revealed decisive factors for the quality and safety of FBT based on the grouped methods of metabolomics combined with biochemical measurements, microbiome sequencing combined with quantitative polymerase chain reaction (PCR), and multiplex analysis. Both the microbiome and quantitative PCR showed that fungi displayed concentrated distribution characteristics in the primary dark tea samples, while bacterial richness increased during the flowering processes and ripening period. All microorganism species, as well as dominant fungi and bacteria, were identified in the distinct processes periods. A total of 178 metabolites were identified, and 34 of them were characterized as critical metabolites responsible for metabolic changes caused by the corresponding processes. Metabolic analysis showed that most metabolites were decreased during the FBT manufacturing processes, with the exception of gallic acid. Multivariate analysis verified that the critical metabolites were correlated with specific dominant microbial species. All the top fungal species except unclassified_g_ Aspergillus showed positive correlations with six critical metabolites (L-The, epigallocatechin (EGC), Gln, tea polyphenol (TP), tea polysaccharides (TPs) and caffeine). Five of the top bacteria species (Cronobacter, Klebsiella, Pantoea, Pluralibacter, and unclassified_ f_Entero-bacteriaceae) showed positive correlations with epigallocatechins and tea polyphenols, while the other 11 top bacterial species correlated negatively with all the critical metabolites. The content of amino acids, tea polyphenols, tea polysaccharides, and flavonoids was reduced during microbial fermentation. In conclusion, our results reveal that microbial composition is the critical factor in changing the metabolic profile of FBT. This discovery provides a theoretical basis for improving the quality of FBT and enhancing its safety.

RevDate: 2021-10-22

Hoen AG, Coker MO, Madan JC, et al (2021)

Association of Cesarean Delivery and Formula Supplementation with the Stool Metabolome of 6-Week-Old Infants.

Metabolites, 11(10): pii:metabo11100702.

Cesarean delivery and formula feeding have both been implicated as important factors associated with perturbations to the infant gut microbiome. To investigate the functional metabolic response of the infant gut microbial milieu to these factors, we profiled the stool metabolomes of 121 infants from a US pregnancy cohort study at approximately 6 weeks of life and evaluated associations with delivery mode and feeding method. Multivariate analysis of six-week stool metabolomic profiles indicated discrimination by both delivery mode and diet. For diet, exclusively breast-fed infants exhibited metabolomic profiles that were distinct from both exclusively formula-fed and combination-fed infants, which were relatively more similar to each other in metabolomic profile. We also identified individual metabolites that were important for differentiating delivery mode groups and feeding groups and metabolic pathways related to delivery mode and feeding type. We conclude based on previous work and this current study that the microbial communities colonizing the gastrointestinal tracts of infants are not only taxonomically, but also functionally distinct when compared according to delivery mode and feeding groups. Further, different sets of metabolites and metabolic pathways define delivery mode and diet metabotypes.

RevDate: 2021-10-22

Thomas SP, JM Denu (2021)

Short-chain fatty acids activate acetyltransferase p300.

eLife, 10: pii:72171 [Epub ahead of print].

Short-chain fatty acids (SCFAs) acetate, propionate, and butyrate are produced in large quantities by the gut microbiome and contribute to a wide array of physiological processes. While the underlying mechanisms are largely unknown, many effects of SCFAs have been traced to changes in the cell's epigenetic state. Here, we systematically investigate how SCFAs alter the epigenome. Using quantitative proteomics of histone modification states, we identified rapid and sustained increases in histone acetylation after addition of butyrate or propionate, but not acetate. While decades of prior observations would have suggested that hyperacetylation induced by SCFAs are attributed to inhibition of histone deacetylases (HDACs), we found that propionate and butyrate instead activate the acetyltransferase p300. Propionate and butyrate are rapidly converted to the corresponding acyl-CoAs which are then used by p300 to catalyze auto-acylation of the autoinhibitory loop, activating the enzyme for histone/protein acetylation. This data challenges the long-held belief that SCFAs mainly regulate chromatin by inhibiting HDACs, and instead reveals a previously unknown mechanism of HAT activation that can explain how an influx of low levels of SCFAs alters global chromatin states.

RevDate: 2021-10-22

Oakley BB, Melgarejo T, Bloom PH, et al (2021)

Emerging Pathogenic Gammaproteobacteria Wohlfahrtiimonas chitiniclastica and Ignatzschineria Species in a Turkey Vulture (Cathartes aura).

Journal of avian medicine and surgery, 35(3):280-289.

New World vultures, such as turkey vultures (Cathartes aura), are obligate scavengers with large geographic ranges. In a preliminary characterization of the turkey vulture (TV) gastrointestinal microbiome in Southern California, we identified 2 recently described emerging bacterial pathogens not previously known to be associated with this avian species. High-throughput sequencing of broad-range 16S rRNA gene amplicons revealed sequences from TV cloacal swabs that were related closest to Wohlfahrtiimonas chitiniclastica and Ignatzschineria species, both Gammaproteobacteria considered by the United States Centers for Disease Control and Prevention as emerging zoonotic pathogens. None of these bacterial sequence types have been previously identified from samples obtained from the turkey vulture gastrointestinal microbiome. With the use of bioinformatics workflows previously established by our research group, we designed specific and sensitive polymerase chain reaction primer sets that represent novel diagnostic assays for the genera Wohlfahrtiimonas and Ignatzschineria. These primer sets were validated by Sanger sequence confirmation from complex TV samples. Because the genera Wohlfahrtiimonas and Ignatzschineria are both known to have dipteran hosts, the molecular diagnostic tools we present here should be useful for better understanding the role of flies, vultures, and other scavengers in the ecology and epidemiology of the genera Wohlfahrtiimonas and Ignatzschineria from a One Health perspective.

RevDate: 2021-10-22

Ma C, He J, Lai L, et al (2021)

Intestinal microbiome and metabolome analyses reveal metabolic disorders in the early stage of renal transplantation.

Molecular omics [Epub ahead of print].

Renal transplantation is the most effective treatment for end-stage renal disease, but the long-term prognosis of organs after transplantation is not ideal. In recent years, the importance of gut microbes and metabolites in the study of disease mechanisms has gradually received attention. However, the coordination between gut microbes and the metabolism of renal transplant patients needs further study. We integrated 16s sequencing and metabolomics data to describe the changes in the serum and fecal metabolites of renal transplant patients. Our data revealed that the gut microbial diversity decreased and the relative abundance of many bacteria, such as Enterococcus and Streptococcus, significantly changed after transplantation. In addition, a large number of amino acids and peptides in serum and feces significantly changed, suggesting an abnormal amino acid metabolism after transplantation. Spearman's correlation analysis revealed the changes in the co-metabolism pattern between gut microbes and the host metabolism after transplantation. Furthermore, Enterococcus was found to be correlated with renal functions and metabolites reflecting renal damage. This study provides potential gut microbes and metabolites impacting renal health, which helps in understanding the renal damage in patients with kidney transplantation.

RevDate: 2021-10-22

Kadurina M, Kazandjieva J, G Bocheva (2021)

Immunopathogenesis and management of polymorphic light eruption.

Dermatologic therapy [Epub ahead of print].

Polymorphic light eruption (PLE) is the most common immunologically-mediated photodermatosis, demonstrating many abnormalities caused by critical failure of UV-induced immunosuppression. The unique expression of antimicrobial peptides (AMPs) in PLE, which is most likely determined by alteration of microbiome components upon UV exposure, implicates their possible triggering role and pathogenic significance in the eruption. The review aims to clarify current knowledge regarding the immunological disturbances corelated withPLE that serve a base for better understanding of molecular pathogenesis of the disease and development of new therapeutic strategies. Preventive treatment with broad spectrum suncreens and sunscreens containing DNA repair enzymes, as well as natural photohardening with graduate exposure to sunlight in early spring could be sufficient in milder cases. Antioxidants and topical calcipotriol are promising approach for adjuvant prevention. Phototherapy, mainly with narrow band UVB, is more appropriate method in severe cases of the disease. The established treatment options for PLE include local and systemic glucocorticoids, systemic non-sedative antihistamines for itch relief, and rarely, immunosuppressive drugs in the refractory cases. Like medical photohardening, afamelanotide has the potential of photoprotection by inducing a melanization of the skin. Afamelanotide is believed to be a possible new treatment option for very severe and refractory cases of PLE. Targeting the main pruritogenic cytokine, IL-31, opens a new road for the development of novel therapeutic approaches to combat moderate and severe itching in cases of PLE with intense pruritus. This article is protected by copyright. All rights reserved.

RevDate: 2021-10-22

Mitchell LK, PSW Davies (2021)

Pre- and probiotics in the management of children with autism and gut issues: a review of the current evidence.

European journal of clinical nutrition [Epub ahead of print].

Manipulation of the gut microbiome offers a promising treatment option for children with autism spectrum disorder (ASD) for whom functional gastrointestinal disorders (FGIDs) are a common comorbidity. Both ASD and FGIDs have been linked to dysfunction of the microbiome-gut-brain (MGB) axis. Dysfunction of this bidirectional network has the ability to impact multiple host processes including gastrointestinal (GI) function, mood and behaviour. Prebiotic and probiotic supplementation aims to produce beneficial shifts within the gut environment, resulting in favourable changes to microbial metabolite production and gastrointestinal function. The aim of this review is to investigate the gut microbiome as a therapeutic target for children with ASD. Evidence for the utility of prebiotics, probiotics or synbiotics (i.e., prebiotic + probiotic) among this cohort is examined. Electronic databases (PubMed, Web of Science, Medline and were searched using keywords or phrases to review the literature from 1 January 2010 to 30 October 2020. Findings suggest limited, but preliminary evidence of efficacy in relieving GI distress, improving ASD-associated behaviours, altering microbiota composition, and reducing inflammatory potential.

RevDate: 2021-10-22

Kingwell K (2021)

A microbiome short circuit in prostate cancer.

RevDate: 2021-10-22

Franasiak JM, Alecsandru D, Forman EJ, et al (2021)

A review of the pathophysiology of recurrent implantation failure.

Fertility and sterility pii:S0015-0282(21)02052-5 [Epub ahead of print].

Implantation is a critical step in human reproduction. The success of this step is dependent on a competent blastocyst, receptive endometrium, and successful cross talk between the embryonic and maternal interfaces. Recurrent implantation failure is the lack of implantation after the transfer of several embryo transfers. As the success of in vitro fertilization has increased and failures have become more unacceptable for patients and providers, the literature on recurrent implantation failure has increased. While this clinical phenomenon is often encountered, there is not a universally agreed-on definition-something addressed in an earlier portion of this Views and Reviews. Implantation failure can result from several different factors. In this review, we discuss factors including the maternal immune system, genetics of the embryo and parents, anatomic factors, hematologic factors, reproductive tract microbiome, and endocrine milieu, which factors into embryo and endometrial synchrony. These potential causes are at various stages of research and not all have clear implications or immediately apparent treatment.

RevDate: 2021-10-22

Sun M, Bao W, Huang C, et al (2021)

A Novel Probiotic Formula, BIOCG, Protects Against Alzheimer's-Related Cognitive Deficits via Regulation of Dendritic Spine Dynamics.

Current Alzheimer research pii:CAR-EPUB-118530 [Epub ahead of print].

BACKGROUND: The brain-gut-microbiome axis has emerged as an important pathway through which perturbations in the gut and/or microbial microenvironment can impact neurological function. Such alterations have been implicated in a variety of neuropsychiatric disorders, includ- ing depression, anxiety, and Alzheimer's Disease (AD) and the use of probiotics as therapy for th- ese diseases remains promising. However, the mechanisms underlying the gut microenvironment's influence on disease pathogenesis and therapy remain unclear.

OBJECTIVE: The objective of this study is to investigate the effect of a novel probiotic formula, BIOCG, on cognitive function and pathobiological mechanisms, including amyloid processing and dendritic spine dynamics, in a mouse model of AD.

METHODS: BIOCG was administered for 3 months to 3xTg or 3xTg; Thy1-YFP AD mice and func- tional outcomes were assessed via behavioral testing and electrophysiology. Mechanisms relevant to AD pathogenesis including dendritic spine morphology and turnover, Amyloid Precursor Pro- tein (APP) processing and microglial phenotype were also evaluated. Finally, we sequenced fecal samples following probiotic treatment to assess the impact on gut microbial composition and corre- late the changes with the above described measures.

RESULTS: Mice treated with BIOCG demonstrated preserved cognitive abilities and stronger Long- Term Potentiation (LTP), spontaneous Excitatory Postsynaptic Currents (sEPSC), and glutamate-in- duced LTPs, indicative of functional and electrophysiological effects. Moreover, we observed atten- uated AD pathogenesis, including reduced Amyloid Beta (Aβ) burden, as well as more mature den- dritic spines in the BIOCG-treated. Our finding of changes in microglial number and phenotype in the treatment group suggests that this formulation may mediate its effects via attenuation of neu- roinflammation. Sequencing data confirmed that the gut microbiome in treated mice was more varied and harbored a greater proportion of "beneficial" bacteria.

CONCLUSION: Overall, our results indicate that treatment with BIOCG enhances microbial diversity and, through gut-brain axis interactions, attenuates neuroinflammation to produce histologic and functional improvement in AD pathogenesis.

RevDate: 2021-10-22

Wu C, Jeong MY, Kim JY, et al (2021)

Activation of ectopic olfactory receptor 544 induces GLP-1 secretion and regulates gut inflammation.

Gut microbes, 13(1):1987782.

Olfactory receptors are ectopically expressed in extra-nasal tissues. The gut is constantly exposed to high levels of odorants where ectopic olfactory receptors may play critical roles. Activation of ectopic olfactory receptor 544 (Olfr544) by azelaic acid (AzA), an Olfr544 ligand, reduces adiposity in mice fed a high-fat diet (HFD) by regulating fuel preference to fats. Herein, we investigated the novel function of Olfr544 in the gut. In GLUTag cells, AzA induces the cAMP-PKA-CREB signaling axis and increases the secretion of GLP-1, an enteroendocrine hormone with anti-obesity effects. In mice fed a HFD and orally administered AzA, GLP-1 plasma levels were elevated in mice. The induction of GLP-1 secretion was negated in cells with Olfr544 gene knockdown and in Olfr544-deficient mice. Gut microbiome analysis revealed that AzA increased the levels of Bacteroides acidifaciens and microbiota associated with antioxidant pathways. In fecal metabolomics analysis, the levels of succinate and trehalose, metabolites correlated with a lean phenotype, were elevated by AzA. The function of Olfr544 in gut inflammation, a key feature in obesity, was further investigated. In RNA sequencing analysis, AzA suppressed LPS-induced activation of inflammatory pathways and reduced TNF-α and IL-6 expression, thereby improving intestinal permeability. The effects of AzA on the gut metabolome, microbiome, and colon inflammation were abrogated in Olfr544-KO mice. These results collectively demonstrated that activation of Olfr544 by AzA in the gut exerts multiple effects by regulating GLP-1 secretion, gut microbiome and metabolites, and colonic inflammation in anti-obesogenic phenotypes and, thus, may be applied for obesity therapeutics.

RevDate: 2021-10-21

Radhakrishnan NA, Ravi A, Joseph BJ, et al (2021)

Phenazine 1-carboxylic acid Producing Seed Harbored Endophytic Bacteria from Cultivated Rice Variety of Kerala and Its Broad Range Antagonism to Diverse Plant Pathogens.

Probiotics and antimicrobial proteins [Epub ahead of print].

Endophytic microorganisms residing within the diverse parts of plants play a significant role in the plant growth and defense response. In the case of the vertically transmitted seed-borne endophytes, they form the promising initiator of the juvenile plant microbiome by supporting the growth and establishment of the seedlings. Hence, the current study emphasizes the isolation and screening of plant beneficial traits of seed endophytes from the cultivated rice variety Jyothi of Kerala, India. Among the 14 bacterial endophytes obtained in the study, the isolate S3 was found to have promising activity against the phytopathogens such as Fusarium oxysporum, Pythium aphanidermatum, Pythium myriotylum, Phytophthora infestans, Rhizoctonia solani, Colletotrichum acutatum, and Sclerotium rolfsii. The isolate S3 was further identified as Paenibacillus polymyxa by the 16S rRNA-based sequence analysis. Furthermore, the isolate was confirmed for its capability for hydrogen cyanide (HCN) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, biofilm formation, and nitrogen fixation. The P. polymyxa S3 was also found to have the potential to provide post-harvest protection to the rice kernels from Sclerotium rolfsii. By the LC-MS/MS analysis, the organism was confirmed for the production of phenazine 1-carboxylic acid which could be the prime chemical basis of its antifungal activity. The in vivo plant growth evaluation has also demonstrated the root length enhancement effect of P. polymyxa S3 in Vigna unguiculata. Here, the root length of P. polymyxa S3-treated plant was enhanced to 12.44 ± 0.58223 cm when compared with distilled water control (10.261 ± 0.38151 cm) and the observed change was statistically significant as per the analysis of variance at P value less than 0.05. Based on all these properties, the isolated P. polymyxa S3 could be considered as a promising agent to be used for the development of competent plant probiotic formulations.

RevDate: 2021-10-21

Wang D, Du Y, Huang S, et al (2021)

Combined supplementation of sodium humate and glutamine reduced diarrhea incidence of weaned calves by intestinal microbiota and metabolites changes.

Journal of animal science pii:6407716 [Epub ahead of print].

This study was conducted to investigate the effects of combined supplementation of sodium humate (HNa) and glutamine (Gln) on growth performance, diarrhea incidence, serum parameters, intestinal microbiome, and metabolites of weaned calves. In Exp. 1, 40 calves were randomly assigned to 4 treatments (1) NC (negative control, basal diet), (2) 1% H+1% G (basal diet extra orally gavaged with 1 g of HNa and 1 g of Gln daily), (3) 3% H+1% G (basal diet extra orally gavaged with 3 g of HNa and 1 g of Gln daily), and (4) 5% H+1% G (basal diet extra orally gavaged with 5 g of HNa and 1 g of Gln daily). The HNa and Gln were together mixed with 100 mL of milk replacer (51-58 days of age) or water (59-72 days of age) and orally administrated to each calf from a bottle before morning feeding. In a 21-day trial, calves on the 5% HNa+1% Gln group had higher (P < 0.05) average daily gain (ADG) and lower (P < 0.05) diarrhea incidence than those in the control group. In Exp. 2, 20 calves were randomly assigned to 2 treatments fed with a basal diet and a basal diet supplemented with 100 mL of 5% HNa+1% Gln. In a 21-day trial, calves supplemented with HNa and Gln had higher (P < 0.05) ADG, IgG concentration and glutathione peroxidase (GSH-Px) and total antioxidant capacity (T-AOC) activities in the serum, but lower (P < 0.05) diarrhea incidence, as well as serum diamine oxidase (DAO), D-isomer of lactic acid (D-lac), tumor necrosis factor-α (TNF-α), and malondialdehyde (MDA) concentrations compared to control group. Results of intestinal microbiota indicated that supplementation with HNa and Gln significantly increased (P < 0.05) the abundance of intestinal beneficial microbiota. Moreover, supplementation with HNa and Gln altered 18 metabolites and enriched 6 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in weaned calves. In conclusion, combined supplementation with HNa and Gln could decrease diarrhea incidence of weaned calves via altering intestinal microbial ecology and metabolism profile.

RevDate: 2021-10-21

Gregory AL, Pensinger DA, AJ Hryckowian (2021)

A short chain fatty acid-centric view of Clostridioides difficile pathogenesis.

PLoS pathogens, 17(10):e1009959 pii:PPATHOGENS-D-21-01381.

Clostridioides difficile is an opportunistic diarrheal pathogen responsible for significant morbidity and mortality worldwide. A disrupted (dysbiotic) gut microbiome, commonly engendered by antibiotic treatment, is the primary risk factor for C. difficile infection, highlighting that C. difficile-microbiome interactions are critical for determining the fitness of this pathogen. Here, we review short chain fatty acids (SCFAs): a major class of metabolites present in the gut, their production by the gut microbiome, and their impacts on the biology of the host and of C. difficile. We use these observations to illustrate a conceptual model whereby C. difficile senses and responds to SCFAs as a marker of a healthy gut and tunes its virulence accordingly in order to maintain dysbiosis. Future work to learn the molecular mechanisms and genetic circuitry underlying the relationships between C. difficile and SCFAs will help to identify precision approaches, distinct from antibiotics and fecal transplant, for mitigating disease caused by C. difficile and will inform similar investigations into other gastrointestinal pathogens.

RevDate: 2021-10-21

Torre E, Sola D, Caramaschi A, et al (2021)

A Pilot Study on Clinical Scores, Immune Cell Modulation, and Microbiota Composition in Allergic Patients with Rhinitis and Asthma Treated with a Probiotic Preparation.

International archives of allergy and immunology pii:000518952 [Epub ahead of print].

BACKGROUND: Specific drugs and/or immunotherapies are widely used to treat allergies, but drug-induced adverse effects recently led to explore new additional strategies. We studied whether a probiotic preparation (iPROB®; Anallergo SpA, Florence, Italy) is effective in allergic patients and the mechanisms underlying clinical outcomes.

METHODS: Eligible patients (n = 28), all suffering from allergic rhinitis with/without bronchial asthma, were consecutively recruited at the Allergology Medical Unit (Novara, Italy) and treated with this probiotic. From each patient, we collected blood and stool samples at the baseline, after 60 days of probiotic supplementation, and after 60 days from probiotic discontinuation. In each blood sample, the percentage of hematopoietic stem cells, eosinophils, and basophils was measured by FACS. To analyze stool microbiota composition, genomic DNA was extracted, bacterial 16S DNA libraries sequenced by Illumina platform (Miseq), and raw sequences processed. Generated data were statistically analyzed.

RESULTS: Probiotic-treated patients showed a significant decrease in Average Rhinitis Total Symptom Score (d = -10.5714), and Visual Analog Scale (d = -2.00) clinical indices, as well as important improvements in quality of life. In whole blood, a significant reduction in the percentage of activated eosinophils and basophils was determined, and this effect persisted after specific cell stimulation. Consistently, the serum levels of IL-4 and IL-5 decreased after probiotic treatment, suggesting a reduction in the Th2 cytokine profile. In addition, microbiome genomic analysis (n = 6) showed an increase in microbiome biodiversity, which positively correlates with clinical and cellular data.

CONCLUSION: Present study suggests that iPROB® preparation has clinical/biological properties to be a valid add-on supplementation in allergic patients with asthma and rhinitis.

RevDate: 2021-10-21

Quintela-Baluja M, Frigon D, Abouelnaga M, et al (2021)

Dynamics of integron structures across a wastewater network - Implications to resistance gene transfer.

Water research, 206:117720 pii:S0043-1354(21)00914-3 [Epub ahead of print].

Class 1 and other integrons are common in wastewater networks, often being associated with antibiotic resistance genes (ARGs). However, the importance of different integron structures in ARG transfer within wastewater systems has only been implied, especially between community and hospital sources, among wastewater treatment plant compartments, and in receiving waters. This uncertainty is partly because current clinical class 1 integron qPCR assays (i.e., that target human-impacted structures, i.e., clintI1) poorly delineate clintI1 from non-impacted class 1 integron structures. They also say nothing about their ARG content. To fill these technical gaps, new real-time qPCR assays were developed for "impacted" class 1 structures (called aint1; i.e., anthropogenic class 1 integrons) and empty aint1 structures (i.e., carry no ARGs; called eaint1). The new assays and other integron assays then were used to examine integron dynamics across a wastewater network. 16S metagenomic sequencing also was performed to characterise associated microbiomes. aint1 abundances per bacterial cell were about 10 times greater in hospital wastewaters compared with other compartments, suggesting aint1 enrichment with ARGs in hospital sources. Conversely, the relative abundance of eaint1 structures were over double in recycled activated sludge compared with other compartments, except receiving waters (RAS; ∼30% of RAS class 1 structures did not carry ARGs). Microbiome analysis showed that human-associated bacterial taxa with mobile integrons also differed in RAS and river sediments. Further, class 1 integrons in RAS bacteria appear to have released ARGs, whereas hospital bacteria have accumulated ARGs. Results show that quantifying integron dynamics can help explain where ARG transfer occurs in wastewater networks, and should be considered in future studies on antibiotic resistance in the environment.

RevDate: 2021-10-21

Belkhou C, Tadeo RT, Bacigalupe R, et al (2021)

Treponema peruense sp. nov., a commensal spirochaete isolated from human faeces.

International journal of systematic and evolutionary microbiology, 71(10):.

A Gram-stain-negative, obligatory anaerobic spirochaete (RCC2812T) was isolated from a faecal sample obtained from an individual residing in a remote Amazonian community in Peru. The bacterium showed highest 16S rRNA gene sequence similarity to the pig intestinal spirochete Treponema succinifaciens (89.48 %). Average nucleotide identity values between strain RCC2812T and all available Treponema genomes from validated type strains were all <73 %, thus clearly lower than the species delineation threshold. The DNA G+C content of RCC2812T was 41.24 mol%. Phenotypic characterization using the API-ZYM and API 20A systems confirmed the divergent position of this bacterium within the genus Treponema. Strain RCC2812T could be differentiated from the phylogenetically most closely related T. succinifaciens by the presence of alkaline phosphatase and α -glucosidase activities. Unlike T. succinifaciens, strain RCC2812T grew equally well with or without serum. Strain RCC2812T is the first commensal Treponema isolated from the human faecal microbiota of remote populations, and based on the collected data represents a novel Treponema species for which the name Treponema peruense sp. nov. is proposed. The type strain is RCC2812T (=LMG 31794T=CIP 111910T).

RevDate: 2021-10-21

Liu TFD, Philippou E, Kolokotroni O, et al (2021)

Gut and airway microbiota and their role in COVID-19 infection and pathogenesis: a scoping review.

Infection [Epub ahead of print].

BACKGROUND: The SARS-CoV-2 virus is responsible for the COVID-19 pandemic. Researchers have been studying the pathogenesis of the virus with the aim to improve our current diagnosis and management strategies. The microbiota have been proposed to play a key role in the pathogenesis of the disease.

PURPOSE: To investigate and report on the current available evidence on any associations between the gut and/or airway microbiota and the pathogenesis of COVID-19.

METHODS: Using a predefined protocol in compliance with the PRISMA guidelines, a search was conducted on MEDLINE, Science Direct, DOAJ and Cochrane databases on primary research studies assessing the association between COVID-19 infection and the gut and/or airway microbiota.

RESULTS: Twenty-two studies were included in the current review; nineteen studies concluded an association between the gut and/or airway dysbiosis and SARS-CoV-2, while 3 studies failed to observe a significant association between the airway microbiome and SARS-CoV-2 infection. Specifically, most studies reported a decrease in microbial diversity and therefore development of intestinal dysbiosis in COVID-19-positive patients compared to healthy controls as well as a possible association between increased intestinal dysbiosis and disease severity.

CONCLUSION: During infection with SARS-CoV-2, there are significant changes in the composition of the gut and airway microbiota. Furthermore, the gut microbiota may have a more important role than the airway microbiota in COVID-19 infection. In the future, studies should be more carefully designed to derive more conclusive evidence on the role of the gut and airway microbiota following infection with SARS-CoV-2 which will lead to the formulation of better management strategies in combating COVID-19.

RevDate: 2021-10-21

Carbajal-Valenzuela IA, Muñoz-Sanchez AH, Hernández-Hernández J, et al (2021)

Microbial Diversity in Cultivated and Feral Vanilla Vanilla planifolia Orchids Affected by Stem and Rot Disease.

Microbial ecology [Epub ahead of print].

The worldwide production of vanilla, a native orchid from Mexico, is greatly affected by stem and root rot disease (SRD), typically associated with Fusarium oxysporum fungi. We hypothesized that the presence of Fusarium species in vanilla is not sufficient for the plant to express symptoms of the disease. We described the taxonomic composition of endophytic microbiomes in symptomatic and asymptomatic vanilla plants using 16S and ITS rDNA metabarcoding, and ITS Sanger sequences generated from fungal isolates. We compared the bacterial and fungal diversity in vanilla plants from a long-term plantation, and from feral plants found near abandoned plantations that did not present SRD symptoms. No significant differences were found in the species richness of the bacterial and fungal microbiome among feral, or asymptomatic and symptomatic cultivated vanilla. However, significant differences were detected in both fungal and bacterial diversity from different organs in the same plant, with roots being more diverse than stems. We found that Proteobacteria and Actinobacteria, as well as the fungal families Nectriaceae and Xylariaceae, constitute the core of the vanilla microbiome that inhabits the root and stem of both cultivated and feral plants. Our work provides information on the microbial diversity associated to root and stem rot in vanilla and lays the groundwork for a better understanding of the role of the microbiome in vanilla fungal diseases.

RevDate: 2021-10-21

Neely WJ, Greenspan SE, Stahl LM, et al (2021)

Habitat Disturbance Linked with Host Microbiome Dispersion and Bd Dynamics in Temperate Amphibians.

Microbial ecology [Epub ahead of print].

Anthropogenic habitat disturbances can dramatically alter ecological community interactions, including host-pathogen dynamics. Recent work has highlighted the potential for habitat disturbances to alter host-associated microbial communities, but the associations between anthropogenic disturbance, host microbiomes, and pathogens are unresolved. Amphibian skin microbial communities are particularly responsive to factors like temperature, physiochemistry, pathogen infection, and environmental microbial reservoirs. Through a field survey on wild populations of Acris crepitans (Hylidae) and Lithobates catesbeianus (Ranidae), we assessed the effects of habitat disturbance and connectivity on environmental bacterial reservoirs, Batrachochytrium dendrobatidis (Bd) infection, and skin microbiome composition. We found higher measures of microbiome dispersion (a measure of community variability) in A. crepitans from more disturbed ponds, supporting the hypothesis that disturbance increases stochasticity in biological communities. We also found that habitat disturbance limited microbiome similarity between locations for both species, suggesting greater isolation of bacterial assemblages in more disturbed areas. Higher disturbance was associated with lower Bd prevalence for A. crepitans, which could signify suboptimal microclimates for Bd in disturbed habitats. Combined, our findings show that reduced microbiome stability stemming from habitat disturbance could compromise population health, even in the absence of pathogenic infection.

RevDate: 2021-10-21

Wang K, Sun G, Conlon MA, et al (2021)

Editorial: Dietary Polyphenols for Improving Gut Health: Volume 1.

Frontiers in nutrition, 8:760917.

RevDate: 2021-10-22

Sun Z, Huang C, Shi Y, et al (2021)

Distinct Bile Acid Profiles in Patients With Chronic Hepatitis B Virus Infection Reveal Metabolic Interplay Between Host, Virus and Gut Microbiome.

Frontiers in medicine, 8:708495.

Hepatitis B virus (HBV) can hijack the host bile acids (BAs) metabolic pathway during infection in cell and animal models. Additionally, microbiome was known to play critical role in the enterohepatic cycle of BAs. However, the impact of HBV infection and associated gut microbiota on the BA metabolism in chronic hepatitis B (CHB) patients is unknown. This study aimed to unveil the distinct BA profiles in chronic HBV infection (CHB) patients with no or mild hepatic injury, and to explore the relationship between HBV, microbiome and BA metabolism with clinical implications. Methods: Serum BA profiles were compared between CHB patients with normal ALT (CHB-NALT, n = 92), with abnormal ALT (CHB-AALT, n = 34) and healthy controls (HCs, n = 28) using UPLC-MS measurement. Hepatic gene expression in CHB patients were explored using previously published transcriptomic data. Fecal microbiome was compared between 30 CHB-NALT and 30 HCs using 16S rRNA sequencing, and key microbial function was predicted by PICRUSt analysis. Results: Significant higher percentage of conjugated BAs and primary BAs was found in CHB patients even without apparent liver injury. Combinatory BA features can discriminate CHB patients and HCs with high accuracy (AUC = 0.838). Up-regulation of BA importer Na+ taurocholate co-transporting peptide (NTCP) and down-regulation of bile salt export pump (BSEP) was found in CHB-NALT patients. The microbial diversity and abundance of Lactobacillus, Clostridium, Bifidobacterium were lower in CHB-NALT patients compared to healthy controls. Suppressed microbial bile salt hydrolases (BSH), 7-alpha-hydroxysteroid dehydrogenase (hdhA) and 3-dehydro-bile acid Delta 4, 6-reductase (BaiN) activity were found in CHB-NALT patients. Conclusion: This study provides new insight into the BA metabolism influenced both by HBV infection and associated gut microbiome modulations, and may lead to novel strategy for clinical management for chronic HBV infection.

RevDate: 2021-10-22

Wang TQ, Li LR, Tan CX, et al (2021)

Effect of Electroacupuncture on Gut Microbiota in Participants With Knee Osteoarthritis.

Frontiers in cellular and infection microbiology, 11:597431.

A close relationship between knee osteoarthritis (KOA) and gut microbiota has recently been described. Herein, we aim to investigate the effect of electroacupuncture (EA) on gut microbiota in participants with KOA. We conducted a study of 60 participants with KOA and 30 matched healthy controls (HCs). Sixty participants were allocated to either EA group (n=30) or sham acupuncture (SA) group (n=30). Five obligatory acupoints and three adjunct acupoints were punctured in the EA group. Eight non-acupoints that were separated from conventional acupoints or meridians were used for the SA group. Participants in both groups received 24 sessions within eight weeks. Fecal microbial analyses by 16S ribosomal RNA gene sequencing were carried out after collecting stools at T 0 and T 8 weeks (Four samples with changed defecation habits were excluded). The results showed that both Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) total score (P=0.043) and NRS score (P=0.002) decreased more in EA group than those in SA group. Moreover, EA could reverse more KOA-related bacteria including Bacteroides, [Eubacterium]_hallii_group, Agathobacter and Streptococcus. The number of significantly different genera between KOA patients and HCs were less after EA treatment than that after SA treatment. This meant that EA modified the composition of the gut microbiome, making it closer to healthy people, while not significantly affecting the microbial diversity. Two genera including Agathobacter (P=0.0163), Lachnoclostridium (P=0.0144) were statistically increased than baseline in EA group (paired Wilcoxon rank sum test). After EA treatment, Bacteroides (P=0.0394) was more abundant and Streptococcus (P=0.0306) was significantly reduced in patients who demonstrated adequate response than in those with inadequate response (Wilcoxon rank-sum test). Spearman correlation test between gut microbe and KOA clinical outcomes indicated that Bacteroides and Agathobacter was negatively correlated with NRS score, WOMAC total score, and WOMAC pain, stiffness and pain scores (P<0.001 or 0.05 or 0.01), while Streptococcus was positively correlated with them (P<0.05 or 0.01). Our study suggests that EA contributes to the improvement of KOA and gut microbiota could be a potential therapeutic target.

RevDate: 2021-10-22

Chen P, Chen P, Guo Y, et al (2021)

Interaction Between Chronic Endometritis Caused Endometrial Microbiota Disorder and Endometrial Immune Environment Change in Recurrent Implantation Failure.

Frontiers in immunology, 12:748447.

Objective: To investigate the Interaction between chronic endometritis (CE) caused endometrial microbiota disorder and endometrial immune environment change in recurrent implantation failure (RIF).

Method: Transcriptome sequencing analysis of the endometrial of 112 patients was preform by using High-Throughput Sequencing. The endometrial microbiota of 43 patients was analyzed by using 16s rRNA sequencing technology.

Result: In host endometrium, CD4 T cell and macrophage exhibited significant differences abundance between CE and non-CE patients. The enrichment analysis indicated differentially expressed genes mainly enriched in immune-related functional terms. Phyllobacterium and Sphingomonas were significantly high infiltration in CE patients, and active in pathways related to carbohydrate metabolism and/or fat metabolism. The increased synthesis of lipopolysaccharide, an important immunomodulator, was the result of microbial disorders in the endometrium.

Conclusion: The composition of endometrial microorganisms in CE and non-CE patients were significantly different. Phyllobacterium and Sphingomonas mainly regulated immune cells by interfering with the process of carbohydrate metabolism and/or fat metabolism in the endometrium. CE endometrial microorganisms might regulate Th17 response and the ratio of Th1 to Th17 through lipopolysaccharide (LPS).

RevDate: 2021-10-21

Li M, Pommier T, Yin Y, et al (2021)

Indirect reduction of Ralstonia solanacearum via pathogen helper inhibition.

The ISME journal [Epub ahead of print].

The rhizosphere microbiome forms a first line of defense against soilborne pathogens. To date, most microbiome enhancement strategies have relied on bioaugmentation with antagonistic microorganisms that directly inhibit pathogens. Previous studies have shown that some root-associated bacteria are able to facilitate pathogen growth. We therefore hypothesized that inhibiting such pathogen helpers may help reduce pathogen densities. We examined tripartite interactions between a model pathogen, Ralstonia solanacearum, two model helper strains and a collection of 46 bacterial isolates recovered from the tomato rhizosphere. This system allowed us to examine the importance of direct (effects of rhizobacteria on pathogen growth) and indirect (effects of rhizobacteria on helper growth) pathways affecting pathogen growth. We found that the interaction between rhizosphere isolates and the helper strains was the major determinant of pathogen suppression both in vitro and in vivo. We therefore propose that controlling microbiome composition to prevent the growth of pathogen helpers may become part of sustainable strategies for pathogen control.

RevDate: 2021-10-21

Chen Y, Ma C, Liu L, et al (2021)

Analysis of gut microbiota and metabolites in patients with rheumatoid arthritis and identification of potential biomarkers.

Aging, 13(undefined): pii:203641 [Epub ahead of print].

Rheumatoid arthritis (RA) is an autoimmune disease described by joint destruction, synovitis and pannus formation. The gut microbiota acts as an environmental factor that plays an important role in RA, but little research regarding the etiopathogenic mechanisms of the microbiome in RA has been carried out. We used an integrated approach of 16S rRNA gene sequencing and ultrahigh-performance liquid chromatography-mass spectrometry-based metabolomics to analyze the structure and diversity of the intestinal flora and metabolites of the gut microbiota in RA patients compared with healthy subjects. In this study, α-diversity analysis of the gut microbiota showed that there was no significant difference between the healthy control (HC) and RA groups. However, β-diversity analysis showed that there was a significant difference between the two groups. Further analysis of alteration of the gut microbiota revealed that at the phylum level, the relative abundance of p_Bacteroidetes was significantly decreased in the RA group, while that of Verrucomicrobia and Proteobacteria was significantly increased in the RA group. At the genus level, Bacteroides, Faecalibacterium and some probiotics were decreased in the RA group, while 97 genera, including Lactobacillus, Streptococcus and Akkermansia, were increased in the RA group. Seventy-four differentially abundant metabolites were identified between the HC and RA groups, and we identified two potential biomarkers (9,12-octadecadiynoic acid and 10Z-nonadecenoic acid) in RA.

RevDate: 2021-10-22
CmpDate: 2021-10-22

Keikha M, M Karbalaei (2021)

Probiotics as the live microscopic fighters against Helicobacter pylori gastric infections.

BMC gastroenterology, 21(1):388.

BACKGROUND: Helicobacter pylori (H. pylori) is the causative agent of stomach diseases such as duodenal ulcer and gastric cancer, in this regard incomplete eradication of this bacterium has become to a serious concern. Probiotics are a group of the beneficial bacteria which increase the cure rate of H. pylori infections through various mechanisms such as competitive inhibition, co-aggregation ability, enhancing mucus production, production of bacteriocins, and modulating immune response.

RESULT: In this study, according to the received articles, the anti-H. pylori activities of probiotics were reviewed. Based on studies, administration of standard antibiotic therapy combined with probiotics plays an important role in the effective treatment of H. pylori infection. According to the literature, Lactobacillus casei, Lactobacillus reuteri, Lactobacillus rhamnosus GG, and Saccharomyces boulardii can effectively eradicate H. pylori infection. Our results showed that in addition to decrease gastrointestinal symptoms, probiotics can reduce the side effects of antibiotics (especially diarrhea) by altering the intestinal microbiome.

CONCLUSION: Nevertheless, antagonist activities of probiotics are H. pylori strain-specific. In general, these bacteria can be used for therapeutic purposes such as adjuvant therapy, drug-delivery system, as well as enhancing immune system against H. pylori infection.

RevDate: 2021-10-23

Shealy NG, Yoo W, MX Byndloss (2021)

Colonization resistance: metabolic warfare as a strategy against pathogenic Enterobacteriaceae.

Current opinion in microbiology, 64:82-90 pii:S1369-5274(21)00133-8 [Epub ahead of print].

The intestine is home to a large and complex bacterial ecosystem (microbiota), which performs multiple beneficial functions for the host, including immune education, nutrition, and protection against invasion by enteric pathogens (colonization resistance). The host and microbiome symbiotic interactions occur in part through metabolic crosstalk. Thus, microbiota members have evolved highly diverse metabolic pathways to inhibit pathogen colonization via activation of protective immune responses and nutrient acquisition and utilization. Conversely, pathogenic Enterobacteriaceae actively induce an inflammation-dependent disruption of the gut microbial ecosystem (dysbiosis) to gain a competitive metabolic advantage against the resident microbiota. This review discusses the recent findings on the crucial role of microbiota metabolites in colonization resistance regulation. Additionally, we summarize metabolic mechanisms used by pathogenic Enterobacteriaceae to outcompete commensal microbes and cause disease.

RevDate: 2021-10-23

Bostanghadiri N, Ziaeefar P, Sameni F, et al (2021)

The controversial association of gut and urinary microbiota with kidney stone formation.

Microbial pathogenesis pii:S0882-4010(21)00531-3 [Epub ahead of print].

Nephrolithiasis (kidney stones) is one of the most common chronic kidney diseases that are typically more common among adult men comparing to adult women. The prevalence of this disease is increasing which is influenced by genetic and environmental factors. Kidney stones are mainly composed of calcium oxalate and urinary oxalate which is considered a dangerous factor in their formation. Besides diverse leading reasons in the progression of nephrolithiasis, the gut and urinary microbiome has been recognized as a major player in the development or prevention of it. These microbes produce metabolites that have diverse effects on host biological functions. Therefore, Changes in the composition and structure of the microbiome (dysbiosis) have been implicated in various diseases. The present review focuses on the roles of gut and urinary in kidney stone formation.

RevDate: 2021-10-23

Li Z, Xiang Y, Wang Y, et al (2021)

Ocular microbial diversity, community structure, and function at high altitude.

Microbial pathogenesis pii:S0882-4010(21)00527-1 [Epub ahead of print].

PURPOSE: To investigate the composition and function of ocular surface microbiome in healthy people from different altitudes.

METHODS: Thirty-two healthy people living in a high altitude region and 30 sex- and age-matched individuals living in a low altitude region were enrolled. Samples were collected from the lower conjunctival sac of one randomly chosen eye for each participant. 16S rRNA sequencing was conducted to study the bacterial community composition and predict gene function using PICRUSt software.

RESULTS: Microbial diversity and richness was significantly decreased in samples from highlanders as calculated by Abundance-based Coverage Estimator (ACE) index, Chao1 index, and observed-species index (all p < 0.01). Principle coordinate analysis (PCoA) suggested significantly distinct clustering of the conjunctival sac bacterial communities between two groups (p = 0.03), especially the dominant genera. The relative abundances of Corynebacterium, Staphylococcus, and Anaerococcus were significantly enriched in highlanders, while those of Pseudomonas and Massilia were significantly decreased as compared with lowlanders (p < 0.01). In the functional annotation analysis, we found that 74 gene pathways, mainly in metabolism, differed in abundance. Pathways related to immune system diseases and infectious diseases were also enriched in highlanders.

CONCLUSION: The composition and function of ocular surface microbiome in highlanders were distinct from those of lowlanders and our study may provide a reference catalog of the healthy conjunctival microbiome in highlanders.

RevDate: 2021-10-23

Li X, Gao X, Zhang H, et al (2021)

The anti-hyperuricemic effects of green alga Enteromorpha prolifera polysaccharide via regulation of the uric acid transporters in vivo.

Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association pii:S0278-6915(21)00663-3 [Epub ahead of print].

A novel polysaccharide obtained from Enteromorpha prolifera (EPP) was purified through diethylaminoethyl cellulose-52 and Sephadex G-75 chromatography. Fourier transform infrared spectroscopy, high-performance liquid chromatography, and nuclear magnetic resonance (NMR) spectroscopy were employed to analyse the structure of EPP. It mainly comprised rhamnose, glucuronic acid, galactose, arabinose, and xylose at a molar ratio of 20.45:12.74:10.99:5.84:1.95, and its average molecular weight was 46.56 kDa. The seven major glycosidic residues identified by NMR were as follows: →2)-α-L-Araf-(1→, →2)-α-L-Rhap-(1→, →4)-α-L-Rhap-(1→, →2,6)-β-D-Galp-(1→, →4)-β-D-GlcpA-(1→, →3,4)-β-D-GlcpA-(1→, and →4)-β-Xylp-(1→. The effect of EPP on hyperuricemic mice was determined by analysing correlative general physical parameters, renal histopathology, renal gene expressions, and gut microbiome. EPP significantly reduced serum uric acid (UA), serum blood urea nitrogen, serum xanthine oxidase (XOD), and hepatic XOD as well as improved histological parameters in hyperuricemic mice. Furthermore, mRNA and protein expression analyses showed the upregulation of UA excretion genes such as ABCG2, OAT1, and NPT1 and downregulation of UA resorption gene URAT1. Moreover, EPP maintained the stability of the intestinal flora and confirmed that Parasutterella is closely related to the regulation of hyperuricemia. This study is the first to demonstrate the anti-hyperuricemic activity of EPP and highlight its therapeutic potential for hyperuricemia-related diseases.

RevDate: 2021-10-23

Zhang F, Wan Y, Zuo T, et al (2021)

Prolonged impairment of short-chain fatty acid and L-isoleucine biosynthesis in gut microbiome in patients with COVID-19.

Gastroenterology pii:S0016-5085(21)03650-7 [Epub ahead of print].

BACKGROUND & AIMS: SARS-CoV-2 infection is associated with altered gut microbiota composition. Phylogenetic groups of gut bacteria involved in the metabolism of short chain fatty acids were depleted in SARS-CoV-2-infected patients. We aimed to characterize functional profile of gut microbiome in patients with COVID-19 before and after disease resolution.

METHODS: We performed shotgun metagenomic sequencing on fecal samples from 66 antibiotics-naïve patients with COVID-19 and 70 non-COVID-19 controls. Serial fecal samples were collected (up to 6 times points) during hospitalization and beyond one month after discharge. We assessed gut microbial pathways in association with disease severity and blood inflammatory markers. We also determined changes of microbial functions in fecal samples before and after disease resolution and validated these functions using targeted analysis of fecal metabolites.

RESULTS: Compared with non-COVID-19 controls, COVID-19 patients with severe/critical illness showed significant alterations in gut microbiome functionality (P < .001), characterized by impaired capacity of gut microbiome for short chain fatty acid (SCFA) and L-isoleucine biosynthesis and enhanced capacity for urea production. Impaired SCFA and L-isoleucine biosynthesis in gut microbiome persisted beyond 30 days after recovery in COVID-19 patients. Targeted analysis of fecal metabolites showed significantly lower fecal concentrations of SCFAs and L-isoleucine in COVID-19 patients before and after disease resolution. Lack of SCFA and L-isoleucine biosynthesis significantly correlated with disease severity and increased plasma concentrations of CXCL-10, NT-proBNP, C-reactive protein (CRP) (all P < .05).

CONCLUSIONS: Gut microbiome of COVID-19 patients displayed impaired capacity for SCFA and L-isoleucine biosynthesis which persisted even after disease resolution. These two microbial functions correlated with host immune response underscoring the importance of gut microbial functions in SARS-CoV-2 infection pathogenesis and outcome.

RevDate: 2021-10-23

Millar EN, Surette MG, KA Kidd (2021)

Altered microbiomes of aquatic macroinvertebrates and riparian spiders downstream of municipal wastewater effluents.

The Science of the total environment pii:S0048-9697(21)06234-3 [Epub ahead of print].

Municipal wastewater treatment plants (WWTPs) contain numerous contaminants, including antimicrobials, that could affect the composition of the beneficial bacterial communities associated with host aquatic organisms. There is also potential for these effects to transfer to terrestrial predators. Riparian spiders and five families of aquatic macroinvertebrates were collected from sites upstream and downstream of two WWTPs, Waterloo and Kitchener, discharging to the Grand River, Ontario, Canada. Whole-body microbiota were analyzed following the extraction, PCR amplification, and sequencing of bacterial DNA using the V3-V4 hypervariable regions of the 16S rRNA genetic barcode. Changes in the relative abundance of major microbiome phyla were observed in all downstream aquatic insects except Hydropsychidae caddisflies, which exhibited little site variation. Shannon alpha diversity differed among sites for Tetragnathidae spiders, Perlidae, Hydropsychidae, and Heptageniidae. Downstream of the Waterloo WWTP alpha diversity decreased in spiders, while downstream of the Kitchener WWTP this measure decreased in Perlidae and increased in spiders. Bray-Curtis beta diversity was dissimilar among sites in all invertebrate taxa; upstream sites differed from those downstream of Waterloo in spiders, Perlidae, and Hydropsychidae, and from those downstream of Kitchener in spiders, Perlidae, and Hydropsychidae. Finally, effluent-derived bacteria were found in the microbiomes of downstream spiders and aquatic insects and not upstream. Overall, results indicated that the microbiomes of invertebrates collected downstream differed from those collected upstream of WWTPs, which has implications for altered host health and transport of WWTP-derived bacteria through aquatic ecosystems.

RevDate: 2021-10-23

Bowd E, Banks S, Bissett A, et al (2021)

Disturbance alters the forest soil microbiome.

Molecular ecology [Epub ahead of print].

Billions of microorganisms perform critical below-ground functions in all terrestrial ecosystems. While largely invisible to the naked eye, they support all higher lifeforms, form symbiotic relationships with ~90% of terrestrial plant species, stabilize soils, and facilitate biogeochemical cycles. Global increases in the frequency of disturbances are driving major changes in the structure and function of forests. However, despite their functional significance, the disturbance responses of forest microbial communities are poorly understood. Here we explore the influence of disturbance on the soil microbiome (archaea, fungi and bacteria) of some of the world's tallest and most carbon-dense forests, the Mountain Ash forests of southeastern Australia. From 80 sites, we identified 23,277 and 19,056 microbial operational taxonomic units from the 0-10 cm and 20-30 cm depths of soil respectively. From this extensive dataset, we found the diversity and composition of these often-cryptic communities has been altered by human and natural disturbance events. For instance, the diversity of ectomycorrhizal fungi declined with clearcut logging, the diversity of archaea declined with salvage logging, and bacterial diversity and overall microbial diversity declined with the number of fires. Moreover, we identified key associations between edaphic (soil properties), environmental (slope, elevation) and spatial variables and the composition of all microbial communities. Specifically, we found that soil pH, manganese, magnesium, phosphorus, iron and nitrate were associated with the composition of all microbial communities. In a period of widespread degradation of global forest ecosystems, our findings provide an important and timely insight into the disturbance responses of soil microbial communities, which may influence key ecological functions.

RevDate: 2021-10-23

Kuznetsova TA, Vecherskii MV, Khayrullin DR, et al (2021)

Dramatic Effect of the Black Soldier Fly Larvae on Fungal Community of a Compost.

Journal of the science of food and agriculture [Epub ahead of print].

BACKGROUND: Black soldier fly larvae (BSFL) are highly promising for the production of cheap and high-quality dietary protein. This insect is able to consume low-quality substrates, including food waste. The properties and safety of the compost obtained are largely determined by its microbiome. However, while the bacterial component of the BSFL-compost microbiome is well studied, little is known about its fungal component. In plant-based rearing substrates both biomass and metabolic activity of fungi often exceed biomass and activity of prokaryotes. So, the purpose of this study was to investigate fungal community of the compost, produced by BSF larvae, reared on a food waste substrate.

RESULTS: Community structure has been determined by metabarcoding of the ITS region. Species composition and abundance have been determined by plating technique and subsequent identification of the isolated pure cultures. It has been found that the primary mycobiome of the used food waste substrate consists of 19 families, represented mainly by phytopathogenic and endophytic genera. Larva incubation leads to complete elimination of all mycelial fungi from the resulting compost. The final mycobiome consists of only two yeast species, Pichia kudriavzevii and Diutina rugosa, with a total abundance of 1.2 × 107 CFU/g.

CONCLUSIONS: BSFL rearing leads to complete elimination of mycelial fungi from its feed substrate. Final compost lacks harmful fungi, including molds. This data may be crucial for BSFL-compost use and utilization. Moreover, it is an interesting aspect of zoomicrobial interactions in nature and agriculture. This article is protected by copyright. All rights reserved.

RevDate: 2021-10-23

Ahmad M, Ling J, Yang Q, et al (2021)

Insight into Bacterial Community Responses to Polycyclic Aromatic Hydrocarbons and the Degradation Potentials of Three Bacterial Isolates in Seagrass Halophila ovalis Sediments.

Current microbiology [Epub ahead of print].

Seagrass meadows constitute a prestigious ecosystem in the marine environment, providing valuable ecological and commercial services. Among the various causes, pollutions are considered one of the significant reasons for seagrass decline globally. This study investigates the impacts of polycyclic aromatic hydrocarbons mixture (pyrene, phenanthrene, and fluorene) on bacterial communities in Halophila ovalis sediments. The seagrass sediment bacterial microbiome was evaluated in a batch culture experiment by Illumina MiSeq sequencing. Culture-able bacterial strains were isolated and characterized by 16S rRNA gene sequencing. The results demonstrated an excellent alpha diversity in the original sediments with a Shannon index of (8.078) compared to the subsequent control group (5.908) and PAH-treated group (PAH-T) (4.916). Three phyla, Proteobacteria, Firmicutes, and Bacteroidetes, were detected in high abundance in the control and PAH-T groups. However, a significant difference (P < 0.05) was observed at the genus level between control and PAH-T group bacterial consortia. Pseudomonas, Mycobacterium, Idiomarina, Hydrogenophaga, Alteromonas, Sphingobacterium, and several others were highly abundant in PAH-T groups. Most of the culture-able isolates recovered in this study showed the closest resemblance to previously identified hydrocarbon-degrading bacteria. Among the three strains, Mix-16 (Citricoccus yambaruensis) and Mix-20 (Gordonia rubripertincta) showed a higher degradation of PAHs than Mix-19 (Isoptericola halotolerans) in the monoculture experiment. The most increased degradation of PAHs was recorded in the co-culture experiment. The present work revealed that PAHs could act as environmental stress and can influence bacterial community succession. Moreover, the co-culture strategy significantly enhanced the biodegradation of PAHs.

RevDate: 2021-10-23

Ai Y, Zhao J, Shi J, et al (2021)

Antibiotic exposure and childhood attention-deficit/hyperactivity disorder: systematic review and meta-analysis.

Psychopharmacology [Epub ahead of print].

BACKGROUND: Disturbances of gastrointestinal microbiome may result in the development of attention-deficit/hyperactivity disorder (ADHD). Antibiotic therapy is commonly known to influence the gastrointestinal microbiome. However, results from studies on the association between antibiotic exposure and ADHD have been inconsistent.

METHODS: Several databases (PubMed, PsychInfo, EMBASE) were searched on January 1, 2021, to identify relevant studies. A random effects model was used to calculate the pooled risk estimate. Statistical heterogeneity was tested using the chi-square test and the I2 statistic.

RESULTS: There were four risk estimates on antibiotic intake during pregnancy and eight risk estimates on antibiotic intake after birth. The pooled odds ratio for ADHD comparing antibiotic exposure with non-exposure during pregnancy was 1.14 (95% confidence interval [CI], 1.10-1.18). The pooled odds ratio with postnatal antibiotic exposure was 1.12 (95% CI, 0.99-1.26). Substantial heterogeneity existed among these analyses. The timing of antibiotic exposure, type of antibiotic, and number of antibiotic intakes might influence the association between antibiotic exposure and ADHD.

CONCLUSIONS: Our findings suggest that maternal antibiotic intake during pregnancy may be associated with an increased risk of ADHD in the offspring. However, there was insufficient evidence for the association between antibiotic intake after birth and ADHD risk. Further studies should be performed before a definitive conclusion can be established.

RevDate: 2021-10-23

Sabater C, Cobo-Díaz JF, Álvarez-Ordóñez A, et al (2021)

Novel methods of microbiome analysis in the food industry.

International microbiology : the official journal of the Spanish Society for Microbiology [Epub ahead of print].

The study of the food microbiome has gained considerable interest in recent years, mainly due to the wide range of applications that can be derived from the analysis of metagenomes. Among these applications, it is worth mentioning the possibility of using metagenomic analyses to determine food authenticity, to assess the microbiological safety of foods thanks to the detection and tracking of pathogens, antibiotic resistance genes and other undesirable traits, as well to identify the microorganisms responsible for food processing defects. Metataxonomics and metagenomics are currently the gold standard methodologies to explore the full potential of metagenomes in the food industry. However, there are still a number of challenges that must be solved in order to implement these methods routinely in food chain monitoring, and for the regulatory agencies to take them into account in their opinions. These challenges include the difficulties of analysing foods and food-related environments with a low microbial load, the lack of validated bioinformatics pipelines adapted to food microbiomes and the difficulty of assessing the viability of the detected microorganisms. This review summarizes the methods of microbiome analysis that have been used, so far, in foods and food-related environments, with a specific focus on those involving Next-Generation Sequencing technologies.

RevDate: 2021-10-23

MacAlpine J, Daniel-Ivad M, Liu Z, et al (2021)

A small molecule produced by Lactobacillus species blocks Candida albicans filamentation by inhibiting a DYRK1-family kinase.

Nature communications, 12(1):6151.

The fungus Candida albicans is an opportunistic pathogen that can exploit imbalances in microbiome composition to invade its human host, causing pathologies ranging from vaginal candidiasis to fungal sepsis. Bacteria of the genus Lactobacillus are colonizers of human mucosa and can produce compounds with bioactivity against C. albicans. Here, we show that some Lactobacillus species produce a small molecule under laboratory conditions that blocks the C. albicans yeast-to-filament transition, an important virulence trait. It remains unexplored whether the compound is produced in the context of the human host. Bioassay-guided fractionation of Lactobacillus-conditioned medium linked this activity to 1-acetyl-β-carboline (1-ABC). We use genetic approaches to show that filamentation inhibition by 1-ABC requires Yak1, a DYRK1-family kinase. Additional biochemical characterization of structurally related 1-ethoxycarbonyl-β-carboline confirms that it inhibits Yak1 and blocks C. albicans biofilm formation. Thus, our findings reveal Lactobacillus-produced 1-ABC can prevent the yeast-to-filament transition in C. albicans through inhibition of Yak1.

RevDate: 2021-10-23

Schut GJ, Thorgersen MP, Poole FL, et al (2021)

Tungsten enzymes play a role in detoxifying food and antimicrobial aldehydes in the human gut microbiome.

Proceedings of the National Academy of Sciences of the United States of America, 118(43):.

Tungsten (W) is a metal that is generally thought to be seldom used in biology. We show here that a W-containing oxidoreductase (WOR) family is diverse and widespread in the microbial world. Surprisingly, WORs, along with the tungstate-specific transporter Tup, are abundant in the human gut microbiome, which contains 24 phylogenetically distinct WOR types. Two model gut microbes containing six types of WOR and Tup were shown to assimilate W. Two of the WORs were natively purified and found to contain W. The enzymes catalyzed the conversion of toxic aldehydes to the corresponding acid, with one WOR carrying out an electron bifurcation reaction coupling aldehyde oxidation to the simultaneous reduction of NAD+ and of the redox protein ferredoxin. Such aldehydes are present in cooked foods and are produced as antimicrobials by gut microbiome metabolism. This aldehyde detoxification strategy is dependent on the availability of W to the microbe. The functions of other WORs in the gut microbiome that do not oxidize aldehydes remain unknown. W is generally beyond detection (<6 parts per billion) in common foods and at picomolar concentrations in drinking water, suggesting that W availability could limit some gut microbial functions and might be an overlooked micronutrient.

RevDate: 2021-10-23

Lee GO, Eisenberg JNS, Uruchima J, et al (2021)

Gut microbiome, enteric infections and child growth across a rural-urban gradient: protocol for the ECoMiD prospective cohort study.

BMJ open, 11(10):e046241 pii:bmjopen-2020-046241.

INTRODUCTION: The functional consequences of the bacterial gut microbiome for child health are not well understood. Characteristics of the early child gut microbiome may influence the course of enteric infections, and enteric infections may change the composition of the gut microbiome, all of which may have long-term implications for child growth and development.

METHODS AND ANALYSIS: We are conducting a community-based birth cohort study to examine interactions between gut microbiome conditions and enteric infections, and how environmental conditions affect the development of the gut microbiome. We will follow 360 newborns from 3 sites along a rural-urban gradient in northern coastal Ecuador, characterising enteric infections and gut microbial communities in the children every 3 to 6 months over their first 2 years of life. We will use longitudinal regression models to assess the correlation between environmental conditions and gut microbiome diversity and presence of specific taxa, controlling for factors that are known to be associated with the gut microbiome, such as diet. From 6 to 12 months of age, we will collect weekly stool samples to compare microbiome conditions in diarrhoea stools versus stools from healthy children prior to, during and after acute enteric infections, using principal-coordinate analysis and other multivariate statistical methods.

ETHICS AND DISSEMINATION: Ethics approvals have been obtained from Emory University and the Universidad San Francisco de Quito institutional review boards. The findings will be disseminated through conference presentations and peer-reviewed journals.

RevDate: 2021-10-23

Dixit AR, Khodadad CLM, Hummerick ME, et al (2021)

Persistence of Escherichia coli in the microbiomes of red Romaine lettuce (Lactuca sativa cv. 'Outredgeous') and mizuna mustard (Brassica rapa var. japonica) - does seed sanitization matter?.

BMC microbiology, 21(1):289.

BACKGROUND: Seed sanitization via chemical processes removes/reduces microbes from the external surfaces of the seed and thereby could have an impact on the plants' health or productivity. To determine the impact of seed sanitization on the plants' microbiome and pathogen persistence, sanitized and unsanitized seeds from two leafy green crops, red Romaine lettuce (Lactuca sativa cv. 'Outredgeous') and mizuna mustard (Brassica rapa var. japonica) were exposed to Escherichia coli and grown in controlled environment growth chambers simulating environmental conditions aboard the International Space Station. Plants were harvested at four intervals from 7 days post-germination to maturity. The bacterial communities of leaf and root were investigated using the 16S rRNA sequencing while quantitative polymerase chain reaction (qPCR) and heterotrophic plate counts were used to reveal the persistence of E. coli.

RESULT: E. coli was detectable for longer periods of time in plants from sanitized versus unsanitized seeds and was identified in root tissue more frequently than in leaf tissue. 16S rRNA sequencing showed dynamic changes in the abundance of members of the phylum Proteobacteria, Firmicutes, and Bacteroidetes in leaf and root samples of both leafy crops. We observed minimal changes in the microbial diversity of lettuce or mizuna leaf tissue with time or between sanitized and unsanitized seeds. Beta-diversity showed that time had more of an influence on all samples versus the E. coli treatment.

CONCLUSION: Our results indicated that the seed surface sanitization, a current requirement for sending seeds to space, could influence the microbiome. Insight into the changes in the crop microbiomes could lead to healthier plants and safer food supplementation.

RevDate: 2021-10-23

Yan W, Zhou Q, Yuan Z, et al (2021)

Impact of the gut microecology on Campylobacter presence revealed by comparisons of the gut microbiota from chickens raised on litter or in individual cages.

BMC microbiology, 21(1):290.

BACKGROUND: Poultry is the major reservoir of Campylobacter that contributes to human campylobacteriosis and threatens food safety. Litter contact has been linked to Campylobacter colonization, but the gut microecological impact underlying this link remains not fully clear. Here, we sought to investigate the impact of the gut microecology on the presence of Campylobacter by examining the microbiota in the duodenum, jejunum, ileum, ceca, and feces from chickens raised on commercial litter and in individual cages at 0-57 days of age.

RESULTS: Through litter contact, the presence of Campylobacter was found to benefit from microecological competition among Lactobacillus, Helicobacter, and genera that are halotolerant and aerobic or facultatively anaerobic in the upper intestine, such as Corynebacterium and Brachybacterium. The presence was also promoted by the increased abundance in obligate anaerobic fermentation microbes, especially members of the orders Clostridiales and Bacteroidales. The longitudinal analysis supported the vertical or pseudo-vertical transmission but suggested that colonization might occur immensely at 7-28 days of age. We observed a host genetic effect on the gut microecology, which might lead to increased heterogeneity of the microecological impact on Campylobacter colonization.

CONCLUSIONS: The findings advance the understanding of the gut microecological impact on Campylobacter presence in the chicken gut under conditions of litter contact and suggest that manipulations of the gut microecology, as well as the microbes identified in the Campylobacter association networks, might be important for the development of intervention strategies.

RevDate: 2021-10-23

Kim D, Jung JY, Oh HS, et al (2021)

Comparison of sampling methods in assessing the microbiome from patients with ulcerative colitis.

BMC gastroenterology, 21(1):396.

BACKGROUND: Dysbiosis of ulcerative colitis (UC) has been frequently investigated using readily accessible stool samples. However, stool samples might insufficiently represent the mucosa-associated microbiome status. We hypothesized that luminal contents including loosely adherent luminal bacteria after bowel preparation may be suitable for diagnosing the dysbiosis of UC.

METHODS: This study included 16 patients with UC (9 men and 7 women, mean age: 52.13 ± 14.09 years) and 15 sex- and age-matched healthy individuals (8 men and 7 women, mean age: 50.93 ± 14.11 years). They donated stool samples before colonoscopy and underwent luminal content aspiration and endoscopic biopsy during the colonoscopy. Then, the composition of each microbiome sample was analyzed by 16S rRNA-based next-generation sequencing.

RESULTS: The microbiome between stool, luminal contents, and biopsy was significantly different in alpha and beta diversities. However, a correlation existed between stool and luminal contents in the Procrustes test (p = 0.001) and Mantel test (p = 0.0001). The stool microbiome was different between patients with UC and the healthy controls. Conversely, no difference was found in the microbiome of luminal content and biopsy samples between the two subject groups. The microbiome of stool and lavage predicted UC, with AUC values of 0.85 and 0.81, respectively.

CONCLUSION: The microbiome of stool, luminal contents, and biopsy was significantly different. However, the microbiome of luminal contents during colonoscopy can predict UC, with AUC values of 0.81. Colonoscopic luminal content aspiration analysis could determine microbiome differences between patients with UC and the healthy control, thereby beneficial in screening dysbiosis via endoscopy.

TRIAL REGISTRATION: This trial was registered at . Registration No.: KCT0003352), Date: 2018-11-13.

RevDate: 2021-10-23

Nakayasu M, Yamazaki S, Aoki Y, et al (2021)

Triterpenoid and Steroidal Saponins Differentially Influence Soil Bacterial Genera.

Plants (Basel, Switzerland), 10(10): pii:plants10102189.

Plant specialized metabolites (PSMs) are secreted into the rhizosphere, i.e., the soil zone surrounding the roots of plants. They are often involved in root-associated microbiome assembly, but the association between PSMs and microbiota is not well characterized. Saponins are a group of PSMs widely distributed in angiosperms. In this study, we compared the bacterial communities in field soils treated with the pure compounds of four different saponins. All saponin treatments decreased bacterial α-diversity and caused significant differences in β-diversity when compared with the control. The bacterial taxa depleted by saponin treatments were higher than the ones enriched; two families, Burkholderiaceae and Methylophilaceae, were enriched, while eighteen families were depleted with all saponin treatments. Sphingomonadaceae, which is abundant in the rhizosphere of saponin-producing plants (tomato and soybean), was enriched in soil treated with α-solanine, dioscin, and soyasaponins. α-Solanine and dioscin had a steroid-type aglycone that was found to specifically enrich Geobacteraceae, Lachnospiraceae, and Moraxellaceae, while soyasaponins and glycyrrhizin with an oleanane-type aglycone did not specifically enrich any of the bacterial families. At the bacterial genus level, the steroidal-type and oleanane-type saponins differentially influenced the soil bacterial taxa. Together, these results indicate that there is a relationship between the identities of saponins and their effects on soil bacterial communities.

RevDate: 2021-10-23

Kriaa A, Jablaoui A, Rhimi S, et al (2021)

SP-1, a Serine Protease from the Gut Microbiota, Influences Colitis and Drives Intestinal Dysbiosis in Mice.

Cells, 10(10): pii:cells10102658.

Increased protease activity has been linked to the pathogenesis of IBD. While most studies have been focusing on host proteases in gut inflammation, it remains unclear how to address the potential contribution of their bacterial counterparts. In the present study, we report a functional characterization of a newly identified serine protease, SP-1, from the human gut microbiota. The serine protease repertoire of gut Clostridium was first explored, and the specificity of SP-1 was analyzed using a combinatorial chemistry method. Combining in vitro analyses and a mouse model of colitis, we show that oral administration of recombinant bacteria secreting SP-1 (i) compromises the epithelial barrier, (ii) alters the microbial community, and (ii) exacerbates colitis. These findings suggest that gut microbial protease activity may constitute a valuable contributor to IBD and could, therefore, represent a promising target for the treatment of the disease.

RevDate: 2021-10-23

Sachdev V, Duta-Mare M, Korbelius M, et al (2021)

Impaired Bile Acid Metabolism and Gut Dysbiosis in Mice Lacking Lysosomal Acid Lipase.

Cells, 10(10): pii:cells10102619.

Lysosomal acid lipase (LAL) is the sole enzyme known to be responsible for the hydrolysis of cholesteryl esters and triglycerides at an acidic pH in lysosomes, resulting in the release of unesterified cholesterol and free fatty acids. However, the role of LAL in diet-induced adaptations is largely unexplored. In this study, we demonstrate that feeding a Western-type diet to Lal-deficient (LAL-KO) mice triggers metabolic reprogramming that modulates gut-liver cholesterol homeostasis. Induction of ileal fibroblast growth factor 15 (three-fold), absence of hepatic cholesterol 7α-hydroxylase expression, and activation of the ERK phosphorylation cascade results in altered bile acid composition, substantial changes in the gut microbiome, reduced nutrient absorption by 40%, and two-fold increased fecal lipid excretion in LAL-KO mice. These metabolic adaptations lead to impaired bile acid synthesis, lipoprotein uptake, and cholesterol absorption and ultimately to the resistance of LAL-KO mice to diet-induced obesity. Our results indicate that LAL-derived lipolytic products might be important metabolic effectors in the maintenance of whole-body lipid homeostasis.

RevDate: 2021-10-23

Żelechowska P, Pastwińska J, Brzezińska-Błaszczyk E, et al (2021)

Do Mast Cells Contribute to the Antifungal Host Defense?.

Cells, 10(10): pii:cells10102510.

The fungal kingdom includes a group of microorganisms that are widely distributed in the environment, and therefore the exposure to them is almost constant. Furthermore, fungal components of the microbiome, i.e., mycobiome, could serve as a reservoir of potentially opportunistic pathogens. Despite close encounters with fungi, defense mechanisms that develop during fungal infections remain unexplored. The strategic location of mast cells (MCs) close to the external environment places them among the first cells to encounter pathogens along with the other innate immune cells. MCs are directly involved in the host defense through the ability to destroy pathogens or indirectly by activating other immune cells. Most available data present MCs' involvement in antibacterial, antiviral, or antiparasitic defense mechanisms. However, less is known about their contribution in defense mechanisms against fungi. MCs may support immune responses to fungi or their specific molecules through initiated degranulation, synthesis and release of cytokines, chemokines, mediators, and generation of reactive oxygen species (ROS), as well as immune cells' recruitment, phagocytosis, or provision of extracellular DNA traps. This review summarizes current knowledge on host defense mechanisms against fungi and MCs' involvement in those processes. It also describes the effects of fungi or fungus-derived constituents on MCs' activity.

RevDate: 2021-10-23

Hummerick ME, Khodadad CLM, Dixit AR, et al (2021)

Spatial Characterization of Microbial Communities on Multi-Species Leafy Greens Grown Simultaneously in the Vegetable Production Systems on the International Space Station.

Life (Basel, Switzerland), 11(10): pii:life11101060.

The establishment of steady-state continuous crop production during long-term deep space missions is critical for providing consistent nutritional and psychological benefits for the crew, potentially improving their health and performance. Three technology demonstrations were completed achieving simultaneous multi-species plant growth and the concurrent use of two Veggie units on the International Space Station (ISS). Microbiological characterization using molecular and culture-based methods was performed on leaves and roots from two harvests of three leafy greens, red romaine lettuce (Lactuca sativa cv. 'Outredgeous'); mizuna mustard, (Brassica rapa var japonica); and green leaf lettuce, (Lactuca sativa cv. Waldmann's) and associated rooting pillow components and Veggie chamber surfaces. Culture based enumeration and pathogen screening indicated the leafy greens were safe for consumption. Surface samples of the Veggie facility and plant pillows revealed low counts of bacteria and fungi and are commonly isolated on ISS. Community analysis was completed with 16S rRNA amplicon sequencing. Comparisons between pillow components, and plant tissue types from VEG-03D, E, and F revealed higher diversity in roots and rooting substrate than the leaves and wick. This work provides valuable information for food production-related research on the ISS and the impact of the plant microbiome on this unique closed environment.

RevDate: 2021-10-23

Siddiqui R, Qaisar R, Goswami N, et al (2021)

Effect of Microgravity Environment on Gut Microbiome and Angiogenesis.

Life (Basel, Switzerland), 11(10): pii:life11101008.

Microgravity environments are known to cause a plethora of stressors to astronauts. Recently, it has become apparent that gut microbiome composition of astronauts is altered following space travel, and this is of significance given the important role of the gut microbiome in human health. Other changes observed in astronauts comprise reduced muscle strength and bone fragility, visual impairment, endothelial dysfunction, metabolic changes, behavior changes due to fatigue or stress and effects on mental well-being. However, the effects of microgravity on angiogenesis, as well as the connection with the gut microbiome are incompletely understood. Here, the potential association of angiogenesis with visual impairment, skeletal muscle and gut microbiome is proposed and explored. Furthermore, metabolites that are effectors of angiogenesis are deliberated upon along with their connection with gut bacterial metabolites. Targeting and modulating the gut microbiome may potentially have a profound influence on astronaut health, given its impact on overall human health, which is thus warranted given the likelihood of increased human activity in the solar system, and the determination to travel to Mars in future missions.

RevDate: 2021-10-23

Jiang S, Su T, Zhao J, et al (2021)

Biodegradation of Polystyrene by Tenebrio molitor, Galleria mellonella, and Zophobas atratus Larvae and Comparison of Their Degradation Effects.

Polymers, 13(20): pii:polym13203539.

Plastic waste pollution and its difficult degradation process have aroused widespread concern. Research has demonstrated that the larvae of Tenebrio molitor (yellow mealworm), Galleria mellonella (greater wax moth), and Zophobas atratus (superworm) possess a biodegradation ability for polystyrene (PS) within the gut microbiota of these organisms. In this study, the difference in PS degradation and the changes of the gut microbiota were compared before and after feeding PS. The results showed that superworm had the strongest PS consumption capacity and the highest survival rate during the 30 d experiment period. They all could degrade PS to different degrees. Superworm showed the highest ability to degrade PS into low-molecular-weight substances, while yellow mealworm depolymerized PS strongly by destroying the benzene ring. The changes of the intestinal microbiome caused by feeding PS showed that after ingesting PS, there was a decrease in community diversity in superworm and yellow mealworm, but an increase in greater wax moth. Meanwhile, Enterococcus and Enterobacteriaceae, found in all three species' larvae upon 20 d of PS feeding, might play an important role in PS degradation. The results will provide more accurate PS degradation comparative data of the three species' larvae and theoretical guidance for further research on the efficient PS biodegradations.

RevDate: 2021-10-23

Hossain F, Majumder S, David J, et al (2021)

Obesity Modulates the Gut Microbiome in Triple-Negative Breast Cancer.

Nutrients, 13(10): pii:nu13103656.

Triple-negative breast cancer (TNBC) is an aggressive, molecularly heterogeneous subtype of breast cancer. Obesity is associated with increased incidence and worse prognosis in TNBC through various potential mechanisms. Recent evidence suggests that the gut microbiome plays a central role in the progression of cancer, and that imbalances or dysbiosis in the population of commensal microbiota can lead to inflammation and contribute to tumor progression. Obesity is characterized by low-grade inflammation, and gut dysbiosis is associated with obesity, chronic inflammation, and failure of cancer immunotherapy. However, the debate on what constitutes a "healthy" gut microbiome is ongoing, and the connection among the gut microbiome, obesity, and TNBC has not yet been addressed. This study aims to characterize the role of obesity in modulating the gut microbiome in a syngeneic mouse model of TNBC. 16S rRNA sequencing and metagenomic analyses were performed to analyze and annotate genus and taxonomic profiles. Our results suggest that obesity decreases alpha diversity in the gut microbiome. Metagenomic analysis revealed that obesity was the only significant factor explaining the similarity of the bacterial communities according to their taxonomic profiles. In contrast to the analysis of taxonomic profiles, the analysis of variation of functional profiles suggested that obesity status, tumor presence, and the obesity-tumor interaction were significant in explaining the variation of profiles, with obesity having the strongest correlation. The presence of tumor modified the profiles to a greater extent in obese than in lean animals. Further research is warranted to understand the impact of the gut microbiome on TNBC progression and immunotherapy.

RevDate: 2021-10-23

Gołębiewski M, Łoś-Rycharska E, Sikora M, et al (2021)

Mother's Milk Microbiome Shaping Fecal and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Analysis.

Nutrients, 13(10): pii:nu13103600.

The child microbiome, including gut and skin communities, is shaped by a multitude of factors, and breastfeeding is one of the most essential. Food allergy (FA) and atopic dermatitis (AD) are among the most common diseases in pediatrics, with the prevalence of each up to 6% and 20%, respectively. Therefore, we aimed at finding differences between the fecal and skin microbiomes of FA and AD patients in the context of breastfeeding, by means of the Illumina sequencing of 16S rRNA gene fragment libraries amplified from the total DNA isolated from samples collected from allergic and healthy infants. We also analyzed milk samples from the mothers of the examined children and searched for patterns of incidence suggesting milk influence on an infant's allergy status. Here we show that a mother's milk influences her child's fecal and skin microbiomes and identify Acinetobacter as the taxon whose abundance is correlated with milk and child-derived samples. We demonstrate that breastfeeding makes allergic children's fecal and skin communities more similar to those of healthy infants than in the case of formula-feeding. We also identify signature taxa that might be important in maintaining health or allergy development.

RevDate: 2021-10-23

Wilson B, Eyice Ö, Koumoutsos I, et al (2021)

Prebiotic Galactooligosaccharide Supplementation in Adults with Ulcerative Colitis: Exploring the Impact on Peripheral Blood Gene Expression, Gut Microbiota, and Clinical Symptoms.

Nutrients, 13(10): pii:nu13103598.

Prebiotics may promote immune homeostasis and reduce sub-clinical inflammation in humans. This study investigated the effect of prebiotic galactooligosaccharide (GOS) supplementation in colonic inflammation. Seventeen patients with active ulcerative colitis (UC) consumed 2.8 g/d GOS for 6 weeks. At baseline and 6 weeks, gene expression (microarray), fecal calprotectin (ELISA), microbiota (16S rRNA), short-chain fatty acids (SCFAs; gas-liquid chromatography), and clinical outcomes (simple clinical colitis activity index (SCCAI), gastrointestinal symptom rating scale (GSRS), and Bristol stool form scale (BSFS)) were measured. Following prebiotics, clinical scores (SCCAI), fecal calprotectin, SCFAs, and pH were unchanged. Five genes were upregulated and two downregulated. Normal stool proportion (BSFS) increased (49% vs. 70%, p = 0.024), and the incidence (46% vs. 23%, p = 0.016) and severity (0.7 vs. 0.5, p = 0.048) of loose stool (GSRS), along with urgency (SCCAI) scores (1.0 vs. 0.5, p = 0.011), were reduced. In patients with a baseline SCCAI ≤2, prebiotics increased the relative abundance of Bifidobacterium from 1.65% (1.97) to 3.99% (5.37) (p = 0.046) and Christensenellaceae from 0.13% (0.33) to 0.31% (0.76) (p = 0.043). Prebiotics did not lower clinical scores or inflammation but normalized stools. Bifidobacterium and Christensenellaceae proportions only increased in patients with less active diseases, indicating that the prebiotic effect may depend on disease activity. A controlled study is required to validate these observations.

RevDate: 2021-10-23

Daliry A, ENGDS Pereira (2021)

Role of Maternal Microbiota and Nutrition in Early-Life Neurodevelopmental Disorders.

Nutrients, 13(10): pii:nu13103533.

The rise in the prevalence of obesity and other related metabolic diseases has been paralleled by an increase in the frequency of neurodevelopmental problems, which has raised the likelihood of a link between these two phenomena. In this scenario, maternal microbiota is a possible linking mechanistic pathway. According to the "Developmental Origins of Health and Disease" paradigm, environmental exposures (in utero and early life) can permanently alter the body's structure, physiology, and metabolism, increasing illness risk and/or speeding up disease progression in offspring, adults, and even generations. Nutritional exposure during early developmental stages may induce susceptibility to the later development of human diseases via interactions in the microbiome, including alterations in brain function and behavior of offspring, as explained by the gut-brain axis theory. This review provides an overview of the implications of maternal nutrition on neurodevelopmental disorders and the establishment and maturation of gut microbiota in the offspring.

RevDate: 2021-10-23

Lombardi M, J Troisi (2021)

Gut Reactions: How Far Are We from Understanding and Manipulating the Microbiota Complexity and the Interaction with Its Host? Lessons from Autism Spectrum Disorder Studies.

Nutrients, 13(10): pii:nu13103492.

Autism is a group of neurodevelopmental disorders, characterized by early onset difficulties in social communication and restricted, repetitive behaviors and interests. It is characterized by familial aggregation, suggesting that genetic factors play a role in disease development, in addition to developmentally early environmental factors. Here, we review the role of the gut microbiome in autism, as it has been characterized in case-control studies. We discuss how methodological differences may have led to inconclusive or contradictory results, even though a disproportion between harmful and beneficial bacteria is generally described in autism. Furthermore, we review the studies concerning the effects of gut microbial-based and dietary interventions on autism symptoms. Also, in this case, the results are not comparable due to the lack of standardized methods. Therefore, autism-specific microbiome signatures and, consequently, possible microbiome-oriented interventions are far from being recognized. We argue that a multi-omic longitudinal implementation may be useful to study metabolic changes connected to microbiome changes.

RevDate: 2021-10-23

Martinez TM, Meyer RK, FA Duca (2021)

Therapeutic Potential of Various Plant-Based Fibers to Improve Energy Homeostasis via the Gut Microbiota.

Nutrients, 13(10): pii:nu13103470.

Obesity is due in part to increased consumption of a Western diet that is low in dietary fiber. Conversely, an increase in fiber supplementation to a diet can have various beneficial effects on metabolic homeostasis including weight loss and reduced adiposity. Fibers are extremely diverse in source and composition, such as high-amylose maize, β-glucan, wheat fiber, pectin, inulin-type fructans, and soluble corn fiber. Despite the heterogeneity of dietary fiber, most have been shown to play a role in alleviating obesity-related health issues, mainly by targeting and utilizing the properties of the gut microbiome. Reductions in body weight, adiposity, food intake, and markers of inflammation have all been reported with the consumption of various fibers, making them a promising treatment option for the obesity epidemic. This review will highlight the current findings on different plant-based fibers as a therapeutic dietary supplement to improve energy homeostasis via mechanisms of gut microbiota.

RevDate: 2021-10-23

Ahrens AP, Culpepper T, Saldivar B, et al (2021)

A Six-Day, Lifestyle-Based Immersion Program Mitigates Cardiovascular Risk Factors and Induces Shifts in Gut Microbiota, Specifically Lachnospiraceae, Ruminococcaceae, Faecalibacterium prausnitzii: A Pilot Study.

Nutrients, 13(10): pii:nu13103459.

Cardiovascular disease (CVD) prevalence remains elevated globally. We have previously shown that a one-week lifestyle "immersion program" leads to clinical improvements and sustained improvements in quality of life in moderate to high atherosclerotic CVD (ASCVD) risk individuals. In a subsequent year of this similarly modeled immersion program, we again collected markers of cardiovascular health and, additionally, evaluated intestinal microbiome composition. ASCVD risk volunteers (n = 73) completed the one-week "immersion program" involving nutrition (100% plant-based foods), stress management education, and exercise. Anthropometric measurements and CVD risk factors were compared at baseline and post intervention. A subgroup (n = 22) provided stool, which we analyzed with 16S rRNA sequencing. We assessed abundance changes within-person, correlated the abundance shifts with clinical changes, and inferred functional pathways using PICRUSt. Reductions in blood pressure, total cholesterol, and triglycerides, were observed without reduction in weight. Significant increases in butyrate producers were detected, including Lachnospiraceae and Oscillospirales. Within-person, significant shifts in relative abundance (RA) occurred, e.g., increased Lachnospiraceae (+58.8% RA, p = 0.0002), Ruminococcaceae (+82.1%, p = 0.0003), Faecalibacterium prausnitzii (+54.5%, p = 0.002), and diversification and richness. Microbiota changes significantly correlated with body mass index (BMI), blood pressure (BP), cholesterol, high-sensitivity C-reactive protein (hsCRP), glucose, and trimethylamine N-oxide (TMAO) changes. Pairwise decreases were inferred in microbial genes corresponding to cancer, metabolic disease, and amino acid metabolism. This brief lifestyle-based intervention improved lipids and BP and enhanced known butyrate producers, without significant weight loss. These results demonstrate a promising non-pharmacological preventative strategy for improving cardiovascular health.

RevDate: 2021-10-23

Henderickx JGE, d'Haens EJ, Hemels MAC, et al (2021)

From Mum to Bum: An Observational Study Protocol to Follow Digestion of Human Milk Oligosaccharides and Glycoproteins from Mother to Preterm Infant.

Nutrients, 13(10): pii:nu13103430.

The nutritional requirements of preterm infants are challenging to meet in neonatal care, yet crucial for their growth, development and health. Aberrant maturation of the gastrointestinal tract and the microbiota could affect the digestion of human milk and its nutritional value considerably. Therefore, the main objective of the proposed research is to investigate how the intestinal microbiota of preterm and full-term infants differ in their ability to extract energy and nutrients from oligosaccharides and glycoproteins in human milk. This pilot study will be an observational, single-center study performed at the Neonatal Intensive Care Unit at Isala Women and Children's Hospital (Zwolle, The Netherlands). A cohort of thirty mother-infant pairs (preterm ≤30 weeks of gestation, n = 15; full-term 37-42 weeks of gestation, n = 15) will be followed during the first six postnatal weeks with follow-up at three- and six-months postnatal age. We will collect human milk of all mothers, gastric aspirates of preterm infants and fecal samples of all infants. A combination of 16S rRNA amplicon sequencing, proteomics, peptidomics, carbohydrate analysis and calorimetric measurements will be performed. The role of the microbiota in infant growth and development is often overlooked yet offers opportunities to advance neonatal care. The 'From Mum to Bum' study is the first study in which the effect of a preterm gut microbiota composition on its metabolic capacity and subsequent infant growth and development is investigated. By collecting human milk of all mothers, gastric aspirates of preterm infants and fecal samples of all infants at each timepoint, we can follow digestion of human milk from the breast of the mother throughout the gastrointestinal tract of the infant, or 'From Mum to Bum'.

RevDate: 2021-10-23

Cheng J, Bar H, E Tako (2021)

Zinc Status Index (ZSI) for Quantification of Zinc Physiological Status.

Nutrients, 13(10): pii:nu13103399.

Zinc (Zn) deficiency is estimated to affect over one billion (17%) of the world's population. Zn plays a key role in various cellular processes such as differentiation, apoptosis, and proliferation, and is used for vital biochemical and structural processes in the body. Widely used biomarkers of Zn status include plasma, whole blood, and urine Zn, which decrease in severe Zn deficiency; however, accurate assessment of Zn status, especially in mild to moderate deficiency, is difficult, as studies with these biomarkers are often contradictory and inconsistent. Thus, sensitive and specific biological markers of Zn physiological status are still needed. In this communication, we provide the Zn status index (ZSI) concept, which consists of a three-pillar formula: (1) the LA:DGLA ratio, (2) mRNA gene expression of Zn-related proteins, and (3) gut microbiome profiling to provide a clear assessment of Zn physiological status and degree of Zn deficiency with respect to assessing dietary Zn manipulation. Analysis of five selected studies found that with lower dietary Zn intake, erythrocyte LA:DGLA ratio increased, mRNA gene expression of Zn-related proteins in duodenal and liver tissues was altered, and gut microbiota populations differed, where the ZSI, a statistical model trained on data from these studies, was built to give an accurate estimation of Zn physiological status. However, the ZSI needs to be tested and refined further to determine its full potential.

RevDate: 2021-10-23

Bellerba F, Muzio V, Gnagnarella P, et al (2021)

The Association between Vitamin D and Gut Microbiota: A Systematic Review of Human Studies.

Nutrients, 13(10): pii:nu13103378.

Recent evidence has shown a number of extra-skeletal functions of Vitamin D (VD), primarily involving the immune system. One of these functions is mediated by the modulation of gut microbiota, whose alterations are linked to many diseases. Our purpose is to contribute to the understanding of existing evidence on the association between VD and gastrointestinal microbiota alterations. A systematic review of studies with human subjects has been conducted up to January 2021. We included publications reporting the association between gut microbiota and VD, including VD supplementation, dietary VD intake and/or level of 25(OH)D. We identified 25 studies: 14 were interventional and 11, observational. VD supplementation was found to be associated with a significant change in microbiome composition, in particular of Firmicutes, Actinobacteria and Bacteroidetes phyla. Furthermore, Firmicutes were found to be correlated with serum VD. Concerning alpha and beta diversity, a high nutritional intake of VD seems to induce a shift in bacterial composition and/or affects the species' richness. Veillonellaceae and Oscillospiraceae families, in the Firmicutes phylum, more frequently decreased with both increasing levels of 25(OH)D and vitamin D supplementation. We found evidence of an association, even though the studies are substantially heterogeneous and have some limitations, resulting sometimes in conflicting results. To further understand the role of VD on the modulation of the gastrointestinal microbiota, future research should be geared toward well-designed animal-based studies or larger randomized controlled trials (RCTs).

RevDate: 2021-10-23

Tanaka Y, Shimizu S, Shirotani M, et al (2021)

Nutrition and Cancer Risk from the Viewpoint of the Intestinal Microbiome.

Nutrients, 13(10): pii:nu13103326.

There are various important factors in reducing the risk of cancer development and progression; these factors may correct an unbalanced intake of nutrients to maintain the living body's homeostasis, detoxify toxic materials, acting as an external factor, and maintain and strengthen the body's immune function. In a normal cell environment, nutrients, such as carbohydrates, lipids, proteins, vitamins, and minerals, are properly digested and absorbed into the body, and, as a result, an environment in which cancer can develop and progress is prevented. It is necessary to prevent toxic materials from entering the body and to detoxify poisons in the body. If these processes occur correctly, cells work normally, and genes cannot be damaged. The most important factor in the fight against cancer and prevention of the development and progression of cancer is the immune system. This requires a nutritional state in which the immune system works well, allowing the intestinal microbiome to carry out all of its roles. In order to grow intestinal microbiota, the consumption of prebiotics, such as organic vegetables, fruits, and dietary fiber, and probiotics of effective intestinal microbiota, such as fermented foods and supplements, is required. Symbiosis, in which these organisms work together, is an effective means of reducing the risk of cancer. In addition, fecal microbiota transplantation (FMT) using ultrafine bubble water, produced specially by the Association for Clinical Research of Fecal Microbiota Transplantation Japan, is also useful for improving the nutritional condition and reducing the risk of cancer.

RevDate: 2021-10-23

Ha S, Oh D, Lee S, et al (2021)

Altered Gut Microbiota in Korean Children with Autism Spectrum Disorders.

Nutrients, 13(10): pii:nu13103300.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social and behavioral impairments. Recent studies have suggested that gut microbiota play a critical role in ASD pathogenesis. Herein, we investigated the fecal microflora of Korean ASD children to determine gut microbiota profiles associated with ASD. Specifically, fecal samples were obtained from 54 children with ASD and 38 age-matched children exhibiting typical development. Systematic bioinformatic analysis revealed that the composition of gut microbiota differed between ASD and typically developing children (TDC). Moreover, the total amounts of short-chain fatty acids, metabolites produced by bacteria, were increased in ASD children. At the phylum level, we found a significant decrease in the relative Bacteroidetes abundance of the ASD group, whereas Actinobacteria abundance was significantly increased. Furthermore, we found significantly lower Bacteroides levels and higher Bifidobacterium levels in the ASD group than in the TDC group at the genus level. Functional analysis of the microbiota in ASD children predicted that several pathways, including genetic information processing and amino acid metabolism, can be associated with ASD pathogenesis. Although more research is needed to determine whether the differences between ASD and TDC are actually related to ASD pathogenesis, these results provide further evidence of altered gut microbiota in children with ASD, possibly providing new perspectives on the diagnosis and therapeutic approaches for ASD patients.

RevDate: 2021-10-23

Raimondi S, Candeliere F, Amaretti A, et al (2021)

Vaginal and Anal Microbiome during Chlamydia trachomatis Infections.

Pathogens (Basel, Switzerland), 10(10): pii:pathogens10101347.

Background.Chlamydia trachomatis (CT) is the agent of the most common bacterial sexually transmitted infection worldwide, with a significant impact on women's health. Despite the increasing number of studies about the vaginal microbiome in women with CT infections, information about the composition of the anal microbiome is still lacking. Here, we assessed the bacterial community profiles of vaginal and anal ecosystems associated or not with CT infection in a cohort of Caucasian young women. Methods. A total of 26 women, including 10 with a contemporary vaginal and ano-rectal CT infection, were enrolled. Composition of vaginal and anal microbiome was studied by 16S rRNA gene profiling. Co-occurrence networks of bacterial communities and metagenome metabolic functions were determined. Results. In case of CT infection, both vaginal and anal environments were characterized by a degree of dysbiosis. Indeed, the vaginal microbiome of CT-positive women were depleted in lactobacilli, with a significant increase in dysbiosis-associated bacteria (e.g., Sneathia, Parvimonas, Megasphaera), whereas the anal microbiota of CT-infected women was characterized by higher levels of Parvimonas and Pseudomonas and lower levels of Escherichia. Interestingly, the microbiome of anus and vagina had numerous bacterial taxa in common, reflecting a significant microbial 'sharing' between the two sites. In the vaginal environment, CT positively correlated with Ezakiella spp. while Gardnerella vaginalis co-occurred with several dysbiosis-related microbes, regardless of CT vaginal infection. The vaginal microbiome of CT-positive females exhibited a higher involvement of chorismate and aromatic amino acid biosynthesis, as well as an increase in mixed acid fermentation. Conclusions. These data could be useful to set up new diagnostic/prognostic tools, offering new perspectives for the control of chlamydial infections.

RevDate: 2021-10-23

He DC, He MH, Amalin DM, et al (2021)

Biological Control of Plant Diseases: An Evolutionary and Eco-Economic Consideration.

Pathogens (Basel, Switzerland), 10(10): pii:pathogens10101311.

Biological control is considered as a promising alternative to pesticide and plant resistance to manage plant diseases, but a better understanding of the interaction of its natural and societal functions is necessary for its endorsement. The introduction of biological control agents (BCAs) alters the interaction among plants, pathogens, and environments, leading to biological and physical cascades that influence pathogen fitness, plant health, and ecological function. These interrelationships generate a landscape of tradeoffs among natural and social functions of biological control, and a comprehensive evaluation of its benefits and costs across social and farmer perspectives is required to ensure the sustainable development and deployment of the approach. Consequently, there should be a shift of disease control philosophy from a single concept that only concerns crop productivity to a multifaceted concept concerning crop productivity, ecological function, social acceptability, and economical accessibility. To achieve these goals, attempts should make to develop "green" BCAs used dynamically and synthetically with other disease control approaches in an integrated disease management scheme, and evolutionary biologists should play an increasing role in formulating the strategies. Governments and the public should also play a role in the development and implementation of biological control strategies supporting positive externality.

RevDate: 2021-10-23

Błaszczyk L, Salamon S, K Mikołajczak (2021)

Fungi Inhabiting the Wheat Endosphere.

Pathogens (Basel, Switzerland), 10(10): pii:pathogens10101288.

Wheat production is influenced by changing environmental conditions, including climatic conditions, which results in the changing composition of microorganisms interacting with this cereal. The group of these microorganisms includes not only endophytic fungi associated with the wheat endosphere, both pathogenic and symbiotic, but also those with yet unrecognized functions and consequences for wheat. This paper reviews the literature in the context of the general characteristics of endophytic fungi inhabiting the internal tissues of wheat. In addition, the importance of epigenetic regulation in wheat-fungus interactions is recognized and the current state of knowledge is demonstrated. The possibilities of using symbiotic endophytic fungi in modern agronomy and wheat cultivation are also proposed. The fact that the current understanding of fungal endophytes in wheat is based on a rather small set of experimental conditions, including wheat genotypes, plant organs, plant tissues, plant development stage, or environmental conditions, is recognized. In addition, most of the research to date has been based on culture-dependent methods that exclude biotrophic and slow-growing species and favor the detection of fast-growing fungi. Additionally, only a few reports of studies on the entire wheat microbiome using high-throughput sequencing techniques exist. Conducting comprehensive research on the mycobiome of the endosphere of wheat, mainly in the context of the possibility of using this knowledge to improve the methods of wheat management, mainly the productivity and health of this cereal, is needed.

RevDate: 2021-10-23

Celik D, A Kantarci (2021)

Vascular Changes and Hypoxia in Periodontal Disease as a Link to Systemic Complications.

Pathogens (Basel, Switzerland), 10(10): pii:pathogens10101280.

The hypoxic microenvironment caused by oral pathogens is the most important cause of the disruption of dynamic hemostasis between the oral microbiome and the immune system. Periodontal infection exacerbates the inflammatory response with increased hypoxia and causes vascular changes. The chronicity of inflammation becomes systemic as a link between oral and systemic diseases. The vascular network plays a central role in controlling infection and regulating the immune response. In this review, we focus on the local and systemic vascular network change mechanisms of periodontal inflammation and the pathological processes of inflammatory diseases. Understanding how the vascular network influences the pathology of periodontal diseases and the systemic complication associated with this pathology is essential for the discovery of both local and systemic proactive control mechanisms.

RevDate: 2021-10-23

Madeen EP, Maldarelli F, JD Groopman (2021)

Environmental Pollutants, Mucosal Barriers, and Pathogen Susceptibility; The Case for Aflatoxin B1 as a Risk Factor for HIV Transmission and Pathogenesis.

Pathogens (Basel, Switzerland), 10(10): pii:pathogens10101229.

HIV transmission risk is dependent on the infectivity of the HIV+ partner and personal susceptibility risk factors of the HIV- partner. The mucosal barrier, as the internal gatekeeper between environment and self, concentrates and modulates the internalization of ingested pathogens and pollutants. In this review, we summarize the localized effects of HIV and dietary toxin aflatoxin B1 (AFB1), a common pollutant in high HIV burden regions, e.g., at the mucosal barrier, and evidence for pollutant-viral interactions. We compiled literature on HIV and AFB1 geographic occurrences, mechanisms of action, related co-exposures, personal risk factors, and HIV key determinants of health. AFB1 exposure and HIV sexual transmission hotspots geographically co-localize in many low-income countries. AFB1 distributes to sexual mucosal tissues generating inflammation, microbiome changes and a reduction of mucosal barrier integrity, effects that are risk factors for increasing HIV susceptibility. AFB1 exposure has a positive correlation to HIV viral load, a risk factor for increasing the infectivity of the HIV+ partner. The AFB1 exposure and metabolism generates inflammation that recruits HIV susceptible cells and generates chemokine/cytokine activation in tissues exposed to HIV. Although circumstantial, the available evidence makes a compelling case for studies of AFB1 exposure as a risk factor for HIV transmission, and a modifiable new component for combination HIV prevention efforts.

RevDate: 2021-10-23

Merkevičius K, Kundelis R, Maleckas A, et al (2021)

Microbiome Changes after Type 2 Diabetes Treatment: A Systematic Review.

Medicina (Kaunas, Lithuania), 57(10): pii:medicina57101084.

Background and objectives: Although the role of the gut microbiome in type 2 diabetes (T2D) pathophysiology is evident, current systematic reviews and meta-analyses analyzing T2D treatment mainly focus on metabolic outcomes. The objective of this study is to evaluate the microbiome and metabolic changes after different types of treatment in T2D patients. Materials and Methods: A systematic search of PubMed, Wiley online library, Science Direct, and Cochrane library electronic databases was performed. Randomized controlled clinical trials published in the last five years that included T2D subjects and evaluated the composition of the gut microbiome alongside metabolic outcomes before and after conventional or alternative glucose lowering therapy were selected. Microbiome changes were evaluated alongside metabolic outcomes in terms of bacteria taxonomic hierarchy, intestinal flora biodiversity, and applied intervention. Results: A total of 16 eligible studies involving 1301 participants were reviewed. Four trials investigated oral glucose-lowering treatment, three studies implemented bariatric surgery, and the rest analyzed probiotic, prebiotic, or synbiotic effects. The most common alterations were increased abundance of Firmicutes and Proteobacteria parallel to improved glycemic control. Bariatric surgery, especially Roux-en-Y gastric bypass, led to the highest variety of changed bacteria phyla. Lower diversity post-treatment was the most significant biodiversity result, which was present with improved glycemic control. Conclusions: Anti-diabetic treatment induced the growth of depleted bacteria. A gut microbiome similar to healthy individuals was achieved during some trials. Further research must explore the most effective strategies to promote beneficial bacteria, lower diversity, and eventually reach a non-T2D microbiome.

RevDate: 2021-10-23

Moon SH, Shin SJ, Tae HJ, et al (2021)

Effects of Colocasia antiquorum var. Esculenta Extract In Vitro and In Vivo against Periodontal Disease.

Medicina (Kaunas, Lithuania), 57(10): pii:medicina57101054.

Background and Objectives: Periodontal disease is a chronic inflammatory disease in which gradual destruction of tissues around teeth is caused by plaque formed by pathogenic bacteria. The purpose of this study was to evaluate the potential of 75% ethanol extract of Colocasia antiquorum var. esculenta (CA) as a prophylactic and improvement agent for periodontal disease in vitro and in vivo. Materials and Methods: The antimicrobial efficacy of CA against Porphyromonas gingivalis (P. gingivalis, ATCC 33277) was evaluated using minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) test, and cytotoxicity was confirmed by CCK-8 assay. For the in vivo study, P. gingivalis was applied by oral gavage to BALB/c mice. Forty-two days after the first inoculation of P. gingivalis, intraoral swabs were taken for microbiome analysis, and the mice were sacrificed to evaluate the alveolar bone loss. Results: The MIC of CA against P. gingivalis was 31.3 μg/mL, the MBC was 62.5 μg/mL, with no cytotoxicity. The diversity of the oral microbiome decreased in the positive control group, while those of the VA (varnish) and VCA (varnish added with CA) groups increased as much as in the negative control group, although the alveolar bone loss was not induced in the mouse model. Conclusions: CA showed antibacterial effects in vitro, and the VA and VCA groups exhibited increased diversity in the oral microbiome, suggesting that CA has potential for improving periodontal disease.

RevDate: 2021-10-23

Chen Y, Wu T, Lu W, et al (2021)

Predicting the Role of the Human Gut Microbiome in Constipation Using Machine-Learning Methods: A Meta-Analysis.

Microorganisms, 9(10): pii:microorganisms9102149.

(1) Background: Constipation is a common condition that affects the health and the quality of life of patients. Recent studies have suggested that the gut microbiome is associated with constipation, but these studies were mainly focused on a single research cohort. Thus, we aimed to construct a classification model based on fecal bacterial and identify the potential gut microbes' biomarkers. (2) Methods: We collected 3056 fecal amplicon sequence data from five research cohorts. The data were subjected to a series of analyses, including alpha- and beta-diversity analyses, phylogenetic profiling analyses, and systematic machine learning to obtain a comprehensive understanding of the association between constipation and the gut microbiome. (3) Results: The alpha diversity of the bacterial community composition was higher in patients with constipation. Beta diversity analysis evidenced significant partitions between the two groups on the base of gut microbiota composition. Further, machine learning based on feature selection was performed to evaluate the utility of the gut microbiome as the potential biomarker for constipation. The Gradient Boosted Regression Trees after chi2 feature selection was the best model, exhibiting a validation performance of 70.7%. (4) Conclusions: We constructed an accurate constipation discriminant model and identified 15 key genera, including Serratia, Dorea, and Aeromonas, as possible biomarkers for constipation.

RevDate: 2021-10-23

Whitworth DE, Sydney N, EJ Radford (2021)

Myxobacterial Genomics and Post-Genomics: A Review of Genome Biology, Genome Sequences and Related 'Omics Studies.

Microorganisms, 9(10): pii:microorganisms9102143.

Myxobacteria are fascinating and complex microbes. They prey upon other members of the soil microbiome by secreting antimicrobial proteins and metabolites, and will undergo multicellular development if starved. The genome sequence of the model myxobacterium Myxococcus xanthus DK1622 was published in 2006 and 15 years later, 163 myxobacterial genome sequences have now been made public. This explosion in genomic data has enabled comparative genomics analyses to be performed across the taxon, providing important insights into myxobacterial gene conservation and evolution. The availability of myxobacterial genome sequences has allowed system-wide functional genomic investigations into entire classes of genes. It has also enabled post-genomic technologies to be applied to myxobacteria, including transcriptome analyses (microarrays and RNA-seq), proteome studies (gel-based and gel-free), investigations into protein-DNA interactions (ChIP-seq) and metabolism. Here, we review myxobacterial genome sequencing, and summarise the insights into myxobacterial biology that have emerged as a result. We also outline the application of functional genomics and post-genomic approaches in myxobacterial research, highlighting important findings to emerge from seminal studies. The review also provides a comprehensive guide to the genomic datasets available in mid-2021 for myxobacteria (including 24 genomes that we have sequenced and which are described here for the first time).

RevDate: 2021-10-23

Van den Abbeele P, Duysburgh C, Cleenwerck I, et al (2021)

Consistent Prebiotic Effects of Carrot RG-I on the Gut Microbiota of Four Human Adult Donors in the SHIME® Model despite Baseline Individual Variability.

Microorganisms, 9(10): pii:microorganisms9102142.

The human gut microbiome is currently recognized to play a vital role in human biology and development, with diet as a major modulator. Therefore, novel indigestible polysaccharides that confer a health benefit upon their fermentation by the microbiome are under investigation. Based on the recently demonstrated prebiotic potential of a carrot-derived pectin extract enriched for rhamnogalacturonan I (cRG-I), the current study aimed to assess the impact of cRG-I upon repeated administration using the M-SHIME technology (3 weeks at 3g cRG-I/d). Consistent effects across four simulated adult donors included enhanced levels of acetate (+21.1 mM), propionate (+17.6 mM), and to a lesser extent butyrate (+4.1 mM), coinciding with a marked increase of OTUs related to Bacteroides dorei and Prevotella species with versatile enzymatic potential likely allowing them to serve as primary degraders of cRG-I. These Bacteroidetes members are able to produce succinate, explaining the consistent increase of an OTU related to the succinate-converting Phascolarctobacterium faecium (+0.47 log10(cells/mL)). While the Bifidobacteriaceae family remained unaffected, a specific OTU related to Bifidobacterium longum increased significantly upon cRG-I treatment (+1.32 log10(cells/mL)). Additional monoculture experiments suggested that Bifidobacterium species are unable to ferment cRG-I structures as such and that B. longum probably feeds on arabinan and galactan side chains of cRG-I, released by aforementioned Bacteroidetes members. Overall, this study confirms the prebiotic potential of cRG-I and additionally highlights the marked consistency of the microbial changes observed across simulated subjects, suggesting the involvement of a specialized consortium in cRG-I fermentation by the human gut microbiome.

RevDate: 2021-10-23

Jung JY, Han SS, Kim ZH, et al (2021)

In-Vitro Characterization of Growth Inhibition against the Gut Pathogen of Potentially Probiotic Lactic Acid Bacteria Strains Isolated from Fermented Products.

Microorganisms, 9(10): pii:microorganisms9102141.

Lactic acid bacteria (LAB) are probiotic candidates that may restore the balance of microbiota populations in intestinal microbial ecosystems by controlling pathogens and thereby promoting host health. The goal of this study was to isolate potential probiotic LAB strains and characterize their antimicrobial abilities against pathogens in intestinal microbiota. Among 54 LAB strains isolated from fermented products, five LAB strains (NSMJ15, NSMJ16, NSMJ23, NSMJ42, and NFFJ04) were selected as potential probiotic candidates based on in vitro assays of acid and bile salt tolerance, cell surface hydrophobicity, adhesion to the intestinal epithelium, and antagonistic activity. Phylogenetic analysis based on 16S rRNA genes showed that they have high similarities of 99.58-100% to Lacticaseibacillus&nbsp;paracasei strains NSMJ15 and NFFJ04, Lentilactobacillus parabuchneri NSMJ16, Levilactobacillus&nbsp;brevis NSMJ23, and Schleiferilactobacillus harbinensis NSMJ42. To characterize their antimicrobial abilities against pathogens in intestinal microbiota, the impact of cell-free supernatant (CFS) treatment in 10% (v/v) fecal suspensions prepared using pooled cattle feces was investigated using in vitro batch cultures. Bacterial community analysis using rRNA amplicon sequencing for control and CFS-treated fecal samples at 8 and 16 h incubation showed the compositional change after CFS treatment for all five LAB strains. The changed compositions were similar among them, but there were few variable increases or decreases in some bacterial groups. Interestingly, as major genera that could exhibit pathogenicity and antibiotic resistance, the members of Bacillus, Escherichia, Leclercia, Morganella, and Vagococcus were decreased at 16 h in all CFS-treated samples. Species-level classification suggested that the five LAB strains are antagonistic to gut pathogens. This study showed the probiotic potential of the five selected LAB strains; in particular, their antimicrobial properties against pathogens present in the intestinal microbiota. These strains would therefore seem to play an important role in modulating the intestinal microbiome of the host.

RevDate: 2021-10-23

Sugino KY, Ma T, Paneth N, et al (2021)

Effect of Environmental Exposures on the Gut Microbiota from Early Infancy to Two Years of Age.

Microorganisms, 9(10): pii:microorganisms9102140.

The gut microbiota undergoes rapid changes during infancy in response to early-life exposures. We have investigated how the infant gut bacterial community matures over time and how exposures such as human milk and antibiotic treatment alter gut microbiota development. We used the LonGP program to create predictive models to determine the contribution of exposures on infant gut bacterial abundances from one month to two years of age. These models indicate that infant antibiotic use, human milk intake, maternal pre-pregnancy BMI, and sample shipping time were associated with changes in gut microbiome composition. In most infants, Bacteroides, Lachnospiraceae unclassified, Faecalibacterium, Akkermansia, and Phascolarctobacterium abundance increased rapidly after 6 months, while Escherichia, Bifidobacterium, Veillonella, and Streptococcus decreased in abundance over time. Individual, time-varying, random effects explained most of the variation in the LonGP models. Multivariate association with linear models (MaAsLin) displayed partial agreement with LonGP in the predicted trajectories over time and in relation to significant factors such as human milk intake. Multiple factors influence the dynamic changes in bacterial composition of the infant gut. Within-individual differences dominate the temporal variations in the infant gut microbiome, suggesting individual temporal variability is an important feature to consider in studies with a longitudinal sampling design.

RevDate: 2021-10-23

Suzuki K, Inoue M, Cho O, et al (2021)

Scalp Microbiome and Sebum Composition in Japanese Male Individuals with and without Androgenetic Alopecia.

Microorganisms, 9(10): pii:microorganisms9102132.

The skin microbiome and sebum may be associated with inflammation-related diseases of the scalp. To assess the pathogenesis and progression of androgenetic alopecia (AGA), we analyzed the composition of sebum and the bacterial and fungal microbiomes of the scalps of 118 Japanese male individuals with and without AGA, then discussed their roles in the pathogenesis of AGA. Sebum triglyceride and palmitic acid contents were higher in the AGA group than in the non-AGA group. Malassezia restricta, a lipophilic fungus that consumes palmitic acid, was abundant on the scalps of patients with AGA. Cutibacterium, Corynebacterium, and Staphylococcus were the most common genera in both groups, and patients with AGA exhibited scalp dysbiosis (increased abundance of Cutibacterium and decreased abundance of Corynebacterium). Our findings suggest that both sebum and the bacterial and fungal microbiomes of the scalp may be involved in the development of AGA.

RevDate: 2021-10-23

Tóthné Bogdányi F, Boziné Pullai K, Doshi P, et al (2021)

Composted Municipal Green Waste Infused with Biocontrol Agents to Control Plant Parasitic Nematodes-A Review.

Microorganisms, 9(10): pii:microorganisms9102130.

The last few years have witnessed the emergence of alternative measures to control plant parasitic nematodes (PPNs). We briefly reviewed the potential of compost and the direct or indirect roles of soil-dwelling organisms against PPNs. We compiled and assessed the most intensively researched factors of suppressivity. Municipal green waste (MGW) was identified and profiled. We found that compost, with or without beneficial microorganisms as biocontrol agents (BCAs) against PPNs, were shown to have mechanisms for the control of plant parasitic nematodes. Compost supports a diverse microbiome, introduces and enhances populations of antagonistic microorganisms, releases nematicidal compounds, increases the tolerance and resistance of plants, and encourages the establishment of a "soil environment" that is unsuitable for PPNs. Our compilation of recent papers reveals that while the scope of research on compost and BCAs is extensive, the role of MGW-based compost (MGWC) in the control of PPNs has been given less attention. We conclude that the most environmentally friendly and long-term, sustainable form of PPN control is to encourage and enhance the soil microbiome. MGW is a valuable resource material produced in significant amounts worldwide. More studies are suggested on the use of MGWC, because it has a considerable potential to create and maintain soil suppressivity against PPNs. To expand knowledge, future research directions shall include trials investigating MGWC, inoculated with BCAs.

RevDate: 2021-10-23

Korneykova M, Nikitin D, V Myazin (2021)

Qualitative and Quantitative Characteristics of Soil Microbiome of Barents Sea Coast, Kola Peninsula.

Microorganisms, 9(10): pii:microorganisms9102126.

The soil microbiome of the Barents Sea coast of the Kola Peninsula is here characterized for the first time. The content of copies of ribosomal genes of archaea, bacteria, and fungi was determined by real-time PCR. Reserves and structure of biomass of soil microorganisms such as total biomass of fungi and prokaryotes, length and diameter of mycelium of fungi and actinomycetes, proportion of mycelium in biomass, number of spores and prokaryotic cells, proportion of small and large fungal propagules, and morphology of mycobiota spores were determined. The largest number of ribosomal gene copies was found for bacteria (from 6.47 × 109 to 3.02 × 1011 per g soil). The number of copies of ribosomal genes of fungi and archaea varied within 107-109 copies of genes/g soil. The biomass of microorganisms (prokaryotes and fungi in total) varied from 0.023 to 0.840 mg/g soil. The share of mycobiota in the microbial biomass ranged from 90% to 97%. The number of prokaryotes was not large and varied from 1.87 × 108 to 1.40 × 109 cells/g of soil, while the biomass of fungi was very significant and varied from 0.021 to 0.715 mg/g of soil. The length of actinomycete mycelium was small-from 0.77 to 88.18 m/g of soil, as was the length of fungal hyphae-an order of magnitude higher (up to 504.22 m/g of soil). The proportion of fungal mycelium, an active component of fungal biomass, varied from 25% to 89%. Most (from 65% to 100%) of mycobiota propagules were represented by specimens of small sizes, 2-3 microns. Thus, it is shown that, despite the extreme position on the mainland land of Fennoscandia, local soils had a significant number of microorganisms, on which the productivity of ecosystems largely depends.

RevDate: 2021-10-23

Ríos-Covian D, Langella P, R Martín (2021)

From Short- to Long-Term Effects of C-Section Delivery on Microbiome Establishment and Host Health.

Microorganisms, 9(10): pii:microorganisms9102122.

The establishment of gut microbiota has been proven to be impacted by several factors during pregnancy, delivery, and neonate periods. The body of evidence describing C-section delivery (CSD) as one of the most disruptive events during early life has expanded in recent years, concluding that CSD results in a drastic change in microbiota establishment patterns. When comparing the gut microbiota composition of CSD babies with vaginally delivered (VD) babies, the former show a microbiome that closely resembles that found in the environment and the mother's skin, while VD babies show a microbiome more similar to the vaginal microbiome. Although these alterations of normal gut microbiota establishment tend to disappear during the first months of life, they still affect host health in the mid-long term since CSD has been correlated with a higher risk of early life infections and non-transmissible diseases, such as inflammatory diseases, allergies, and metabolic diseases. In recent years, this phenomenon has also been studied in other mammals, shedding light on the mechanisms involved in the effects of a CSD on host health. In addition, strategies to revert the disruptions in gut microbiomes caused by a CSD are currently in the process of development and evaluation. In this review, we discuss the recent advances in CSD research, from the alteration of gut microbiota establishment to the possible effects on host health during early life and development.

RevDate: 2021-10-23

Shi J, Yang Y, Xu W, et al (2021)

Sex-Specific Associations between Gut Microbiome and Non-Alcoholic Fatty Liver Disease among Urban Chinese Adults.

Microorganisms, 9(10): pii:microorganisms9102118.

Non-alcoholic fatty liver disease (NAFLD) has been linked to altered gut microbiome; however, evidence from large population-based studies is limited. We compared gut microbiome profiles of 188 male and 233 female NAFLD cases with 571 male and 567 female controls from two longitudinal studies of urban Chinese adults. History of NAFLD was assessed during surveys administered in 2004-2017. Microbiota were assessed using 16S rRNA sequencing of stool samples collected in 2015-2018. Associations of NAFLD with microbiome diversity and composition were evaluated by generalized linear or logistic regression models. Compared with controls, male cases had lower microbial α-diversity, higher abundance of genera Dialister and Streptococcus and Bifidobacterium species, lower abundance of genus Phascolarctobacterium, and lower prevalence of taxa including order RF39 (all p < 0.05). In contrast, female cases had higher α-diversity, higher abundance of genus Butyricimonas and a family of order Clostridiales, lower abundance of Dialister and Bifidobacterium species, and higher prevalence of RF39. Significant NAFLD-sex interactions were found for α-diversity and above taxa (all false discovery rate < 0.1). In conclusion, we observed sex-specific gut microbiome features related to history of NAFLD. Further studies are needed to validate our findings and evaluate the health effects of NAFLD-related gut microbiota.

RevDate: 2021-10-23

Dogra SK, Cheong KC, Wang D, et al (2021)

Nurturing the Early Life Gut Microbiome and Immune Maturation for Long Term Health.

Microorganisms, 9(10): pii:microorganisms9102110.

Early life is characterized by developmental milestones such as holding up the head, turning over, sitting up and walking that are typically achieved sequentially in specific time windows. Similarly, the early gut microbiome maturation can be characterized by specific temporal microorganism acquisition, colonization and selection with differential functional features over time. This orchestrated microbial sequence occurs from birth during the first years of age before the microbiome reaches an adult-like composition and function between 3 and 5 years of age. Increasingly, these different steps of microbiome development are recognized as crucial windows of opportunity for long term health, primarily linked to appropriate immune and metabolic development. For instance, microbiome disruptors such as preterm and Cesarean-section birth, malnutrition and antibiotic use are associated with increased risk to negatively affect long-term immune and metabolic health. Different age discriminant microbiome taxa and functionalities are used to describe age-appropriate microbiome development, and advanced modelling techniques enable an understanding and visualization of an optimal microbiome maturation trajectory. Specific microbiome features can be related to later health conditions, however, whether such features have a causal relationship is the topic of intense research. Early life nutrition is an important microbiome modulator, and 'Mother Nature' provides the model with breast milk as the sole source of nutrition for the early postnatal period, while dietary choices during the prenatal and weaning period are to a large extent guided by tradition and culture. Increasing evidence suggests prenatal maternal diet and infant and child nutrition impact the infant microbiome trajectory and immune competence development. The lack of a universal feeding reference for such phases represents a knowledge gap, but also a great opportunity to provide adequate nutritional guidance to maintain an age-appropriate microbiome for long term health. Here, we provide a narrative review and perspective on our current understanding of age-appropriate microbiome maturation, its relation to long term health and how nutrition shapes and influences this relationship.

RevDate: 2021-10-23

Mohamed YH, Uematsu M, Morinaga Y, et al (2021)

Conjunctival Sac Microbiome in Infectious Conjunctivitis.

Microorganisms, 9(10): pii:microorganisms9102095.

Acute bacterial conjunctival infections are common, and this study identified the conjunctival bacterial community in infectious conjunctivitis cases seen at the outpatient clinic of Khanh Hoa General Hospital in Nha Trang, Vietnam from October 2016 through December 2017. Conjunctival swabs were collected and tested using conventional culture, PCR, and 16S ribosomal RNA sequencing. The study included 47 randomly selected patients. More than 98% of all DNA reads represented five bacterial phyla. Three of these phyla constituted 92% of all sequences (Firmicutes (35%), Actinobacteria (31%), and Proteobacteria (26%)). At the genus level, there were 12 common genera that constituted about 61% of all sequence reads. Seven of those genera were common (Streptococcus (10%), Cutibacterium (10%), Staphylococcus (7%), Nocardioides (7%), Corynebacterium 1 (5%), Anoxybacillus (5%), and Acinetobacter (5%)), which encompassed 49% of all reads. As for diversity analysis, there was no difference on PERMANOVA analysis (unweighted UniFrac) for sex (p = 0.087), chemosis (p = 0.064), and unclassified eyedrops (p = 0.431). There was a significant difference in cases with bilateral conjunctivitis (p = 0.017) and for using antibiotics (p = 0.020). Of the predominant phyla, Firmicutes had the highest abundance in bacterial conjunctivitis in this study. Pseudomonas as a resident commensal microbiota may have an important role in the prevention of infection.

RevDate: 2021-10-23

Parkar SG, Rosendale DI, Stoklosinski HM, et al (2021)

Complementary Food Ingredients Alter Infant Gut Microbiome Composition and Metabolism In Vitro.

Microorganisms, 9(10): pii:microorganisms9102089.

We examined the prebiotic potential of 32 food ingredients on the developing infant microbiome using an in vitro gastroileal digestion and colonic fermentation model. There were significant changes in the concentrations of short-chain fatty-acid metabolites, confirming the potential of the tested ingredients to stimulate bacterial metabolism. The 16S rRNA gene sequencing for a subset of the ingredients revealed significant increases in the relative abundances of the lactate- and acetate-producing Bifidobacteriaceae, Enterococcaceae, and Lactobacillaceae, and lactate- and acetate-utilizing Prevotellaceae, Lachnospiraceae, and Veillonellaceae. Selective changes in specific bacterial groups were observed. Infant whole-milk powder and an oat flour enhanced Bifidobacteriaceae and lactic acid bacteria. A New Zealand-origin spinach powder enhanced Prevotellaceae and Lachnospiraceae, while fruit and vegetable powders increased a mixed consortium of beneficial gut microbiota. All food ingredients demonstrated a consistent decrease in Clostridium perfringens, with this organism being increased in the carbohydrate-free water control. While further studies are required, this study demonstrates that the selected food ingredients can modulate the infant gut microbiome composition and metabolism in vitro. This approach provides an opportunity to design nutrient-rich complementary foods that fulfil infants' growth needs and support the maturation of the infant gut microbiome.

RevDate: 2021-10-23

Parkin K, Christophersen CT, Verhasselt V, et al (2021)

Risk Factors for Gut Dysbiosis in Early Life.

Microorganisms, 9(10): pii:microorganisms9102066.

Dysbiosis refers to a reduction in microbial diversity, combined with a loss of beneficial taxa, and an increase in pathogenic microorganisms. Dysbiosis of the intestinal microbiota can have a substantial effect on the nervous and immune systems, contributing to the onset of several inflammatory diseases. Epidemiological studies provided insight in how changes in the living environment have contributed to an overall loss of diversity and key taxa in the gut microbiome, coinciding with increased reports of atopy and allergic diseases. The gut microbiome begins development at birth, with major transition periods occurring around the commencement of breastfeeding, and the introduction of solid foods. As such, the development of the gut microbiome remains highly plastic and easily influenced by environmental factors until around three years of age. Developing a diverse and rich gut microbiome during this sensitive period is crucial to setting up a stable gut microbiome into adulthood and to prevent gut dysbiosis. Currently, the delivery route, antibiotic exposure, and diet are the best studied drivers of gut microbiome development, as well as risk factors of gut dysbiosis during infancy. This review focuses on recent evidence regarding key environmental factors that contribute to promoting gut dysbiosis.

RevDate: 2021-10-23

Zhang C, Burch M, Wylie K, et al (2021)

Characterization of the Eukaryotic Virome of Mice from Different Sources.

Microorganisms, 9(10): pii:microorganisms9102064.

Accumulating studies show that the host microbiome influences the development or progression of many diseases. The eukaryotic virome, as a key component of the microbiome, plays an important role in host health and disease in humans and animals, including research animals designed to model human disease. To date, the majority of research on the microbiome has focused on bacterial populations, while less attention has been paid to the viral component. Members of the eukaryotic virome interact with the commensal bacterial microbiome through trans-kingdom interactions, and influence host immunity and disease phenotypes as a collective microbial ecosystem. As such, differences in the virome may affect the reproducibility of animal models, and supplementation of the virome may enhance the translatability of animal models of human disease. However, there are minimal empirical data regarding differences in the virome of mice from different commercial sources. Our hypotheses were that the mice obtained from pet store sources and lab mice differ in their eukaryotic virome, and that lab mice from different sources would also have different viromes. To test this hypothesis, the ViroCap platform was used to characterize the eukaryotic virome in multiple tissues of mice from different sources including three sources of laboratory mice and two pet stores. As expected, pet store mice harbored a much greater diversity within the virome compared to lab mice. This included an ostensibly novel norovirus strain identified in one source of these mice. Viruses found in both laboratory and pet store populations included four strains of endogenous retroviruses and murine astrovirus with the latter being restricted to one source of lab mice. Considering the relatively high richness virome within different samples from healthy humans, these data suggest that mouse models from alternative sources may be more translational to the human condition. Moreover, these data demonstrate that, by characterizing the eukaryotic murine virome from different sources, novel viruses may be identified for use as field strains in biomedical research.

RevDate: 2021-10-23

Huyben D, Chiasson M, Lumsden JS, et al (2021)

Dietary Microencapsulated Blend of Organic Acids and Plant Essential Oils Affects Intestinal Morphology and Microbiome of Rainbow Trout (Oncorhynchus mykiss).

Microorganisms, 9(10): pii:microorganisms9102063.

A study was conducted on 500 juvenile rainbow trout (122 ± 4 g) fed either a control diet or a treatment diet containing 300 mg/kg of a microencapsulated blend of organic acids and essential oils to elucidate effects on intestinal morphology and microbiome. Proximal intestinal villi length was significantly increased in fish fed the treatment diet. Despite no differences in gut inflammation scores, edema, lamina propria inflammation and apoptosis were completely absent in the distal intestine of fish fed the treatment diet. Next-generation sequencing of the 16S rDNA showed no differences in alpha and beta diversity, and gut bacteria were mainly composed of Firmicutes, Bacteroidetes and Proteobacteria. On the genus level, LefSe analysis of indicator OTUs showed Bacteroides, Sporosarcina, Veillonella, Aeromonas and Acinetobacter were associated with the control diet whereas Streptococcus, Fusobacterium and Escherichia were associated with the treatment diet. Aeromonas hydrophila and Acinetobacter spp. are opportunistic pathogens and several strains have been found to be resistant to antibiotics. The increase in villi length and reduction of specific pathogens indicates that feeding a microencapsulated blend of organic acids and essential oils improves gut health and may serve as a part of an effective strategy to reduce antibiotic use in aquaculture.

RevDate: 2021-10-23

Xu W, Wang F, Wang R, et al (2021)

Seasonal Characterization of the Endophytic Fungal Microbiome of Mulberry (Morus spp.) Cultivars Resistant and Susceptible to Sclerotiniosis.

Microorganisms, 9(10): pii:microorganisms9102052.

The endophytic microbiome is thought to play an important role in promoting plant growth and health. Using culture-independent and culture-dependent protocols, this study characterized the seasonal shifts in the endophytic fungal microbiota of four mulberry (Morus L.) cultivars having different levels of resistance to mulberry fruit sclerotiniosis. Core endophytes can be obtained by two approaches, and they were divided into two clusters by season. Spring samples harbored higher operational taxonomic units (OTUs) and α-diversity, while autumn samples had more sequences or isolates of the fungal class Dothideomycetes with the representative orders Capnodiales and Pleosporales. While comparing different mulberry cultivars, we found that the total number of OTUs in susceptible cultivars was higher than that of resistant cultivars, and Cladosporium sp. were observed in all. Notably, the causal agent of fruit sclerotiniosis (Scleromitrula shiraiana) was only detected in susceptible cultivars. Collectively, our work elucidated significant variations in the mulberry endophytic microbiome, mainly because of seasonal shifts, and the fact that the host cultivars and mulberry endophytic fungal community appeared to have a certain connection with the resistance level of mulberry fruit to sclerotiniosis. These results provided valuable information on the isolation and culturing of mulberry endophytes that could be applied to improve mulberry fruit production and health.

RevDate: 2021-10-23

Fujii T, Fujitomo T, Tsuji R, et al (2021)

Effects of Heat-Killed Lactococcus lactis Strain Plasma on Skin Homeostasis-Related Genes and the Skin Microbiome among Healthy Adults: A Randomized Controlled Double-Blind Study.

Microorganisms, 9(10): pii:microorganisms9102029.

Lactococcus lactis subsp. lactis strain plasma (LC-plasma) is a bacterial strain that activates plasmacytoid dendritic cells and induces viral resistance genes via the TLR9/MyD88 pathway. We recently showed that oral administration of LC-plasma prevents skin infection by Staphylococcus aureus, possibly by activating skin immunity. In this study, we conducted a double-blind clinical trial to investigate the effect of oral administration of heat-killed LC-plasma on the skin microbiome, gene expression in the skin, and the skin condition of healthy volunteers. Seventy healthy volunteers were randomly assigned to receive either heat-killed LC-plasma or a placebo for eight weeks. Analysis of the skin microbiome by next-generation sequencing suggested that the alpha-diversity of the skin microbiome did not change during the test period in either group. However, the proportion of species that changed significantly during the test period was 10-fold smaller in the LC-plasma group than in the placebo group, suggesting that LC-plasma may maintain the skin microbiome. Quantitative PCR analysis indicated that tight-junction genes, such as CLDN1 and CLDN12, and the antimicrobial peptide gene BD3 were significantly up-regulated in the LC-plasma group but not in the placebo group. Our results suggest that administration of LC-plasma helps to maintain the skin microbiome and that it affects homeostasis-related genes.

RevDate: 2021-10-23

Alzahrani KJ (2021)

Microbiome Studies from Saudi Arabia over the Last 10 Years: Achievements, Gaps, and Future Directions.

Microorganisms, 9(10): pii:microorganisms9102021.

In the past ten years, microbiome studies have shown tremendous potentiality for implementation of understanding microbiome structures and functions of various biomes and application of this knowledge for human betterment. Saudi Arabia is full of geographical, ecological, ethnical, and industrial diversities and scientific capacities. Therefore, there is a great potential in Saudi Arabia to conduct and implement microbiome-based research and applications. However, there is no review available on where Saudi Arabia stands with respect to global microbiome research trends. This review highlights the metagenome-assisted microbiome research from Saudi Arabia compared to the global focuses on microbiome research. Further, it also highlights the gaps and areas that should be focused on by Saudi microbiome researchers and the possible initiatives to be taken by Saudi government and universities. This literature review shows that the global trends of microbiome research cover a broad spectrum of human and animal health conditions and diseases, environmental and antimicrobial resistance surveillance, surveillance of food and food processing, production of novel industrial enzymes and bioactive pharmaceutical products, and space applications. However, Saudi microbiome studies are mostly confined to very few aspects of health (human and animal) and environment/ecology in last ten years, without much application. Therefore, Saudi Arabia should focus more on applied microbiome research through government, academic, and industry initiatives and global cooperation to match the global trends.

RevDate: 2021-10-23

Rocha R, Vaz Velho M, Santos J, et al (2021)

Serra da Estrela PDO Cheese Microbiome as Revealed by Next Generation Sequencing.

Microorganisms, 9(10): pii:microorganisms9102007.

Serra da Estrela PDO cheese is the oldest traditional cheese manufactured in Portugal. In this work, its microbiome as well as the main raw materials used in cheese production, raw ewes' milk and thistle flowers (Cynara cardunculus L.), were characterized using next generation sequencing. Samples were accordingly retrieved from a local producer over two consecutive production campaigns and at different time periods within each campaign. The bacterial and fungi communities associated with each matrix were accessed through sequencing of V3-V4 and Internal Transcribed Spacer 2 regions of rRNA gene amplicons, respectively. A high microbial diversity was found associated to each matrix, differing significantly (p < 0.05) from each other. Over 500 taxa were identified in each analyzed matrix, ranging from dominant (relative abundance > 1%), sub-dominant (0.01-1%) and rare taxa (<0.01%). Specifically, in cheese, 30 taxa were present in all analyzed samples (core taxa), including species of Leuconostoc spp. and Lactococcus spp. for bacteria and Candida spp., Debaryomyces spp. and Yarrowia spp. for fungi, that were cumulatively the most prevalent genera in Serra da Estrela PDO cheese (average relative abundance ≥10%). Ultimately, this characterization study may contribute to a better understanding of the microbial dynamics of this traditional PDO product, namely the influence of raw materials on cheese microbiome, and could assist producers interested in preserving the identity, quality and safety of Serra da Estrela PDO cheese.

RevDate: 2021-10-23

Guccione C, Yadlapati R, Shah S, et al (2021)

Challenges in Determining the Role of Microbiome Evolution in Barrett's Esophagus and Progression to Esophageal Adenocarcinoma.

Microorganisms, 9(10): pii:microorganisms9102003.

Esophageal adenocarcinoma (EAC) claims the lives of half of patients within the first year of diagnosis, and its incidence has rapidly increased since the 1970s despite extensive research into etiological factors. The changes in the microbiome within the distal esophagus in modern populations may help explain the growth in cases that other common EAC risk factors together cannot fully explain. The precursor to EAC is Barrett's esophagus (BE), a metaplasia adapted to a reflux-mediated microenvironment that can be challenging to diagnose in patients who do not undergo endoscopic screening. Non-invasive procedures to detect microbial communities in saliva, oral swabs and brushings from the distal esophagus allow us to characterize taxonomic differences in bacterial population abundances within patients with BE versus controls, and may provide an alternative means of BE detection. Unique microbial communities have been identified across healthy esophagus, BE, and various stages of progression to EAC, but studies determining dynamic changes in these communities, including migration from proximal stomach and oral cavity niches, and their potential causal role in cancer formation are lacking. Helicobacter pylori is negatively associated with EAC, and the absence of this species has been implicated in the evolution of chromosomal instability, a main driver of EAC, but joint analyses of microbiome and host genomes are needed. Acknowledging technical challenges, future studies on the prediction of microbial dynamics and evolution within BE and the progression to EAC will require larger esophageal microbiome datasets, improved bioinformatics pipelines, and specialized mathematical models for analysis.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )