@article {pmid33472193, year = {2021}, author = {Aburahma, A and Pachhain, S and Choudhury, SR and Rana, S and Phuntumart, V and Larsen, R and Sprague, JE}, title = {Potential Contribution of the Intestinal Microbiome to Phenethylamine-Induced Hyperthermia.}, journal = {Brain, behavior and evolution}, volume = {}, number = {}, pages = {1-16}, doi = {10.1159/000512098}, pmid = {33472193}, issn = {1421-9743}, abstract = {Phenethylamines (e.g., methamphetamine) are a common source of drug toxicity. Phenethylamine-induced hyperthermia (PIH) can activate a cascade of events that may result in rhabdomyolysis, coagulopathy, and even death. Here, we review recent evidence that suggests a potential link between the gut-brain axis and PIH. Within the preoptic area of the hypothalamus, phenethylamines lead to changes in catecholamine levels, that activate the sympathetic nervous system (SNS) and increase the peripheral levels of norepinephrine (NE), resulting in: (1) the loss of heat dissipation through α1 adrenergic receptor (α1-AR)-mediated vasoconstriction, (2) heat generation through β-AR activation and subsequent free fatty acid (FFA) activation of uncoupling proteins (UCPs) in brown and white adipose tissue, and (3) alteration of the gut microbiome and its link to the gut-brain axis. Recent studies have shown that phenethylamine derivatives can influence the composition of the gut microbiome and thus its metabolic potential. Phenethylamines increase the relative level of Proteuswhich has been linked to enhanced NE turnover. Bidirectional fecal microbial transplants (FMT) between PIH-tolerant and PIH-naïve rats demonstrated that the transplantation of gut microbiome can confer phenotypic hyperthermic and tolerant responses to phenethylamines. These phenethylamine-mediated changes in the gut microbiome were also associated with epigenetic changes in the mediators of thermogenesis. Given the significant role that the microbiome has been shown to play in the maintenance of body temperature, we outline current studies demonstrating the effects of phenethylamines on the gut microbiome and how these microbiome changes may mechanistically contribute to alterations in body temperature.}, } @article {pmid33472009, year = {2021}, author = {Ray, LA and Grodin, EN}, title = {Clinical Neuroscience of Addiction: What Clinical Psychologists Need to Know and Why.}, journal = {Annual review of clinical psychology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-clinpsy-081219-114309}, pmid = {33472009}, issn = {1548-5951}, abstract = {The last three decades in psychological research have been marked by interdisciplinary science. Addiction represents a prime example of a disorder marked by a complex interaction among psychosocial and biological factors. This review highlights critical findings in the basic neuroscience of addiction and translates them into clinical language that can inform clinical psychologists in their research, teaching, and practice. From mechanisms of reward processing, learning and memory, allostasis, incentive-sensitization, withdrawal, tolerance, goal-directed decision making, habit learning, genetics, inflammation, and the microbiome, the common theme of this review is to illustrate the clinical utility of basic neuroscience research and to identify opportunities for clinical science. The thoughtful integration of basic and clinical science provides a powerful tool to fulfill the scientific mission of improving health care. Clinical psychologists have a crucial role to play in the translational science of addiction. Expected final online publication date for the Annual Review of Clinical Psychology, Volume 17 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, } @article {pmid33472004, year = {2021}, author = {Baumgarth, N}, title = {The Shaping of a B Cell Pool Maximally Responsive to Infections.}, journal = {Annual review of immunology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-immunol-042718-041238}, pmid = {33472004}, issn = {1545-3278}, abstract = {B cell subsets differ in development, tissue distribution, and mechanisms of activation. In response to infections, however, all can differentiate into extrafollicular plasmablasts that rapidly provide highly protective antibodies, indicating that these plasmablasts are the main humoral immune response effectors. Yet, the effectiveness of this response type depends on the presence of antigen-specific precursors in the circulating mature B cell pool, a pool that is generated initially through the stochastic processes of B cell receptor assembly. Importantly, germinal centers then mold the repertoire of this B cell pool to be increasingly responsive to pathogens by generating a broad array of antimicrobial memory B cells that act as highly effective precursors of extrafollicular plasmablasts. Such B cell repertoire molding occurs in two ways: continuously via the chronic germinal centers of mucosal lymphoid tissues, driven by the presence of the microbiome, and via de novo generated germinal centers following acute infections. For effectively evaluating humoral immunity as a correlate of immune protection, it might be critical to measure memory B cell pools in addition to antibody titers. Expected final online publication date for the Annual Review of Immunology, Volume 39 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, } @article {pmid33471121, year = {2021}, author = {Shah, N and Molloy, EK and Pop, M and Warnow, T}, title = {TIPP2: metagenomic taxonomic profiling using phylogenetic markers.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btab023}, pmid = {33471121}, issn = {1367-4811}, abstract = {MOTIVATION: Metagenomics has revolutionized microbiome research by enabling researchers to characterize the composition of complex microbial communities. Taxonomic profiling is one of the critical steps in metagenomic analyses. Marker genes, which are single-copy and universally found across Bacteria and Archaea, can provide accurate estimates of taxon abundances in the sample.

RESULTS: We present TIPP2, a marker gene-based abundance profiling method, that combines phylogenetic placement with statistical techniques to control classification precision and recall. TIPP2 includes an updated set of reference packages and several algorithmic improvements over the original TIPP method. We find that TIPP2 provides comparable or better estimates of abundance than other profiling methods (including Bracken, mOTUsv2, and MetaPhlAn2), and strictly dominates other methods when there are under-represented (novel) genomes present in the dataset.

The code for our method is freely available in open source form at https://github.com/smirarab/sepp/blob/tipp2/README.TIPP.mdThe code and procedure to create new reference packages for TIPP2 are available at https://github.com/shahnidhi/TIPP_reference_package.

SUPPLEMENTARY INFORMATION: Not available online.}, } @article {pmid33471054, year = {2021}, author = {Yu, D and Nguyen, SM and Yang, Y and Xu, W and Cai, H and Wu, J and Cai, Q and Long, J and Zheng, W and Shu, XO}, title = {Long-term diet quality is associated with gut microbiome diversity and composition among urban Chinese adults.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1093/ajcn/nqaa350}, pmid = {33471054}, issn = {1938-3207}, abstract = {BACKGROUND: Few population-based studies have evaluated the influence of long-term diet on the gut microbiome, and data among Asian populations are lacking.

OBJECTIVE: We examined the association of long-term diet quality, comprising 8 food groups (fruit, vegetables, dairy, fish/seafood, nuts/legumes, refined grains, red meat, and processed meat), with gut microbiome among Chinese adults.

METHODS: Included were 1920 men and women, enrolled in 2 prospective cohorts (baseline 1996-2006), who remained free of cardiovascular diseases, diabetes, and cancer at stool collection (2015-2018) and had no diarrhea or antibiotic use in the last 7 d before stool collection. Microbiome was profiled by 16S rRNA sequencing. Long-term diet was assessed by repeated surveys at baseline and follow-ups (1996-2011), with intervals of 5.2 to 20.5 y between dietary surveys and stool collection. Associations of dietary variables with microbiome diversity and composition were evaluated by linear or negative binomial hurdle models, adjusting for potential confounders. False discovery rate (FDR) <0.1 was considered significant.

RESULTS: The mean ± SD age at stool collection was 68 ± 1.5 y. Diet quality was positively associated with microbiome α-diversity (P = 0.03) and abundance of Firmicutes, Actinobacteria, Tenericutes, and genera/species within these phyla, including Coprococcus, Faecalibacterium/Faecalibacterium prausnitzii, Bifidobacterium / Bifidobacterium adolescentis, and order RF39 (all FDRs <0.1). Significant associations were also observed for intakes of dairy, fish/seafood, nuts/legumes, refined grains, and processed meat, including a positive association of dairy with Bifidobacterium and inverse associations of processed meat with Roseburia /Roseburia faecis. Most associations were similar, with or without adjustment for BMI and hypertension status or excluding participants with antibiotic use in the past 6 mo.

CONCLUSION: Among apparently healthy Chinese adults, long-term diet quality is positively associated with fecal microbiome diversity and abundance of fiber-fermenting bacteria, although magnitudes are generally small. Future studies are needed to examine if these bacteria may mediate or modify diet-disease relations.}, } @article {pmid33471045, year = {2021}, author = {Zinöcker, MK and Svendsen, K and Dankel, SN}, title = {The homeoviscous adaptation to dietary lipids (HADL) model explains controversies over saturated fat, cholesterol, and cardiovascular disease risk.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1093/ajcn/nqaa322}, pmid = {33471045}, issn = {1938-3207}, abstract = {SFAs play the leading role in 1 of the greatest controversies in nutrition science. Relative to PUFAs, SFAs generally increase circulating concentrations of LDL cholesterol, a risk factor for atherosclerotic cardiovascular disease (ASCVD). However, the purpose of regulatory mechanisms that control the diet-induced lipoprotein cholesterol dynamics is rarely discussed in the context of human adaptive biology. We argue that better mechanistic explanations can help resolve lingering controversies, with the potential to redefine aspects of research, clinical practice, dietary advice, public health management, and food policy. In this paper we propose a novel model, the homeoviscous adaptation to dietary lipids (HADL) model, which explains changes in lipoprotein cholesterol as adaptive homeostatic adjustments that serve to maintain cell membrane fluidity and hence optimal cell function. Due to the highly variable intake of fatty acids in humans and other omnivore species, we propose that circulating lipoproteins serve as a buffer to enable the rapid redistribution of cholesterol molecules between specific cells and tissues that is necessary with changes in dietary fatty acid supply. Hence, circulating levels of LDL cholesterol may change for nonpathological reasons. Accordingly, an SFA-induced raise in LDL cholesterol in healthy individuals could represent a normal rather than a pathologic response. These regulatory mechanisms may become disrupted secondarily to pathogenic processes in association with insulin resistance and the presence of other ASCVD risk factors, as supported by evidence showing diverging lipoprotein responses in healthy individuals as opposed to those with metabolic disorders such as insulin resistance and obesity. Corresponding with the model, we suggest alternative contributing factors to the association between elevated LDL cholesterol concentrations and ASCVD, involving dietary factors beyond SFAs, such as an increased endotoxin load from diet-gut microbiome interactions and subsequent chronic low-grade inflammation that interferes with fine-tuned signaling pathways.}, } @article {pmid33470871, year = {2021}, author = {Neubert, H and Alley, SC and Lee, A and Jian, W and Buonarati, M and Edmison, A and Garofolo, F and Gorovits, B and Haidar, S and Mylott, B and Nouri, P and Qian, M and Vinter, S and Voelker, T and Welink, J and Wu, J and Yang, E and Yu, H and Evans, C and Summerfield, S and Wang, J and Bateman, K and Boer, J and Dean, B and Dillen, L and Faustino, P and Ferrari, L and Hughes, N and Luo, L and Olah, T and Post, N and Spellman, DS and Sydor, J and Zhang, H and Zhang, J and Zhang, J and Fandozzi, C and Wilson, A and Fraier, D and Beaver, CJ and Dandamudi, S and Dasgupta, A and Elliott, R and Ji, A and Li, W and McGuinness, M and Lima Santos, GM and Mirza, T and Savoie, N and Shakleya, D and Sporring, S and Stojdl, S and Sundman, P and Tampal, N and Woolf, E}, title = {2020 White Paper on Recent Issues in Bioanalysis: BMV of Hybrid Assays, Acoustic MS, HRMS, Data Integrity, Endogenous Compounds, Microsampling and Microbiome (Part 1 - Recommendations on Industry/Regulators Consensus on BMV of Biotherapeutics by LCMS, Advanced Application in Hybrid Assays, Regulatory Challenges in Mass Spec, Innovation in Small Molecules, Peptides and Oligos).}, journal = {Bioanalysis}, volume = {}, number = {}, pages = {}, doi = {10.4155/bio-2020-0324}, pmid = {33470871}, issn = {1757-6199}, abstract = {The 14th edition of the Workshop on Recent Issues in Bioanalysis (14th WRIB) was held virtually on June 15-29, 2020 with an attendance of over 1000 representatives from pharmaceutical/biopharmaceutical companies, biotechnology companies, contract research organizations, and regulatory agencies worldwide. The 14th WRIB included three Main Workshops, seven Specialized Workshops that together spanned 11 days in order to allow exhaustive and thorough coverage of all major issues in bioanalysis, biomarkers, immunogenicity, gene therapy, cell therapy and vaccine. Moreover, a comprehensive vaccine assays track; an enhanced cytometry track and updated Industry/Regulators consensus on BMV of biotherapeutics by Mass Spectrometry (hybrid assays, LCMS and HRMS) were special features in 2020. As in previous years, this year's WRIB continued to gather a wide diversity of international industry opinion leaders and regulatory authority experts working on both small and large molecules to facilitate sharing and discussions focused on improving quality, increasing regulatory compliance and achieving scientific excellence on bioanalytical issues. This 2020 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop and is aimed to provide the Global Bioanalytical Community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2020 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication covers the recommendations on (Part 1) Hybrid Assays, Innovation in Small Molecules, & Regulated Bioanalysis. Part 2A (BAV, PK LBA, Flow Cytometry Validation and Cytometry Innovation), Part 2B (Regulatory Input) and Part 3 (Vaccine, Gene/Cell Therapy, NAb Harmonization and Immunogenicity) are published in volume 13 of Bioanalysis, issues 5, and 6 (2021), respectively.}, } @article {pmid33470492, year = {2021}, author = {Harbison, JE and Thomson, RL and Wentworth, JM and Louise, J and Roth-Schulze, A and Battersby, RJ and Ngui, KM and Penno, MAS and Colman, PG and Craig, ME and Barry, SC and Tran, CD and Makrides, M and Harrison, LC and Couper, JJ}, title = {Associations between diet, the gut microbiome and short chain fatty acids in youth with islet autoimmunity and type 1 diabetes.}, journal = {Pediatric diabetes}, volume = {}, number = {}, pages = {}, doi = {10.1111/pedi.13178}, pmid = {33470492}, issn = {1399-5448}, abstract = {AIM: We aimed to characterise associations between diet and the gut microbiome and short chain fatty acid products in youth with islet autoimmunity or type 1 diabetes (IA/T1D) in comparison with controls.

RESEARCH DESIGN AND METHODS: 80 participants (25 diagnosed with T1D, 17 with confirmed IA, 38 sibling or unrelated controls) from the Australian Type 1 Diabetes Gut Study cohort were studied [median (IQR) age 11.7 (8.9,14.0) years, 43% female]. A Food Frequency Questionnaire characterised daily macronutrient intake over the preceding 6 months. Plasma and fecal short chain fatty acids were measured by gas chromatography; gut microbiome composition and diversity by 16S rRNA gene sequencing.

RESULTS: A 10g increase in daily carbohydrate intake associated with higher plasma acetate in IA/T1D [adjusted estimate +5.2 (95% CI 1.1, 9.2) μmol/L p=0.01] and controls [adjusted estimate +4.1 (95% CI 1.7, 8.5) μmol/L p=0.04]. A 5g increase in total fat intake associated with lower plasma acetate in IA/T1D and controls. A five percent increase in non-core (junk) food intake associated with reduced richness [adjusted estimate -4.09 (95%CI -7.83, -0.35) p=0.03] and evenness [-1.25 (95% CI -2.00, -0.49) p<0.01] of the gut microbiome in IA/T1D. Fiber intake associated with community structure of the microbiome in IA/T1D.

CONCLUSIONS: Modest increments in carbohydrate and fat intake associated with plasma acetate in all youth. Increased junk food intake associated with reduced diversity of the gut microbiome in IA/T1D alone. These associations with the gut microbiome in IA/T1D support future efforts to promote short chain fatty acids by using dietary interventions. This article is protected by copyright. All rights reserved.}, } @article {pmid33469669, year = {2021}, author = {Zhang, K and He, C and Xu, Y and Zhang, C and Li, C and Jing, X and Wang, M and Yang, Y and Suo, L and Kalds, P and Song, J and Wang, X and Brugger, D and Wu, Y and Chen, Y}, title = {Taxonomic and functional adaption of the gastrointestinal microbiome of goats kept at high altitude (4800 m) under intensive or extensive rearing conditions.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab009}, pmid = {33469669}, issn = {1574-6941}, abstract = {The gut microbiota composition is influenced by the diet as well as the environment in both wild and domestic animals. We studied the effects of two feeding systems on the rumen and hindgut microbiome of semi-feral Tibetan goats kept at high altitude (∼4800 m) using 16S rRNA gene and metagenomic sequencing. Intensive drylot feeding resulted in significantly higher zootechnical performance, narrower ruminal acetate: propionate ratios and a drop in the average rumen pH at slaughter to ∼5.04. Hindgut microbial adaption appeared to be more diverse in the drylot group suggesting a higher influx of undegraded complex non-starch polysaccharides from the rumen. Despite their higher fiber levels in the diet, grazing goats exhibited lower counts of Methanobrevibacter and genes associated with the hydrogenotrophic methanogenesis pathway, presumably reflecting the scarce dietary conditions (low energy density) when rearing goats on pasture from extreme alpine environments. These conditions appeared to promote a relevant abundance of bacitracin genes. In parallel, we recognized a significant increase in the abundance of antibiotic resistance genes in the digestive tracts of drylot animals. In summary, this study provides a deeper insight into the metataxonomic and functional adaption of the gastrointestinal microbiome of goats subject to intensive drylot and extensive pasture rearing conditions at high altitude.}, } @article {pmid33469555, year = {2020}, author = {Qi, R and Qiu, X and Du, L and Wang, J and Wang, Q and Huang, J and Liu, Z}, title = {Changes of Gut Microbiota and Its Correlation With Short Chain Fatty Acids and Bioamine in Piglets at the Early Growth Stage.}, journal = {Frontiers in veterinary science}, volume = {7}, number = {}, pages = {617259}, doi = {10.3389/fvets.2020.617259}, pmid = {33469555}, issn = {2297-1769}, abstract = {The change characteristics of intestinal microbial succession and the correlation with the production of two important types of bacterial metabolites (short chain fatty acids and bioamine) in piglets during the early stage were fully explored in this study. Six piglets from different litters with the same birth time were selected, weighted and euthanized at 1, 7, 14, 21, 28, 35, and 42 days of age. During this stage, the piglets grew quickly with gradual increases in blood levels of growth hormone and insulin, and in the intestinal developmental index and immunity. 16s rRNA analysis indicated the alpha diversity of colonic microbiome community was higher than ileum. However, the composition change in the ileal microbiota was more dramatic over time. Lactobacillus genus was the dominant bacteria in piglets' ileum while Prevotella and Ruminococcaceae genera were the dominant bacteria in colon up to weaning. Gut bacterial community of the piglets showed obvious differences between the three different phases: newborn, before weaning, and post weaning. This was similar to the morphological change pattern of pigs' gut. Total SCFA content in the colon of pigs showed almost a 20-fold increase at day 42 compared to the value at day 1. The percentage of acetic acid among the total SCFAs dropped quickly from 74.5% at day 1 to 36.5% at day 42, while butyric acid and propionic acid showed significant increases at the stage. The histamine level increased and putrescine level decreased markedly in the colon with time while the amounts of total bioamines, tyramine and spermidine were devoid of changes. Dozens bacteria taxa showed highly correlations with SCFAs and bioamines. These findings provide an expanded view of the dynamic pig gut and gut microbiome at the important early growth stage.}, } @article {pmid33469518, year = {2020}, author = {Emery, DC and Cerajewska, TL and Seong, J and Davies, M and Paterson, A and Allen-Birt, SJ and West, NX}, title = {Comparison of Blood Bacterial Communities in Periodontal Health and Periodontal Disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {577485}, doi = {10.3389/fcimb.2020.577485}, pmid = {33469518}, issn = {2235-2988}, abstract = {The use of Next Generation Sequencing (NGS) techniques has generated a wide variety of blood microbiome data. Due to the large variation in bacterial DNA profiles between studies and the likely high concentrations of cell-free bacterial DNA in the blood, it is still not clear how such microbiome data relates to viable microbiota. For these reasons much remains to be understood about the true nature of any possible healthy blood microbiota and of bacteraemic events associated with disease. The gut, reproductive tracts, skin, and oral cavity are all likely sources of blood-borne bacteria. Oral bacteria, especially those associated with periodontal diseases, are also commonly associated with cardiovascular diseases such as infective endocarditis, and also have been linked to rheumatoid arthritis and Alzheimer's disease. Periodontal treatment, dental probing, and toothbrushing have been shown to cause transient bacteraemia and oral bacteria from the phyla Firmicutes (e.g. Streptococci) and Bacteroidetes (e.g. Porphyromonas) are found in cardiovascular lesions (CVD). Many studies of blood bacterial DNA content however, find Proteobacteria DNA to be the dominant microbiome component, suggesting a gut origin. Most studies of this type use total DNA extracted from either whole blood or blood fractions, such as buffy coat. Here, using a method that purifies DNA from intact bacterial cells only, we examined blood donated by those with active, severe periodontitis and periodontally healthy controls and show that 43-52% of bacterial species in blood are classified as oral. Firmicutes, consisting largely of members of the Streptococcus mitis group and Staphylococcus epidermidis, were predominant at 63.5% of all bacterial sequences detected in periodontal health and, little changed at 66.7% in periodontitis. Compared to studies using total DNA Proteobacteria were found here at relatively low levels in blood at 13.3% in periodontitis and 17.6% in health. This study reveals significant phylogenetic differences in blood bacterial population profiles when comparing periodontal health to periodontal disease cohorts.}, } @article {pmid33469457, year = {2020}, author = {Wakefield, D and Clarke, D and McCluskey, P}, title = {Recent Developments in HLA B27 Anterior Uveitis.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {608134}, doi = {10.3389/fimmu.2020.608134}, pmid = {33469457}, issn = {1664-3224}, abstract = {There has been steady progress in understanding the pathogenesis, clinical features, and effective treatment of acute anterior uveitis (AU) over the past 5 years. Large gene wide association studies have confirmed that AU is a polygenic disease, with overlaps with the seronegative arthropathies and inflammatory bowel diseases, associations that have been repeatedly confirmed in clinical studies. The role of the microbiome in AU has received increased research attention, with recent evidence indicating that human leukocyte antigen B27 (HLA B27) may influence the composition of the gut microbiome in experimental animals. Extensive clinical investigations have confirmed the typical features of acute AU (AAU) and its response to topical, regional and systemic immunosuppressive treatment. Increased understanding of the role of cytokines has resulted in studies confirming the value of anti-cytokine therapy [anti-tumor necrosis factor (anti-TNF) and interleukin 6 (IL-6) therapy] in severe and recurrent cases of AAU, particularly in subjects with an associated spondyloarthopathy (SpA) and in juvenile idiopathic arthritis (JIA)-associated AAU.}, } @article {pmid33469451, year = {2020}, author = {Zhou, H and Zeng, X and Sun, D and Chen, Z and Chen, W and Fan, L and Limpanont, Y and Dekumyoy, P and Maleewong, W and Lv, Z}, title = {Monosexual Cercariae of Schistosoma japonicum Infection Protects Against DSS-Induced Colitis by Shifting the Th1/Th2 Balance and Modulating the Gut Microbiota.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {606605}, doi = {10.3389/fmicb.2020.606605}, pmid = {33469451}, issn = {1664-302X}, abstract = {Inflammatory bowel disease (IBD)-related inflammation is closely associated with the initiation and progression of colorectal cancer. IBD is generally treated with 5-aminosalicylic acid and immune-modulating medication, but side effects and limitations of these therapies are emerging. Thus, the development of novel preventative or therapeutic approaches is imperative. Here, we constructed a dextran sodium sulphate (DSS)-induced IBD mouse model that was infected with monosexual Schistosoma japonicum cercariae (mSjci) at day 1 or administered dexamethasone (DXM) from days 3 to 5 as a positive control. The protective effect of mSjci on IBD mice was evaluated through their assessments of their clinical signs, histopathological lesions and intestinal permeability. To uncover the underlying mechanism, the Th1/Th2 balance and Treg cell population were also examined. Additionally, the alterations in the gut microbiota were assessed to investigate the interaction between the mSjci-modulated immune response and pathogenic microbiome. Mice treated with DSS and mSjci showed fewer IBD clinical signs and less impaired intestinal permeability than DSS-treated mice. Mechanistically, mSjci modulated the Th1/Th2 balance by repressing IFN-γ production, promoting IL-10 expression and enhancing the Treg subset population. Moreover, mSjci notably reshaped the structure, diversity and richness of the gut microbiota community and subsequently exerted immune-modulating effects. Our findings provide evidence showing that mSjci might serve as a novel and effective protective strategy and that the gut microbiota might be a new therapeutic target in IBD.}, } @article {pmid33469450, year = {2020}, author = {Barua, N and Herken, AM and Stern, KR and Reese, S and Powers, RL and Morrell-Falvey, JL and Platt, TG and Hansen, RR}, title = {Simultaneous Discovery of Positive and Negative Interactions Among Rhizosphere Bacteria Using Microwell Recovery Arrays.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {601788}, doi = {10.3389/fmicb.2020.601788}, pmid = {33469450}, issn = {1664-302X}, abstract = {Understanding microbe-microbe interactions is critical to predict microbiome function and to construct communities for desired outcomes. Investigation of these interactions poses a significant challenge due to the lack of suitable experimental tools available. Here we present the microwell recovery array (MRA), a new technology platform that screens interactions across a microbiome to uncover higher-order strain combinations that inhibit or promote the function of a focal species. One experimental trial generates 104 microbial communities that contain the focal species and a distinct random sample of uncharacterized cells from plant rhizosphere. Cells are sequentially recovered from individual wells that display highest or lowest levels of focal species growth using a high-resolution photopolymer extraction system. Interacting species are then identified and putative interactions are validated. Using this approach, we screen the poplar rhizosphere for strains affecting the growth of Pantoea sp. YR343, a plant growth promoting bacteria isolated from Populus deltoides rhizosphere. In one screen, we montiored 3,600 microwells within the array to uncover multiple antagonistic Stenotrophomonas strains and a set of Enterobacter strains that promoted YR343 growth. The later demonstrates the unique ability of the platform to discover multi-membered consortia that generate emergent outcomes, thereby expanding the range of phenotypes that can be characterized from microbiomes. This knowledge will aid in the development of consortia for Populus production, while the platform offers a new approach for screening and discovery of microbial interactions, applicable to any microbiome.}, } @article {pmid33469429, year = {2020}, author = {Foxx, CL and Heinze, JD and González, A and Vargas, F and Baratta, MV and Elsayed, AI and Stewart, JR and Loupy, KM and Arnold, MR and Flux, MC and Sago, SA and Siebler, PH and Milton, LN and Lieb, MW and Hassell, JE and Smith, DG and Lee, KAK and Appiah, SA and Schaefer, EJ and Panitchpakdi, M and Sikora, NC and Weldon, KC and Stamper, CE and Schmidt, D and Duggan, DA and Mengesha, YM and Ogbaselassie, M and Nguyen, KT and Gates, CA and Schnabel, K and Tran, L and Jones, JD and Vitaterna, MH and Turek, FW and Fleshner, M and Dorrestein, PC and Knight, R and Wright, KP and Lowry, CA}, title = {Effects of Immunization With the Soil-Derived Bacterium Mycobacterium vaccae on Stress Coping Behaviors and Cognitive Performance in a "Two Hit" Stressor Model.}, journal = {Frontiers in physiology}, volume = {11}, number = {}, pages = {524833}, doi = {10.3389/fphys.2020.524833}, pmid = {33469429}, issn = {1664-042X}, abstract = {Previous studies demonstrate that Mycobacterium vaccae NCTC 11659 (M. vaccae), a soil-derived bacterium with anti-inflammatory and immunoregulatory properties, is a potentially useful countermeasure against negative outcomes to stressors. Here we used male C57BL/6NCrl mice to determine if repeated immunization with M. vaccae is an effective countermeasure in a "two hit" stress exposure model of chronic disruption of rhythms (CDR) followed by acute social defeat (SD). On day -28, mice received implants of biotelemetric recording devices to monitor 24-h rhythms of locomotor activity. Mice were subsequently treated with a heat-killed preparation of M. vaccae (0.1 mg, administered subcutaneously on days -21, -14, -7, and 27) or borate-buffered saline vehicle. Mice were then exposed to 8 consecutive weeks of either stable normal 12:12 h light:dark (LD) conditions or CDR, consisting of 12-h reversals of the LD cycle every 7 days (days 0-56). Finally, mice were exposed to either a 10-min SD or a home cage control condition on day 54. All mice were exposed to object location memory testing 24 h following SD. The gut microbiome and metabolome were assessed in fecal samples collected on days -1, 48, and 62 using 16S rRNA gene sequence and LC-MS/MS spectral data, respectively; the plasma metabolome was additionally measured on day 64. Among mice exposed to normal LD conditions, immunization with M. vaccae induced a shift toward a more proactive behavioral coping response to SD as measured by increases in scouting and avoiding an approaching male CD-1 aggressor, and decreases in submissive upright defensive postures. In the object location memory test, exposure to SD increased cognitive function in CDR mice previously immunized with M. vaccae. Immunization with M. vaccae stabilized the gut microbiome, attenuating CDR-induced reductions in alpha diversity and decreasing within-group measures of beta diversity. Immunization with M. vaccae also increased the relative abundance of 1-heptadecanoyl-sn-glycero-3-phosphocholine, a lysophospholipid, in plasma. Together, these data support the hypothesis that immunization with M. vaccae stabilizes the gut microbiome, induces a shift toward a more proactive response to stress exposure, and promotes stress resilience.}, } @article {pmid33469166, year = {2021}, author = {Robbins, SJ and Song, W and Engelberts, JP and Glasl, B and Slaby, BM and Boyd, J and Marangon, E and Botté, ES and Laffy, P and Thomas, T and Webster, NS}, title = {A genomic view of the microbiome of coral reef demosponges.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {33469166}, issn = {1751-7370}, abstract = {Sponges underpin the productivity of coral reefs, yet few of their microbial symbionts have been functionally characterised. Here we present an analysis of ~1200 metagenome-assembled genomes (MAGs) spanning seven sponge species and 25 microbial phyla. Compared to MAGs derived from reef seawater, sponge-associated MAGs were enriched in glycosyl hydrolases targeting components of sponge tissue, coral mucus and macroalgae, revealing a critical role for sponge symbionts in cycling reef organic matter. Further, visualisation of the distribution of these genes amongst symbiont taxa uncovered functional guilds for reef organic matter degradation. Genes for the utilisation of sialic acids and glycosaminoglycans present in sponge tissue were found in specific microbial lineages that also encoded genes for attachment to sponge-derived fibronectins and cadherins, suggesting these lineages can utilise specific structural elements of sponge tissue. Further, genes encoding CRISPR and restriction-modification systems used in defence against mobile genetic elements were enriched in sponge symbionts, along with eukaryote-like gene motifs thought to be involved in maintaining host association. Finally, we provide evidence that many of these sponge-enriched genes are laterally transferred between microbial taxa, suggesting they confer a selective advantage within the sponge niche and therefore play a critical role in host ecology and evolution.}, } @article {pmid33469094, year = {2021}, author = {Zha, H and Liu, F and Ling, Z and Chang, K and Yang, J and Li, L}, title = {Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1824}, pmid = {33469094}, issn = {2045-2322}, support = {82003441//National Natural Science Foundation of China/ ; 81790631//National Natural Science Foundation of China/ ; 2018YFC2000500//National Key Research and Development Program of China/ ; }, abstract = {Type 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.}, } @article {pmid33468706, year = {2021}, author = {Jing, G and Liu, L and Wang, Z and Zhang, Y and Qian, L and Gao, C and Zhang, M and Li, M and Zhang, Z and Liu, X and Xu, J and Su, X}, title = {Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33468706}, issn = {2379-5077}, abstract = {Metagenomic data sets from diverse environments have been growing rapidly. To ensure accessibility and reusability, tools that quickly and informatively correlate new microbiomes with existing ones are in demand. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes in the global metagenome data space based on the taxonomic or functional similarity of a whole microbiome to those in the database. MSE 2 consists of (i) a well-organized and regularly updated microbiome database that currently contains over 250,000 metagenomic shotgun and 16S rRNA gene amplicon samples associated with unified metadata collected from 798 studies, (ii) an enhanced search engine that enables real-time and fast (<0.5 s per query) searches against the entire database for best-matched microbiomes using overall taxonomic or functional profiles, and (iii) a Web-based graphical user interface for user-friendly searching, data browsing, and tutoring. MSE 2 is freely accessible via http://mse.ac.cn For standalone searches of customized microbiome databases, the kernel of the MSE 2 search engine is provided at GitHub (https://github.com/qibebt-bioinfo/meta-storms).IMPORTANCE A search-based strategy is useful for large-scale mining of microbiome data sets, such as a bird's-eye view of the microbiome data space and disease diagnosis via microbiome big data. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes against the existing microbiome data sets on the basis of their similarity in taxonomic structure or functional profile. Key improvements include database extension, data compatibility, a search engine kernel, and a user interface. The new ability to search the microbiome space via functional similarity greatly expands the scope of search-based mining of the microbiome big data.}, } @article {pmid33468687, year = {2021}, author = {Beilsmith, K and Perisin, M and Bergelson, J}, title = {Natural Bacterial Assemblages in Arabidopsis thaliana Tissues Become More Distinguishable and Diverse during Host Development.}, journal = {mBio}, volume = {12}, number = {1}, pages = {}, pmid = {33468687}, issn = {2150-7511}, abstract = {To study the spatial and temporal dynamics of bacterial colonization under field conditions, we planted and sampled Arabidopsis thaliana during 2 years at two Michigan sites and surveyed colonists by sequencing 16S rRNA gene amplicons. Mosaic and dynamic assemblages revealed the plant as a patchwork of tissue habitats that differentiated with age. Although assemblages primarily varied between roots and shoots, amplicon sequence variants (ASVs) also differentiated phyllosphere tissues. Increasing assemblage diversity indicated that variants dispersed more widely over time, decreasing the importance of stochastic variation in early colonization relative to tissue differences. As tissues underwent developmental transitions, the root and phyllosphere assemblages became more distinct. This pattern was driven by common variants rather than those restricted to a particular tissue or transiently present at one developmental stage. Patterns also depended critically on fine phylogenetic resolution: when ASVs were grouped at coarse taxonomic levels, their associations with host tissue and age weakened. Thus, the observed spatial and temporal variation in colonization depended upon bacterial traits that were not broadly shared at the family level. Some colonists were consistently more successful at entering specific tissues, as evidenced by their repeatable spatial prevalence distributions across sites and years. However, these variants did not overtake plant assemblages, which instead became more even over time. Together, these results suggested that the increasing effect of tissue type was related to colonization bottlenecks for specific ASVs rather than to their ability to dominate other colonists once established.IMPORTANCE Developing synthetic microbial communities that can increase plant yield or deter pathogens requires basic research on several fronts, including the efficiency with which microbes colonize plant tissues, how plant genes shape the microbiome, and the microbe-microbe interactions involved in community assembly. Findings on each of these fronts depend upon the spatial and temporal scales at which plant microbiomes are surveyed. In our study, phyllosphere tissues housed increasingly distinct microbial assemblages as plants aged, indicating that plants can be considered collections of tissue habitats in which microbial colonists-natural or synthetic-are established with differing success. Relationships between host genes and community diversity might vary depending on when samples are collected, given that assemblages grew more diverse as plants aged. Both spatial and temporal trends weakened when colonists were grouped by family, suggesting that functional rather than taxonomic profiling will be necessary to understand the basis for differences in colonization success.}, } @article {pmid33468594, year = {2021}, author = {Nhu, NTQ and Lee, JS and Wang, HJ and Dufour, YS}, title = {Alkaline pH increases swimming speed and facilitates mucus penetration for Vibrio cholerae.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JB.00607-20}, pmid = {33468594}, issn = {1098-5530}, abstract = {Intestinal mucus is the first line of defense against intestinal pathogens. It acts as a physical barrier between epithelial tissues and the lumen that enteropathogens must overcome to establish a successful infection. We investigated the motile behavior of two V. cholerae strains (El Tor C6706 and Classical O395) in mucus using single cell tracking in unprocessed porcine intestinal mucus. We determined that V. cholerae is able to penetrate mucus using flagellar motility and that alkaline pH increases swimming speed, and consequently, improves mucus penetration. Microrheological measurements indicate that changes in pH between 6 and 8 (the physiological range for the human small intestine) had little effect on the viscoelastic properties of mucus. Finally, we determined that acidic pH promotes surface attachment by activating the mannose-sensitive haemagglutinin (MshA) pilus in V. cholerae El Tor C6706 without a measurable change in the total cellular concentration of the secondary messenger cyclic dimeric guanosine monophosphate (c-di-GMP). Overall, our results support that pH is an important factor affecting the motile behavior of V. cholerae and its ability to penetrate mucus. Therefore, changes in pH along the human small intestine may play a role in determining the preferred site for V. cholerae during infection.IMPORTANCE The diarrheal disease cholera is still a burden for populations in developing countries with poor sanitation. To develop effective vaccines and prevention strategies against Vibrio cholerae, we must understand the initial steps of infection leading to the colonization of the small intestine. To infect the host and deliver the cholera toxin, V. cholerae has to penetrate the mucus layer protecting the intestinal tissues. However, the interaction of V. cholerae with intestinal mucus has not been extensively investigated. In this report, we demonstrated using single cell tracking that V. cholerae is able to penetrate intestinal mucus using flagellar motility. In addition, we observed that alkaline pH improves the ability of V. cholerae to penetrate mucus. This finding has important implications for understanding the dynamics of infection because pH varies significantly along the small intestine, between individuals, and between species. Blocking mucus penetration by interfering with flagellar motility in V. cholerae, reinforcing the mucosa, controlling intestinal pH, or manipulating the intestinal microbiome, will offer new strategies to fight cholera.}, } @article {pmid33468585, year = {2021}, author = {Swaney, MH and Kalan, LR}, title = {Living in your Skin: Microbes, Molecules and Mechanisms.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1128/IAI.00695-20}, pmid = {33468585}, issn = {1098-5522}, abstract = {Human skin functions as a physical, chemical, and immune barrier against the external environment, while also providing a protective niche for its resident microbiota, known as the skin microbiome. Cooperation between the microbiota, host skin cells, and the immune system is responsible for maintenance of skin health, and a disruption to this delicate balance, such as by pathogen invasion or a breach in the skin barrier, may lead to impaired skin function. In this minireview, we describe the role of the microbiome in microbe, host, and immune interactions under distinct skin states, including homeostasis, tissue repair, and wound infection. Furthermore, we highlight the growing number of diverse microbial metabolites and products that have been identified to mediate these interactions, particularly those involved in host-microbe communication and defensive symbiosis. We also address the contextual pathogenicity exhibited by many skin commensals and provide insight into future directions in the skin microbiome field.}, } @article {pmid33468234, year = {2021}, author = {Toresson, L and Steiner, JM and Suchodolski, JS}, title = {Cholestyramine treatment in two dogs with presumptive bile acid diarrhoea: a case report.}, journal = {Canine medicine and genetics}, volume = {8}, number = {1}, pages = {1}, pmid = {33468234}, issn = {2662-9380}, abstract = {BACKGROUND: In people, bile acid diarrhoea is a prevalent complication of Crohn's disease and diarrhoea-associated irritable bowel syndrome. Affected patients typically respond to bile acid sequestrants, such as cholestyramine, but human gastroenterologists often fail to recognize bile acid diarrhoea. Consequently, bile acid diarrhoea is regarded as an underrecognized and undertreated condition in human medicine. Due to lack of diagnostic tools, clinical response to bile acid sequestrants is often used to confirm a diagnosis of bile acid diarrhoea in people. Several recent studies have shown that bile acid dysmetabolism also occurs in dogs with chronic enteropathies. It has further been shown that dogs with chronic enteropathies have significantly decreased expression of a bile acid transport protein in the ileum compared to healthy dogs, which correlates with faecal bile acid dysmetabolism. Consequently, in spite of the lack of reports in the literature, bile acid diarrhoea is likely to exist in dogs as well.

CASE DESCRIPTIONS: Two dogs, an 8-year old Rottweiler and a 4.5-year old Siberian Husky were evaluated for chronic watery diarrhoea. Neither dog responded to dietary trials, probiotics, cyclosporine, faecal microbial transplantations or metronidazole. One of the dogs responded to high daily doses of corticosteroids, which were however associated with unacceptable side effects. The other dog was refractory to all standard treatment protocols, including cyclosporine and corticosteroids. Since none of the dogs responded satisfactorily to standard treatment or modulation of the intestinal microbiome, a suspicion of possible bile acid diarrhoea was raised. Treatment with cholestyramine, a bile acid sequestrant was initiated and resulted in marked improvement of faecal consistency, frequency of defecation and activity level in both dogs.

CONCLUSION: This report presents two dogs with presumed bile acid diarrhoea that were successfully treated with cholestyramine. Therefore, bile acid diarrhoea should be considered as a possible diagnosis in dogs with treatment-refractory chronic diarrhoea.}, } @article {pmid33468221, year = {2021}, author = {Xu, C and Zhou, M and Xie, Z and Li, M and Zhu, X and Zhu, H}, title = {LightCUD: a program for diagnosing IBD based on human gut microbiome data.}, journal = {BioData mining}, volume = {14}, number = {1}, pages = {2}, pmid = {33468221}, issn = {1756-0381}, support = {31671366, 32070667//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The diagnosis of inflammatory bowel disease (IBD) and discrimination between the types of IBD are clinically important. IBD is associated with marked changes in the intestinal microbiota. Advances in next-generation sequencing (NGS) technology and the improved hospital bioinformatics analysis ability motivated us to develop a diagnostic method based on the gut microbiome.

RESULTS: Using a set of whole-genome sequencing (WGS) data from 349 human gut microbiota samples with two types of IBD and healthy controls, we assembled and aligned WGS short reads to obtain feature profiles of strains and genera. The genus and strain profiles were used for the 16S-based and WGS-based diagnostic modules construction respectively. We designed a novel feature selection procedure to select those case-specific features. With these features, we built discrimination models using different machine learning algorithms. The machine learning algorithm LightGBM outperformed other algorithms in this study and thus was chosen as the core algorithm. Specially, we identified two small sets of biomarkers (strains) separately for the WGS-based health vs IBD module and ulcerative colitis vs Crohn's disease module, which contributed to the optimization of model performance during pre-training. We released LightCUD as an IBD diagnostic program built with LightGBM. The high performance has been validated through five-fold cross-validation and using an independent test data set. LightCUD was implemented in Python and packaged free for installation with customized databases. With WGS data or 16S rRNA sequencing data of gut microbiome samples as the input, LightCUD can discriminate IBD from healthy controls with high accuracy and further identify the specific type of IBD. The executable program LightCUD was released in open source with instructions at the webpage http://cqb.pku.edu.cn/ZhuLab/LightCUD/ . The identified strain biomarkers could be used to study the critical factors for disease development and recommend treatments regarding changes in the gut microbial community.

CONCLUSIONS: As the first released human gut microbiome-based IBD diagnostic tool, LightCUD demonstrates a high-performance for both WGS and 16S sequencing data. The strains that either identify healthy controls from IBD patients or distinguish the specific type of IBD are expected to be clinically important to serve as biomarkers.}, } @article {pmid33468220, year = {2021}, author = {Chen, H and Mozzicafreddo, M and Pierella, E and Carletti, V and Piersanti, A and Ali, SM and Ame, SM and Wang, C and Miceli, C}, title = {Dissection of the gut microbiota in mothers and children with chronic Trichuris trichiura infection in Pemba Island, Tanzania.}, journal = {Parasites & vectors}, volume = {14}, number = {1}, pages = {62}, pmid = {33468220}, issn = {1756-3305}, abstract = {BACKGROUND: Soil-transmitted helminthiases are important neglected tropical diseases that result in a notably high number of disability-adjusted life years worldwide. Characterizing the interactions between the human intestinal microbiome and helminths is of interest in the development of alternative treatments that do not rely on chemotherapeutics and do not lead to drug resistance.

METHODS: We recruited and obtained fecal samples from 32 pairs of mothers and children on Pemba Island and monitored their intestinal microbiota using 16S rRNA gene sequencing.

RESULTS: We observed that microbial changes occur in the gut microbiota of infected mothers and children. Some short-chain fatty acid (SCFA)-producing bacteria and carbohydrate-degrading bacteria exhibited lower abundance in the infected individuals. Potentially pathogenic Campylobacter and proinflammatory Methanobrevibacter in infected mothers and opportunistic Enterococcus in infected children exhibited greater abundance.

CONCLUSIONS: Our findings could reveal the microbiota profiling in T. trichiura-infected individuals, indicate the potential roles of key microbiota in the host and aid to the development of novel strategies to control T. trichiura infection.}, } @article {pmid33468211, year = {2021}, author = {Beard, D and Stannard, HJ and Old, JM}, title = {Morphological identification of ticks and molecular detection of tick-borne pathogens from bare-nosed wombats (Vombatus ursinus).}, journal = {Parasites & vectors}, volume = {14}, number = {1}, pages = {60}, pmid = {33468211}, issn = {1756-3305}, abstract = {BACKGROUND: Ticks are obligate haematophagous ectoparasites of vertebrate hosts and transmit the widest range of pathogenic organisms of any arthropod vector. Seven tick species are known to feed on bare-nosed wombats (Vombatus ursinus), in addition to the highly prevalent Sarcoptes scabiei mite which causes fatal sarcoptic mange in most bare-nosed wombat populations. Little is known about the pathogens carried by most wombat ticks or how they may impact wombats and wombat handlers.

METHODS: Wombat ticks were sourced from wildlife hospitals and sanctuaries across Australia and identified to species level using taxonomic keys. Genomic DNA was extracted from a subsample, and following the amplification of the bacterial 16S rRNA gene V3-V4 hypervariable region, next-generation sequencing (NGS) on the Illumina MiSeq platform was used to assess the microbial composition.

RESULTS: A total of 447 tick specimens were collected from 47 bare-nosed wombats between January 2019 and January 2020. Five species of ticks were identified comprising wombat tick Bothriocroton auruginans (n = 420), wallaby tick Haemaphysalis bancrofti (n = 8), bush tick Haemaphysalis longicornis (n = 3), common marsupial tick Ixodes tasmani (n = 12), and Australian paralysis tick Ixodes holocyclus (n = 4). Tick infestations ranged from one to 73 ticks per wombat. The wombat tick was the most prevalent tick species comprising 94% of the total number of samples and was present on 97.9% (46/47) of wombat hosts. NGS results revealed the 16S rRNA gene diversity profile was predominantly Proteobacteria (55.1%) followed by Firmicutes (21.9%) and Actinobacteria (18.4%). A species of Coxiella sharing closest sequence identity to Coxiella burnetii (99.07%), was detected in 72% of B. auruginans and a Rickettsiella endosymbiont dominated the bacterial profile for I. tasmani.

CONCLUSIONS: A new host record for H. longicornis is the bare-nosed wombat. One adult male and two engorged adult female specimens were found on an adult male wombat from Coolagolite in New South Wales, and more specimens should be collected to confirm this host record. The most prevalent tick found on bare-nosed wombats was B. auruginans, confirming previous records. Analysis of alpha-diversity showed high variability across both sample locations and instars, similar to previous studies. The detection of various Proteobacteria in this study highlights the high bacterial diversity in native Australian ticks.}, } @article {pmid33468103, year = {2021}, author = {Boddy, SL and Giovannelli, I and Sassani, M and Cooper-Knock, J and Snyder, MP and Segal, E and Elinav, E and Barker, LA and Shaw, PJ and McDermott, CJ}, title = {The gut microbiome: a key player in the complexity of amyotrophic lateral sclerosis (ALS).}, journal = {BMC medicine}, volume = {19}, number = {1}, pages = {13}, pmid = {33468103}, issn = {1741-7015}, support = {1U54DE02378901//NIH Human Microbiome Project/ ; }, abstract = {BACKGROUND: Much progress has been made in mapping genetic abnormalities linked to amyotrophic lateral sclerosis (ALS), but the majority of cases still present with no known underlying cause. Furthermore, even in families with a shared genetic abnormality there is significant phenotypic variability, suggesting that non-genetic elements may modify pathogenesis. Identification of such disease-modifiers is important as they might represent new therapeutic targets. A growing body of research has begun to shed light on the role played by the gut microbiome in health and disease with a number of studies linking abnormalities to ALS.

MAIN BODY: The microbiome refers to the genes belonging to the myriad different microorganisms that live within and upon us, collectively known as the microbiota. Most of these microbes are found in the intestines, where they play important roles in digestion and the generation of key metabolites including neurotransmitters. The gut microbiota is an important aspect of the environment in which our bodies operate and inter-individual differences may be key to explaining the different disease outcomes seen in ALS. Work has begun to investigate animal models of the disease, and the gut microbiomes of people living with ALS, revealing changes in the microbial communities of these groups. The current body of knowledge will be summarised in this review. Advances in microbiome sequencing methods will be highlighted, as their improved resolution now enables researchers to further explore differences at a functional level. Proposed mechanisms connecting the gut microbiome to neurodegeneration will also be considered, including direct effects via metabolites released into the host circulation and indirect effects on bioavailability of nutrients and even medications.

CONCLUSION: Profiling of the gut microbiome has the potential to add an environmental component to rapidly advancing studies of ALS genetics and move research a step further towards personalised medicine for this disease. Moreover, should compelling evidence of upstream neurotoxicity or neuroprotection initiated by gut microbiota emerge, modification of the microbiome will represent a potential new avenue for disease modifying therapies. For an intractable condition with few current therapeutic options, further research into the ALS microbiome is of crucial importance.}, } @article {pmid33468056, year = {2021}, author = {Zaidi, SSA and Kayani, MUR and Zhang, X and Ouyang, Y and Shamsi, IH}, title = {Prediction and analysis of metagenomic operons via MetaRon: a pipeline for prediction of Metagenome and whole-genome opeRons.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {60}, pmid = {33468056}, issn = {1471-2164}, support = {2012GB316504//National Basic Research Program of China (973 Program)/ ; 31750110462, 31961143008//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Efficient regulation of bacterial genes in response to the environmental stimulus results in unique gene clusters known as operons. Lack of complete operonic reference and functional information makes the prediction of metagenomic operons a challenging task; thus, opening new perspectives on the interpretation of the host-microbe interactions.

RESULTS: In this work, we identified whole-genome and metagenomic operons via MetaRon (Metagenome and whole-genome opeRon prediction pipeline). MetaRon identifies operons without any experimental or functional information. MetaRon was implemented on datasets with different levels of complexity and information. Starting from its application on whole-genome to simulated mixture of three whole-genomes (E. coli MG1655, Mycobacterium tuberculosis H37Rv and Bacillus subtilis str. 16), E. coli c20 draft genome extracted from chicken gut and finally on 145 whole-metagenome data samples from human gut. MetaRon consistently achieved high operon prediction sensitivity, specificity and accuracy across E. coli whole-genome (97.8, 94.1 and 92.4%), simulated genome (93.7, 75.5 and 88.1%) and E. coli c20 (87, 91 and 88%,), respectively. Finally, we identified 1,232,407 unique operons from 145 paired-end human gut metagenome samples. We also report strong association of type 2 diabetes with Maltose phosphorylase (K00691), 3-deoxy-D-glycero-D-galacto-nononate 9-phosphate synthase (K21279) and an uncharacterized protein (K07101).

CONCLUSION: With MetaRon, we were able to remove two notable limitations of existing whole-genome operon prediction methods: (1) generalizability (ability to predict operons in unrelated bacterial genomes), and (2) whole-genome and metagenomic data management. We also demonstrate the use of operons as a subset to represent the trends of secondary metabolites in whole-metagenome data and the role of secondary metabolites in the occurrence of disease condition. Using operonic data from metagenome to study secondary metabolic trends will significantly reduce the data volume to more precise data. Furthermore, the identification of metabolic pathways associated with the occurrence of type 2 diabetes (T2D) also presents another dimension of analyzing the human gut metagenome. Presumably, this study is the first organized effort to predict metagenomic operons and perform a detailed analysis in association with a disease, in this case type 2 diabetes. The application of MetaRon to metagenomic data at diverse scale will be beneficial to understand the gene regulation and therapeutic metagenomics.}, } @article {pmid33467657, year = {2021}, author = {Hasebe, K and Kendig, MD and Morris, MJ}, title = {Mechanisms Underlying the Cognitive and Behavioural Effects of Maternal Obesity.}, journal = {Nutrients}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/nu13010240}, pmid = {33467657}, issn = {2072-6643}, support = {APP1126929//National Health and Medical Research Council/ ; }, abstract = {The widespread consumption of 'western'-style diets along with sedentary lifestyles has led to a global epidemic of obesity. Epidemiological, clinical and preclinical evidence suggests that maternal obesity, overnutrition and unhealthy dietary patterns programs have lasting adverse effects on the physical and mental health of offspring. We review currently available preclinical and clinical evidence and summarise possible underlying neurobiological mechanisms by which maternal overnutrition may perturb offspring cognitive function, affective state and psychosocial behaviour, with a focus on (1) neuroinflammation; (2) disrupted neuronal circuities and connectivity; and (3) dysregulated brain hormones. We briefly summarise research implicating the gut microbiota in maternal obesity-induced changes to offspring behaviour. In animal models, maternal obesogenic diet consumption disrupts CNS homeostasis in offspring, which is critical for healthy neurodevelopment, by altering hypothalamic and hippocampal development and recruitment of glial cells, which subsequently dysregulates dopaminergic and serotonergic systems. The adverse effects of maternal obesogenic diets are also conferred through changes to hormones including leptin, insulin and oxytocin which interact with these brain regions and neuronal circuits. Furthermore, accumulating evidence suggests that the gut microbiome may directly and indirectly contribute to these maternal diet effects in both human and animal studies. As the specific pathways shaping abnormal behaviour in offspring in the context of maternal obesogenic diet exposure remain unknown, further investigations are needed to address this knowledge gap. Use of animal models permits investigation of changes in neuroinflammation, neurotransmitter activity and hormones across global brain network and sex differences, which could be directly and indirectly modulated by the gut microbiome.}, } @article {pmid33467644, year = {2021}, author = {Lamichhane, S and Sen, P and Alves, MA and Ribeiro, HC and Raunioniemi, P and Hyötyläinen, T and Orešič, M}, title = {Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations.}, journal = {Metabolites}, volume = {11}, number = {1}, pages = {}, doi = {10.3390/metabo11010055}, pmid = {33467644}, issn = {2218-1989}, support = {323171 to S.L.//Academy of Finland/ ; NNF19OC0057418 to M.O.),//Novo Nordisk Foundation/ ; No. 2016-05176 to T.H.//Swedish Research Council/ ; 2018-02629 to M.O.).//Swedish Research Council/ ; }, abstract = {Various studies aiming to elucidate the role of the gut microbiome-metabolome co-axis in health and disease have primarily focused on water-soluble polar metabolites, whilst non-polar microbial lipids have received less attention. The concept of microbiota-dependent lipid biotransformation is over a century old. However, only recently, several studies have shown how microbial lipids alter intestinal and circulating lipid concentrations in the host, thus impacting human lipid homeostasis. There is emerging evidence that gut microbial communities play a particularly significant role in the regulation of host cholesterol and sphingolipid homeostasis. Here, we review and discuss recent research focusing on microbe-host-lipid co-metabolism. We also discuss the interplay of human gut microbiota and molecular lipids entering host systemic circulation, and its role in health and disease.}, } @article {pmid33467528, year = {2021}, author = {Sharpton, TJ and Stagaman, K and Sieler, MJ and Arnold, HK and Davis, EW}, title = {Phylogenetic Integration Reveals the Zebrafish Core Microbiome and Its Sensitivity to Environmental Exposures.}, journal = {Toxics}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/toxics9010010}, pmid = {33467528}, issn = {2305-6304}, support = {1R01ES030226/ES/NIEHS NIH HHS/United States ; }, abstract = {Zebrafish are increasingly used to study how environmental exposures impact vertebrate gut microbes. However, we understand little about which microbial taxa are common to the zebrafish gut across studies and facilities. Here, we define the zebrafish core gut microbiome to resolve microbiota that are both relatively robust to study or facility effects and likely to drive proper microbiome assembly and functioning due to their conservation. To do so, we integrated publicly available gut microbiome 16S gene sequence data from eight studies into a phylogeny and identified monophyletic clades of gut bacteria that are unexpectedly prevalent across individuals. Doing so revealed 585 core clades of bacteria in the zebrafish gut, including clades within Aeromonas, Pseudomonas, Cetobacterium, Shewanella, Chitinibacter, Fluviicola, Flectobacillus, and Paucibacter. We then applied linear regression to discern which of these core clades are sensitive to an array of different environmental exposures. We found that 200 core clades were insensitive to any exposure we assessed, while 134 core clades were sensitive to more than two exposures. Overall, our analysis defines the zebrafish core gut microbiome and its sensitivity to exposure, which helps future studies to assess the robustness of their results and prioritize taxa for empirical assessments of how gut microbiota mediate the effects of exposure on the zebrafish host.}, } @article {pmid33467395, year = {2021}, author = {Fajardo, C and Blánquez, A and Domínguez, G and Borrero-López, AM and Valencia, C and Hernández, M and Arias, ME and Rodríguez, J}, title = {Assessment of Sustainability of Bio Treated Lignocellulose-Based Oleogels.}, journal = {Polymers}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/polym13020267}, pmid = {33467395}, issn = {2073-4360}, support = {Project CTQ2014-56038-C3-2-R//Spanish Ministry of Economy and Competitiveness/ ; }, abstract = {The development of biological strategies to obtain new high-added value biopolymers from lignocellulosic biomass is a current challenge for scientific community. This study evaluates the biodegradability and ecotoxicity of new formulated oleogels obtained from fermented agricultural residues with Streptomyces, previously reported to show improved rheological and tribological characteristics compared to commercial mineral lubricants. Both new oleogels exhibited higher biodegradation rates than the commercial grease. Classical ecotoxicological bioassays using eukaryotic organisms (Lactuca sativa, Caenorhabditis elegans) showed that the toxic impact of the produced bio-lubricants was almost negligible and comparable to the commercial grease for the target organisms. In addition, high throughput molecular techniques using emerging next-generation DNA-sequencing technologies (NGS) were applied to study the structural changes of lubricant-exposed microbial populations of a standard soil. Results obtained showed that disposal of biomass-based lubricants in the soil environment did not substantially modify the structure and phylogenetic composition of the microbiome. These findings point out the feasibility and sustainability, in terms of biodegradability and eco-safety, of the new bio-lubricants in comparison with commercial mineral greases. This technology entails a promising biological strategy to replace fossil and non-renewable raw materials as well as to obtain useful biopolymers from agricultural residues with potential for large-scale applications.}, } @article {pmid33467340, year = {2019}, author = {Pickering, C and Kiely, J}, title = {The Development of a Personalised Training Framework: Implementation of Emerging Technologies for Performance.}, journal = {Journal of functional morphology and kinesiology}, volume = {4}, number = {2}, pages = {}, doi = {10.3390/jfmk4020025}, pmid = {33467340}, issn = {2411-5142}, abstract = {Over the last decade, there has been considerable interest in the individualisation of athlete training, including the use of genetic information, alongside more advanced data capture and analysis techniques. Here, we explore the evidence for, and practical use of, a number of these emerging technologies, including the measurement and quantification of epigenetic changes, microbiome analysis and the use of cell-free DNA, along with data mining and machine learning. In doing so, we develop a theoretical model for the use of these technologies in an elite sport setting, allowing the coach to better answer six key questions: (1) To what training will my athlete best respond? (2) How well is my athlete adapting to training? (3) When should I change the training stimulus (i.e., has the athlete reached their adaptive ceiling for this training modality)? (4) How long will it take for a certain adaptation to occur? (5) How well is my athlete tolerating the current training load? (6) What load can my athlete handle today? Special consideration is given to whether such an individualised training framework will outperform current methods as well as the challenges in implementing this approach.}, } @article {pmid33467216, year = {2021}, author = {Kedves, O and Shahab, D and Champramary, S and Chen, L and Indic, B and Bóka, B and Nagy, VD and Vágvölgyi, C and Kredics, L and Sipos, G}, title = {Epidemiology, Biotic Interactions and Biological Control of Armillarioids in the Northern Hemisphere.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, doi = {10.3390/pathogens10010076}, pmid = {33467216}, issn = {2076-0817}, support = {GINOP-2.3.2-15-2016-00052//Széchenyi 2020 Programme/ ; }, abstract = {Armillarioids, including the genera Armillaria, Desarmillaria and Guyanagaster, represent white-rot specific fungal saprotrophs with soilborne pathogenic potentials on woody hosts. They propagate in the soil by root-like rhizomorphs, connecting between susceptible root sections of their hosts, and often forming extended colonies in native forests. Pathogenic abilities of Armillaria and Desarmillaria genets can readily manifest in compromised hosts, or hosts with full vigour can be invaded by virulent mycelia when exposed to a larger number of newly formed genets. Armillaria root rot-related symptoms are indicators of ecological imbalances in native forests and plantations at the rhizosphere levels, often related to abiotic environmental threats, and most likely unfavourable changes in the microbiome compositions in the interactive zone of the roots. The less-studied biotic impacts that contribute to armillarioid host infection include fungi and insects, as well as forest conditions. On the other hand, negative biotic impactors, like bacterial communities, antagonistic fungi, nematodes and plant-derived substances may find applications in the environment-friendly, biological control of armillarioid root diseases, which can be used instead of, or in combination with the classical, but frequently problematic silvicultural and chemical control measures.}, } @article {pmid33467150, year = {2021}, author = {Checa-Ros, A and Jeréz-Calero, A and Molina-Carballo, A and Campoy, C and Muñoz-Hoyos, A}, title = {Current Evidence on the Role of the Gut Microbiome in ADHD Pathophysiology and Therapeutic Implications.}, journal = {Nutrients}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/nu13010249}, pmid = {33467150}, issn = {2072-6643}, abstract = {Studies suggest that the bidirectional relationship existent between the gut microbiome (GM) and the central nervous system (CNS), or so-called the microbiome-gut-brain axis (MGBA), is involved in diverse neuropsychiatric diseases in children and adults. In pediatric age, most studies have focused on patients with autism. However, evidence of the role played by the MGBA in attention deficit/hyperactivity disorder (ADHD), the most common neurodevelopmental disorder in childhood, is still scanty and heterogeneous. This review aims to provide the current evidence on the functioning of the MGBA in pediatric patients with ADHD and the specific role of omega-3 polyunsaturated fatty acids (ω-3 PUFAs) in this interaction, as well as the potential of the GM as a therapeutic target for ADHD. We will explore: (1) the diverse communication pathways between the GM and the CNS; (2) changes in the GM composition in children and adolescents with ADHD and association with ADHD pathophysiology; (3) influence of the GM on the ω-3 PUFA imbalance characteristically found in ADHD; (4) interaction between the GM and circadian rhythm regulation, as sleep disorders are frequently comorbid with ADHD; (5) finally, we will evaluate the most recent studies on the use of probiotics in pediatric patients with ADHD.}, } @article {pmid33467110, year = {2021}, author = {Schaid, MD and Zhu, Y and Richardson, NE and Patibandla, C and Ong, IM and Fenske, RJ and Neuman, JC and Guthery, E and Reuter, A and Sandhu, HK and Fuller, MH and Cox, ED and Davis, DB and Layden, BT and Brasier, AR and Lamming, DW and Ge, Y and Kimple, ME}, title = {Systemic Metabolic Alterations Correlate with Islet-Level Prostaglandin E2 Production and Signaling Mechanisms That Predict β-Cell Dysfunction in a Mouse Model of Type 2 Diabetes.}, journal = {Metabolites}, volume = {11}, number = {1}, pages = {}, doi = {10.3390/metabo11010058}, pmid = {33467110}, issn = {2218-1989}, support = {K01 DK080845/DK/NIDDK NIH HHS/United States ; R01 DK102598/DK/NIDDK NIH HHS/United States ; R01 AG056771/AG/NIA NIH HHS/United States ; UL1 TR002373/TR/NCATS NIH HHS/United States ; R01 DK104927/DK/NIDDK NIH HHS/United States ; R01 DK111848/DK/NIDDK NIH HHS/United States ; U01 DK127378/DK/NIDDK NIH HHS/United States ; P30 DK020595/DK/NIDDK NIH HHS/United States ; I01 BX003700/BX/BLRD VA/United States ; I01 BX004031/BX/BLRD VA/United States ; I01 BX003382/BX/BLRD VA/United States ; T32 AG000213/AG/NIA NIH HHS/United States ; 1-14-BS-115//American Diabetes Association Research Foundation/ ; UW2020 grant//Wisconsin Alumni Research Foundation/ ; P30 CA014520/CA/NCI NIH HHS/United States ; }, abstract = {The transition from β-cell compensation to β-cell failure is not well understood. Previous works by our group and others have demonstrated a role for Prostaglandin EP3 receptor (EP3), encoded by the Ptger3 gene, in the loss of functional β-cell mass in Type 2 diabetes (T2D). The primary endogenous EP3 ligand is the arachidonic acid metabolite prostaglandin E2 (PGE2). Expression of the pancreatic islet EP3 and PGE2 synthetic enzymes and/or PGE2 excretion itself have all been shown to be upregulated in primary mouse and human islets isolated from animals or human organ donors with established T2D compared to nondiabetic controls. In this study, we took advantage of a rare and fleeting phenotype in which a subset of Black and Tan BRachyury (BTBR) mice homozygous for the Leptinob/ob mutation-a strong genetic model of T2D-were entirely protected from fasting hyperglycemia even with equal obesity and insulin resistance as their hyperglycemic littermates. Utilizing this model, we found numerous alterations in full-body metabolic parameters in T2D-protected mice (e.g., gut microbiome composition, circulating pancreatic and incretin hormones, and markers of systemic inflammation) that correlate with improvements in EP3-mediated β-cell dysfunction.}, } @article {pmid33466861, year = {2021}, author = {Wu, L and Han, Y and Zheng, Z and Peng, G and Liu, P and Yue, S and Zhu, S and Chen, J and Lv, H and Shao, L and Sheng, Y and Wang, Y and Li, L and Li, L and Wang, B}, title = {Altered Gut Microbial Metabolites in Amnestic Mild Cognitive Impairment and Alzheimer's Disease: Signals in Host-Microbe Interplay.}, journal = {Nutrients}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/nu13010228}, pmid = {33466861}, issn = {2072-6643}, support = {81790633, 81790630//Major Program of National Natural Science Foundation of China/ ; 2019-I2M-5-045//CAMS Innovation Fund for Medical Sciences/ ; }, abstract = {Intimate metabolic host-microbiome crosstalk regulates immune, metabolic, and neuronal response in health and disease, yet remains untapped for biomarkers or intervention for disease. Our recent study identified an altered microbiome in patients with pre-onset amnestic mild cognitive impairment (aMCI) and dementia Alzheimer's disease (AD). Thus, we aimed to characterize the gut microbial metabolites among AD, aMCI, and healthy controls (HC). Here, a cohort of 77 individuals (22 aMCI, 27 AD, and 28 HC) was recruited. With the use of liquid-chromatography/gas chromatography mass spectrometry metabolomics profiling, we identified significant differences between AD and HC for tryptophan metabolites, short-chain fatty acids (SCFAs), and lithocholic acid, the majority of which correlated with altered microbiota and cognitive impairment. Notably, tryptophan disorders presented in aMCI and SCFAs decreased progressively from aMCI to AD. Importantly, indole-3-pyruvic acid, a metabolite from tryptophan, was identified as a signature for discrimination and prediction of AD, and five SCFAs for pre-onset and progression of AD. This study showed fecal-based gut microbial signatures were associated with the presence and progression of AD, providing a potential target for microbiota or dietary intervention in AD prevention and support for the host-microbe crosstalk signals in AD pathophysiology.}, } @article {pmid33466802, year = {2021}, author = {Fu, SC and Lee, CH and Wang, H}, title = {Exploring the Association of Autism Spectrum Disorders and Constipation through Analysis of the Gut Microbiome.}, journal = {International journal of environmental research and public health}, volume = {18}, number = {2}, pages = {}, doi = {10.3390/ijerph18020667}, pmid = {33466802}, issn = {1660-4601}, support = {107-2118-M-009 -002 -MY2//Ministry of Science and Technology, Taiwan/ ; }, abstract = {Over the past two decades, research into the role of the gut microbiome in regulating the central nervous system has rapidly increased. Several neurodevelopmental diseases have been linked to the unbalance of gut microbiota, including autism. Children on the autism spectrum often suffer from gastrointestinal symptoms, including constipation, which is four times more prevalent than it is in children without autism spectrum disorders (ASD). Although studies in animals have shown the crucial role of the microbiota in key aspects of neurodevelopment, there is currently no consensus on how the alteration of microbial composition affects the pathogenesis of ASD, let alone how it exerts an impact on the following comorbidities. In our study, we were able to control the effects of constipation on gut dysbiosis and distinguish neuropathological-related and gastrointestinal-related bacteria in ASD patients separately. By analyzing published data, eight additional bacteria significantly altered in autistic individuals were identified in our study. All of them had a decreased relative abundance in ASD patients, except Lactobacillaceae and Peptostreptococcaceae. Eighteen and eleven bacteria were significantly correlated with ASD symptoms and constipation, respectively. Among those, six bacteria were overlapped between the groups. We have found another six bacteria highly associated with constipation status in ASD patients only. By conducting Welch's t-test, we were able to demonstrate the critical roles of microbes in ASD core and gastrointestinal symptoms and raised the hypotheses of their confounding and mediating effects on the relationship between the two symptoms.}, } @article {pmid33466662, year = {2021}, author = {Singh, AK and Kim, WK}, title = {Effects of Dietary Fiber on Nutrients Utilization and Gut Health of Poultry: A Review of Challenges and Opportunities.}, journal = {Animals : an open access journal from MDPI}, volume = {11}, number = {1}, pages = {}, doi = {10.3390/ani11010181}, pmid = {33466662}, issn = {2076-2615}, abstract = {Many fibrous ingredients incorporated in poultry feed to reduce production costs have low digestibility and cause poor growth in poultry. However, all plant-based fibers are not equal, and thus exert variable physiological effects on the birds, including but not limited to, digestibility, growth performance, and microbial fermentation. Several types of fibers, especially oligosaccharides, when supplemented in poultry diets in isolated form, exhibit prebiotic effects by enhancing beneficial gut microbiota, modulating gut immunity, boosting intestinal mucosal health, and increasing the production of short-chain fatty acids (SCFA) in the gut. Recently, poultry producers are also facing the challenge of limiting the use of antibiotic growth promoters (AGP) in poultry feed. In addition to other alternatives in use, exogenous non-starch polysaccharides digesting enzymes (NSPase) and prebiotics are being used to provide substrates to support the gut microbiome. We also conducted a meta-analysis of different studies conducted in similar experimental conditions to evaluate the variability and conclusiveness in effects of NSPase on growth performance of broilers fed fibrous ingredients. This review presents a holistic approach in discussing the existing challenges of incorporating high-fiber ingredients in poultry feed, as well as strategies to fully utilize the potential of such ingredients in improving feed efficiency and gut health of poultry.}, } @article {pmid33465774, year = {2021}, author = {Chu, AHY and Godfrey, KM}, title = {Gestational Diabetes Mellitus and Developmental Programming.}, journal = {Annals of nutrition & metabolism}, volume = {}, number = {}, pages = {1-12}, doi = {10.1159/000509902}, pmid = {33465774}, issn = {1421-9697}, abstract = {During normal pregnancy, increased insulin resistance acts as an adaptation to enhance materno-foetal nutrient transfer and meet the nutritional needs of the developing foetus, particularly in relation to glucose requirements. However, about 1 in 6 pregnancies worldwide is affected by the inability of the mother's metabolism to maintain normoglycaemia, with the combination of insulin resistance and insufficient insulin secretion resulting in gestational diabetes mellitus (GDM). A growing body of epidemiologic work demonstrates long-term implications for adverse offspring health resulting from exposure to GDM in utero. The effect of GDM on offspring obesity and cardiometabolic health may be partly influenced by maternal obesity; this suggests that improving glucose and weight control during early pregnancy, or better still before conception, has the potential to lessen the risk to the offspring. The consequences of GDM for microbiome modification in the offspring and the impact upon offspring immune dysregulation are actively developing research areas. Some studies have suggested that GDM impacts offspring neurodevelopmental and cognitive outcomes; confirmatory studies will need to separate the effect of GDM exposure from the complex interplay of social and environmental factors. Animal and human studies have demonstrated the role of epigenetic modifications in underpinning the predisposition to adverse health in offspring exposed to suboptimal hyperglycaemic in utero environment. To date, several epigenome-wide association studies in human have extended our knowledge on linking maternal diabetes-related DNA methylation marks with childhood adiposity-related outcomes. Identification of such epigenetic marks can help guide future research to develop candidate diagnostic biomarkers and preventive or therapeutic strategies. Longer-term interventions and longitudinal studies will be needed to better understand the causality, underlying mechanisms, or impact of GDM treatments to optimize the health of future generations.}, } @article {pmid33465759, year = {2021}, author = {Wang, ST and Meng, XZ and Dai, YF and Zhang, JH and Shen, Y and Xu, XY and Wang, RQ and Li, JL}, title = {Characterization of the intestinal digesta and mucosal microbiome of the grass carp (Ctenopharyngodon idella).}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {37}, number = {}, pages = {100789}, doi = {10.1016/j.cbd.2021.100789}, pmid = {33465759}, issn = {1878-0407}, abstract = {The intestinal microbiome plays a pivotal role in the nutritional digestion and metabolism of the grass carp (Ctenopharyngodon idella). Here, we characterized the digesta and mucosal microbiome of the anterior, middle, and posterior intestine of the grass carp, using 16S rRNA next-generation sequencing. Based on 16S rRNA amplicon data, Proteobacteria, Firmicutes and Bacteroides were the dominant phyla in the intestine of grass carp. Our results also showed that microbial communities of the middle intestine exhibited higher alpha diversity indices compared with the anterior and posterior intestine. The clustering of microbial communities that had either colonized in the digesta or were attached to the mucosa, were significantly tighter in the posterior intestine, based on average unweighted Unifrac distances (P < 0.05). The digesta or mucosa of the anterior and middle intestines were similar in microbial composition, but were significantly different to the posterior intestine (P < 0.05). In digesta and mucosa samples from the posterior intestine, we observed a significantly increased abundance of cellulose-degrading microbiomes, such as Bacteroides, Clostridiales and Spirochaetia (P < 0.05). Our results suggested that the microbiomes of the posterior intestine, either attached to the mucosa or colonized in the digesta, were distinct from the microbiomes of the anterior and middle intestine in grass carp.}, } @article {pmid33465728, year = {2021}, author = {Wu, Q and Liu, J and Wu, S and Xie, X}, title = {The impact of antibiotics on efficacy of immune checkpoint inhibitors in malignancies: A study based on 44 cohorts.}, journal = {International immunopharmacology}, volume = {92}, number = {}, pages = {107303}, doi = {10.1016/j.intimp.2020.107303}, pmid = {33465728}, issn = {1878-1705}, abstract = {BACKGROUND: Pre-clinical and clinical data had revealed the gut microbiome plays a critical role in immune checkpoint inhibitors (ICIs) efficacy. This study was designed to investigate whether antibiotics (ATBs) affect the prognosis of malignancies treated with ICIs.

METHODS: Electronic databases were searched to identify relevant trials that evaluated the impact of ATBs on ICIs efficacy. The primary endpoints were overall survival (OS) and progression-free survival (PFS) measured by HRs with corresponding 95%CIs. Subgroup analyses were performed based on cancer type, study design, ICIs agent, and time of ATBs administration.

RESULTS: Totally, 12,492 individuals in the 44 cohorts were recruited. Pooled results showed that ATBs administration was significantly correlated with a worse objective remission rate (ORR) (OR = 0.61, 95%CI (0.42-0.90), P = 0.0128), PFS (HR = 1.18, 95%CI (1.11-1.25), P < 0.0001), and OS (HR = 1.20, 95%CI (1.15-1.25), P < 0.0001) in patients treated with ICIs. In subgroup analyses, patients treated with ICIs exposed to ATBs suffered an evidently worse ORR in arms of renal cell carcinoma (RCC) (OR = 0.30, 95%CI (0.14-0.67), P = 0.0034), multiple (OR = 0.44, 95%CI (0.27-0.73), P = 0.0016), and before ICIs initiation (OR = 0.47, 95%CI (0.32-0.71), P = 0.0003) without heterogeneity; experienced a worse PFS and OS in arms of non-small cell lung cancer, melanoma, RCC, urothelial carcinoma, multiple, prospective, retrospective, PD-(L)1 alone, PD-(L)1 plus CTLA-4, before ICIs initiation, before ICIs initiation and concurrent, and before or after ICIs within 1 month, while a better PFS and OS in concurrent with ICIs arm.

CONCLUSIONS: ATBs administration was negatively associated with ORR, PFS and OS in malignancies treated with ICIs, while the time of ATBs exposure might impact ICIs efficacy.}, } @article {pmid33465665, year = {2021}, author = {Hernandez, BY and Zhu, X and Sotto, P and Paulino, Y}, title = {Oral exposure to environmental cyanobacteria toxins: Implications for cancer risk.}, journal = {Environment international}, volume = {148}, number = {}, pages = {106381}, doi = {10.1016/j.envint.2021.106381}, pmid = {33465665}, issn = {1873-6750}, abstract = {BACKGROUND: Areca nut/betel quid (AN/BQ) chewing, a prevalent practice in parts of the Pacific and Asia, is an independent cause of cancers of the oral cavity and esophagus and may be linked to liver cancer. The mechanisms of AN/BQ-associated carcinogenesis are unclear. In a Guam population, we previously demonstrated that AN/BQ chewing alters the oral bacterial microbiome including in chewers with oral premalignant lesions. Enrichment of specific taxa, including Cyanobacteria, was observed.

OBJECTIVES: We undertook an investigation to evaluate Areca catechu and/or Piper betle plants as potential sources of Cyanobacteria and cyanotoxins in AN/BQ chewers in Guam.

METHODS: We evaluated bacterial 16S rRNA with Illumina MiSeq in 122 oral samples and 30 Areca catechu nut and Piper betle leaf samples. Cyanobacteria sequences were interrogated using the NCBI database to identify candidate species and their reference sequences were evaluated for secondary metabolite toxins using AntiSMASH 5.0. Selected toxins were measured by ELISA in extracts from 30 plant samples and in a subset of 25 saliva samples.

RESULTS: Cyanobacteria was the predominant taxa in Areca catechu and Piper betle plants, comprising 75% of sequences. Cyanobacteria was detected at low levels in oral samples but 90-fold higher in current AN/BQ chewers compared to former/never chewers (p = 0.001). Microcystin/nodularin was detected in saliva (15 of 25 samples) and Piper betle leaves (6 of 10 samples). Cylindrospermopsin was detected in all saliva and leaf samples and 7 of 10 nut/husks. Salivary cylindrospermopsin levels were significantly higher in current chewers of betel quid (i.e., crushed Areca catechu nut wrapped in Piper betle leaf) compared to those chewing Areca nut alone. Anabaenopeptin was detected in saliva (10 of 25 samples), all leaf samples, and 7 of 10 nut/husks. Salivary anabaenopeptin concentration was weakly, albeit significantly, correlated with oral Cyanobacteria relative abundance.

DISCUSSION: Our study demonstrates that Cyanobacteria can contaminate AN/BQ plants and expose chewers to potent hepatotoxins. With worldwide increases in climate-related overgrowth of Cyanobacteria, our findings have broad implications for cancer risk across populations.}, } @article {pmid33465627, year = {2021}, author = {Wu, N and Wang, X and Yan, Z and Xu, X and Xie, S and Liang, J}, title = {Transformation of pig manure by passage through the gut of black soldier fly larvae (Hermetia illucens): Metal speciation, potential pathogens and metal-related functional profiling.}, journal = {Ecotoxicology and environmental safety}, volume = {211}, number = {}, pages = {111925}, doi = {10.1016/j.ecoenv.2021.111925}, pmid = {33465627}, issn = {1090-2414}, abstract = {Black soldier fly larvae (BSFL) have great potential in livestock manure disposal. However, the changes in metal speciation, microbial communities, potential pathogens during the manure transformation process by BSFL is still largely uncharacterized, as well as the underlying metal tolerance mechanism of larval gut microbiome. Here we used BSFL to convert pig manure (PM) into larval feces (BF), and investigated the metal and microbial changes in the conversion process. Physicochemical parameters (e.g. pH, electrical conductivity, total nitrogen, total phosphorus and total potassium) in PM were significantly altered compared to BF. After conversion, less than 10% of Cu and Zn were accumulated in larval bodies. The bioavailable fraction of Cu (88.3%-86.2%) and Zn (80.6%-82.3%) occupied as the primary form in PM and BF. Genera Enterococcus, Clostridium_sensu_stricto_1, Terrisporobacter and Romboutsia were substantially enriched in the final BSFL gut (GF) compared with initial gut (GI). BSFL transformation substantially reduced pathogen abundances (decreased by 89%) derived from pig manure. Functional genes involved in metal homeostasis and resistance (e.g. CutC, pcoC, cusR, zurR and zntB) were obviously strengthened (by 2.3-7.7 folds) in GF than in GI, which might partly explain the metal tolerance ability of BSFL during the livestock manure transformation process.}, } @article {pmid33465548, year = {2021}, author = {Nikoloudaki, O and Lemos Junior, WJF and Campanaro, S and Di Cagno, R and Gobbetti, M}, title = {Role prediction of Gram-negative species in the resistome of raw cow's milk.}, journal = {International journal of food microbiology}, volume = {340}, number = {}, pages = {109045}, doi = {10.1016/j.ijfoodmicro.2021.109045}, pmid = {33465548}, issn = {1879-3460}, abstract = {Extended use of antibiotics in dairy farming for therapeutic and prophylactic reasons, but also the higher prevalence of antibiotic resistant bacteria (ARB) in the farm environment raised the concern of consuming raw cow's milk and its derived products. The aim of this study was to predict by shotgun metagenomic analyses the presence of antibiotic resistance genes (ARGs) mainly correlated with Gram-negative bacteria in antibiotic residue free raw cow's milk derived exclusively from healthy animal from South Tyrol (Northern Italy), chosen as a model system. Assessment of shotgun metagenomic data of reconstructed scaffolds, revealed the existence of Pseudomonas spp. as the most abundant Gram-negative species in the raw cow's milk samples bearing ARGs. Besides, ARGs also linked to lactic acid bacteria such as Lactococcus sp. and Lactobacillus sp. ARGs correlated to microbiome found in milk samples conferred resistance towards aminoglycoside-streptothricin, beta-lactamase, macrolide, tetracycline, carbapenem, cephalosporin, penam, peptide, penem, fluoroquinolone, chloramphenicol and elfamycin antibiotics. Further bioinformatic processing included de-novo reassembly of all metagenomic sequences from all milk samples in one, to reconstruct metagenome assembled genomes (MAGs), which were further used to investigate mobile genetic elements (MGE). Analyses of the reconstructed MAGs showed that, MAG 9 (Pseudomonas sp1.) contained the oriT gene (origin of transfer gene) needed for transferring virulent factors. Although the presence of Pseudomonas is common in raw cow's milk, pasteurization treatment reduces their survivability. Nevertheless, attention should be paid on Pseudomonas spp. due to their intrinsic resistance to antibiotics and their capability of transferring virulent factors to other bacteria.}, } @article {pmid33465423, year = {2021}, author = {Shareefdeen, H and Hynes, AP}, title = {Does over a century of aerobic phage work provide a solid framework for the study of phages in the gut?.}, journal = {Anaerobe}, volume = {}, number = {}, pages = {102319}, doi = {10.1016/j.anaerobe.2021.102319}, pmid = {33465423}, issn = {1095-8274}, abstract = {Bacterial viruses (bacteriophages, phages) of the gut have increasingly become a focus in microbiome studies, with an understanding that they are likely key players in health and disease. However, characterization of the virome remains largely based on bioinformatic approaches, with the impact of these viromes inferred based on a century of knowledge from aerobic phage work. Studying the phages infecting anaerobes is difficult, as they are often technically demanding to isolate and propagate. In this review, we primarily discuss the phages infecting three well-studied anaerobes in the gut: Bifidobacterium, Clostridia and Bacteroides, with a particular focus on the challenges in isolating and characterizing these phages. We contrast the lessons learned from these to other anaerobic work on phages infecting facultative anaerobes of the gut: Enterococcus and Lactobacillus. Phages from the gut do appear to adhere to the lessons learned from aerobic work, but the additional challenges of working on them has required ingenious new approaches to enable their study. This, in turn, has uncovered remarkable biology likely underpinning phage-host relationships in many stable environments.}, } @article {pmid33465324, year = {2021}, author = {Senga, SS and Grose, RP}, title = {Hallmarks of cancer-the new testament.}, journal = {Open biology}, volume = {11}, number = {1}, pages = {200358}, doi = {10.1098/rsob.200358}, pmid = {33465324}, issn = {2046-2441}, abstract = {Diagnosis and treatment of disease demand a sound understanding of the underlying mechanisms, determining any Achilles' heel that can be targeted in effective therapies. Throughout history, this endeavour to decipher the origin and mechanism of transformation of a normal cell into cancer has led to various theories-from cancer as a curse to an understanding at the level of single-cell heterogeneity, meaning even among a single sub-type of cancer there are myriad molecular challenges to overcome. With increasing insight into cancer genetics and biology, the disease has become ever more complex to understand. The complexity of cancer as a disease was distilled into key traits by Hanahan and Weinberg in their seminal 'Hallmarks of Cancer' reviews. This lucid conceptualization of complex cancer biology is widely accepted and has helped advance cancer therapeutics by targeting the various hallmarks but, with the advancement in technologies, there is greater granularity in how we view cancer as a disease, and the additional understanding over the past decade requires us to revisit the hallmarks of cancer. Based on extensive study of the cancer research literature, we propose four novel hallmarks of cancer, namely, the ability of cells to regress from a specific specialized functional state, epigenetic changes that can affect gene expression, the role of microorganisms and neuronal signalling, to be included in the hallmark conceptualization along with evidence of various means to exploit them therapeutically.}, } @article {pmid33464726, year = {2021}, author = {Cho, J and Park, YJ and Gonzales-Portillo, B and Saft, M and Cozene, B and Sadanandan, N and Borlongan, CV}, title = {Gut dysbiosis in stroke and its implications on Alzheimer's disease-like cognitive dysfunction.}, journal = {CNS neuroscience & therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1111/cns.13613}, pmid = {33464726}, issn = {1755-5949}, support = {R01NS090962/NH/NIH HHS/United States ; R01NS102395/NH/NIH HHS/United States ; R21NS109575/NH/NIH HHS/United States ; }, abstract = {Various neurological disorders, such as stroke and Alzheimer's disease (AD), involve neuroinflammatory responses. The advent of the gut-brain axis enhances our understanding of neurological disease progression and secondary cell death. Gut microbiomes, especially those associated with inflammation, may reflect the dysbiosis of both the brain and the gut, opening the possibility to utilize inflammatory microbiomes as biomarkers and therapeutic targets. The gut-brain axis may serve as a contributing factor to disease pathology and offer innovative approaches in cell-based regenerative medicine for the treatment of neurological diseases. In reviewing the pathogenesis of stroke and AD, we also discuss the effects of gut microbiota on cognitive decline and brain pathology. Although the underlying mechanism of primary cell death from either disease is clearly distinct, both may be linked to gut-microbial dysfunction as a consequential aberration that is unique to each disease. Targeting peripheral cell death pathways that exacerbate disease symptoms, such as those arising from the gut, coupled with conventional central therapeutic approach, may improve stroke and AD outcomes.}, } @article {pmid33464013, year = {2021}, author = {Vielot, NA and González, F and Reyes, Y and Zepeda, O and Blette, B and Paniagua, M and Toval-Ruíz, C and Diez-Valcarce, M and Hudgens, MG and Gutiérrez, L and Blandón, P and Herrera, R and Cuadra, EC and Bowman, N and Vilchez, S and Vinjé, J and Becker-Dreps, S and Bucardo, F}, title = {Risk Factors and Clinical Profile of Sapovirus-associated Acute Gastroenteritis in Early Childhood: A Nicaraguan Birth Cohort Study.}, journal = {The Pediatric infectious disease journal}, volume = {}, number = {}, pages = {}, doi = {10.1097/INF.0000000000003015}, pmid = {33464013}, issn = {1532-0987}, abstract = {BACKGROUND: Sapovirus is increasingly recognized as an important cause of acute gastroenteritis (AGE) in children. We identified risk factors and characterized the clinical profile of sapovirus AGE in a birth cohort in León, Nicaragua.

METHODS: We conducted a case-control study nested within a birth cohort (n = 444). Fieldworkers conducted weekly household AGE surveillance. AGE stools were tested for sapovirus by reverse transcriptase quantitative polymerase chain reaction. For each first sapovirus episode, we selected 2 healthy age-matched controls and estimated independent risk factors of sapovirus AGE using conditional logistic regression. We compared clinical characteristics of sapovirus AGE episodes with episodes associated with other etiologies and identified co-infections with other enteric pathogens.

RESULTS: From June 2017 to July 2019, we identified 63 first sapovirus AGE episodes and selected 126 controls. Having contact with an individual with AGE symptoms and vaginal delivery were independent risk factors for sapovirus AGE. All cases experienced diarrhea, lasting a median 6 days; 23% experienced vomiting. Compared to children with AGE due to another etiology, sapovirus AGE was similar in severity, with less reported fever. Most cases experienced co-infections and were more likely than controls to be infected with diarrheagenic Escherichia coli or astrovirus.

CONCLUSIONS: Sapovirus was a commonly identified AGE etiology in this Central American setting, and symptoms were similar to AGE associated with other etiologies. The association between vaginal delivery and sapovirus is a novel finding. Gut microbiome composition might mediate this relationship, or vaginal delivery might be a proxy for other risk factors. Further investigation into more specific biological mechanisms is warranted.}, } @article {pmid33463949, year = {2020}, author = {Riffelmacher, T and Kronenberg, M}, title = {Metabolic Triggers of Invariant Natural Killer T-Cell Activation during Sterile Autoinflammatory Disease.}, journal = {Critical reviews in immunology}, volume = {40}, number = {5}, pages = {367-378}, doi = {10.1615/CritRevImmunol.2020035158}, pmid = {33463949}, issn = {1040-8401}, abstract = {Ample evidence exists for activation of invariant natural killer T (iNKT) cells in a sterile manner by endogenous ligands or microbial antigens from the commensal flora, indicating that iNKT cells are not truly self-tolerant. Their controlled autoreactivity state is disturbed in many types of sterile inflammatory disease, resulting in their central role in modulating autoimmune responses. This review focuses on sterile iNKT-cell responses that are initiated by metabolic triggers, such as obesity-associated inflammation and fatty liver disease, as a manifestation of metabolic disease and dyslipidemia, as well as ischemia reperfusion injuries and sickle cell disease, characterized by acute lack of oxygen and oxidative stress response on reperfusion. In the intestine, inflammation and iNKT-cell response type are shaped by the microbiome as an extended "self". Disease- and organ-specific differences in iNKT-cell response type are summarized and help to define common pathways that shape iNKT-cell responses in the absence of exogenous antigen.}, } @article {pmid33463536, year = {2021}, author = {Bao, R and Hesser, LA and He, Z and Zhou, X and Nadeau, KC and Nagler, CR}, title = {Fecal microbiome and metabolome differ in healthy and food-allergic twins.}, journal = {The Journal of clinical investigation}, volume = {131}, number = {2}, pages = {}, doi = {10.1172/JCI141935}, pmid = {33463536}, issn = {1558-8238}, abstract = {BACKGROUNDThere has been a striking generational increase in the prevalence of food allergies. We have proposed that this increase can be explained, in part, by alterations in the commensal microbiome.METHODSTo identify bacterial signatures and metabolic pathways that may influence the expression of this disease, we collected fecal samples from a unique, well-controlled cohort of twins concordant or discordant for food allergy. Samples were analyzed by integrating 16S rRNA gene amplicon sequencing and liquid chromatography-tandem mass spectrometry metabolite profiling.RESULTSA bacterial signature of 64 operational taxonomic units (OTUs) distinguished healthy from allergic twins; the OTUs enriched in the healthy twins were largely taxa from the Clostridia class. We detected significant enrichment in distinct metabolite pathways in each group. The enrichment of diacylglycerol in healthy twins is of particular interest for its potential as a readily measurable fecal biomarker of health. In addition, an integrated microbial-metabolomic analysis identified a significant association between healthy twins and Phascolarctobacterium faecium and Ruminococcus bromii, suggesting new possibilities for the development of live microbiome-modulating biotherapeutics.CONCLUSIONTwin pairs exhibited significant differences in their fecal microbiomes and metabolomes through adulthood, suggesting that the gut microbiota may play a protective role in patients with food allergies beyond the infant stage.TRIAL REGISTRATIONParticipants in this study were recruited as part of an observational study (ClinicalTrials.gov NCT01613885) at multiple sites from 2014 to 2018.FUNDINGThis work was supported by the Sunshine Charitable Foundation; the Moss Family Foundation; the National Institute of Allergy and Infectious Diseases (NIAID) (R56AI134923 and R01AI 140134); the Sean N. Parker Center for Allergy and Asthma Research; the National Heart, Lung, and Blood Institute (R01 HL 118612); the Orsak family; the Kepner family; and the Stanford Institute for Immunity, Transplant and Infection.}, } @article {pmid33463464, year = {2021}, author = {Floden, AM and Sohrabi, M and Nookala, S and Cao, JJ and Combs, CK}, title = {Salivary Aβ Secretion and Altered Oral Microbiome in Mouse Models of AD.}, journal = {Current Alzheimer research}, volume = {}, number = {}, pages = {}, doi = {10.2174/1567205018666210119151952}, pmid = {33463464}, issn = {1875-5828}, abstract = {BACKGROUND: Beta amyloid (Aβ) peptide containing plaque aggregations in the brain are a hallmark of Alzheimer's Disease (AD). However, Aβ is produced by cell types outside of the brain suggesting that the peptide may serve a broad physiologic purpose.

OBJECTIVE: Based upon our prior work documenting expression of amyloid β precursor protein (APP) in intestinal epithelium we hypothesized that salivary epithelium might also express APP and be a source of Aβ.

METHODS: To begin testing this idea, we compared human age-matched control and AD salivary glands to C57BL/6 wild type, App NL-G-F , and APP/PS1 mice.

RESULTS: Both male and female AD, App NL-G-F , and APP/PS1 glands demonstrated robust APP and Aβ immunoreactivity. Female App NL-G-F mice had significantly higher levels of pilocarpine stimulated Aβ 1-42 compared to both wild type and APP/PS1 mice. No differences in male salivary Aβ levels were detected. No significant differences in total pilocarpine stimulated saliva volumes were observed in any group. Both male and female App NL-G-F but not APP/PS1 mice demonstrated significant differences in oral microbiome phylum and genus abundance compared to wild type mice. Male, but not female, APP/PS1 and App NL-G-F mice had significantly thinner molar enamel compared to their wild type counterparts.

CONCLUSION: These data support the idea that oral microbiome changes exist during AD in addition to changes in salivary Aβ and oral health.}, } @article {pmid33462863, year = {2021}, author = {Pestana-Oliveira, N and Nahey, DB and Hartson, R and Weber, B and Johnson, TJ and Collister, JP}, title = {DOCA-salt hypertension and the role of the OVLT-sympathetic-gut microbiome axis.}, journal = {Clinical and experimental pharmacology & physiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1440-1681.13457}, pmid = {33462863}, issn = {1440-1681}, support = {19AIREA34380525//American Heart Association/ ; }, abstract = {Hypertension is a multifaceted condition influenced by genetic and environmental factors and estimated to cause 9.4 million deaths globally every year. Recently, there has been growing interest in understanding the gut microbe-host interaction in the maintenance of health or disease states, but relatively few studies have shown an association between the gut microbiome and specific types of hypertension. The deoxycorticosterone acetate (DOCA)-salt model of hypertension in rats is known to have a neurogenic component linked to increased sympathetic nervous system activity. As such, our lab has recently shown the hypertensive response in DOCA treated rats requires an intact organum vasculosum of the lamina terminalis (OVLT), a central hypothalamic circumventricular organ. Currently, we hypothesize the OVLT mediates changes in the gut microbiome associated with concomitant hypertension. Herein, we report that the hypertensive effects of DOCA-salt treatment were significantly attenuated throughout the 24-hour day/night cycle in OLVT lesioned rats on days 1, 3, and 9-21 of DOCA treatment compared with sham rats. Increased blood pressure (BP) in DOCA-salt treated rats was accompanied by specific changes in regional gut microbial populations yet was mitigated and offset by lesion of the OVLT. Furthermore, bacterial populations in OVLT-lesioned rats with attenuated hypertension more closely resembled those in normal control rats. We conclude that DOCA-salt hypertension is associated with specific microbiome changes in the gut, and the attenuated hypertensive effects of DOCA-salt in OVLT-lesioned rats is mediated in part through counteracting changes in these bacterial populations.}, } @article {pmid33462700, year = {2021}, author = {Moroenyane, I and Mendes, L and Tremblay, J and Tripathi, B and Yergeau, É}, title = {Plant Compartments and Developmental Stages Modulate the Balance between Niche-Based and Neutral Processes in Soybean Microbiome.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33462700}, issn = {1432-184X}, support = {RGPIN 2014-05274//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Understanding the dynamics of plant-associated microbial communities within agriculture is well documented. However, the ecological processes that assemble the plant microbiome are not well understood. This study elucidates the relative dominance of assembly processes across plant compartments (root, stem, and leaves) and developmental stages (emergence, growth, flowering, and maturation). Bacterial community composition and assembly processes were assessed using 16S rRNA gene amplicon sequencing. Null models that couple phylogenetic community composition and species distribution models were used to evaluate ecological assembly processes of bacterial communities. All models highlighted that the balance between the assembly process was modulated by compartments and developmental stages. Dispersal limitation dominated amongst the epiphytic communities and at the maturation stage. Homogeneous selection dominated assembly across plant compartments and development stages. Overall, both sets of models were mostly in agreement in predicting the prevailing assembly processes. Our results show, for the first time, that even though niche-based processes dominate in the plant environment, the relative influence of dispersal limitation in community assembly is important.}, } @article {pmid33462612, year = {2021}, author = {Pietzner, M and Budde, K and Rühlemann, M and Völzke, H and Homuth, G and Weiss, FU and Lerch, MM and Frost, F}, title = {Exocrine Pancreatic Function Modulates Plasma Metabolites Through Changes in Gut Microbiota Composition.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1210/clinem/dgaa961}, pmid = {33462612}, issn = {1945-7197}, abstract = {PURPOSE: Exocrine pancreatic function is critically involved in regulating the gut microbiota composition. At the same time, its impairment acutely affects human metabolism. How these 2 roles are connected is unknown. We studied how the exocrine pancreas contributes to metabolism via modulation of gut microbiota.

DESIGN: Fecal samples were collected in 2226 participants of the population-based Study of Health in Pomerania (SHIP/SHIP-TREND) to determine exocrine pancreatic function (pancreatic elastase enzyme-linked immunosorbent assay) and intestinal microbiota profiles (16S ribosomal ribonucleic acid gene sequencing). Plasma metabolite levels were determined by mass spectrometry.

RESULTS: Exocrine pancreatic function was associated with changes in the abundance of 28 taxa and, simultaneously, with those of 16 plasma metabolites. Mediation pathway analysis revealed that a significant component of how exocrine pancreatic function affects the blood metabolome is mediated via gut microbiota abundance changes, most prominently, circulating serotonin and lysophosphatidylcholines.

CONCLUSION: These results imply that the effect of exocrine pancreatic function on intestinal microbiota composition alters the availability of microbial-derived metabolites in the blood and thus directly contributes to the host metabolic changes associated with exocrine pancreatic dysfunction.}, } @article {pmid33462485, year = {2021}, author = {Kurilshikov, A and Medina-Gomez, C and Bacigalupe, R and Radjabzadeh, D and Wang, J and Demirkan, A and Le Roy, CI and Raygoza Garay, JA and Finnicum, CT and Liu, X and Zhernakova, DV and Bonder, MJ and Hansen, TH and Frost, F and Rühlemann, MC and Turpin, W and Moon, JY and Kim, HN and Lüll, K and Barkan, E and Shah, SA and Fornage, M and Szopinska-Tokov, J and Wallen, ZD and Borisevich, D and Agreus, L and Andreasson, A and Bang, C and Bedrani, L and Bell, JT and Bisgaard, H and Boehnke, M and Boomsma, DI and Burk, RD and Claringbould, A and Croitoru, K and Davies, GE and van Duijn, CM and Duijts, L and Falony, G and Fu, J and van der Graaf, A and Hansen, T and Homuth, G and Hughes, DA and Ijzerman, RG and Jackson, MA and Jaddoe, VWV and Joossens, M and Jørgensen, T and Keszthelyi, D and Knight, R and Laakso, M and Laudes, M and Launer, LJ and Lieb, W and Lusis, AJ and Masclee, AAM and Moll, HA and Mujagic, Z and Qibin, Q and Rothschild, D and Shin, H and Sørensen, SJ and Steves, CJ and Thorsen, J and Timpson, NJ and Tito, RY and Vieira-Silva, S and Völker, U and Völzke, H and Võsa, U and Wade, KH and Walter, S and Watanabe, K and Weiss, S and Weiss, FU and Weissbrod, O and Westra, HJ and Willemsen, G and Payami, H and Jonkers, DMAE and Arias Vasquez, A and de Geus, EJC and Meyer, KA and Stokholm, J and Segal, E and Org, E and Wijmenga, C and Kim, HL and Kaplan, RC and Spector, TD and Uitterlinden, AG and Rivadeneira, F and Franke, A and Lerch, MM and Franke, L and Sanna, S and D'Amato, M and Pedersen, O and Paterson, AD and Kraaij, R and Raes, J and Zhernakova, A}, title = {Large-scale association analyses identify host factors influencing human gut microbiome composition.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {33462485}, issn = {1546-1718}, support = {024.004.017//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 024.004.017//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, abstract = {To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microbial composition showed high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples. A genome-wide association study of host genetic variation regarding microbial taxa identified 31 loci affecting the microbiome at a genome-wide significant (P < 5 × 10-8) threshold. One locus, the lactase (LCT) gene locus, reached study-wide significance (genome-wide association study signal: P = 1.28 × 10-20), and it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.95 × 10-10 < P < 5 × 10-8) but enriched for taxa showing high heritability and for genes expressed in the intestine and brain. A phenome-wide association study and Mendelian randomization identified enrichment of microbiome trait loci in the metabolic, nutrition and environment domains and suggested the microbiome might have causal effects in ulcerative colitis and rheumatoid arthritis.}, } @article {pmid33462482, year = {2021}, author = {Rühlemann, MC and Hermes, BM and Bang, C and Doms, S and Moitinho-Silva, L and Thingholm, LB and Frost, F and Degenhardt, F and Wittig, M and Kässens, J and Weiss, FU and Peters, A and Neuhaus, K and Völker, U and Völzke, H and Homuth, G and Weiss, S and Grallert, H and Laudes, M and Lieb, W and Haller, D and Lerch, MM and Baines, JF and Franke, A}, title = {Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {33462482}, issn = {1546-1718}, support = {SFB1182//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 03ZZ0921E//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; ESF/14-BM-A55_0045/16//EC | Directorate-General for Employment, Social Affairs and Inclusion | European Social Fund (Fondo Social Europeo)/ ; }, abstract = {The intestinal microbiome is implicated as an important modulating factor in multiple inflammatory1,2, neurologic3 and neoplastic diseases4. Recent genome-wide association studies yielded inconsistent, underpowered and rarely replicated results such that the role of human host genetics as a contributing factor to microbiome assembly and structure remains uncertain5-11. Nevertheless, twin studies clearly suggest host genetics as a driver of microbiome composition11. In a genome-wide association analysis of 8,956 German individuals, we identified 38 genetic loci to be associated with single bacteria and overall microbiome composition. Further analyses confirm the identified associations of ABO histo-blood groups and FUT2 secretor status with Bacteroides and Faecalibacterium spp. Mendelian randomization analysis suggests causative and protective effects of gut microbes, with clade-specific effects on inflammatory bowel disease. This holistic investigative approach of the host, its genetics and its associated microbial communities as a 'metaorganism' broaden our understanding of disease etiology, and emphasize the potential for implementing microbiota in disease treatment and management.}, } @article {pmid33462291, year = {2021}, author = {Jeong, J and Yun, K and Mun, S and Chung, WH and Choi, SY and Nam, YD and Lim, MY and Hong, CP and Park, C and Ahn, Y and Han, K}, title = {The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1727}, pmid = {33462291}, issn = {2045-2322}, support = {2019R1A6C1010033//Korea Basic Science Institute (National research Facilities and Equipment Center)/ ; 2019R1A6C1010033//Korea Basic Science Institute (National research Facilities and Equipment Center)/ ; }, abstract = {Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium, Bacteroides, and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.}, } @article {pmid33462163, year = {2020}, author = {Townsend, JR and Vantrease, WC and Jones, MD and Sapp, PA and Johnson, KD and Beuning, CN and Haase, AA and Boot, CM}, title = {Plasma Amino Acid Response to Whey Protein Ingestion Following 28 Days of Probiotic (Bacillus subtilis DE111) Supplementation in Active Men and Women.}, journal = {Journal of functional morphology and kinesiology}, volume = {6}, number = {1}, pages = {}, doi = {10.3390/jfmk6010001}, pmid = {33462163}, issn = {2411-5142}, support = {n/a//Deerland Enzymes/ ; }, abstract = {We sought to determine if 28 days of probiotic supplementation influenced the plasma amino acid (AA) response to acute whey protein feeding.

METHODS: Twenty-two recreationally active men (n = 11; 24.3 ± 3.2 yrs; 89.3 ± 7.2 kg) and women (n = 11; 23.0 ± 2.8 yrs; 70.2 ± 15.2 kg) participated in this double-blind, placebo-controlled, randomized study. Before (PRE) and after 28 days of supplementation (POST), participants reported to the lab following a 10-hr fast and provided a resting blood draw (0 min), then subsequently consumed 25 g of whey protein. Blood samples were collected at 15-min intervals for 2 h post-consumption (15-120 min) and later analyzed for plasma leucine, branched-chain AA (BCAA), essential AA (EAA), and total AA (TAA). Participants received a probiotic (PROB) consisting of 1 x10-9 colony forming units (CFU) Bacillus subtilis DE111 (n = 11) or a maltodextrin placebo (PL) (n = 11) for 28 days. Plasma AA response and area under the curve (AUC) values were analyzed via repeated measures analysis of variance.

RESULTS: Our analysis indicated no significant (p < 0.05) differential responses for plasma leucine, BCAA, EAA, or TAA between PROB and PL from PRE to POST. AUC analysis revealed no group × time interaction for plasma leucine (p = 0.524), BCAA (p = 0.345), EAA (p = 0.512), and TAA (p = 0.712).

CONCLUSION: These data indicate that 28 days of Bacillus subtilis DE111 does not affect plasma AA appearance following acute whey protein ingestion.}, } @article {pmid33461965, year = {2021}, author = {Yaskolka Meir, A and Rinott, E and Tsaban, G and Zelicha, H and Kaplan, A and Rosen, P and Shelef, I and Youngster, I and Shalev, A and Blüher, M and Ceglarek, U and Stumvoll, M and Tuohy, K and Diotallevi, C and Vrhovsek, U and Hu, F and Stampfer, M and Shai, I}, title = {Effect of green-Mediterranean diet on intrahepatic fat: the DIRECT PLUS randomised controlled trial.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2020-323106}, pmid = {33461965}, issn = {1468-3288}, abstract = {OBJECTIVE: To examine the effectiveness of green-Mediterranean (MED) diet, further restricted in red/processed meat, and enriched with green plants and polyphenols on non-alcoholic fatty liver disease (NAFLD), reflected by intrahepatic fat (IHF) loss.

DESIGN: For the DIRECT-PLUS 18-month randomized clinical trial, we assigned 294 participants with abdominal obesity/dyslipidaemia into healthy dietary guidelines (HDG), MED and green-MED weight-loss diet groups, all accompanied by physical activity. Both isocaloric MED groups consumed 28 g/day walnuts (+440 mg/day polyphenols provided). The green-MED group further consumed green tea (3-4 cups/day) and Mankai (a Wolffia globosa aquatic plant strain; 100 g/day frozen cubes) green shake (+1240 mg/day total polyphenols provided). IHF% 18-month changes were quantified continuously by proton magnetic resonance spectroscopy (MRS).

RESULTS: Participants (age=51 years; 88% men; body mass index=31.3 kg/m2; median IHF%=6.6%; mean=10.2%; 62% with NAFLD) had 89.8% 18-month retention-rate, and 78% had eligible follow-up MRS. Overall, NAFLD prevalence declined to: 54.8% (HDG), 47.9% (MED) and 31.5% (green-MED), p=0.012 between groups. Despite similar moderate weight-loss in both MED groups, green-MED group achieved almost double IHF% loss (-38.9% proportionally), as compared with MED (-19.6% proportionally; p=0.035 weight loss adjusted) and HDG (-12.2% proportionally; p<0.001). After 18 months, both MED groups had significantly higher total plasma polyphenol levels versus HDG, with higher detection of Naringenin and 2-5-dihydroxybenzoic-acid in green-MED. Greater IHF% loss was independently associated with increased Mankai and walnuts intake, decreased red/processed meat consumption, improved serum folate and adipokines/lipids biomarkers, changes in microbiome composition (beta-diversity) and specific bacteria (p<0.05 for all).

CONCLUSION: The new suggested strategy of green-Mediterranean diet, amplified with green plant-based proteins/polyphenols as Mankai, green tea, and walnuts, and restricted in red/processed meat can double IHF loss than other healthy nutritional strategies and reduce NAFLD in half.

TRIAL REGISTRATION NUMBER: NCT03020186.}, } @article {pmid33461660, year = {2021}, author = {Urban, L and Holzer, A and Baronas, JJ and Hall, MB and Braeuninger-Weimer, P and Scherm, MJ and Kunz, DJ and Perera, SN and Martin-Herranz, DE and Tipper, ET and Salter, SJ and Stammnitz, MR}, title = {Freshwater monitoring by nanopore sequencing.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, doi = {10.7554/eLife.61504}, pmid = {33461660}, issn = {2050-084X}, support = {Graduate Student Fellowship//Gates Cambridge Trust/ ; OPP1144//Bill and Melinda Gates Foundation/ ; OpenPlant Fund (BBSRC BB/L014130/1)/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; Public Engagement Starter Grant (RCUK Catalyst Seed Fund)//University of Cambridge/ ; Graduate Student Fellowship//European Bioinformatics Institute/ ; Graduate Student Fellowship (203828/Z/16/A, 203828/Z/16/Z)/WT_/Wellcome Trust/United Kingdom ; Graduate Student Fellowship (102453/Z/13/Z)/WT_/Wellcome Trust/United Kingdom ; Graduate Student Fellowship//Oliver Gatty Studentship/ ; Standard Grant (NE/P011659/1)//Natural Environment Research Council/ ; }, abstract = {While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices.}, } @article {pmid33461494, year = {2021}, author = {Dhungel, E and Mreyoud, Y and Gwak, HJ and Rajeh, A and Rho, M and Ahn, TH}, title = {MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {25}, pmid = {33461494}, issn = {1471-2105}, support = {1564894//National Science Foundation/ ; }, abstract = {BACKGROUND: Diverse microbiome communities drive biogeochemical processes and evolution of animals in their ecosystems. Many microbiome projects have demonstrated the power of using metagenomics to understand the structures and factors influencing the function of the microbiomes in their environments. In order to characterize the effects from microbiome composition for human health, diseases, and even ecosystems, one must first understand the relationship of microbes and their environment in different samples. Running machine learning model with metagenomic sequencing data is encouraged for this purpose, but it is not an easy task to make an appropriate machine learning model for all diverse metagenomic datasets.

RESULTS: We introduce MegaR, an R Shiny package and web application, to build an unbiased machine learning model effortlessly with interactive visual analysis. The MegaR employs taxonomic profiles from either whole metagenome sequencing or 16S rRNA sequencing data to develop machine learning models and classify the samples into two or more categories. It provides various options for model fine tuning throughout the analysis pipeline such as data processing, multiple machine learning techniques, model validation, and unknown sample prediction that can be used to achieve the highest prediction accuracy possible for any given dataset while still maintaining a user-friendly experience.

CONCLUSIONS: Metagenomic sample classification and phenotype prediction is important particularly when it applies to a diagnostic method for identifying and predicting microbe-related human diseases. MegaR provides various interactive visualizations for user to build an accurate machine-learning model without difficulty. Unknown sample prediction with a properly trained model using MegaR will enhance researchers to identify the sample property in a fast turnaround time.}, } @article {pmid33461422, year = {2021}, author = {Stephenson, T and Lee, K and Griffith, JE and McLelland, DJ and Wilkes, A and Bird, PS and Trott, DJ and Speight, KN and Hemmatzadeh, F and Woolford, L}, title = {Pulmonary Actinomycosis in South Australian Koalas (Phascolarctos cinereus).}, journal = {Veterinary pathology}, volume = {}, number = {}, pages = {300985820973459}, doi = {10.1177/0300985820973459}, pmid = {33461422}, issn = {1544-2217}, abstract = {Pneumonia has been reported in both free-ranging and captive koalas and a number of causative agents have been described. Between 2016 and 2019, 16 free-ranging and 1 captive koala (Phascolarctos cinereus) from the Mount Lofty Ranges of South Australia were identified with pyogranulomatous lobar pneumonia, which involved the left caudal lobe in 14/17 (82%) cases. Within lesions, numerous gram-positive or gram-variable, non-acid-fast filamentous bacteria were observed in association with Splendore-Hoeppli phenomenon. Culture yielded growth of anaerobic bacteria, which were unidentifiable by MALDI-TOF-MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry) analysis in 5/5 cases. Sequencing of the bacterial 16S rRNA gene identified a novel Actinomyces species in 4 samples, confirming a diagnosis of pulmonary actinomycosis. Concurrent examination of resin lung casts from healthy koalas suggested greater laminar flow of air to the left caudal lung lobe in koalas. Actinomyces spp. have been reported as commensals of the oral microbiome in other species, and an association with similar pulmonary lesions in other species. Considering the predilection for involvement of the left caudal lung lobe, aspiration is suggested as the likely cause in some cases of pulmonary actinomycosis in koalas. Pulmonary actinomycosis has not been previously described in koalas and further work needs to be undertaken in order to classify this organism within the Actinomyces genus.}, } @article {pmid33456404, year = {2018}, author = {Ahmed, I and Umar, S}, title = {Microbiome and Colorectal Cancer.}, journal = {Current colorectal cancer reports}, volume = {14}, number = {6}, pages = {217-225}, pmid = {33456404}, issn = {1556-3790}, support = {R01 CA185322/CA/NCI NIH HHS/United States ; }, abstract = {Purpose of Review: The trillions of microbes collectively referred to as the human microbiota, inhabit the human body and establish a beneficial relationship with the host. It is clear however that dysbiosis impacting microbial diversity in the gut, may lead to development of inflammatory and malignant gastrointestinal diseases including colorectal cancer (CRC). We provide a literature review of the recent influx of information related to the alterations in gut microbiota composition that influences CRC incidence and progression.

Recent Findings: A growing body of evidence implicates altered gut microbiota in the development of CRC. Profiles of CRC associated microbiota have been shown to differ from those in healthy subjects and bacterial phylotypes vary depending on the primary tumor location. The compositional variation in the microbial profile is not restricted to cancerous tissue however and is different between cancers of the proximal and distal colons, respectively. More recently, studies have shed light on the "driver-passenger" model for CRC wherein, driver bacteria cause inflammation, increased cell proliferation and production of genotoxic substances to contribute towards mutational acquisition associated with adenoma-carcinoma sequence. These changes facilitate gradual replacement of driver bacteria by passengers that either promote or suppress tumor progression. Significant advances have also been made in associating individual bacterial species to consensus molecular subtypes (CMS) of CRC and this remarkable development is expected to galvanize scientific community into advancing therapeutic strategies for CRC.

Summary: Increasing evidence suggests a link between the intestinal microbiota and CRC development although the mechanisms through which the bacterial constituents of the microbiome contribute towards CRC are complex and yet to be fully fathomed. Thus, more exhaustive and mechanistic studies are needed to identify key interactions amongst diet, microbial community and metabolites that help facilitate the adenoma-carcinoma sequence evolution in CRC. It is expected that development of therapeutics based on microbial association with CMS will likely facilitate the translation of molecular subtypes into the clinic for CRCs and potentially other malignancies.}, } @article {pmid33454868, year = {2021}, author = {Feng, ZP and Xin, HY and Zhang, ZW and Liu, CG and Yang, Z and You, H and Xin, HW}, title = {Gut microbiota homeostasis restoration may become a novel therapy for breast cancer.}, journal = {Investigational new drugs}, volume = {}, number = {}, pages = {}, pmid = {33454868}, issn = {1573-0646}, support = {81872412//National Natural Science Foundation of China/ ; 2020007//Innovation Fund Designated for Graduate Students of Yangtze University Health Science Center/ ; }, abstract = {Breast cancer is the most diagnosed cancer in women. It significantly impairs a patient's physical and mental health. Gut microbiota comprise the bacteria residing in a host's gastrointestinal tract. Through studies over the last decade, we now know that alterations in the composition of the gut microbiome are associated with protection against colonization by pathogens and other diseases, such as diabetes and cancer. This review focuses on how gut microbiota can affect breast cancer development through estrogen activity and discusses the types of bacteria that may be involved in the onset and the progression of breast cancer. We also describe potential therapies to curtail the risk of breast cancer by restoring gut microbiota homeostasis and reducing systemic estrogen levels. This review will further explore the relationship between intestinal microbes and breast cancer and propose a method to treat breast cancer by improving intestinal microbes. We aimed at discovering new methods to prevent or treat BC by changing intestinal microorganisms.}, } @article {pmid33454779, year = {2021}, author = {Druzhinin, VG and Matskova, LV and Demenkov, PS and Baranova, ED and Volobaev, VP and Minina, VI and Larionov, AV and Titov, VA and Fucic, A}, title = {Genetic damage in lymphocytes of lung cancer patients is correlated to the composition of the respiratory tract microbiome.}, journal = {Mutagenesis}, volume = {}, number = {}, pages = {}, doi = {10.1093/mutage/geab004}, pmid = {33454779}, issn = {1464-3804}, abstract = {Recent findings indicate that the microbiome may have significant impact on the development of lung cancer by its effects on inflammation, dysbiosis or genome damage. The aim of this study was to compare the sputum microbiome of lung cancer (LC) patients with the chromosomal aberration (CA) and micronuclei (MN) frequency in peripheral blood lymphocytes. In the study, the taxonomic composition of the sputum microbiome of 66 men with untreated LC were compared to 62 control subjects with respect to CA and MN frequency and centromere FISH analysis. Results showed a significant increase in CA (4.11 ± 2.48% vs 2.08 ± 1.18%) and MN (1.53 ± 0.67% vs 0.87 ± 0.49%) frequencies respectively in LC patients as compared to control subjects. The higher frequency of centromeric positive MN of LC patients was mainly due to aneuploidy. A significant increase in Streptococcus, Bacillus, Gemella and Haemophilus in LC patients, in comparison to the control subjects while 18 bacterial genera were significantly reduced, which indicates a decrease in the beta diversity in the microbiome of LC patients. Although, the CA frequency in LC patients is significantly associated with an increased presence of the genera Bacteroides, Lachnoanaerobaculum, Porphiromonas, Mycoplasma and Fusobacterium in their sputum, and a decrease for the genus Granulicatella after application of false discovery rate (FDR) correction significance was not any more present. The decrease of MN frequency of LC patients is significantly associated with a increase in Megasphaera genera and Selenonomas bovis. In conclusion, a significant difference in beta diversity of microbiome between LC and control subjects and association between the sputum microbiome composition and genome damage of LC patients was detected, thus supporting previous studies suggesting an etiological connection between the airway microbiome and LC.}, } @article {pmid33454743, year = {2021}, author = {Lee, AH and Vidal, S and Oba, PM and Wyss, R and Miao, Y and Adesokan, Y and Swanson, KS}, title = {Evaluation of a novel animal milk oligosaccharide biosimilar: Macronutrient digestibility and gastrointestinal tolerance, fecal metabolites, and fecal microbiota of healthy adult dogs and in vitro genotoxicity assays.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skab014}, pmid = {33454743}, issn = {1525-3163}, abstract = {Milk oligosaccharides (MO) are bioactive compounds in mammalian milk that provide health benefits to neonates beyond essential nutrients. GNU100, a novel animal MO biosimilar, was recently tested in vitro, with results showing beneficial shifts in microbiota and increased short-chain fatty acid (SCFA) production, but other effects of GNU100 were unknown. Three studies were conducted to evaluate the safety, palatability and gastrointestinal (GI) tolerance of GNU100. In Study 1, the mutagenic potential of GNU100 was tested using a bacterial reverse mutation assay and a mammalian cell micronucleus test. In Study 2, palatability was assessed by comparing diets containing 0% vs. 1% GNU100 in 20 adult dogs. In Study 3, 32 adult dogs were used in a completely randomized design to assess the safety and GI tolerance of GNU100 and explore utility. Following a 2-wk baseline, dogs were assigned to one of four treatments and fed for 26 wk: 0%, 0.5%, 1% and 1.5% GNU100. On wk 2, 4 and 26, fresh fecal samples were collected to measure stool quality, immunoglobulin A, and calprotectin, and blood samples were collected to measure serum chemistry and inflammatory markers and hematology. On wk 2 and 4, fresh fecal samples were collected to measure metabolites and microbiota. On wk 4, total feces were collected to assess apparent total tract macronutrient digestibility. Although revertant numbers were greater compared to the solvent control in WP2uvrA(pKM101) in presence of metabolic activation (S9) in the initial experiment, they remained below the threshold for a positive mutagenic response in follow-up confirmatory tests, supporting that GNU100 is not mutagenic. Similarly, no cytotoxicity or chromosome damage were observed in the cell micronucleus test. The palatability test showed that 1% GNU100 was strongly preferred (P < 0.05; 3.6:1 consumption ratio) over to the control. In Study 3, all dogs were healthy and had no signs of GI intolerance or illness. All diets were well-accepted and food intake, fecal characteristics and metabolite concentrations and macronutrient digestibilities were not altered. GNU100 modulated fecal microbiota, increasing evenness and Catenibacterium, Megamonas, and Prevotella (SCFA producers) and reducing Collinsella. Overall, results suggest that GNU100 is palatable and well-tolerated, causes no genotoxicity or adverse effects on health, and beneficially shifts the fecal microbiota, supporting the safety of GNU100 for inclusion in canine diets.}, } @article {pmid33453902, year = {2020}, author = {Balty, C and Guillot, A and Fradale, L and Brewee, C and Lefranc, B and Herrero, C and Sandström, C and Leprince, J and Berteau, O and Benjdia, A}, title = {Biosynthesis of the sactipeptide Ruminococcin C by the human microbiome: Mechanistic insights into thioether bond formation by radical SAM enzymes.}, journal = {The Journal of biological chemistry}, volume = {295}, number = {49}, pages = {16665-16677}, doi = {10.1074/jbc.RA120.015371}, pmid = {33453902}, issn = {1083-351X}, abstract = {Despite its major importance in human health, the metabolic potential of the human gut microbiota is still poorly understood. We have recently shown that biosynthesis of Ruminococcin C (RumC), a novel ribosomally synthesized and posttranslationally modified peptide (RiPP) produced by the commensal bacterium Ruminococcus gnavus, requires two radical SAM enzymes (RumMC1 and RumMC2) catalyzing the formation of four Cα-thioether bridges. These bridges, which are essential for RumC's antibiotic properties against human pathogens such as Clostridium perfringens, define two hairpin domains giving this sactipeptide (sulfur-to-α-carbon thioether-containing peptide) an unusual architecture among natural products. We report here the biochemical and spectroscopic characterizations of RumMC2. EPR spectroscopy and mutagenesis data support that RumMC2 is a member of the large family of SPASM domain radical SAM enzymes characterized by the presence of three [4Fe-4S] clusters. We also demonstrate that this enzyme initiates its reaction by Cα H-atom abstraction and is able to catalyze the formation of nonnatural thioether bonds in engineered peptide substrates. Unexpectedly, our data support the formation of a ketoimine rather than an α,β-dehydro-amino acid intermediate during Cα-thioether bridge LC-MS/MS fragmentation. Finally, we explored the roles of the leader peptide and of the RiPP precursor peptide recognition element, present in myriad RiPP-modifying enzymes. Collectively, our data support a more complex role for the peptide recognition element and the core peptide for the installation of posttranslational modifications in RiPPs than previously anticipated and suggest a possible reaction intermediate for thioether bond formation.}, } @article {pmid33453859, year = {2020}, author = {Duan, CJ and Baslé, A and Liberato, MV and Gray, J and Nepogodiev, SA and Field, RA and Juge, N and Ndeh, D}, title = {Ascertaining the biochemical function of an essential pectin methylesterase in the gut microbe Bacteroides thetaiotaomicron.}, journal = {The Journal of biological chemistry}, volume = {295}, number = {52}, pages = {18625-18637}, doi = {10.1074/jbc.RA120.014974}, pmid = {33453859}, issn = {1083-351X}, abstract = {Pectins are a major dietary nutrient source for the human gut microbiota. The prominent gut microbe Bacteroides thetaiotaomicron was recently shown to encode the founding member (BT1017) of a new family of pectin methylesterases essential for the metabolism of the complex pectin rhamnogalacturonan-II (RG-II). However, biochemical and structural knowledge of this family is lacking. Here, we showed that BT1017 is critical for the metabolism of an RG-II-derived oligosaccharide ΔBT1017oligoB generated by a BT1017 deletion mutant (ΔBT1017) during growth on carbohydrate extract from apple juice. Structural analyses of ΔBT1017oligoB using a combination of enzymatic, mass spectrometric, and NMR approaches revealed that it is a bimethylated nonaoligosaccharide (GlcA-β1,4-(2-O-Me-Xyl-α1,3)-Fuc-α1,4-(GalA-β1,3)-Rha-α1,3-Api-β1,2-(Araf-α1,3)-(GalA-α1,4)-GalA) containing components of the RG-II backbone and its side chains. We showed that the catalytic module of BT1017 adopts an α/β-hydrolase fold, consisting of a central twisted 10-stranded β-sheet sandwiched by several α-helices. This constitutes a new fold for pectin methylesterases, which are predominantly right-handed β-helical proteins. Bioinformatic analyses revealed that the family is dominated by sequences from prominent genera of the human gut microbiota, including Bacteroides and Prevotella. Our re-sults not only highlight the critical role played by this family of enzymes in pectin metabolism but also provide new insights into the molecular basis of the adaptation of B. thetaiotaomicron to the human gut.}, } @article {pmid33461019, year = {2021}, author = {Oz, M and Lorke, DE}, title = {Multifunctional angiotensin converting enzyme 2, the SARS-CoV-2 entry receptor, and critical appraisal of its role in acute lung injury.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {136}, number = {}, pages = {111193}, doi = {10.1016/j.biopha.2020.111193}, pmid = {33461019}, issn = {1950-6007}, abstract = {The recent emergence of coronavirus disease-2019 (COVID-19) as a pandemic affecting millions of individuals has raised great concern throughout the world, and the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was identified as the causative agent for COVID-19. The multifunctional protein angiotensin converting enzyme 2 (ACE2) is accepted as its primary target for entry into host cells. In its enzymatic function, ACE2, like its homologue ACE, regulates the renin-angiotensin system (RAS) critical for cardiovascular and renal homeostasis in mammals. Unlike ACE, however, ACE2 drives an alternative RAS pathway by degrading Ang-II and thus operates to balance RAS homeostasis in the context of hypertension, heart failure, and cardiovascular as well as renal complications of diabetes. Outside the RAS, ACE2 hydrolyzes key peptides, such as amyloid-β, apelin, and [des-Arg9]-bradykinin. In addition to its enzymatic functions, ACE2 is found to regulate intestinal amino acid homeostasis and the gut microbiome. Although the non-enzymatic function of ACE2 as the entry receptor for SARS-CoV-2 has been well established, the contribution of enzymatic functions of ACE2 to the pathogenesis of COVID-19-related lung injury has been a matter of debate. A complete understanding of this central enzyme may begin to explain the various symptoms and pathologies seen in SARS-CoV-2 infected individuals, and may aid in the development of novel treatments for COVID-19.}, } @article {pmid33460987, year = {2021}, author = {Zhang, J and Cook, J and Nearing, JT and Zhang, J and Raudonis, R and Glick, BR and Langille, MGI and Cheng, Z}, title = {Harnessing the plant microbiome to promote the growth of agricultural crops.}, journal = {Microbiological research}, volume = {245}, number = {}, pages = {126690}, doi = {10.1016/j.micres.2020.126690}, pmid = {33460987}, issn = {1618-0623}, abstract = {The rhizosphere microbiome is composed of diverse microbial organisms, including archaea, viruses, fungi, bacteria as well as eukaryotic microorganisms, which occupy a narrow region of soil directly associated with plant roots. The interactions between these microorganisms and the plant can be commensal, beneficial or pathogenic. These microorganisms can also interact with each other, either competitively or synergistically. Promoting plant growth by harnessing the soil microbiome holds tremendous potential for providing an environmentally friendly solution to the increasing food demands of the world's rapidly growing population, while also helping to alleviate the associated environmental and societal issues of large-scale food production. There recently have been many studies on the disease suppression and plant growth promoting abilities of the rhizosphere microbiome; however, these findings largely have not been translated into the field. Therefore, additional research into the dynamic interactions between crop plants, the rhizosphere microbiome and the environment are necessary to better guide the harnessing of the microbiome to increase crop yield and quality. This review explores the biotic and abiotic interactions that occur within the plant's rhizosphere as well as current agricultural practices, and how these biotic and abiotic factors, as well as human practices, impact the plant microbiome. Additionally, some limitations, safety considerations, and future directions to the study of the plant microbiome are discussed.}, } @article {pmid33460787, year = {2021}, author = {Higgins, MA and Ryan, KS}, title = {Generating a fucose permease deletion mutant in Bifidobacterium longum subspecies infantis ATCC 15697.}, journal = {Anaerobe}, volume = {}, number = {}, pages = {102320}, doi = {10.1016/j.anaerobe.2021.102320}, pmid = {33460787}, issn = {1095-8274}, abstract = {Bifidobacterium longum subsp. infantis ATCC 15697 has emerged as a model for infant gut-associated bifidobacterial strains. Here we present a genetic system for B. longum subsp. infantis ATCC 15697 using its own DNA restriction-modification systems and create a fucose permease deletion mutant lacking the ability to use free fucose as a carbon source.}, } @article {pmid33460570, year = {2021}, author = {Combs, MP and Wheeler, DS and Luth, JE and Falkowski, NR and Walker, NM and Erb-Downward, JR and Lama, VN and Dickson, RP}, title = {Lung microbiota predict chronic rejection in healthy lung transplant recipients: a prospective cohort study.}, journal = {The Lancet. Respiratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2213-2600(20)30405-7}, pmid = {33460570}, issn = {2213-2619}, abstract = {BACKGROUND: Alterations in the respiratory microbiome are common in chronic lung diseases, correlate with decreased lung function, and have been associated with disease progression. The clinical significance of changes in the respiratory microbiome after lung transplant, specifically those related to development of chronic lung allograft dysfunction (CLAD), are unknown. The aim of this study was to evaluate the effect of lung microbiome characteristics in healthy lung transplant recipients on subsequent CLAD-free survival.

METHODS: We prospectively studied a cohort of lung transplant recipients at the University of Michigan (Ann Arbor, MI, USA). We analysed characteristics of the respiratory microbiome in acellular bronchoalveolar lavage fluid (BALF) collected from asymptomatic patients during per-protocol surveillance bronchoscopy 1 year after lung transplantation. For our primary endpoint, we evaluated a composite of development of CLAD or death at 500 days after the 1-year surveillance bronchoscopy. Our primary microbiome predictor variables were bacterial DNA burden (total 16S rRNA gene copies per mL of BALF, quantified via droplet digital PCR) and bacterial community composition (determined by bacterial 16S rRNA gene sequencing). Patients' lung function was followed serially at least every 3 months by spirometry, and CLAD was diagnosed according to International Society of Heart and Lung Transplant 2019 guidelines.

FINDINGS: We analysed BALF from 134 patients, collected during 1-year post-transplant surveillance bronchoscopy between Oct 21, 2005, and Aug 25, 2017. Within 500 days of follow-up from the time of BALF sampling, 24 (18%) patients developed CLAD, five (4%) died before confirmed development of CLAD, and 105 (78%) patients remained CLAD-free with complete follow-up. Lung bacterial burden was predictive of CLAD development or death within 500 days of the surveillance bronchoscopy, after controlling for demographic and clinical factors, including immunosuppression and bacterial culture results, in a multivariable survival model. This relationship was evident when burden was analysed as a continuous variable (per log10 increase in burden, HR 2·49 [95% CI 1·38-4·48], p=0·0024) or by tertiles (middle vs lowest bacterial burden tertile, HR 4·94 [1·25-19·42], p=0·022; and highest vs lowest, HR 10·56 [2·53-44·08], p=0·0012). In patients who developed CLAD or died, composition of the lung bacterial community significantly differed to that in patients who survived and remained CLAD-free (on permutational multivariate analysis of variance, p=0·047 at the taxonomic level of family), although differences in community composition were associated with bacterial burden. No individual bacterial taxa were definitively associated with CLAD development or death.

INTERPRETATION: Among asymptomatic lung transplant recipients at 1-year post-transplant, increased lung bacterial burden is predictive of chronic rejection and death. The lung microbiome represents an understudied and potentially modifiable risk factor for lung allograft dysfunction.

FUNDING: US National Institutes of Health, Cystic Fibrosis Foundation, Brian and Mary Campbell and Elizabeth Campbell Carr research gift fund.}, } @article {pmid33460452, year = {2021}, author = {Byrd, DA and Vogtmann, E and Wu, Z and Han, Y and Wan, Y and Clegg-Lamptey, JN and Yarney, J and Wiafe-Addai, B and Wiafe, S and Awuah, B and Ansong, D and Nyarko, K and Hullings, AG and Hua, X and Ahearn, T and Goedert, JJ and Shi, J and Knight, R and Figueroa, JD and Brinton, LA and Garcia-Closas, M and Sinha, R}, title = {Associations of fecal microbial profiles with breast cancer and non-malignant breast disease in the Ghana Breast Health Study.}, journal = {International journal of cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/ijc.33473}, pmid = {33460452}, issn = {1097-0215}, abstract = {The gut microbiota may play a role in breast cancer etiology by regulating hormonal, metabolic, and immunologic pathways. We investigated associations of fecal bacteria with breast cancer and non-malignant breast disease in a case-control study conducted in Ghana, a country with rising breast cancer incidence and mortality. To do this, we sequenced the V4 region of the 16S rRNA gene to characterize bacteria in fecal samples collected at the time of breast biopsy (N = 379 breast cancer cases, N = 102 non-malignant breast disease cases, N = 414 population-based controls). We estimated associations of alpha diversity (observed amplicon sequence variants [ASVs], Shannon index, and Faith's phylogenetic diversity), beta diversity (Bray Curtis and unweighted/weighted UniFrac distance), and presence and relative abundance of select taxa with breast cancer and non-malignant breast disease using multivariable unconditional polytomous logistic regression. All alpha diversity metrics were strongly, inversely associated with odds of breast cancer and for those in the highest relative to lowest tertile of observed ASVs, the odds ratio (95% confidence interval) was 0.21 (0.13-0.36; Ptrend < 0.001). Alpha diversity associations were similar for non-malignant breast disease and breast cancer grade/molecular subtype. All beta diversity distance matrices and multiple taxa with possible estrogen-conjugating and immune-related functions were strongly associated with breast cancer (all P's < 0.001). There were no statistically significant differences between breast cancer and non-malignant breast disease cases in any microbiota metric. In conclusion, fecal bacteria characteristics were strongly and similarly associated with breast cancer and non-malignant breast disease. Our findings provide novel insight into potential microbially-mediated mechanisms of breast disease. This article is protected by copyright. All rights reserved.}, } @article {pmid33460261, year = {2020}, author = {Rehan, M and Al-Bahadly, I and Thomas, DG and Avci, E}, title = {Capsule robot for gut microbiota sampling using shape memory alloy spring.}, journal = {The international journal of medical robotics + computer assisted surgery : MRCAS}, volume = {16}, number = {5}, pages = {1-14}, doi = {10.1002/rcs.2140}, pmid = {33460261}, issn = {1478-596X}, support = {//Massey University Research Fund (MURF) 2019/ ; 5-1/HRD/UESTPI(Batch-V)/2421/2018/HEC//Higher Education Commision, Pakistan/ ; }, abstract = {BACKGROUND: Human gut microbiota can provide lifelong health information and even influence mood and behaviour. We currently lack the tools to obtain a microbial sample, directly from the small intestine, without contamination.

METHODS: Shape memory alloy springs are used in concentric configuration to develop an axial actuator. A novel design of sampling mechanism is fabricated for collecting the sample from the gut. Storage chamber (500 µl) is used to protect the sample from downstream contamination.

RESULTS: The developed actuator occupies a small space (5 × Ø5.75 mm) and produces sufficient output force (1.75 N) to operate the sampling mechanism. A non-invasive capsule robot was tested ex vivo on the animal intestine, and it captured an average of 134 µl content which was sufficient for microbiome assessment.

CONCLUSIONS: Laboratory testing revealed that the collected sample had an amino acid signature indicative of microbiota, mucus and digesta, which provided a proof of concept for the proposed design.}, } @article {pmid33459951, year = {2021}, author = {Martin, C and Stebbins, B and Ajmani, A and Comendul, A and Hamner, S and Hasan, NA and Colwell, R and Ford, T}, title = {Nanopore-based metagenomics analysis reveals prevalence of mobile antibiotic and heavy metal resistome in wastewater.}, journal = {Ecotoxicology (London, England)}, volume = {}, number = {}, pages = {}, pmid = {33459951}, issn = {1573-3017}, abstract = {In-depth studies of the microbiome and mobile resistome profile of different environments is central to understanding the role of the environment in antimicrobial resistance (AMR), which is one of the urgent threats to global public health. In this study, we demonstrated the use of a rapid (and easily portable) sequencing approach coupled with user-friendly bioinformatics tools, the MinION (Oxford Nanopore Technologies), on the evaluation of the microbial as well as mobile metal and antibiotic resistome profile of semi-rural wastewater. A total of 20 unique phyla, 43 classes, 227 genera, and 469 species were identified in samples collected from the Amherst Wastewater Treatment Plant, both from primary and secondary treated wastewater. Alpha diversity indices indicated that primary samples were significantly richer and more microbially diverse than secondary samples. A total of 1041 ARGs, 68 MRGs, and 17 MGEs were detected in this study. There were more classes of AMR genes in primary than secondary wastewater, but in both cases multidrug, beta-lactam and peptide AMR predominated. Of note, OXA β-lactamases, some of which are also carbapenemases, were enriched in secondary samples. Metal resistance genes against arsenic, copper, zinc and molybdenum were the dominant MRGs in the majority of the samples. A larger proportion of resistome genes were located in chromosome-derived sequences except for mobilome genes, which were predominantly located in plasmid-derived sequences. Genetic elements related to transposase were the most common MGEs in all samples. Mobile or MGE/plasmid-associated resistome genes that confer resistance to last resort antimicrobials such as carbapenems and colistin were detected in most samples. Worryingly, several of these potentially transferable genes were found to be carried by clinically-relevant hosts including pathogenic bacterial species in the orders Aeromonadales, Clostridiales, Enterobacterales and Pseudomonadales. This study demonstrated that the MinION can be used as a metagenomics approach to evaluate the microbiome, resistome, and mobilome profile of primary and secondary wastewater.}, } @article {pmid33459875, year = {2021}, author = {Balasubramanian, VK and Dampanaboina, L and Cobos, CJ and Yuan, N and Xin, Z and Mendu, V}, title = {Induced secretion system mutation alters rhizosphere bacterial composition in Sorghum bicolor (L.) Moench.}, journal = {Planta}, volume = {253}, number = {2}, pages = {33}, pmid = {33459875}, issn = {1432-2048}, abstract = {MAIN CONCLUSION: A novel inducible secretion system mutation in Sorghum named Red root has been identified. The mutant plant root exudes pigmented compounds that enriches Actinobacteria in its rhizosphere compared to BTx623. Favorable plant-microbe interactions in the rhizosphere positively influence plant growth and stress tolerance. Sorghum bicolor, a staple biomass and food crop, has been shown to selectively recruit Gram-positive bacteria (Actinobacteria) in its rhizosphere under drought conditions to enhance stress tolerance. However, the genetic/biochemical mechanism underlying the selective enrichment of specific microbial phyla in the sorghum rhizosphere is poorly known due to the lack of available mutants with altered root secretion systems. Using a subset of sorghum ethyl methanesulfonate (EMS) mutant lines, we have isolated a novel Red root (RR) mutant with an increased accumulation and secretion of phenolic compounds in roots. Genetic analysis showed that RR is a single dominant mutation. We further investigated the effect of root-specific phenolic compounds on rhizosphere microbiome composition under well-watered and water-deficit conditions. The microbiome diversity analysis of the RR rhizosphere showed that Actinobacteria were enriched significantly under the well-watered condition but showed no significant change under the water-deficit condition. BTx623 rhizosphere showed a significant increase in Actinobacteria under the water-deficit condition. Overall, the rhizosphere of RR genotype retained a higher bacterial diversity and richness relative to the rhizosphere of BTx623, especially under water-deficit condition. Therefore, the RR mutant provides an excellent genetic resource for rhizosphere-microbiome interaction studies as well as to develop drought-tolerant lines. Identification of the RR gene and the molecular mechanism through which the mutant selectively enriches microbial populations in the rhizosphere will be useful in designing strategies for improving sorghum productivity and stress tolerance.}, } @article {pmid33459777, year = {2021}, author = {Pan, HB and Li, MY and Wu, W and Wang, ZL and Yu, XP}, title = {Host-Plant Induced Shifts in Microbial Community Structure in Small Brown Planthopper, Laodelphax striatellus (Homoptera: Delphacidae).}, journal = {Journal of economic entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jee/toaa316}, pmid = {33459777}, issn = {1938-291X}, abstract = {Microbiome associated with insects play vital roles in host ecology and physiology. The small brown planthopper (SBPH), Laodelphax striatellus, is a polyphagous insect pest that caused enormous damage to a wide range of cereal crops. Previous studies have assessed the effects of environmental factors, such as antibiotics, insecticide, and geographical habitat on the bacterial composition of SBPH. However, the influence of host plants on the microbial community in SBPH still unclear. Here, we characterized and compared the microbial community in three SBPH populations feeding on rice, barley, and wheat, respectively, using high-throughput amplicon sequencing. Our observations revealed that the microbiome harbored by SBPH was abundant and diverse. Ten phyla comprising 141 genera of bacteria were annotated, and four fungal phyla consisting of 47 genera were assigned. The bacteria belonging to the phylum Proteobacteria were the most prevalent and the fungi with the highest abundance were from the order Hypocreales. Comparative analysis showed that host plants could significantly induce structural changes of SBPH microbiome. Significant differences in abundance were observed in two main bacterial orders (Rickettsiales and Rhodospirillales) and three fungal classes (Sordariomycetes, an unclassified class in Ascomycota and Eurotiomycetes) among three host-adapted SBPH populations. Our results could broaden our understanding of interactions among SBPH, its microbial associates and host plants, and also represented the basis of future SBPH biological management.}, } @article {pmid33459632, year = {2021}, author = {Cuñé Castellana, J}, title = {[Microbioma and lithiasis.].}, journal = {Archivos espanoles de urologia}, volume = {74}, number = {1}, pages = {157-170}, pmid = {33459632}, issn = {0004-0614}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Lithiasis ; Prebiotics ; *Probiotics ; *Urinary Tract ; }, abstract = {Human microbiome understanding and its relationship with health has represented a revolution in biomedicine, facilitated by the emergence of new molecular microbiology techniques. Lithiasic pathology has not been alien to this new approach to etiological knowledge. As a result of this research activity, it has been possible to elucidate the importance of the intestine-kidney axis, understood as the impact of the intestinal microbiota on nephrourinary health. In this regard the ability to use oxalate as an energy source by certain intestinal microorganisms has been used as a target form odulators of the intestinal microbiota in order to correcthyperoxaluria, both primary and secondary. However,the importance of the microbiome configuration, and its role in oxalocalcic lithiasis, transcends the existence of certain trophic networks. In particular, intestinal microbiome has the ability to promote tubular lesions resulting from oxidative stress caused by chronic low-grade inflammation, closely linked to the composition of the microbiota and the dialogue established with the immune system at the intestinal level. The importance of the urobiome, a stable microbia lstructure residing in the urinary tract, allowed to calibrate the importance of urinary microorganisms in lithiasic pathology, breaking with the paradigm of urine sterility in healthy conditions. Thus, recent studies suggest that the composition and structure of the urobiome have a crucial impact on infectious but also non-infectious lithiasis, since certain microorganisms can act as nucleants and promoters of the lithogenic process. Associated with the advances in the study of binomial microbiota and lithiasic pathology, new ways are opened for patient management, in terms of prevention and treatment, based on intervention on the microbiome. Future therapeutic arsenal, in addition to probiotics and prebiotics, will integrate consortia of different microbial groups and microbiota transplantation, both urinary and intestinal.}, } @article {pmid33459618, year = {2021}, author = {Wagner, CA}, title = {Etiopathogenic factors of urolithiasis.}, journal = {Archivos espanoles de urologia}, volume = {74}, number = {1}, pages = {16-23}, pmid = {33459618}, issn = {0004-0614}, mesh = {Humans ; *Kidney Calculi/etiology/genetics ; Recurrence ; *Renal Insufficiency, Chronic ; Risk Factors ; *Urolithiasis/epidemiology/etiology ; }, abstract = {INTRODUCTION: Kidney stone disease affects 1 in 10 persons at least once per life-time worldwide, in 2% the disease is recurrent. For the individual stone disease can be painful and lead even to chronic kidney disease, while the costs for the health system and economy can be very high. Thus, factors causing stone disease need to be identified in order to prevent or reduce the incidence of disease.

AIM: This review will discuss major risk factors contributing to stone disease with special emphasis on genetic and dietary risk factors. RESULTS: Stone disease is multifactorial with a strong genetic component, gender-specific risks and prevalence, and a modifiable contribution of nutrition. The different factors contributing to the risk for developing stones are discussed.

DISCUSSION: Urolithiasis is a frequent disorder affecting almost 10% of the population with a high risk of recurrence. Treatment and prevention have to be tailored to the individual causes of disease and require an assessment of underlying predispositions and interacting modifiable environmental factors.}, } @article {pmid33458858, year = {2021}, author = {Darch, HT and Collins, MK and O'Riordan, KJ and Cryan, JF}, title = {Microbial Memories: Sex-dependent Impact of the Gut Microbiome on Hippocampal Plasticity.}, journal = {The European journal of neuroscience}, volume = {}, number = {}, pages = {}, doi = {10.1111/ejn.15119}, pmid = {33458858}, issn = {1460-9568}, abstract = {Germ-free rodents, raised in the absence of a measurable gut microbiome, have been a key model to study the microbiome-gut-brain axis. Germ free mice exhibit marked behavioural and neurochemical differences to their conventionally raised counterparts. It is as yet unclear how these neurochemical differences lead to the behavioural differences. Here, we test the electrophysiological properties of hippocampal plasticity in adult germ-free mice and compare them to conventionally raised counterparts. Whilst basal synaptic efficacy and pre-synaptic short-term plasticity appears normal, we find a striking alteration of hippocampal long-term potentiation specifically in male germ-free slices. However, the spike output of these neurons remains normal along with altered input-output coupling, potentially indicating homeostatic compensatory mechanisms, or an altered excitation/inhibition balance. To our knowledge this is the first time the electrophysiological properties of the hippocampus have been assessed in a microbiome deficient animal. Our data indicate that the absence of a microbiome alters integration of dendritic signalling in the CA1 region in mice.}, } @article {pmid33458792, year = {2021}, author = {Zhong, C and He, L and Lee, SY and Chang, H and Zhang, Y and Threadgill, DW and Yuan, Y and Zhou, F and Celniker, SE and Xia, Y and Snijders, AM and Mao, JH}, title = {Host genetics and gut microbiota cooperatively contribute to azoxymethane-induced acute toxicity in Collaborative Cross mice.}, journal = {Archives of toxicology}, volume = {}, number = {}, pages = {}, pmid = {33458792}, issn = {1432-0738}, support = {DE AC02-05CH11231//Lawrence Berkeley National Laboratory/ ; R01ES031322/ES/NIEHS NIH HHS/United States ; 81961128022//National Natural Science Foundation of China/ ; 81872481//National Natural Science Foundation of China/ ; }, abstract = {Azoxymethane (AOM) is a widely used carcinogen to study chemical-induced colorectal carcinogenesis and is an agent for studying fulminant hepatic failure. The inter-strain susceptibility to acute toxicity by AOM has been reported, but its association with host genetics or gut microbiota remains largely unexplored. Here a cohort of genetically diverse Collaborative Cross (CC) mice was used to assess the contribution of host genetics and the gut microbiome to AOM-induced acute toxicity. We observed variation in AOM-induced acute liver failure across CC strains. Quantitative trait loci (QTL) analysis revealed three chromosome regions significantly associated with AOM toxicity. Genes located within these QTL, including peroxisome proliferator-activated receptor alpha (Ppara), were enriched for enzyme activator and nucleoside-triphosphatase regulator activity. We further demonstrated that the protein level of PPARα in liver tissues from sensitive strains was remarkably lower compared to levels in resistant strains, consistent with protective role of PPAR family in liver injury. We discovered that the abundance levels of gut microbial families Anaeroplasmataceae, Ruminococcaceae, Lactobacillaceae, Akkermansiaceae and Clostridiaceae were significantly higher in the sensitive strains compared to the resistant strains. Using a random forest classifier method, we determined that the relative abundance levels of these microbial families predicted AOM toxicity with the area under the receiver-operating curve (AUC) of 0.75. Combining the three genetic loci and five microbial families increased the predictive accuracy of AOM toxicity (AUC of 0.99). Moreover, we found that Ruminococcaceae and Lactobacillaceae acted as mediators between host genetics and AOM toxicity. In conclusion, this study shows that host genetics and specific microbiome members play a critical role in AOM-induced acute toxicity, which provides a framework for analysis of the health effects from environmental toxicants.}, } @article {pmid33457180, year = {2020}, author = {Shaw, J and Tate, V and Hanson, J and Bajaj, JS}, title = {What diet should I recommend my patient with Hepatic Encephalopathy?.}, journal = {Current hepatology reports}, volume = {19}, number = {1}, pages = {13-22}, pmid = {33457180}, issn = {2195-9595}, support = {I01 CX001076/CX/CSRD VA/United States ; R01 HS025412/HS/AHRQ HHS/United States ; R21 TR002024/TR/NCATS NIH HHS/United States ; }, abstract = {Purpose of Review: The burden of malnutrition is high in patients with cirrhosis, especially in those with hepatic encephalopathy (HE). This has a bearing on increased morbidity and mortality. Heightened attention needs to be paid to screen the patients at high nutritional risk both in the outpatient and hospitalized settings. This review summarizes the current evidence for nutritional support in HE patients and compares the recommendations about nutritional requirement as laid out by various organizations.

Recent Findings: On survey of the literature, there is a consensus on avoiding protein restriction of the diets in HE patients along with uniform recommendations on caloric requirements. An exciting field of manipulating the gut microbiome in nutritional sciences may hold promise as well as there may be a future role for branched chain amino acids in nutritional management of HE patients.

Summary: Even though the data suggest that nutritional improvement lead to better outcomes including lower readmission rates in cirrhosis, operationalizing these into practice remains a challenge. To achieve this, a multi-disciplinary approach with nutritional education of the frontline care providers, earlier nutritional risk screening of patients, involvement of the nutrition professionals as part of the team and repeated dietary counseling for the patient and caregiver/s is required. Ultimately, this may need more focus, resource allocation and uniform guidelines across all countries to make this a success.}, } @article {pmid33457168, year = {2021}, author = {Chandra, A and Gaur, V and Tripathi, P}, title = {Microbiome analysis of rhizospheres of plant and winter-initiated ratoon crops of sugarcane grown in sub-tropical India: utility to improve ratoon crop productivity.}, journal = {3 Biotech}, volume = {11}, number = {1}, pages = {34}, pmid = {33457168}, issn = {2190-572X}, abstract = {One plant and one to two ratoon crops are the predominant patterns of sugarcane cultivation in sub-tropical part of India. Despite high agricultural inputs, yield of ratoon crop gets dwindled in the subsequent years. The microbial community, particularly bacteria and fungi, in the rhizosphere and their interaction with the root system, in general influences plant productivity. For the present study, an early maturing sugarcane variety (CoLk 94184), was used to establish plant and winter-initiated ratoon crops in 2016-2018. Soils pertaining to both plant and ratoon rhizospheres were subjected to biochemical analysis, microbial DNA isolation and high-throughput sequencing of 16S rRNA genes to assess the microbial diversity and associated characteristics impacting cane yield. Although alpha diversity of bacterial community was observed high in the soils of both plant and ratoon crops, the species richness/diversity was more in plant crop. Bacterial community structure in the rhizosphere of plant crop was predominantly consisted of phyla Actinobacteria (35.68%), Gemmatimonadetes (29.26%), Chloroflexi (26.73%) and Proteobacteria (16.68%), while ratoon rhizosphere revealed dominance of Acidobacteria (20.77%) and Bacteroidetes (10.7%). Though studies revealed the presence of rich bacterial community in the rhizospheres of both plant and ratoon crops of sugarcane, dominance of Acidobacteria and meager proportion of Actinobacteria and Proteobacteria in ratoon crop possibly limited its productivity. Along with high total phenols (7.27 mg/g dry wt), ratoon crop depicted less active root system as revealed by scanning electron microscopy. Dominance of thermophilic bacterial phyla Chloroflexi and Gemmatimonadetes which was observed in sugarcane rhizosphere supports better crop growth in drought. However, management of soil microbial community is required to improve the ratoon crop productivity.}, } @article {pmid33456723, year = {2020}, author = {Willis, JR and Iraola-Guzmán, S and Saus, E and Ksiezopolska, E and Cozzuto, L and Bejarano, LA and Andreu-Somavilla, N and Alloza-Trabado, M and Puig-Sola, A and Blanco, A and Broglio, E and Carolis, C and Hecht, J and Ponomarenko, J and Gabaldón, T}, title = {Oral microbiome in down syndrome and its implications on oral health.}, journal = {Journal of oral microbiology}, volume = {13}, number = {1}, pages = {1865690}, pmid = {33456723}, issn = {2000-2297}, abstract = {Introduction: The oral cavity harbors an abundant and diverse microbial community (i.e. the microbiome), whose composition and roles in health and disease have been the focus of intense research. Down syndrome (DS) is associated with particular characteristics in the oral cavity, and with a lower incidence of caries and higher incidence of periodontitis and gingivitis compared to control populations. However, the overall composition of the oral microbiome in DS and how it varies with diverse factors like host age or the pH within the mouth are still poorly understood. Methods: Using a Citizen-Science approach in collaboration with DS associations in Spain, we performed 16S rRNA metabarcoding and high-throughput sequencing, combined with culture and proteomics-based identification of fungi to survey the bacterial and fungal oral microbiome in 27 DS persons (age range 7-55) and control samples matched by geographical distribution, age range, and gender. Results: We found that DS is associated with low salivary pH and less diverse oral microbiomes, which were characterized by lower levels of Alloprevotella, Atopobium, Candidatus Saccharimonas, and higher amounts of Kingella, Staphylococcus, Gemella, Cardiobacterium, Rothia, Actinobacillus, and greater prevalence of Candida.Conclusion: Altogether, our study provides a first global snapshot of the oral microbiome in DS. Future studies are required to establish whether the observed differences are related to differential pathology in the oral cavity in DS.}, } @article {pmid33456534, year = {2021}, author = {Shigeishi, H and Su, CY and Kaneyasu, Y and Matsumura, M and Nakamura, M and Ishikawa, M and Saito, A and Ohta, K and Sugiyama, M}, title = {Association of oral HPV16 infection with periodontal inflammation and the oral microbiome in older women.}, journal = {Experimental and therapeutic medicine}, volume = {21}, number = {2}, pages = {167}, pmid = {33456534}, issn = {1792-0981}, abstract = {The present preliminary study aimed to investigate the association between oral human papillomavirus type 16 (HPV16) DNA prevalence and periodontal inflammation in older women. The association between oral HPV16 infection and oral health status has not been fully elucidated in older Japanese women. The present study investigated older women aged ≥60 years who visited Hiroshima University Hospital. The present study excluded subjects with clinical factors affecting HPV infection, such as current smoking, oral cancer and pre-malignant lesions, and immunodeficiency. Finally, 46 female patients (mean age, 74.6 years) were analyzed. Quantitative PCR analysis was performed to detect HPV16 DNA in oral rinse samples. A total of 4 participants (8.7%) were HPV16 DNA positive. There was a significant association between the HPV16 DNA positivity rate and bleeding on probing (P=0.03). Additionally, Prevotella intermedia positive cases exhibited a significantly higher HPV16 DNA positivity rate than negative cases (33.3 vs 3.8%). Furthermore, analysis of 16S ribosomal RNA in bacterial flora was performed to examine microbiome diversity in participants with ≥6 mm periodontal pockets and bleeding on probing. Importantly, the average percentage of Porphyromonas was significantly higher in HPV16 DNA positive cases compared with in HPV16 DNA negative cases (5.57 vs. 1.44%). By contrast, the average percentage of Veillonella was significantly lower in HPV16 DNA positive cases than in HPV16 DNA negative cases (2.43 vs. 8.51%). Prevotella was also lower in HPV16 DNA positive cases than in HPV16 DNA negative cases (4.0 vs. 8.23%). These results indicated that people with both deep periodontal pocket inflammation and oral HPV16 infection may not have Prevotella- or Veillonella-dominant oral microbiomes, and their microbiomes may exhibit their own distinctive characteristics. In conclusion, the results suggested that oral HPV16 infection may be associated with periodontal inflammation in older Japanese women. Further research is required to clarify the detailed association between oral HPV infection and the oral microbiome.}, } @article {pmid33456248, year = {2020}, author = {Deo, PN and Deshmukh, R}, title = {Oral microbiome and oral cancer - The probable nexus.}, journal = {Journal of oral and maxillofacial pathology : JOMFP}, volume = {24}, number = {2}, pages = {361-367}, pmid = {33456248}, issn = {0973-029X}, abstract = {Oral squamous cell carcinoma is one of the most common malignancies and is the leading cause of morbidity and mortality. The known risk factors for oral cancer are tobacco, alcohol consumption and betel quid chewing. Nutritional deficiencies and certain microorganisms are also associated with oral cancer. Oral cavity is a host to numerous microorganisms, majority of which are bacterial communities along with fungi and viruses. A possibility of the dysregulation of the oral microbiome cannot be ignored. Oral microbiome is defined as the collective genome of microorganisms that reside in the oral cavity. With the development of culture-independent techniques, the detection and identification of the bacteria which cannot be cultured has become possible. Revolution in technology has led to increased research in this area in an attempt to find the role of microbiome in health and disease. Before identifying the exact role the microbiome plays in the development of oral cancer, it is essential to profile the microbiome in healthy individuals and patients with oral cancer. It is essential to note that oral cancer may sometimes occur without any habit too!! This article is an attempt to review the role of oral microbiome in oral cancer with a focus on the bacteriome, its related studies and in brief about the omics technologies in understanding the microbiome.}, } @article {pmid33455754, year = {2021}, author = {Samarasinghe, MB and Sehested, J and Weisbjerg, MR and Vestergaard, M and Hernández-Castellano, LE}, title = {Milk supplemented with dried seaweed affects the systemic innate immune response in preweaning dairy calves.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2020-19528}, pmid = {33455754}, issn = {1525-3198}, abstract = {Intact seaweed or seaweed extracts are used as feed supplements to improve the gut microbiome in young animals. Seaweeds provide functional polysaccharides, and they are a good source of vitamins, minerals, and phenolic compounds, all of which are relevant for immune system development. However, literature on the effects of dried seaweed supplementation on immune system development is limited, especially in calves. This experiment aimed to study the effect of feeding milk supplemented with Ulva lactuca, Ascophyllum nodosum, or Saccharina latissima on the systemic immune status of preweaning dairy calves. Forty male Holstein calves with birth body weight 41 ± 4 kg and plasma Brix percentage ≥8.7% at d 2 after birth were used in this study. Calves were fed 4 L of cow milk twice a day (total 8 L/d). From d 2 to d 28, calves in the control group (n = 10) received milk without seaweed supplementation. Over the same period, experimental calves received milk supplemented with Ulva lactuca (SW1; n = 10), Ascophyllum nodosum (SW2; n = 10), or Saccharina latissima (SW3, n = 10). Dried and ground seaweeds were offered at a daily allowance of 50 g/8 L of milk (i.e., approximately 5% inclusion rate on a dry matter basis). Blood samples were collected from a jugular vein on d 2, 4, 7, 14, 21, and 28 after birth. Plasma concentrations of total protein, albumin, immunoglobulins, and acute-phase proteins (i.e., serum amyloid A, fibrinogen, and haptoglobin) were measured. We detected no differences in average daily gain, plasma immunoglobulins, albumin, or total protein. However, the contrast analysis revealed that plasma concentrations of fibrinogen (SW1 and SW2) and serum amyloid A (SW2 and SW3) were significantly higher in the seaweed groups compared with the control group. We also found a tendency for high plasma haptoglobin in the seaweed groups (SW1 and SW2) compared with the control group. Differences in acute-phase protein concentrations could be partially explained by the large differences in micromineral intake between control and seaweed-supplemented calves. Feeding milk supplemented with dried seaweed increased plasma concentrations of variables related to the innate immune response in preweaning dairy calves.}, } @article {pmid33453564, year = {2021}, author = {Bourdillon, AT and Edwards, HA}, title = {Review of probiotic use in otolaryngology.}, journal = {American journal of otolaryngology}, volume = {42}, number = {2}, pages = {102883}, doi = {10.1016/j.amjoto.2020.102883}, pmid = {33453564}, issn = {1532-818X}, abstract = {OBJECTIVE: Probiotics have garnered considerable attention as an intervention for various conditions common to otolaryngology. The purpose of this review is to evaluate the current literature to offer recommendations about the safety and efficacy of probiotic management in otolaryngologic conditions.

STUDY DESIGN: Narrative review.

METHODS: PubMed and Google Scholar were queried using pertinent keywords to retrieve relevant studies with particular focus in the recent 5 years. All abstracts were assessed and studies, reviews and meta-analyses achieving evaluation of probiotic therapies or characterization of microbiome changes were included for further review. Studies were categorized by condition or anatomic region across various subspecialties. Key data parameters were extracted and evaluated across studies and treatment types.

RESULTS: Strong evidence exists for the use probiotic agents to improve symptoms for allergic rhinitis, chronic rhinosinusitis and certain dental conditions. Despite promising results, further investigation is needed to evaluate and optimize probiotic delivery for mitigating otitis media, oropharyngeal inflammation and upper respiratory tract infections. Preclinical studies suggest that probiotics may potentially offer benefit for voice prosthesis maintenance, wound healing and mitigation of oral dysplasia.

CONCLUSION: Probiotic therapies may offer clinical benefit in a variety of contexts within the field of otolaryngology, especially for short-term relief of certain inflammatory conditions of the oral cavity, auditory and nasal cavities. Further investigation is warranted for evaluation of long-term outcomes and pathogenic deterrence.}, } @article {pmid33453422, year = {2021}, author = {Tao, S and Wang, Z and Quan, C and Ge, Y and Qian, Q}, title = {The effects of ALA-PDT on microbiota in pilosebaceous units of patients with severe acne: A metagenomic study.}, journal = {Photodiagnosis and photodynamic therapy}, volume = {}, number = {}, pages = {102050}, doi = {10.1016/j.pdpdt.2020.102050}, pmid = {33453422}, issn = {1873-1597}, abstract = {BACKGROUND: 5-aminolevulinic acid mediated photodynamic therapy (ALA-PDT) is increasingly used to control severe acne. However, its impact on skin microbiota remains uncertain.

OBJECTIVES: We aimed to compare the makeup, diversity, and function of the microbiota in pilosebaceous units of patients with severe acne before and after ALA-PDT.

METHODS: A longitudinal cohort study was performed on 11 participants with severe facial acne. All patients were given 5%ALA-PDT every two weeks for three sessions in total. The contents of lesions were sampled for metagenomic sequencing at baseline and two weeks after of the first ALA-PDT.

RESULTS: Cutibacterium acnes was the most dominant species followed by Staphylococcus epidermidis and Pseudomonas fluorescens. Treatment with ALA-PDT led to clinical improvements in acne severity concurrent with a significant reduction in the relative abundance of C. acnes, while P. fluorescens increased significantly after ALA-PDT. No significant change was identified in other species. ALA-PDT administration was associated with an increased microbiota diversity and reductions in the relative abundance of the functional genes involved in energy metabolism and DNA replication.

CONCLUSIONS: ALA-PDT plays a therapeutic role by killingC. acnes, increasing P. fluorescens and the microbiome diversity, while inhibiting the function of microbiota in pilosebaceous units of severe acne.}, } @article {pmid33453153, year = {2021}, author = {Stacy, A and Andrade-Oliveira, V and McCulloch, JA and Hild, B and Oh, JH and Perez-Chaparro, PJ and Sim, CK and Lim, AI and Link, VM and Enamorado, M and Trinchieri, G and Segre, JA and Rehermann, B and Belkaid, Y}, title = {Infection trains the host for microbiota-enhanced resistance to pathogens.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2020.12.011}, pmid = {33453153}, issn = {1097-4172}, abstract = {The microbiota shields the host against infections in a process known as colonization resistance. How infections themselves shape this fundamental process remains largely unknown. Here, we show that gut microbiota from previously infected hosts display enhanced resistance to infection. This long-term functional remodeling is associated with altered bile acid metabolism leading to the expansion of taxa that utilize the sulfonic acid taurine. Notably, supplying exogenous taurine alone is sufficient to induce this alteration in microbiota function and enhance resistance. Mechanistically, taurine potentiates the microbiota's production of sulfide, an inhibitor of cellular respiration, which is key to host invasion by numerous pathogens. As such, pharmaceutical sequestration of sulfide perturbs the microbiota's composition and promotes pathogen invasion. Together, this work reveals a process by which the host, triggered by infection, can deploy taurine as a nutrient to nourish and train the microbiota, promoting its resistance to subsequent infection.}, } @article {pmid33452946, year = {2021}, author = {Xiaoming, W and Jing, L and Yuchen, P and Huili, L and Miao, Z and Jing, S}, title = {Characteristics of the vaginal microbiomes in prepubertal girls with and without vulvovaginitis.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {33452946}, issn = {1435-4373}, support = {2017YFC1703205//National Key R&D Program of China/ ; }, abstract = {The present study focused on the characteristics of the vaginal microbiomes in prepubertal girls with and without vulvovaginitis. We collected 24 vaginal samples and 16 fecal samples from 10 girls aged 3-9 years with vulvovaginitis and 16 healthy girls of the same age. The samples were divided into three groups: fecal swabs from healthy controls (HF), vaginal swabs from healthy controls (HVS), and vaginal swabs from girls with vulvovaginitis (VVS). Sequencing of the V3-V4 region of the 16S rDNA gene was performed with the NovaSeq PE250 platform to reveal the vaginal microbial community structure in healthy prepubertal girls and vulvovaginitis-associated microbiota. The intestinal microbiomes of healthy children were also analyzed for comparison. This study revealed that the healthy vaginal tract in prepubertal girls was dominated by Prevotella, Porphyromonas, Ezakiella, and Peptoniphilus species, with a high diversity of microbiota. The vulvovaginitis-associated microbiota were dominated by Streptococcus, Prevotella, Haemophilus, and Granulicatella, with lower diversity than that in healthy girls. Furthermore, the compositions of the vaginal and intestinal microbiomes were completely different. ANOSIM, MRPP, Adonis, and AMOVA were used to analyze the beta diversity, and the results showed that there were significant differences in the microbial communities among the three groups. Lactobacillus deficiency and high bacterial diversity were characteristics of the vaginal microbiome in healthy prepubertal girls; this is inconsistent with that in reproductive-age women. The vulvovaginitis-associated vaginal microbiota differed dramatically from normal microbiota, and the main causative agents were not fecal in origin.}, } @article {pmid33452896, year = {2021}, author = {Bergo, NM and Bendia, AG and Ferreira, JCN and Murton, BJ and Brandini, FP and Pellizari, VH}, title = {Microbial Diversity of Deep-Sea Ferromanganese Crust Field in the Rio Grande Rise, Southwestern Atlantic Ocean.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33452896}, issn = {1432-184X}, support = {14/50820-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {Seamounts are often covered with Fe and Mn oxides, known as ferromanganese (Fe-Mn) crusts. Future mining of these crusts is predicted to have significant effects on biodiversity in mined areas. Although microorganisms have been reported on Fe-Mn crusts, little is known about the role of crusts in shaping microbial communities. Here, we investigated microbial communities based on 16S rRNA gene sequences retrieved from Fe-Mn crusts, coral skeleton, calcarenite, and biofilm at crusts of the Rio Grande Rise (RGR). RGR is a prominent topographic feature in the deep southwestern Atlantic Ocean with Fe-Mn crusts. Our results revealed that crust field of the RGR harbors a usual deep-sea microbiome. No differences were observed on microbial community diversity among Fe-Mn substrates. Bacterial and archaeal groups related to oxidation of nitrogen compounds, such as Nitrospirae, Nitrospinae phyla, Candidatus Nitrosopumilus within Thaumarchaeota group, were present on those substrates. Additionally, we detected abundant assemblages belonging to methane oxidation, i.e., Methylomirabilales (NC10) and SAR324 (Deltaproteobacteria). The chemolithoautotrophs associated with ammonia-oxidizing archaea and nitrite-oxidizing bacteria potentially play an important role as primary producers in the Fe-Mn substrates from RGR. These results provide the first insights into the microbial diversity and potential ecological processes in Fe-Mn substrates from the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region.}, } @article {pmid33452882, year = {2021}, author = {Varsadiya, M and Urich, T and Hugelius, G and Bárta, J}, title = {Microbiome structure and functional potential in permafrost soils of the Western Canadian Arctic.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab008}, pmid = {33452882}, issn = {1574-6941}, abstract = {Substantial amounts of topsoil organic matter (OM) in Arctic Cryosols have been translocated by the process of cryoturbation into deeper soil horizons (cryoOM), reducing its decomposition. Recent Arctic warming deepens the Cryosols´ active layer, making more topsoil and cryoOM carbon accessible for microbial transformation. To quantify bacteria, archaea, and selected microbial groups (methanogens- mcrA gene and diazotrophs- nifH gene) and to investigate bacterial and archaeal diversity, we collected 83 soil samples from four different soil horizons of three distinct tundra types located in Qikiqtaruk (Hershel Island, Western Canada). In general, the abundance of bacteria and diazotrophs decreased from topsoil to permafrost, but not for cryoOM. No such difference was observed for archaea and methanogens. CryoOM was enriched with oligotrophic (slow-growing microorganism) taxa capable of recalcitrant OM degradation. We found distinct microbial patterns in each tundra type: topsoil from wet-polygonal tundra had the lowest abundance of bacteria and diazotrophs, but the highest abundance of methanogens. Wet-polygonal tundra, therefore, represented a hotspot for methanogenesis. Oligotrophic and copiotrophic (fast-growing microorganism) genera of methanogens and diazotrophs were distinctly distributed in topsoil and cryoOM, resulting in different rates of nitrogen flux into these horizons affecting OM vulnerability and potential CO2 and CH4 release.}, } @article {pmid33452880, year = {2021}, author = {Lindsay, EL and Faustoferri, RC and Quivey, RG}, title = {Repression of the TreR transcriptional regulator in Streptococcus mutans by the global regulator, CcpA.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnab004}, pmid = {33452880}, issn = {1574-6968}, abstract = {Streptococcus mutans, the etiologic agent of dental caries in humans, is considered a dominating force in the oral microbiome due to its highly-evolved propensity for survival. The oral pathogen encodes an elaborate array of regulatory elements, including the carbon catabolite-responsive regulator, CcpA, a global regulator key in the control of sugar metabolism and in stress tolerance response mechanisms. The recently characterized trehalose utilization operon, integral for the catabolism of the disaccharide trehalose, is controlled by a local regulator, TreR, which has been implicated in a number of cellular functions outside of trehalose catabolism. Electrophoretic mobility shift assays demonstrated that CcpA bound a putative cre site in the treR promoter. Loss of ccpA resulted in elevated expression of treR in cultures of the organism grown in glucose or trehalose, indicating that CcpA not only acts as a repressor of trehalose catabolism genes, but also the local regulator. The loss of both CcpA and TreR in S. mutans resulted in an impaired growth rate and fitness response, supporting the hypothesis that these regulators are involved in carbon catabolism control and in induction of components of the organism's stress response.}, } @article {pmid33452801, year = {2021}, author = {Ta, AD and Ollberding, NJ and Karns, R and Haberman, Y and Alazraki, AL and Hercules, D and Baldassano, R and Markowitz, J and Heyman, MB and Kim, S and Kirschner, B and Shapiro, JM and Noe, J and Oliva-Hemker, M and Otley, A and Pfefferkorn, M and Kellermayer, R and Snapper, S and Rabizadeh, S and Xavier, R and Dubinsky, M and Hyams, J and Kugathasan, S and Jegga, AG and Dillman, JR and Denson, LA}, title = {Association of Baseline Luminal Narrowing With Ileal Microbial Shifts and Gene Expression Programs and Subsequent Transmural Healing in Pediatric Crohn Disease.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izaa339}, pmid = {33452801}, issn = {1536-4844}, abstract = {BACKGROUND: Transmural healing (TH) is associated with better long-term outcomes in Crohn disease (CD), whereas pretreatment ileal gene signatures encoding myeloid inflammatory responses and extracellular matrix production are associated with stricturing. We aimed to develop a predictive model for ileal TH and to identify ileal genes and microbes associated with baseline luminal narrowing (LN), a precursor to strictures.

MATERIALS AND METHODS: Baseline small bowel imaging obtained in the RISK pediatric CD cohort study was graded for LN. Ileal gene expression was determined by RNASeq, and the ileal microbial community composition was characterized using 16S rRNA amplicon sequencing. Clinical, demographic, radiologic, and genomic variables were tested for association with baseline LN and future TH.

RESULTS: After controlling for ileal location, baseline ileal LN (odds ratio [OR], 0.3; 95% confidence interval [CI], 0.1-0.8), increasing serum albumin (OR, 4; 95% CI, 1.3-12.3), and anti-Saccharomyces cerevisiae antibodies IgG serology (OR, 0.97; 95% CI, 0.95-1) were associated with subsequent TH. A multivariable regression model including these factors had excellent discriminant power for TH (area under the curve, 0.86; positive predictive value, 80%; negative predictive value, 87%). Patients with baseline LN exhibited increased Enterobacteriaceae and inflammatory and extracellular matrix gene signatures, coupled with reduced levels of butyrate-producing commensals and a respiratory electron transport gene signature. Taxa including Lachnospiraceae and the genus Roseburia were associated with increased respiratory and decreased inflammatory gene signatures, and Aggregatibacter and Blautia bacteria were associated with reduced extracellular matrix gene expression.

CONCLUSIONS: Pediatric patients with CD with LN at diagnosis are less likely to achieve TH. The association between specific microbiota, wound healing gene programs, and LN may suggest future therapeutic targets.}, } @article {pmid33452800, year = {2021}, author = {Roy Paladhi, U and Harb, AH and Daniel, SG and Dawwas, GK and Schnellinger, EM and Wollack, C and Aberra, FN and Bewtra, M and Green, JA and Klaproth, JA and Lichtenstein, GR and Saxena, A and Berera, S and Buchner, A and Mehta, SJ and Osterman, MT and Rashid, F and Tomov, V and Caldera, F and Sumona, S and Mahadevan, U and Roy, A and Nessel, L and Wu, GD and Bittinger, K and Lewis, JD}, title = {The Impact of Introducing Patient-Reported Inflammatory Bowel Disease Symptoms via Electronic Survey on Clinic Visit Length, Patient and Provider Satisfaction, and the Environment Microbiome.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izaa356}, pmid = {33452800}, issn = {1536-4844}, } @article {pmid33452691, year = {2021}, author = {Yan, XT and Ye, ZX and Wang, X and Zhang, CX and Chen, JP and Li, JM and Huang, HJ}, title = {Insight into different host range of three planthoppers by transcriptomic and microbiomic analysis.}, journal = {Insect molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imb.12695}, pmid = {33452691}, issn = {1365-2583}, abstract = {Brown planthopper (BPH), white-backed planthopper (WBPH), and small brown planthopper (SBPH), are the closely related rice pests that perform differentially on wheat plants. Using fecundity as a fitness measure, we found that SBPH well-adapted on wheat plants, followed by WBPH, while BPH had the worst performance. The transcriptomic responses of SBPH and BPH to wheat plants have been compared previously. To understand the different fitness mechanisms of three planthoppers, this study firstly investigated the transcriptomic responses of WBPH to rice and wheat plants. Genes involved in detoxification, transportation and proteasome were significantly enriched in WBPH in response to different diets. Moreover, comparative analysis demonstrated that most co-regulated genes in BPH and SBPH showed different expression changes; whereas most co-regulated genes in BPH and WBPH exhibited similar expression changes. Subsequently, this study also investigated the influences of host plants on the bacterial community of three planthoppers. The three planthoppers harbored distant diversity of bacterial communities. However, there was no dramatic change in bacterial diversity or relative abundance in planthoppers colonized on different hosts. This study illustrates generic and species-specific changes of three rice planthoppers in response to different plants, which deepen our understanding towards the host fitness for planthopper species.}, } @article {pmid33452507, year = {2021}, author = {}, title = {A case of 'stomach flu' arms the microbiome against invaders.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-021-00078-z}, pmid = {33452507}, issn = {1476-4687}, } @article {pmid33452327, year = {2021}, author = {Yuan, ZS and Liu, F and Liu, ZY and Huang, QL and Zhang, GF and Pan, H}, title = {Structural variability and differentiation of niches in the rhizosphere and endosphere bacterial microbiome of moso bamboo (Phyllostachys edulis).}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1574}, pmid = {33452327}, issn = {2045-2322}, support = {MYK19027//the Scientific Research Project of Minjiang University/ ; }, abstract = {The plant microbiota play a key role in plant productivity, nutrient uptake, resistance to stress and flowering. The flowering of moso bamboo has been a focus of study. The mechanism of flowering is related to nutrient uptake, temperature, hormone balance and regulation of key genes. However, the connection between microbiota of moso bamboo and its flowering is unknown. In this study, samples of rhizosphere soil, rhizomes, roots and leaves of flowering and nonflowering plants were collected, and 16S rRNA amplicon Illumina sequencing was utilized to separate the bacterial communities associated with different flowering stages of moso bamboo. We identified 5442 OTUs, and the number of rhizosphere soil OTUs was much higher than those of other samples. Principal component analysis (PCA) and hierarchical clustering (Bray Curtis dis) analysis revealed that the bacterial microorganisms related to rhizosphere soil and endophytic tissues of moso bamboo differed significantly from those in bulk soil and rhizobacterial and endosphere microbiomes. In addition, the PCA analyses of root and rhizosphere soil revealed different structures of microbial communities between bamboo that is flowering and not flowering. Through the analysis of core microorganisms, it was found that Flavobacterium, Bacillus and Stenotrophomonas played an important role in the absorption of N elements, which may affect the flowering time of moso bamboo. Our results delineate the complex host-microbe interactions of this plant. We also discuss the potential influence of bacterial microbiome in flowering, which can provide a basis for the development and utilization of moso bamboo.}, } @article {pmid33452177, year = {2021}, author = {Ding, Z and Wang, W and Zhang, K and Ming, F and Yangdai, T and Xu, T and Shi, H and Bao, Y and Yao, H and Peng, H and Han, C and Jiang, W and Liu, J and Hou, X and Lin, R}, title = {Novel scheme for non-invasive gut bioinformation acquisition with a magnetically controlled sampling capsule endoscope.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2020-322465}, pmid = {33452177}, issn = {1468-3288}, abstract = {OBJECTIVE: Intestinal flora and metabolites are associated with multiple systemic diseases. Current approaches for acquiring information regarding microbiota/metabolites have limitations. We aimed to develop a precise magnetically controlled sampling capsule endoscope (MSCE) for the convenient, non-invasive and accurate acquisition of digestive bioinformation for disease diagnosis and evaluation.

DESIGN: The MSCE and surgery were both used for sampling both jejunal and ileal GI content in the control and antibiotic-induced diarrhoea groups. The GI content was then used for microbiome profiling and metabolomics profiling.

RESULTS: Compared with surgery, our data showed that the MSCE precisely acquired data regarding the intestinal flora and metabolites, which was effectively differentiated in different intestinal regions and disease models. Using MSCE, we detected a dramatic decrease in the abundance of Bacteroidetes, Patescibacteria and Actinobacteria and hippuric acid levels, as well as an increase in the abundance of Escherichia-Shigella and the 2-pyrrolidinone levels were detected in the antibiotic-induced diarrhoea model by MSCE. MSCE-mediated sampling revealed specific gut microbiota/metabolites including Enterococcus, Lachnospiraceae, acetyl-L-carnitine and succinic acid, which are related to metabolic diseases, cancers and nervous system disorders. Additionally, the MSCE exhibited good sealing characteristics with no contamination after sampling.

CONCLUSIONS: We present a newly developed MSCE that can non-invasively and accurately acquire intestinal bioinformation via direct visualization under magnetic control, which may further aid in disease prevention, diagnosis, prognosis and treatment.}, } @article {pmid33452033, year = {2021}, author = {Wolff, BA and Clements, WH and Hall, EK}, title = {Metals alter membership but not diversity of a headwater stream microbiome.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02635-20}, pmid = {33452033}, issn = {1098-5336}, abstract = {Metal contamination from mining or natural weathering is a common feature of surface waters in the American west. Advances in microbial analyses have created the potential for routine sampling of aquatic microbiomes as a tool to assess the quality of stream habitat. We sought to determine if microbiome diversity and membership were affected by metal contamination and identify candidate microbial taxa to be used to indicate metal stress in stream ecosystems. We evaluated microbiome membership from sediments at multiple sites within the principal drainage of an EPA superfund site near the headwaters of the Upper Arkansas River, Leadville, CO. From each sample, we extracted DNA and sequenced the 16S rRNA gene amplicon on the Illumina MiSeq platform. We used the remaining sediments to simultaneously evaluate environmental metal concentrations. We also conducted an artificial stream mesocosm experiment using sediments collected from two of the observational study sites. The mesocosm experiment had a 2x2 factorial design: 1) location (upstream or downstream of contaminating tributary), and 2) treatment (metal exposure or control). We found no difference in diversity between upstream and downstream sites in the field. Similarly, diversity changed very little following experimental metal exposure. However, microbiome membership differed between upstream and downstream locations and experimental metal exposure changed microbiome membership in a manner that depended on origin of the sediments used in each mesocosm.Importance Our results suggest that microbiomes can be reliable indicators of ecosystem metal stress even when surface water chemistry and other metrics used to assess ecosystem health do not indicate ecosystem stress. Results presented in this study in combination with previously published work on this same ecosystem are consistent with the idea that a microbial response to metals at the base of the food web may be affecting primary consumers. If effects of metals are mediated through shifts in the microbiome, then microbial metrics, as presented here, may aid in the assessment of stream ecosystem health which currently does not include assessments of the microbiome.}, } @article {pmid33452027, year = {2021}, author = {Meziti, A and Rodriguez-R, LM and Hatt, JK and Peña-Gonzalez, A and Levy, K and Konstantinidis, KT}, title = {How reliably do metagenome-assembled genomes (MAGs) represent natural populations? Insights from comparing MAGs against isolate genomes derived from the same fecal sample.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02593-20}, pmid = {33452027}, issn = {1098-5336}, abstract = {The recovery of metagenome-assembled genomes (MAGs) from metagenomic data has recently become a common task for microbial studies. The strengths and limitations of the underlying bioinformatics algorithms are well appreciated by now based on performance tests with mock datasets of known composition. However, these mock datasets do not capture the complexity and diversity often observed within natural populations, since their construction typically relies on only a single genome of a given organism. Further, it remains unclear if MAGs can recover population variable (e.g., shared by >10% but <90% of the members of the population) as efficiently as core genes (e.g., shared by >90% of the members). To address these issues, we compared the gene variability of pathogenic Escherichia coli isolates from eight diarrheal samples, for which the isolate was the causative agent, against their corresponding MAGs recovered from the companion metagenomic dataset. Our analysis revealed that MAGs with completeness estimates near 95% captured only 77% of the population core genes and 50% of the variable genes, on average. Further, about 5% of the genes of these MAG were conservatively identified as missing in the isolate and were of different (non-Enterobacteriaceae) taxonomic origin, suggesting errors at the genome binning step, even though contamination estimates based on commonly used pipelines were only 1.5%. Therefore, the quality of MAGs may oftentimes be worse than estimated, and we offer examples of how to recognize and improve such MAGs to sufficient quality by -for instance- employing only contigs longer than 1,000bp for binning.IMPORTANCE Metagenome assembly and recovery of metagenome-assembled genomes (MAGs) have recently become common tasks for microbiome studies across environmental and clinical settings. However, to what extent MAGs can capture the genes of the population they represent remains speculative. Current approaches to evaluate MAG quality are limited to the recovery and copy number of universal, housekeeping genes but these genes represent a small fraction of the total genome, leaving the majority of the genome essentially inaccessible. If MAG quality in reality is lower than these approaches would estimate, this could have dramatic consequences for all downstream analyses and interpretations. In this study, we evaluated this issue using a novel approach that employs comparisons of MAGs to isolate genomes derived from the same samples. Further, our samples originated from a diarrhea case-control study, and thus our results are relevant for recovering the virulence factors of pathogens from metagenomic datasets.}, } @article {pmid33452025, year = {2021}, author = {Fracchia, F and Mangeot-Peter, L and Jacquot, L and Martin, F and Veneault-Fourrey, C and Deveau, A}, title = {Colonization of naïve roots from Populus tremula x alba involves successive waves of fungi and bacteria with different trophic abilities.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02541-20}, pmid = {33452025}, issn = {1098-5336}, abstract = {Through their roots, trees interact with a highly complex community of microorganisms belonging to various trophic guilds and contributing to tree nutrition, development and protection against stresses. Tree roots select for specific microbial species from the bulk soil communities. The root microbiome formation is a dynamic process but little is known on how the different microorganisms colonize the roots and how the selection occurs. To decipher if the final composition of the root microbiome is the product of several waves of colonization by different guilds of microorganisms, we planted sterile rooted cuttings of Gray Poplar obtained from plantlets propagated in axenic conditions in natural poplar stand-soil. We analyzed the root microbiome at different time points between 2 and 50 days of culture by combining high-throughput Illumina MiSeq sequencing of fungal rDNA ITS and bacterial 16S rRNA amplicons with Confocal Laser Scanning Microscope observations. The microbial colonisation of poplar roots took place in three stages but the dynamic was different between bacteria and fungi. Root bacterial communities were clearly different from the soil after two days of culture. By contrast, if fungi were also already colonizing roots after two days, the initial communities were very close to the one of the soil and were dominated by saprotrophs. Those were slowly replaced by endophytes and ectomycorhizal fungi. The replacement of the most abundant fungal and bacterial community members observed in poplar roots along time suggest potential competition effect between microorganisms and/or a selection by the host.IMPORTANCE The tree root microbiome is composed of a very diverse set of bacterial and fungal communities. These microorganisms have a profound impact on tree growth, development and protection against different types of stress. They mainly originate from the bulk soil and colonize the root system which provides a unique nutrient rich-environment for a diverse assemblage of microbial communities. In order to better understand how the tree root microbiome is shaped along time, we observed the composition of root-associated microbial communities of naïve plantlets of poplar transferred in natural soil. The composition of the final root microbiome rely on a series of colonization stages characterized by the dominance of different fungal guilds and bacterial community members along time. Our observations suggest an early stabilization of bacterial communities, whereas fungal communities are established following a more gradual pattern.}, } @article {pmid33452024, year = {2021}, author = {Zhu, HZ and Zhang, ZF and Zhou, N and Jiang, CY and Wang, BJ and Cai, L and Wang, HM and Liu, SJ}, title = {Intensive Bacterial Cultivation and Genome Assembly Reveal Previously Unknown Bacteria and Metabolic Potential in Karst Caves.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02440-20}, pmid = {33452024}, issn = {1098-5336}, abstract = {Karst caves are widely distributed subsurface systems, and the microbiomes therein are proposed to be the driving force for cave evolution and biogeochemical cycling. In past years, culture-independent studies on the microbiomes of cave systems have been conducted, yet intensive microbial cultivation is still needed to validate the sequence-derived hypothesis and to disclose the microbial functions in cave ecosystems. In this study, the microbiomes of two karst caves in Guizhou Province in southwest China were examined. A total of 3,562 bacterial strains were cultivated from rock, water, and sediment samples, and 329 species (including 14 newly described species) of 102 genera were found. We created a cave bacterial genome collection of 218 bacterial genomes from a karst cave microbiome through the extraction of 204 database-derived genomes and de novo sequencing of 14 new bacterial genomes. The cultivated genome collection obtained in this study and the metagenome data from previous studies were used to investigate the bacterial metabolism and potential involvement in the carbon, nitrogen, and sulfur biogeochemical cycles in the cave ecosystem. New N2-fixing Azospirillum and alkane-oxidizing Oleomonas species were documented in the karst cave microbiome. Two pcaIJ clusters of the β-ketoadipate pathway that were abundant in both the cultivated microbiomes and the metagenomic data were identified, and their representatives from the cultivated bacterial genomes were functionally demonstrated. This large-scale cultivation of a cave microbiome represents the most intensive collection of cave bacterial resources to date and provides valuable information and diverse microbial resources for future cave biogeochemical research.IMPORTANCE Karst caves are oligotrophic environments that are dark, humid, and have a relative stable annual temperature. The bacteria diversity and their metabolisms are crucial for understanding the biogeochemical cycling in cave ecosystems. We integrated large-scale bacterial cultivation with metagenomic data-mining to explore the composition and metabolisms of the microbiomes in two karst cave systems. Our results reveal the presence of a highly diversified cave bacterial community, and 14 new bacterial species were described and genome-sequenced. In this study, we obtained the most intensive collection of cultivated microbial resources from karst caves to date and predicted the various important routes for the biogeochemical cycling of elements in cave ecosystems.}, } @article {pmid33451726, year = {2020}, author = {Li, L and Figeys, D}, title = {Proteomics and Metaproteomics Add Functional, Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-luminal Interface.}, journal = {Molecular & cellular proteomics : MCP}, volume = {19}, number = {9}, pages = {1409-1417}, doi = {10.1074/mcp.R120.002051}, pmid = {33451726}, issn = {1535-9484}, abstract = {Recent efforts in gut microbiome studies have highlighted the importance of explicitly describing the ecological processes beyond correlative analysis. However, we are still at the early stage of understanding the organizational principles of the gut ecosystem, partially because of the limited information provided by currently used analytical tools in ecological modeling practices. Proteomics and metaproteomics can provide a number of insights for ecological studies, including biomass, matter and energy flow, and functional diversity. In this Mini Review, we discuss proteomics and metaproteomics-based experimental strategies that can contribute to studying the ecology, in particular at the mucosal-luminal interface (MLI) where the direct host-microbiome interaction happens. These strategies include isolation protocols for different MLI components, enrichment methods to obtain designated array of proteins, probing for specific pathways, and isotopic labeling for tracking nutrient flow. Integration of these technologies can generate spatiotemporal and site-specific biological information that supports mathematical modeling of the ecosystem at the MLI.}, } @article {pmid33451555, year = {2020}, author = {Doellinger, J and Schneider, A and Hoeller, M and Lasch, P}, title = {Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics Based on Acid Extraction.}, journal = {Molecular & cellular proteomics : MCP}, volume = {19}, number = {1}, pages = {209-222}, doi = {10.1074/mcp.TIR119.001616}, pmid = {33451555}, issn = {1535-9484}, abstract = {The main challenge of bottom-up proteomic sample preparation is to extract proteomes in a manner that enables efficient protein digestion for subsequent mass spectrometric analysis. Today's sample preparation strategies are commonly conceptualized around the removal of detergents, which are essential for extraction but strongly interfere with digestion and LC-MS. These multi-step preparations contribute to a lack of reproducibility as they are prone to losses, biases and contaminations, while being time-consuming and labor-intensive. We report a detergent-free method, named Sample Preparation by Easy Extraction and Digestion (SPEED), which consists of three mandatory steps, acidification, neutralization and digestion. SPEED is a universal method for peptide generation from various sources and is easily applicable even for lysis-resistant sample types as pure trifluoroacetic acid (TFA) is used for highly efficient protein extraction by complete sample dissolution. The protocol is highly reproducible, virtually loss-less, enables very rapid sample processing and is superior to the detergent/chaotropic agent-based methods FASP, ISD-Urea and SP3 for quantitative proteomics. SPEED holds the potential to dramatically simplify and standardize sample preparation while improving the depth of proteome coverage especially for challenging samples.}, } @article {pmid33451015, year = {2021}, author = {Adam, T and Becker, TM and Chua, W and Bray, V and Roberts, TL}, title = {The Multiple Potential Biomarkers for Predicting Immunotherapy Response-Finding the Needle in the Haystack.}, journal = {Cancers}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/cancers13020277}, pmid = {33451015}, issn = {2072-6694}, abstract = {Immune checkpoint inhibitors (ICIs) are being increasingly utilised in a variety of advanced malignancies. Despite promising outcomes in certain patients, the majority will not derive benefit and are at risk of potentially serious immune-related adverse events (irAEs). The development of predictive biomarkers is therefore critical to personalise treatments and improve outcomes. A number of biomarkers have shown promising results, including from tumour (programmed cell death ligand 1 (PD-L1), tumour mutational burden (TMB), stimulator of interferon genes (STING) and apoptosis-associated speck-like protein containing a CARD (ASC)), from blood (peripheral blood mononuclear cells (PBMCs), circulating tumour DNA (ctDNA), exosomes, cytokines and metal chelators) and finally the microbiome.}, } @article {pmid33450667, year = {2020}, author = {Ezzat-Zadeh, Z and Henning, SM and Yang, J and Woo, SL and Lee, RP and Huang, J and Thames, G and Gilbuena, I and Tseng, CH and Heber, D and Li, Z}, title = {California strawberry consumption increased the abundance of gut microorganisms related to lean body weight, health and longevity in healthy subjects.}, journal = {Nutrition research (New York, N.Y.)}, volume = {85}, number = {}, pages = {60-70}, doi = {10.1016/j.nutres.2020.12.006}, pmid = {33450667}, issn = {1879-0739}, abstract = {It was our hypothesis that foods high in polyphenols and fiber have prebiotic activity. This human intervention study aimed to determine if daily consumption of freeze-dried California strawberry powder (SBP) leads to changes in the intestinal microbiota, fecal cholesterol and bile acid (BA) microbial metabolites. Fifteen healthy adults consumed a beige diet+26 g of SBP for 4 weeks, followed by 2 weeks of beige diet only. Stool samples were collected at 0, 4, and 6 weeks. Fecal microbiota was analyzed by 16S rRNA sequencing; fecal cholesterol, BA, and microbial metabolites by gas chromatography. Confirming compliance, urine concentration of pelargonidin, urolithin A glucuronide and dimethylellagic acid glucuronide were present after 4 weeks of SBP consumption. Daily SBP altered the abundance of 24 operational taxonomic units (OTUs). Comparing week 4 to baseline the most significant increases were observed for one OTU from Firmicutes\Clostridia\ Christensenellaceae\NA, one OTU from Firmicutes\ Clostridia\Mogibacteriacea\NA, one OTU from Verrucomicrobia\ Verrucomicrobiaceae\Akkermansia\Muciniphila, one OTU from Actinobacteria\ Bifidobacteriaceae\Bifidobacterium\NA, and one OTU from Bacteroidetes\Bacteroidia\ Bacteroidaceae\Bacteroides and decrease of one OTU from Proteobacteria\ Betaproteobacteria\Alcaligenaceae\Sutterella. Comparing week 4 to 6, we observed a reversal of the same OTUs from C Christensenellaceae, V muciniphilia and C Mogibacteriaceae. Fecal short chain fatty acids and most of the fecal markers including cholesterol, coprostanol, primary and secondary BAs were not changed significantly except for lithocholic acid, which was increased significantly at week 6 compared to baseline. In summary, SBP consumption increased the abundance of gut microorganisms related to lean body weight, health and longevity, and increased fecal lithocholic acid at week 6 in healthy study participants.}, } @article {pmid33450498, year = {2021}, author = {Srinivasan, M and Adnane, M and Archunan, G}, title = {Significance of cervico-vaginal microbes in bovine reproduction and pheromone production - A hypothetical review.}, journal = {Research in veterinary science}, volume = {135}, number = {}, pages = {66-71}, doi = {10.1016/j.rvsc.2021.01.003}, pmid = {33450498}, issn = {1532-2661}, abstract = {The vaginal microbiota has been studied in animal reproduction and fertility, in particular little information of vaginal microbes in reference to bovine reproduction and pheromone production is known. The vaginal mucosa in healthy cow is colonized by an equilibrated and dynamic composition of aerobic, facultative anaerobic and obligate anaerobic microbes. Cervico-vaginal mucus (CVM) composition, viscosity and volume vary with the cyclicity and health status of the reproductive tract. In addition, CVM contains pheromones, volatile compounds, and proteins that attract males for coitus. Commensal microbiota plays a key role in protection of the genital tract from pathogenic microbes by competition effect. In the bovine species, the microbial composition, its abundance and diversity in the female gut, vagina, urine, saliva, and feces, and the associated chemical communication remains poorly documented. The impact of microbes in the reproductive tract of cow, buffalo and certain mammals are discussed in this review. Since the microbial population diversity of CVM is modified during estrus phase it presumes that it may have a role for pheromone production in conspecific. Herein, we would like to critically discuss the current state of knowledge on microbially produced signals in animals and the role of genital and CVM microbiota in estrous cycle and pregnancy.}, } @article {pmid33450310, year = {2021}, author = {Widyarman, AS and Udawatte, NS and Theodorea, CF and Apriani, A and Richi, M and Astoeti, TE and Seneviratne, CJ}, title = {Casein phosphopeptide-amorphous calcium phosphate fluoride treatment enriches the symbiotic dental plaque microbiome in children.}, journal = {Journal of dentistry}, volume = {}, number = {}, pages = {103582}, doi = {10.1016/j.jdent.2021.103582}, pmid = {33450310}, issn = {1879-176X}, abstract = {OBJECTIVES: The dysbiotic oral microbiome plays a key role in the pathogenesis of caries in children. Topical application of casein phosphopeptide-amorphous calcium phosphate containing fluoride (CPP-ACP/F) is an effective treatment modality for children with caries (CC). Hitherto the mechanism by which CPP-ACP/F modules the oral microbiome in CC has not been investigated. The study aimed to examine the CPP-ACP/F effect on the dental plaque microbiome of children group with caries.

METHODS: This preliminary prospective clinical cohort included 10 children with caries. The children received topical fluoride CPP-ACP/F once-a-week for one month. Plaque samples were collected before and after treatment and subjected to 16S rDNA-based next-generation-sequencing. Microbial composition, diversity and functional roles were analyzed in comparison to the clinical characteristics of cohort using standard bioinformatics tools.

RESULTS: CPP-ACP/F treatment modulated dysbiotic oral microbiome towards healthier community as the higher proportion of Proteobacteria and certain microbial protective species were enriched following CPP-ACP/F treatment. Despite overall uniformity of community structure in children with caries between the groups, some bacterial species were differentially represented in a statistically significant manner between pre- and post- treatments. Three bacterial species were found to be predictive of strongly sensitive to the CPP-ACP/F treatment, marked by decreased abundance of Lautropia mirabalis and increased abundance of Gemella haemolysans and Schwartzia succinivorans.

CONCLUSION: Within the limits of the current study, it could be concluded that the CPP-ACP/F varnish treatment modulated the microbial composition of the dental plaque microbiome towards symbiosis. These symbiotic changes may demonstrate the potential clinical significance of CPP-ACP/F varnish treatment.}, } @article {pmid33450288, year = {2021}, author = {Sibeko, L and Johns, T}, title = {Global survey of medicinal plants during lactation and postpartum recovery: evolutionary perspectives and contemporary health implications.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {113812}, doi = {10.1016/j.jep.2021.113812}, pmid = {33450288}, issn = {1872-7573}, abstract = {Cross-cultural comparison of plants used during lactation and the postpartum period offers insight into a largely overlooked area of ethnopharmacological research. Potential roles of phytochemicals in emerging models of interaction among immunity, inflammation, microbiome and nervous system effects on perinatal development have relevance for the life-long health of individuals and of populations in both traditional and contemporary contexts.

AIM OF THE STUDY: Delineate and interpret patterns of traditional and contemporary global use of medicinal plants ingested by mothers during the postpartum period relative to phytochemical activity on immune development and gastrointestinal microbiome of breastfed infants, and on maternal health.

MATERIALS AND METHODS: Published reviews and surveys on galactagogues and postpartum recovery practices plus ethnobotanical studies from around the world were used to identify and rank plants, and ascertain regional use patterns. Scientific literature for 20 most-cited plants based on frequency of publication was assessed for antimicrobial, antioxidant, anti-inflammatory, immunomodulatory, antidepressant, analgesic, galactagogic and safety properties.

RESULTS: From compilation of 4418 use reports related to 1948 species, 105 plant taxa were recorded ≥ 7 times, with the most frequently cited species, Foeniculum vulgare, Trigonella foenum-graecum, Pimpinella anisum, Euphorbia hirta and Asparagus racemosus, 81, 64, 42, 40 and 38 times, respectively. Species and use vary globally, illustrated by the pattern of aromatic plants of culinary importance versus latex-producing plants utilized in North Africa/Middle East and Sub-Saharan Africa with opposing predominance. For 18/20 of the plants a risk/benefit perspective supports assessment that positive immunomodulation and related potential exceed any safety concerns. Published evidence does not support a lactation-enhancing effect for nearly all the most-cited plants while antidepressant data for the majority of plants are predominately limited to animal studies.

CONCLUSIONS: Within a biocultural context traditional postpartum plant use serves adaptive functions for the mother-infant dyad and contributes phytochemicals absent in most contemporary diets and patterns of ingestion, with potential impacts on allergic, inflammatory and other conditions. Polyphenolics and other phytochemicals are widely immunologically active, present in breast milk and predominately non-toxic. Systematic analysis of phytochemicals in human milk, infant lumen and plasma, and immunomodulatory studies that differentiate maternal ingestion during lactation from pregnancy, are needed. Potential herb-drug interaction and other adverse effects should remain central to obstetric advising, but unless a plant is specifically shown as harmful, considering potential contributions to health of individuals and populations, blanket advisories against postpartum herbal use during lactation appear empirically unwarranted.}, } @article {pmid33450094, year = {2021}, author = {Bhat, SF and Pinney, SE and Kennedy, KM and McCourt, CR and Mundy, MA and Surette, MG and Sloboda, DM and Simmons, RA}, title = {Exposure to high fructose corn syrup during adolescence in the mouse alters hepatic metabolism and the microbiome in a sex-specific manner.}, journal = {The Journal of physiology}, volume = {}, number = {}, pages = {}, doi = {10.1113/JP280034}, pmid = {33450094}, issn = {1469-7793}, abstract = {KEY POINTS: The prevalence of obesity and non-alcoholic fatty liver disease in children is dramatically increasing at the same time as consumption of foods with a high sugar content. Intake of high fructose corn syrup (HFCS) is a possible etiology as it is thought to be more lipogenic than glucose. In a mouse model, HFCS intake during adolescence increased fat mass and hepatic lipid levels in male and female mice. However, only males showed impaired glucose tolerance. Multiple metabolites including lipids, bile acids, carbohydrates, and amino acids were altered in liver in a sex-specific manner at 6 weeks of age. Some of these changes were also present in adulthood even though HFCS exposure ended at 6 weeks. HFCS significantly altered the gut microbiome which was associated with changes in key microbial metabolites. These results suggest that HFCS intake during adolescence has profound metabolic changes that are linked to changes in the microbiome and these changes are sex-specific.

ABSTRACT: The rapid increase in obesity, diabetes and fatty liver disease in children over the past 20 years has been linked to increased high fructose corn syrup (HFCS) consumption making it essential to determine the short and long-term effects of HFCS during this vulnerable developmental window. We hypothesized that HFCS exposure during adolescence significantly impairs hepatic metabolic signaling pathways and alters gut microbial composition contributing to changes in energy metabolism with sex-specific effects. C57bl/6J mice with free access to HFCS during adolescence (3-6 weeks of age) underwent glucose tolerance and body composition testing and hepatic metabolomics, gene expression and triglyceride content analysis at 6 and 30 weeks of age (n = 6-8 per sex). At 6 weeks HFCS-exposed mice had significant increases in fat mass, glucose intolerance, hepatic triglycerides (females) and de novo lipogenesis gene expression (ACC, DGAT, FAS, ChREBP, SCD, SREBP, CPT and PPARα) with sex-specific effects. At 30 weeks HFCS-exposed mice also had abnormalities in glucose tolerance (males) and fat mass (females). HFCS exposure enriched carbohydrate, amino acid, long chain fatty acid and secondary bile acid metabolism at 6 weeks with changes in secondary bile metabolism at 6 and 30 weeks. Microbiome studies performed immediately before and after HFCS exposure identified profound shifts of microbial species in male mice only. In summary, a short-term HFCS exposure during adolescence induces fatty liver, alters important metabolic pathways, some of which continue to be altered in adulthood, and changes the microbiome in a sex-specific manner. This article is protected by copyright. All rights reserved.}, } @article {pmid33450018, year = {2020}, author = {Chu, XJ and Cao, NW and Zhou, HY and Meng, X and Guo, B and Zhang, HY and Li, BZ}, title = {The oral and gut microbiome in rheumatoid arthritis patients: a systematic review.}, journal = {Rheumatology (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/rheumatology/keaa835}, pmid = {33450018}, issn = {1462-0332}, abstract = {BACKGROUND: Recently, researchers have proposed a possible relationship between RA and the microbiome of the oral cavity and gut. However, this relation has not been systematically established. Herein, we conducted a comprehensive review of the pertinent literature to describe this possible association.

METHODS: We systematically performed searches in databases, namely EMBASE, the Cochrane Library, and PubMed, from inception to 7 June 2020 to identify case-control studies that compared the oral and gut microbiome in adult RA patients with those of controls. The primary outcome was specific bacterial changes between RA and controls. The secondary outcome was microbial diversity changes between RA and controls.

RESULTS: In total, 26 articles were considered eligible for inclusion and reported some differences. Therein, ≥3 articles reported decreased Faecalibacterium in the gut of early-RA (ERA)/RA patients compared with healthy controls (HCs). Also, ≥3 articles reported decreased Streptococcus and Haemophilus and increased Prevotella in the oral cavity of ERA/RA patients compared with HCs. In addition, some Prevotella species, including P. histicola and P. oulorum, showed increased trends in RA patients' oral cavity, compared with HCs. The α-diversity of the microbiome was either increased or not changed in the oral cavity of RA patients, but it was more commonly either decreased or not changed in the gut of RA patients.

CONCLUSIONS: In this systematic review, we identified the microbiome associated with RA patients in comparison with controls. More research is needed in the future to find the deep relationship between RA and the microbiome.}, } @article {pmid33449810, year = {2021}, author = {Roshanravan, N and Bastani, S and Tutunchi, H and Kafil, B and Nikpayam, O and Mesri Alamdari, N and Hadi, A and Sotoudeh, S and Ghaffari, S and Ostadrahimi, A}, title = {A comprehensive systematic review of the effectiveness of Akkermansia muciniphila, a member of the gut microbiome, for the management of obesity and associated metabolic disorders.}, journal = {Archives of physiology and biochemistry}, volume = {}, number = {}, pages = {1-11}, doi = {10.1080/13813455.2021.1871760}, pmid = {33449810}, issn = {1744-4160}, abstract = {AIMS AND BACKGROUND: Obesity is recognised as a significant public health burden worldwide. Recently the cross-talk between gut microbiota and obesity has attracted much attention. To that end, Akkermansia muciniphila has been proposed as a promising microbe to manage obesity. In the present systematic review, we evaluated evidence on the effectiveness and mechanisms of action of Akkermansia muciniphila supplementation in the management of obesity.

METHODS: Electronic databases of MEDLINE, PubMed, Scopus, Web of Science, and Google Scholar were searched thought March 2020 to identify relevant published articles, and eligible articles were systematically reviewed.

RESULTS AND CONCLUSIONS: Fifteen studies were included in the present study. Findings from the present review, which included human and animal (rodent) models support the effectiveness of Akkermansia supplementation as a novel therapeutic approach for the management of obesity and metabolic complications associated with obesity. However, future clinical trials are warranted to verify these outcomes.}, } @article {pmid33449574, year = {2021}, author = {Lemberger, U and Quhal, F and Bruchbacher, A and Shariat, SF and Hiess, M}, title = {The microbiome in urinary tract infections in children - an update.}, journal = {Current opinion in urology}, volume = {}, number = {}, pages = {}, doi = {10.1097/MOU.0000000000000858}, pmid = {33449574}, issn = {1473-6586}, abstract = {PURPOSE OF REVIEW: Urinary tract infection (UTI) is one of the most common pediatric infections worldwide. Recently introduced 16S rRNA sequencing allows detailed identification of bacteria involved in UTI on a species-based level. The urogenital microbiome in children is scarcely investigated, with underlying conditions differing from adults. Improvement in diagnostic and therapeutic approaches can help to minimize unnecessary antibiotic treatments, thereby protecting the physiological microbiome.

RECENT FINDINGS: Healthy bladders of children display a distinct microbiome than those of adults. UTI is characterized by changes in bacterial composition, with a high prevalence of Enterobacterales. There is a correlation between bacterial species and the pH of the urine, so a characteristic age-related pathogen pattern can be found due to the acidic urine in infants and more alkaline urine in older children. Recently, new methods were proposed to overcome the suboptimal diagnostic performance of urine cultures and urine dipstick test. This allows precise treatment decisions and helps to prevent chronification of UTI, related voiding dysfunctions and renal scaring, systemic abiosis, and the development of antibiotic resistance.

SUMMARY: Uropathogens involved in UTIs in children should be identified with precision to allow targeted therapeutic decisions. This can also help preventing the destruction of the microbiome homeostasis, which could result in a life-long dysbiosis. New treatment approaches and recolonization with probiotics are necessary due to increasing intrinsic antibiotic resistance of bacteria.}, } @article {pmid33449409, year = {2021}, author = {Schmidt, KM and Haddad, EN and Sugino, KY and Vevang, KR and Peterson, LA and Koratkar, R and Gross, MD and Kerver, JM and Comstock, SS}, title = {Dietary and plasma carotenoids are positively associated with alpha diversity in the fecal microbiota of pregnant women.}, journal = {Journal of food science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1750-3841.15586}, pmid = {33449409}, issn = {1750-3841}, support = {CHEAR P&F 2018-PF05//Children's Health Exposure Analysis Resource (CHEAR) Pilot and Feasibility (P&F) Program/ ; 1U2CES026533/NH/NIH HHS/United States ; }, abstract = {Because microbes use carotenoids as an antioxidant for protection, dietary carotenoids could be associated with gut microbiota composition. We aimed to determine associations among reported carotenoid intake, plasma carotenoid concentrations, and fecal bacterial communities in pregnant women. Pregnant women (n = 27) were enrolled in a two-arm study designed to assess feasibility of biospecimen collection and delivery of a practical nutrition intervention. Plasma and fecal samples were collected and women were surveyed with a 24-hr dietary checklist and recalls. Plasma carotenoids were analyzed by HPLC using photodiode array detection. Fecal bacteria were analyzed by 16S rRNA DNA sequencing. Results presented are cross-sectional from the 36-week gestational study visit combined across both study arms due to lack of significant differences between intervention and usual care groups (n = 23 women with complete data). Recent intake of carotenoid-containing foods included carrots, sweet potatoes, mangos, apricots, and/or bell peppers for 48% of women; oranges/orange juice (17%); egg (39%); tomato/tomato-based sauces (52%); fruits (83%); and vegetables (65%). Average plasma carotenoid concentrations were 6.4 µg/dL α-carotene (AC), 17.7 µg/dL β-carotene (BC), 11.4 µg/dL cryptoxanthin, 39.0 µg/dL trans-lycopene, and 29.8 µg/dL zeaxanthin and lutein. AC and BC concentrations were higher in women who recently consumed foods high in carotenoids. CR concentrations were higher in women who consumed oranges/orange juice. Microbiota α-diversity positively correlated with AC and BC. Microbiota β-diversity differed significantly across reported intake of carotenoid containing foods and plasma concentrations of AC. This may reflect an effect of high fiber or improved overall dietary quality, rather than a specific effect of carotenoids. PRACTICAL APPLICATION: Little is known about the association between the gut microbiome and specific dietary microconstituents, such as carotenoids, especially during pregnancy. This research demonstrates that a carotenoid-rich diet during pregnancy supports a diverse microbiota, which could be one mechanism by which carotenoids promote health.}, } @article {pmid33449153, year = {2021}, author = {Strickland, AB and Shi, M}, title = {Mechanisms of fungal dissemination.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {}, number = {}, pages = {}, pmid = {33449153}, issn = {1420-9071}, support = {AI131219/NH/NIH HHS/United States ; AI131905/NH/NIH HHS/United States ; }, abstract = {Fungal infections are an increasing threat to global public health. There are more than six million fungal species worldwide, but less than 1% are known to infect humans. Most of these fungal infections are superficial, affecting the hair, skin and nails, but some species are capable of causing life-threatening diseases. The most common of these include Cryptococcus neoformans, Aspergillus fumigatus and Candida albicans. These fungi are typically innocuous and even constitute a part of the human microbiome, but if these pathogens disseminate throughout the body, they can cause fatal infections which account for more than one million deaths worldwide each year. Thus, systemic dissemination of fungi is a critical step in the development of these deadly infections. In this review, we discuss our current understanding of how fungi disseminate from the initial infection sites to the bloodstream, how immune cells eliminate fungi from circulation and how fungi leave the blood and enter distant organs, highlighting some recent advances and offering some perspectives on future directions.}, } @article {pmid33449130, year = {2021}, author = {Zai, X and Luo, W and Bai, W and Li, Y and Xiao, X and Gao, X and Wang, E and Wei, G and Chen, W}, title = {Effect of Root Diameter on the Selection and Network Interactions of Root-Associated Bacterial Microbiomes in Robinia pseudoacacia L.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33449130}, issn = {1432-184X}, support = {31870476//the National Natural Science Foundation of China/ ; 41830755//the National Natural Science Foundation of China/ ; }, abstract = {The high plasticity of root morphology, physiology, and function influences root-associated microbiomes. However, the variation in root-associated microbiome diversity and structures in response to root diameter at different root depths remains poorly understood. Here, we selected black locust (Robinia pseudoacacia L.) as a model plant to investigate the selection and network interactions of rhizospheric and root endophytic bacterial microbiomes associated with roots of different diameters (1, 1-2, and > 2 mm) among root depths of 0-100 cm via the Illumina sequencing of the 16S rRNA gene. The results showed that the alpha diversity of the root-associated bacterial communities decreased with increasing root diameters among different root depths; fewer orders with higher relative abundance, especially in the endosphere, were enriched in association with coarse roots (> 2 mm) than fine roots among root depths. Furthermore, the variation in the enriched bacterial orders associated with different root diameters was explained by bulk soil properties. Higher co-occurrence network complexity and stability emerged in the rhizosphere microbiomes of fine roots than those of coarse roots, in contrast to the situation in the endosphere microbiomes. In particular, the endosphere of roots with a diameter of 1-2 mm exhibited the lowest network complexity and stability and a high proportion of keystone taxa (e.g., Cytophagia, Flavobacteriia, Sphingobacteriia, β-Proteobacteria, and γ-Proteobacteria), suggesting a keystone taxon-reliant strategy in this transitional stage. In summary, this study indicated that root diameter at different root depths differentially affects rhizospheric and endophytic bacterial communities, which implies a close relationship between the bacterial microbiome, root function, and soil properties.}, } @article {pmid33448927, year = {2021}, author = {Mortensen, MS and Rasmussen, MA and Stokholm, J and Brejnrod, AD and Balle, C and Thorsen, J and Krogfelt, KA and Bisgaard, H and Sørensen, SJ}, title = {Modeling transfer of vaginal microbiota from mother to infant in early life.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, doi = {10.7554/eLife.57051}, pmid = {33448927}, issn = {2050-084X}, support = {R93-A8944//Lundbeckfonden/ ; R16-A1694//Lundbeckfonden/ ; 903516//Danish Ministry of Health/ ; 0603-00280B//Strategiske Forskningsråd/ ; }, abstract = {Early-life microbiota has been linked to the development of chronic inflammatory diseases. It has been hypothesized that maternal vaginal microbiota is an important initial seeding source and therefore might have lifelong effects on disease risk. To understand maternal vaginal microbiota's role in seeding the child's microbiota and the extent of delivery mode-dependent transmission, we studied 665 mother-child dyads from the COPSAC2010 cohort. The maternal vaginal microbiota was evaluated twice in the third trimester and compared with the children's fecal (at 1 week, 1 month, and 1 year of age) and airway microbiota (at 1 week, 1 month, and 3 months). Based on the concept of weighted transfer ratios (WTRs), we have identified bacterial orders for which the WTR displays patterns indicate persistent or transient transfer from the maternal vaginal microbiome, as well as orders that are shared at later time points independent of delivery mode, indicating a common reservoir.}, } @article {pmid33448595, year = {2020}, author = {Dury, GJ and Moczek, AP and Schwab, DB}, title = {Maternal and larval niche construction interact to shape development, survival, and population divergence in the dung beetle Onthophagus taurus.}, journal = {Evolution & development}, volume = {22}, number = {5}, pages = {358-369}, doi = {10.1111/ede.12348}, pmid = {33448595}, issn = {1525-142X}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; 1256689//National Science Foundation, Division of Integrative Organismal Systems/ ; 1901680//National Science Foundation, Division of Integrative Organismal Systems/ ; 61369//John Templeton Foundation/ ; }, abstract = {Through niche construction, organisms modify their environments in ways that can alter how selection acts on themselves and their offspring. However, the role of niche construction in shaping developmental and evolutionary trajectories, and its importance for population divergences and local adaptation, remains largely unclear. In this study, we manipulated both maternal and larval niche construction and measured the effects on fitness-relevant traits in two rapidly diverging populations of the bull-headed dung beetle, Onthophagus taurus. We find that both types of niche construction enhance adult size, peak larval mass, and pupal mass, which when compromised lead to a synergistic decrease in survival. Furthermore, for one measure, duration of larval development, we find that the two populations have diverged in their reliance on niche construction: larval niche construction appears to buffer against compromised maternal niche construction only in beetles from Western Australia, but not in beetles from the Eastern United States. We discuss our results in the context of rapid adaptation to novel conditions and the role of niche construction therein.}, } @article {pmid33447816, year = {2020}, author = {Vandeplassche, E and Sass, A and Ostyn, L and Burmølle, M and Kragh, KN and Bjarnsholt, T and Coenye, T and Crabbé, A}, title = {Antibiotic susceptibility of cystic fibrosis lung microbiome members in a multispecies biofilm.}, journal = {Biofilm}, volume = {2}, number = {}, pages = {100031}, pmid = {33447816}, issn = {2590-2075}, abstract = {The lungs of cystic fibrosis (CF) patients are often chronically colonized by multiple microbial species that can form biofilms, including the major CF pathogen Pseudomonas aeruginosa. Herewith, lower microbial diversity in CF airways is typically associated with worse health outcomes. In an attempt to treat CF lung infections patients are frequently exposed to antibiotics, which may affect microbial diversity. This study aimed at understanding if common antibiotics that target P. aeruginosa influence microbial diversity. To this end, a microaerophilic multispecies biofilm model of frequently co-isolated members of the CF lung microbiome (Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus anginosus, Achromobacter xylosoxidans, Rothia mucilaginosa, and Gemella haemolysans) was exposed to antipseudomonal antibiotics. We found that antibiotics that affected several dominant species (i.e. ceftazidime, tobramycin) resulted in higher species evenness compared to colistin, which is only active against P. aeruginosa. Furthermore, susceptibility of individual species in the multispecies biofilm following antibiotic treatment was compared to that of the respective single-species biofilms, showing no differences. Adding three anaerobic species (Prevotella melaninogenica, Veillonella parvula, and Fusobacterium nucleatum) to the multispecies biofilm did not influence antibiotic susceptibility. In conclusion, our study demonstrates antibiotic-dependent effects on microbial community diversity of multispecies biofilms comprised of CF microbiome members.}, } @article {pmid33447811, year = {2020}, author = {Zea, L and McLean, RJC and Rook, TA and Angle, G and Carter, DL and Delegard, A and Denvir, A and Gerlach, R and Gorti, S and McIlwaine, D and Nur, M and Peyton, BM and Stewart, PS and Sturman, P and Velez Justiniano, YA}, title = {Potential biofilm control strategies for extended spaceflight missions.}, journal = {Biofilm}, volume = {2}, number = {}, pages = {100026}, pmid = {33447811}, issn = {2590-2075}, support = {80NSSC17K0036/ImNASA/Intramural NASA/United States ; }, abstract = {Biofilms, surface-adherent microbial communities, are associated with microbial fouling and corrosion in terrestrial water-distribution systems. Biofilms are also present in human spaceflight, particularly in the Water Recovery System (WRS) on the International Space Station (ISS). The WRS is comprised of the Urine Processor Assembly (UPA) and the Water Processor Assembly (WPA) which together recycles wastewater from human urine and recovered humidity from the ISS atmosphere. These wastewaters and various process streams are continually inoculated with microorganisms primarily arising from the space crew microbiome. Biofilm-related fouling has been encountered and addressed in spacecraft in low Earth orbit, including ISS and the Russian Mir Space Station. However, planned future missions beyond low Earth orbit to the Moon and Mars present additional challenges, as resupplying spare parts or support materials would be impractical and the mission timeline would be in the order of years in the case of a mission to Mars. In addition, future missions are expected to include a period of dormancy in which the WRS would be unused for an extended duration. The concepts developed in this review arose from a workshop including NASA personnel and representatives with biofilm expertise from a wide range of industrial and academic backgrounds. Here, we address current strategies that are employed on Earth for biofilm control, including antifouling coatings and biocides and mechanisms for mitigating biofilm growth and damage. These ideas are presented in the context of their applicability to spaceflight and identify proposed new topics of biofilm control that need to be addressed in order to facilitate future extended, crewed, spaceflight missions.}, } @article {pmid33447732, year = {2021}, author = {Shen, H and Ding, L and Baig, M and Tian, J and Wang, Y and Huang, W}, title = {Improving glucose and lipids metabolism: drug development based on bile acid related targets.}, journal = {Cell stress}, volume = {5}, number = {1}, pages = {1-18}, pmid = {33447732}, issn = {2523-0204}, support = {R01 DK124627/DK/NIDDK NIH HHS/United States ; }, abstract = {Bariatric surgery is one of the most effective treatment options for severe obesity and its comorbidities. However, it is a major surgery that poses several side effects and risks which impede its clinical use. Therefore, it is urgent to develop alternative safer pharmacological approaches to mimic bariatric surgery. Recent studies suggest that bile acids are key players in mediating the metabolic benefits of bariatric surgery. Bile acids can function as signaling molecules by targeting bile acid nuclear receptors and membrane receptors, like FXR and TGR5 respectively. In addition, the composition of bile acids is regulated by either the hepatic sterol enzymes such as CYP8B1 or the gut microbiome. These bile acid related targets all play important roles in regulating metabolism. Drug development based on these targets could provide new hope for patients without the risks of surgery and at a lower cost. In this review, we summarize the most updated progress on bile acid related targets and development of small molecules as drug candidates based on these targets.}, } @article {pmid33446997, year = {2020}, author = {Liu, F and Liu, M and Liu, Y and Guo, C and Zhou, Y and Li, F and Xu, R and Liu, Z and Deng, Q and Li, X and Zhang, C and Pan, Y and Ning, T and Dong, X and Hu, Z and Bao, H and Cai, H and Silva, IDS and He, Z and Ke, Y}, title = {Oral microbiome and risk of malignant esophageal lesions in a high-risk area of China: A nested case-control study.}, journal = {Chinese journal of cancer research = Chung-kuo yen cheng yen chiu}, volume = {32}, number = {6}, pages = {742-754}, pmid = {33446997}, issn = {1000-9604}, abstract = {Objective: We aimed to prospectively evaluate the association of oral microbiome with malignant esophageal lesions and its predictive potential as a biomarker of risk.

Methods: We conducted a case-control study nested within a population-based cohort with up to 8 visits of oral swab collection for each subject over an 11-year period in a high-risk area for esophageal cancer in China. The oral microbiome was evaluated with 16S ribosomal RNA (rRNA) gene sequencing in 428 pre-diagnostic oral specimens from 84 cases with esophageal lesions of severe squamous dysplasia and above (SDA) and 168 matched healthy controls. DESeq analysis was performed to identify taxa of differential abundance. Differential oral species together with subject characteristics were evaluated for their potential in predicting SDA risk by constructing conditional logistic regression models.

Results: A total of 125 taxa including 37 named species showed significantly different abundance between SDA cases and controls (all P<0.05 & false discovery rate-adjusted Q<0.10). A multivariate logistic model including 11 SDA lesion-related species and family history of esophageal cancer provided an area under the receiver operating characteristic curve (AUC) of 0.89 (95% CI, 0.84-0.93). Cross-validation and sensitivity analysis, excluding cases diagnosed within 1 year of collection of the baseline specimen and their matched controls, or restriction to screen-endoscopic-detected or clinically diagnosed case-control triads, or using only bacterial data measured at the baseline, yielded AUCs>0.84.

Conclusions: The oral microbiome may play an etiological and predictive role in esophageal cancer, and it holds promise as a non-invasive early warning biomarker for risk stratification for esophageal cancer screening programs.}, } @article {pmid33446825, year = {2021}, author = {Corrêa, R and de Oliveira Santos, I and Braz-de-Melo, HA and de Sant'Ana, LP and das Neves Almeida, R and Pasquarelli-do-Nascimento, G and Prado, PS and Kobinger, GP and Maurice, CF and Magalhães, KG}, title = {Gut microbiota modulation induced by Zika virus infection in immunocompetent mice.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1421}, pmid = {33446825}, issn = {2045-2322}, support = {193.001.621/2016//Fundação de Apoio à Pesquisa do Distrito Federal/ ; }, abstract = {Gut microbiota composition can modulate neuroendocrine function, inflammation, and cellular and immunological responses against different pathogens, including viruses. Zika virus (ZIKV) can infect adult immunocompetent individuals and trigger brain damage and antiviral responses. However, it is not known whether ZIKV infection could impact the gut microbiome from adult immunocompetent mice. Here, we investigated modifications induced by ZIKV infection in the gut microbiome of immunocompetent C57BL/6J mice. Adult C57BL/6J mice were infected with ZIKV and the gut microbiota composition was analyzed by next-generation sequencing of the V4 hypervariable region present in the bacterial 16S rDNA gene. Our data showed that ZIKV infection triggered a significant decrease in the bacteria belonging to Actinobacteria and Firmicutes phyla, and increased Deferribacteres and Spirochaetes phyla components compared to uninfected mice. Interestingly, ZIKV infection triggered a significant increase in the abundance of bacteria from the Spirochaetaceae family in the gut microbiota. Lastly, we demonstrated that modulation of microbiota induced by ZIKV infection may lead to intestinal epithelium damage and intense leukocyte recruitment to the intestinal mucosa. Taken together, our data demonstrate that ZIKV infection can impact the gut microbiota composition and colon tissue homeostasis in adult immunocompetent mice.}, } @article {pmid33446697, year = {2021}, author = {Marcos-Fernández, R and Ruiz, L and Blanco-Míguez, A and Margolles, A and Sánchez, B}, title = {Precision modification of the human gut microbiota targeting surface-associated proteins.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1270}, pmid = {33446697}, issn = {2045-2322}, support = {AGL2016-78311-R//Agencia Estatal de Investigación/ ; AGL2016-78311-R//Agencia Estatal de Investigación/ ; IDI/2018/000236//Plan Regional de Investigación del Principado de Asturias/ ; IDI/2018/000236//Plan Regional de Investigación del Principado de Asturias/ ; PS-2016//AECC/ ; }, abstract = {This work describes a new procedure that allows the targeted modification of the human gut microbiota by using antibodies raised against bacterial surface-associated proteins specific to the microorganism of interest. To this end, a polyclonal antibody recognising the surface-associated protein Surface Layer Protein A of Lactobacillus acidophilus DSM20079T was developed. By conjugating this antibody with fluorescent probes and magnetic particles, we were able to specifically identify this bacterium both in a synthetic, and in real gut microbiotas by means of a flow cytometry approach. Further, we demonstrated the applicability of this antibody to deplete complex human gut microbiotas from L. acidophilus in a single step. L. acidophilus was found to interact with other bacteria both in synthetic and in real microbiotas, as reflected by its concomitant depletion together with other species. Further optimization of the procedure including a trypsin step enabled to achieve the selective and complete isolation of this species. Depleting a single species from a gut microbiota, using antibodies recognizing specific cell surface elements of the target organism, will open up novel ways to tackle research on the specific immunomodulatory and metabolic contributions of a bacterium of interest in the context of a complex human gut microbiota, including the investigation into therapeutic applications by adding/depleting a key bacterium. This represents the first work in which an antibody/flow-cytometry based application enabled the targeted edition of human gut microbiotas, and represents the basis for the design of precision microbiome-based therapies.}, } @article {pmid33446688, year = {2021}, author = {Monteiro, MF and Altabtbaei, K and Kumar, PS and Casati, MZ and Ruiz, KGS and Sallum, EA and Nociti-Junior, FH and Casarin, RCV}, title = {Parents with periodontitis impact the subgingival colonization of their offspring.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1357}, pmid = {33446688}, issn = {2045-2322}, support = {2015/50264-0//Sao Paolo Research Foundation/ ; }, abstract = {Early acquisition of a pathogenic microbiota and the presence of dysbiosis in childhood is associated with susceptibility to and the familial aggregation of periodontitis. This longitudinal interventional case-control study aimed to evaluate the impact of parental periodontal disease on the acquisition of oral pathogens in their offspring. Subgingival plaque and clinical periodontal metrics were collected from 18 parents with a history of generalized aggressive periodontitis and their children (6-12 years of age), and 18 periodontally healthy parents and their parents at baseline and following professional oral prophylaxis. 16S rRNA amplicon sequencing revealed that parents were the primary source of the child's microbiome, affecting their microbial acquisition and diversity. Children of periodontitis parents were preferentially colonized by Filifactor alocis, Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Streptococcus parasanguinis, Fusobacterium nucleatum and several species belonging to the genus Selenomonas even in the absence of periodontitis, and these species controlled inter-bacterial interactions. These pathogens also emerged as robust discriminators of the microbial signatures of children of parents with periodontitis. Plaque control did not modulate this pathogenic pattern, attesting to the microbiome's resistance to change once it has been established. This study highlights the critical role played by parental disease in microbial colonization patterns in their offspring and the early acquisition of periodontitis-related species and underscores the need for greater surveillance and preventive measures in families of periodontitis patients.}, } @article {pmid33446604, year = {2021}, author = {Sulaiman, I and Wu, BG and Li, Y and Tsay, JC and Sauthoff, M and Scott, AS and Ji, K and Koralov, SB and Weiden, M and Clemente, J and Jones, D and Huang, YJ and Stringer, KA and Zhang, L and Geber, A and Banakis, S and Tipton, L and Ghedin, E and Segal, LN}, title = {Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism.}, journal = {The European respiratory journal}, volume = {}, number = {}, pages = {}, doi = {10.1183/13993003.03434-2020}, pmid = {33446604}, issn = {1399-3003}, abstract = {RATIONALE: Microbiome studies of the lower airway based on bacterial 16S rRNA gene sequencing assess microbial community structure but can only infer functional characteristics. Microbial products, such as short chain fatty acids (SCFAs), in the lower airways have significant impact on the host's immune tone. Thus, functional approaches to the analyses of the microbiome are necessary.

METHODS: Here we used upper and lower airway samples from a research bronchoscopy smoker cohort. In addition, we validated our results in an experimental mouse model.

MEASUREMENTS: We extended our microbiota characterisation beyond 16S rRNA gene sequencing with the use of whole genome (WGS) and RNA metatranscriptome sequencing. Short chain fatty acids (SCFA) were also measured in lower airway samples and correlated with each of the sequencing datasets. In the mouse model, 16S rRNA gene and RNA metatranscriptome sequencing were performed.

MAIN RESULTS: Functional evaluations of the lower airway microbiota using inferred metagenome, WGS and metatranscriptome were dissimilar. Comparison with measured levels of SCFAs shows that the inferred metagenome from the 16S rRNA gene sequencing data was poorly correlated, while better correlations were noted when SCFAs levels were compared with WGS and metatranscriptome. Modelling lower airway aspiration with oral commensals in a mouse model showed that the metatranscriptome most efficiently captures transient active microbial metabolism, which was overestimated by 16S rRNA gene sequencing.

CONCLUSIONS: Functional characterisation of the lower airway microbiota through metatranscriptome identify metabolically active organisms capable of producing metabolites with immunomodulatory capacity such as SCFAs.}, } @article {pmid33446262, year = {2021}, author = {Maldonado-Ruiz, LP and Neupane, S and Park, Y and Zurek, L}, title = {The bacterial community of the lone star tick (Amblyomma americanum).}, journal = {Parasites & vectors}, volume = {14}, number = {1}, pages = {49}, pmid = {33446262}, issn = {1756-3305}, support = {GAČR 19-04301S//Grantová Agentura České Republiky/ ; }, abstract = {BACKGROUND: The lone star tick (Amblyomma americanum), an important vector of a wide range of human and animal pathogens, is very common throughout the East and Midwest of the USA. Ticks are known to carry non-pathogenic bacteria that may play a role in their vector competence for pathogens. Several previous studies using the high throughput sequencing (HTS) technologies reported the commensal bacteria in a tick midgut as abundant and diverse. In contrast, in our preliminary survey of the field collected adult lone star ticks, we found the number of culturable/viable bacteria very low.

METHODS: We aimed to analyze the bacterial community of A. americanum by a parallel culture-dependent and a culture-independent approach applied to individual ticks.

RESULTS: We analyzed 94 adult females collected in eastern Kansas and found that 60.8% of ticks had no culturable bacteria and the remaining ticks carried only 67.7 ± 42.8 colony-forming units (CFUs)/tick representing 26 genera. HTS of the 16S rRNA gene resulted in a total of 32 operational taxonomic units (OTUs) with the dominant endosymbiotic genera Coxiella and Rickettsia (> 95%). Remaining OTUs with very low abundance were typical soil bacterial taxa indicating their environmental origin.

CONCLUSIONS: No correlation was found between the CFU abundance and the relative abundance from the culture-independent approach. This suggests that many culturable taxa detected by HTS but not by culture-dependent method were not viable or were not in their culturable state. Overall, our HTS results show that the midgut bacterial community of A. americanum is very poor without a core microbiome and the majority of bacteria are endosymbiotic.}, } @article {pmid33446094, year = {2021}, author = {Short, MI and Hudson, R and Besasie, BD and Reveles, KR and Shah, DP and Nicholson, S and Johnson-Pais, TL and Weldon, K and Lai, Z and Leach, RJ and Fongang, B and Liss, MA}, title = {Comparison of rectal swab, glove tip, and participant-collected stool techniques for gut microbiome sampling.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {26}, pmid = {33446094}, issn = {1471-2180}, support = {U01 CA086402/NH/NIH HHS/United States ; P30 CA054174/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Studies of the gut microbiome are becoming increasingly important. Such studies require stool collections that can be processed or frozen in a timely manner so as not to alter the microbial content. Due to the logistical difficulties of home-based stool collection, there has been a challenge in selecting the appropriate sample collection technique and comparing results from different microbiome studies. Thus, we compared stool collection and two alternative clinic-based fecal microbiome collection techniques, including a newer glove-based collection method.

RESULTS: We prospectively enrolled 22 adult men from our prostate cancer screening cohort SABOR (San Antonio Biomarkers of Risk for prostate cancer) in San Antonio, TX, from 8/2018 to 4/2019. A rectal swab and glove tip sample were collected from each participant during a one-time visit to our clinics. A single stool sample was collected at the participant's home. DNA was isolated from the fecal material and 16 s rRNA sequencing of the V1-V2 and V3-V4 regions was performed. We found the gut microbiome to be similar in richness and evenness, noting no differences in alpha diversity among the collection methods. The stool collection method, which remains the gold-standard method for the gut microbiome, proved to have different community composition compared to swab and glove tip techniques (p< 0.001) as measured by Bray-Curtis and unifrac distances. There were no significant differences in between the swab and glove tip samples with regard to beta diversity (p> 0.05). Despite differences between home-based stool and office-based fecal collection methods, we noted that the distance metrics for the three methods cluster by participant indicating within-person similarities. Additionally, no taxa differed among the methods in a Linear Discriminant Analysis Effect Size (LEfSe) analysis comparing all-against-all sampling methods.

CONCLUSION: The glove tip method provides similar gut microbiome results as rectal swab and stool microbiome collection techniques. The addition of a new office-based collection technique could help easy and practical implementation of gut microbiome research studies and clinical practice.}, } @article {pmid33446027, year = {2021}, author = {Berard, AR and Miller, C and Araínga, M and Broedlow, CA and Noël-Romas, L and Schifanella, L and Hensley-McBain, T and Roederer, A and Driscoll, C and Coronado, E and Manuzak, J and McKinnon, LR and Villinger, FJ and Hope, TJ and Burgener, AD and Klatt, NR}, title = {SIV susceptibility, immunology and microbiome in the female genital tract of adolescent versus adult pigtail macaques.}, journal = {AIDS research and human retroviruses}, volume = {}, number = {}, pages = {}, doi = {10.1089/AID.2020.0271}, pmid = {33446027}, issn = {1931-8405}, abstract = {In Sub-Saharan Africa, young women aged 15-24 account for nearly 30% of all new HIV infections, however biological and epidemiological factors underlying this disproportionate infection rate are unclear. Here, we assessed biological contributors of SIV/HIV susceptibility in the female genital tract (FGT) using adolescent (n=9) and adult (n=10) pigtail macaques (PTMs) with weekly low-dose intravaginal challenges of SIV. Immunological variables were captured in vaginal tissue of PTMs by flow cytometry and cytokine assays. Vaginal biopsies were profiled by proteomic analysis. The vaginal microbiome was assessed by 16S rRNA sequencing. We were powered to detect a 2.2-fold increase in infection rates between age groups, however we identified no significant differences in susceptibility. This model cannot capture epidemiological factors or may not best represent biological differences of HIV susceptibility. No immune cell subsets measured were significantly different between groups. Inflammatory marker MCP-1 was significantly higher (adj p=0.02), and sCD40L trended higher (adj p=0.06) in vaginal cytobrushes of adults. Proteomic analysis of vaginal biopsies showed no significant (adj p<0.05) protein or pathway differences between groups. Vaginal microbiomes were not significantly different between groups. No differences were observed between age groups in this PTM model, however these animals may not reflect biological factors contributing to HIV risk such as those found in their human counterparts. This model is therefore not appropriate to explore human adolescent differences in HIV risk. Young women remain a key population at risk for HIV infection, and there is still a need for comprehensive assessments and interventions strategies for epidemic control of this uniquely vulnerable population.}, } @article {pmid33446008, year = {2021}, author = {DeDecker, L and Coppedge, B and Avelar-Barragan, J and Karnes, W and Whiteson, K}, title = {Microbiome distinctions between the CRC carcinogenic pathways.}, journal = {Gut microbes}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/19490976.2020.1854641}, pmid = {33446008}, issn = {1949-0984}, abstract = {Colorectal cancer (CRC) is the third most commonly diagnosed cancer, the third leading cause of cancer-related deaths, and has been on the rise among young adults in the United States. Research has established that the colonic microbiome is different in patients with CRC compared to healthy controls, but few studies have investigated if and how the microbiome may relate to CRC progression through the serrated pathway versus the adenoma-carcinoma sequence. Our view is that progress in CRC microbiome research requires consideration of how the microbiome may contribute to CRC carcinogenesis through the distinct pathways that lead to CRC, which could enable the creation of novel and tailored prevention, screening, and therapeutic interventions. We first highlight the limitations in existing CRC microbiome research and offer corresponding solutions for investigating the microbiome's role in the adenoma-carcinoma sequence and serrated pathway. We then summarize the findings in the select human studies that included data points related to the two major carcinogenic pathways. These studies investigate the microbiome in CRC carcinogenesis and 1) utilize mucosal samples and 2) compare polyps or tumors by histopathologic type, molecular/genetic type, or location in the colon. Key findings from these studies include: 1) Fusobacterium is associated with right-sided, more advanced, and serrated lesions; 2) the colons of people with CRC have bacteria typically associated with normal oral flora; and 3) colons from people with CRC have more biofilms, and these biofilms are predominantly located in the proximal colon (single study).}, } @article {pmid33445765, year = {2021}, author = {Wassermann, B and Korsten, L and Berg, G}, title = {Plant Health and Sound Vibration: Analyzing Implications of the Microbiome in Grape Wine Leaves.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, doi = {10.3390/pathogens10010063}, pmid = {33445765}, issn = {2076-0817}, support = {ZA 01/2019//Servicestelle für Mobilitätsprogramme des österreichischen Bundesministeriums für Bildung, Wissenschaft und Forschung, KulturKontakt Austria/ ; }, abstract = {Understanding the plant microbiome is a key for plant health and controlling pathogens. Recent studies have shown that plants are responsive towards natural and synthetic sound vibration (SV) by perception and signal transduction, which resulted in resistance towards plant pathogens. However, whether or not native plant microbiomes respond to SV and the underlying mechanism thereof remains unknown. Within the present study we compared grapevine-associated microbiota that was perpetually exposed to classical music with a non-exposed control group from the same vineyard in Stellenbosch, South Africa. By analyzing the 16S rRNA gene and ITS fragment amplicon libraries we found differences between the core microbiome of SV-exposed leaves and the control group. For several of these different genera, e.g., Bacillus, Kocuria and Sphingomonas, a host-beneficial or pathogen-antagonistic effect has been well studied. Moreover, abundances of taxa identified as potential producers of volatile organic compounds that contribute to sensory characteristics of wines, e.g., Methylobacterium, Sphingomonas, Bacillus and Sporobolomyces roseus, were either increased or even unique within the core music-exposed phyllosphere population. Results show an as yet unexplored avenue for improved plant health and the terroir of wine, which are important for environmentally friendly horticulture and consumer appreciation. Although our findings explain one detail of the long-term positive experience to improve grapevine's resilience by this unusual but innovative technique, more mechanistic studies are necessary to understand the whole interplay.}, } @article {pmid33445571, year = {2021}, author = {Moore, EK}, title = {Trimethylornithine Membrane Lipids: Discovered in Planctomycetes and Identified in Diverse Environments.}, journal = {Metabolites}, volume = {11}, number = {1}, pages = {}, doi = {10.3390/metabo11010049}, pmid = {33445571}, issn = {2218-1989}, abstract = {Intact polar membrane lipids (IPLs) are the building blocks of all cell membranes. There is a wide range of phosphorus-free IPL structures, including amino acid containing IPLs, that can be taxonomically specific. Trimethylornithine membrane lipids (TMOs) were discovered in northern wetland Planctomycete species that were isolated and described in the last decade. The trimethylated terminal nitrogen moiety of the ornithine amino acid in the TMO structure gives the lipid a charged polar head group, similar to certain phospholipids. Since their discovery, TMOs have been identified in various other recently described northern latitude Planctomycete species, and in diverse environments including tundra soil, a boreal eutrophic lake, meso-oligotrophic lakes, and hot springs. The majority of environments or enrichment cultures in which TMOs have been observed include predominately heterotrophic microbial communities involved in the degradation of recalcitrant material and/or low oxygen methanogenic conditions at primarily northern latitudes. Other ecosystems occupied with microbial communities that possess similar metabolic pathways, such as tropical peatlands or coastal salt marshes, may include TMO producing Planctomycetes as well, further allowing these lipids to potentially be used to understand microbial community responses to environmental change in a wide range of systems. The occurrence of TMOs in hot springs indicates that these unique lipids could have broad environmental distribution with different specialized functions. Opportunities also exist to investigate the application of TMOs in microbiome studies, including forensic necrobiomes. Further environmental and microbiome lipidomics research involving TMOs will help reveal the evolution, functions, and applications of these unique membrane lipids.}, } @article {pmid33445538, year = {2021}, author = {Fliegerova, KO and Podmirseg, SM and Vinzelj, J and Grilli, DJ and Kvasnová, S and Schierová, D and Sechovcová, H and Mrázek, J and Siddi, G and Arenas, GN and Moniello, G}, title = {The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic Fungi.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/microorganisms9010157}, pmid = {33445538}, issn = {2076-2607}, abstract = {This work investigated the changes of the rumen microbiome of goats switched from a forage to a concentrate diet with special attention to anaerobic fungi (AF). Female goats were fed an alfalfa hay (AH) diet (0% grain; n = 4) for 20 days and were then abruptly shifted to a high-grain (HG) diet (40% corn grain, 60% AH; n = 4) and treated for another 10 days. Rumen content samples were collected from the cannulated animals at the end of each diet period (day 20 and 30). The microbiome structure was studied using high-throughput sequencing for bacteria, archaea (16S rRNA gene) and fungi (ITS2), accompanied by qPCR for each group. To further elucidate unclassified AF, clone library analyses were performed on the ITS1 spacer region. Rumen pH was significantly lower in HG diet fed goats, but did not induce subacute ruminal acidosis. HG diet altered prokaryotic communities, with a significant increase of Bacteroidetes and a decrease of Firmicutes. On the genus level Prevotella 1 was significantly boosted. Methanobrevibacter and Methanosphaera were the most abundant archaea regardless of the diet and HG induced a significant augmentation of unclassified Thermoplasmatales. For anaerobic fungi, HG triggered a considerable rise in Feramyces observed with both ITS markers, while a decline of Tahromyces was detected by ITS2 and decrease of Joblinomyces by ITS1 only. The uncultured BlackRhino group revealed by ITS1 and further elucidated in one sample by LSU analysis, formed a considerable part of the AF community of goats fed both diets. Results strongly indicate that the rumen ecosystem still acts as a source for novel microorganisms and unexplored microbial interactions and that initial rumen microbiota of the host animal considerably influences the reaction pattern upon diet change.}, } @article {pmid33444573, year = {2021}, author = {Saha, S and Mara, K and Pardi, DS and Khanna, S}, title = {Long-term Safety of Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2021.01.010}, pmid = {33444573}, issn = {1528-0012}, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is highly effective for treating recurrent Clostridioides difficile infection (CDI), with emerging data on intermediate and long-term safety.

METHODS: A prospective survey-based study was conducted (9/2012-6/2018) in patients undergoing FMT for recurrent CDI. Data on demographics and comorbidities were abstracted from medical records. Patients were contacted at 1 week, 1 month, 6 months, 1 year (short-term), ≥2 years post-FMT (long-term). Symptoms and new medical diagnoses were recorded at each time point. Data were weighted to account for survey non-response bias. Multivariate logistic regression models for adverse events were built using age (per 10-year increment), sex, time of survey and comorbidities. P<0.05 was considered statistically significant.

RESULTS: Overall, 609 patients underwent FMT; median age 56 years (range, 18-94), 64.8% were female, 22.8% had inflammatory bowel disease (IBD). At short-term follow up (n=609), >60% patients had diarrhea, <33% had constipation. At 1 year, 9.5% reported additional CDI episodes. On multivariable analysis, patients with IBD, dialysis dependent kidney disease and multiple FMTs had higher risk of diarrhea; risk of constipation was higher in females and lower in IBD (all p<0.05). For long-term follow up (n=447), median time of follow up was 3.7 years (range, 2.0-6.8). Overall, 73 new diagnoses were reported- 13% gastrointestinal, 10% weight gain, 11.8% new infections (all deemed unrelated to FMT). Median time to infections was 29 months (range, 0-73) post-FMT.

CONCLUSION: FMT appears safe with low risk of transmission of infections. Several new diagnoses were reported, which should be explored in future studies.}, } @article {pmid33444433, year = {2021}, author = {Kerkhof, LJ}, title = {Is oxford nanopore sequencing ready for analyzing complex microbiomes?.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiab001}, pmid = {33444433}, issn = {1574-6941}, abstract = {This minireview will discuss the improvements in Oxford Nanopore sequencing technology which make the MinION a viable platform for microbial ecology studies. Specific issues being addressed are the increase in sequence accuracy from 65-96.5% during the last 5 years, the ability to obtain a quantifiable/predictive signal from the MinION with respect to target molecule abundance, simple-to-use GUI-based pathways for data analysis, and the modest additional equipment needs for sequencing in the field. Coupling these recent improvements with the low capital costs for equipment and the reasonable per sample cost makes MinION sequencing an attractive option for virtually any laboratory.}, } @article {pmid33444319, year = {2021}, author = {McKinney, CA and Bedenice, D and Pacheco, AP and Oliveira, BCM and Paradis, MR and Mazan, M and Widmer, G}, title = {Assessment of clinical and microbiota responses to fecal microbial transplantation in adult horses with diarrhea.}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0244381}, doi = {10.1371/journal.pone.0244381}, pmid = {33444319}, issn = {1932-6203}, abstract = {BACKGROUND AND AIMS: Fecal microbial transplantation (FMT) is empirically implemented in horses with colitis to facilitate resolution of diarrhea. The purpose of this study was to assess FMT as a clinical treatment and modulator of fecal microbiota in hospitalized horses with colitis.

METHODS: A total of 22 horses with moderate to severe diarrhea, consistent with a diagnosis of colitis, were enrolled at two referral hospitals (L1: n = 12; L2: n = 10). FMT was performed in all 12 patients on 3 consecutive days at L1, while treatment at L2 consisted of standard care without FMT. Manure was collected once daily for 4 days from the rectum in all colitis horses, prior to FMT for horses at L1, and from each manure sample used for FMT. Fecal samples from 10 clinically healthy control horses housed at L2, and 30 healthy horses located at 5 barns in regional proximity to L1 were also obtained to characterize the regional healthy equine microbiome. All fecal microbiota were analyzed using 16S amplicon sequencing.

RESULTS AND CONCLUSIONS: As expected, healthy horses at both locations showed a greater α-diversity and lower β-diversity compared to horses with colitis. The fecal microbiome of healthy horses clustered by location, with L1 horses showing a higher prevalence of Kiritimatiellaeota. Improved manure consistency (lower diarrhea score) was associated with a greater α-diversity in horses with colitis at both locations (L1: r = -0.385, P = 0.006; L2: r = -0.479, P = 0.002). Fecal transplant recipients demonstrated a greater overall reduction in diarrhea score (median: 4±3 grades), compared to untreated horses (median: 1.5±3 grades, P = 0.021), with a higher incidence in day-over-day improvement in diarrhea (22/36 (61%) vs. 10/28 (36%) instances, P = 0.011). When comparing microbiota of diseased horses at study conclusion to that of healthy controls, FMT-treated horses showed a lower mean UniFrac distance (0.53±0.27) than untreated horses (0.62±0.26, P<0.001), indicating greater normalization of the microbiome in FMT-treated patients.}, } @article {pmid33443802, year = {2021}, author = {Wang, M and Zhao, H and Wen, X and Ho, CT and Li, S}, title = {Citrus flavonoids and the intestinal barrier: Interactions and effects.}, journal = {Comprehensive reviews in food science and food safety}, volume = {20}, number = {1}, pages = {225-251}, doi = {10.1111/1541-4337.12652}, pmid = {33443802}, issn = {1541-4337}, support = {2019ABA100//Hubei Province Technical Innovation Special Project/ ; 81803548//National Natural Science Foundation of China/ ; 19JCQNJC12400//Natural Science Foundation of Tianjin City/ ; TD13-5087//Tianjin Innovative Research Team Grant/ ; }, abstract = {The intestinal barrier plays a central role in sustaining gut homeostasis and, when dysfunctional, may contribute to diseases. Dietary flavonoids derived from Citrus genus represent one of the main naturally occurring phytochemicals with multiple potential benefits for the intestinal barrier function. In the intestine, citrus flavonoids (CFs) undergo ingestion from the lumen, biotransformation in the epithelial cells and/or crosstalk with luminal microbiota to afford various metabolites that may in turn exert protective actions on gut barrier along with their parental compounds. Specifically, the health-promoting properties of CFs and their metabolic bioactives for the intestinal barrier include their capacity to (a) modulate barrier permeability; (b) protect mucus layer; (c) regulate intestinal immune system; (d) fight against oxidative stress; and (e) positively shape microbiome and metabolome. Notably, local effects of CFs can also generate systemic benefits, for instance, improvement of gut microbial dysbiosis helpful to orchestrate gut homeostasis and leading to alleviation of systemic dysmetabolism. Given the important role of the intestinal barrier in overall health, further understanding of underlying action mechanisms and ultimate health effects of CFs as well as their metabolites on the intestine is of great significance to future application of citrus plants and their bioactives as dietary supplements and/or functional ingredients in medical foods.}, } @article {pmid33443749, year = {2020}, author = {Hens, K}, title = {[You should exercise a bit more - The ethics of lifestyle and mental health].}, journal = {Tijdschrift voor psychiatrie}, volume = {62}, number = {11}, pages = {976-980}, pmid = {33443749}, issn = {0303-7339}, abstract = {BACKGROUND: The fact that environmental factors and lifestyle play a role in mental health is well known. In the last decades more research has gone into the link between environment and genetics: epigenetics has shown us the molecular link between these two, and the influence of the microbiome on mental health has demonstrated the importance of food. Still, ethical questions remain about how lifestyle advice can be integrated in clinical practice in an ethical way. AIM: To describe the normative import of our view on biology and individual responsibility and the place of lifestyle in the debate. METHOD: A consideration of ethical aspects of lifestyle and lifestyle advice. RESULTS: The normative import of our view on biology and individual responsibility and the place of lifestyle in the debate is described. It is argued that lifestyle has a unique place between biological and psychosocial concepts. Finally, the pitfalls and opportunities of introducing lifestyle in clinical practice are shown. CONCLUSION: Lifestyle is conceptually situated between the biological and the psychosocial, and sheds new light on the importance of certain explanations for recovery, and the relation with specific treatments. Lifestyle advice can only be used optimally in therapy if mental health care professionals also include a dialogue about assumptions and expectations.}, } @article {pmid33443714, year = {2021}, author = {Yang, H and Zhang, Y and Chuang, S and Cao, W and Ruan, Z and Xu, X and Jiang, J}, title = {Bioaugmentation of acetamiprid-contaminated soil with Pigmentiphaga sp. strain D-2 and its effect on the soil microbial community.}, journal = {Ecotoxicology (London, England)}, volume = {}, number = {}, pages = {}, pmid = {33443714}, issn = {1573-3017}, support = {2018YFA0901200//National Key R&D Program of china/ ; 2018YFA0901200//National Key R&D Program of china/ ; 2018YFA0901200//National Key R&D Program of china/ ; 41977120//National Natural Science Foundation of China/ ; }, abstract = {Bioaugmentation, a strategy based on microbiome engineering, has been proposed for bioremediation of pollutant-contaminated environments. However, the complex microbiome engineering processes for soil bioaugmentation, involving interactions among the exogenous inoculum, soil environment, and indigenous microbial microbiome, remain largely unknown. Acetamiprid is a widely used neonicotinoid insecticide which has caused environmental contaminations. Here, we used an acetamiprid-degrading strain, Pigmentiphaga sp. D-2, as inoculum to investigate the effects of bioaugmentation on the soil microbial community and the process of microbiome reassembly. The bioaugmentation treatment removed 94.8 and 92.5% of acetamiprid within 40 days from soils contaminated with 50 and 200 mg/kg acetamiprid, respectively. A decrease in bacterial richness and diversity was detected in bioaugmentation treatments, which later recovered with the removal of acetamiprid from soil. Moreover, the bioaugmentation treatment significantly influenced the bacterial community structure, whereas application of acetamiprid alone had little influence on the soil microbial community. Furthermore, the bioaugmentation treatment improved the growth of bacteria associated with acetamiprid degradation, and the inoculated and recruited taxa significantly influenced the keystone taxa of the indigenous microbiome, resulting in reassembly of the bacterial community yielding higher acetamiprid-degrading efficiency than that of the indigenous and acetamiprid-treated communities. Our results provide valuable insights into the mechanisms of microbiome engineering for bioaugmentation of acetamiprid-contaminated soils.}, } @article {pmid33443222, year = {2021}, author = {Wang, Q and Kim, SY and Matsushita, H and Wang, Z and Pandyarajan, V and Matsuda, M and Ohashi, K and Tsuchiya, T and Roh, YS and Kiani, C and Zhao, Y and Chan, M and Devkota, S and Lu, SC and Hayashi, T and Carson, DA and Seki, E}, title = {Oral administration of PEGylated TLR7 ligand ameliorates alcohol-associated liver disease via the induction of IL-22.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {1}, pages = {}, doi = {10.1073/pnas.2020868118}, pmid = {33443222}, issn = {1091-6490}, abstract = {Effective therapies for alcohol-associated liver disease (ALD) are limited; therefore, the discovery of new therapeutic agents is greatly warranted. Toll-like receptor 7 (TLR7) is a pattern recognition receptor for single-stranded RNA, and its activation prevents liver fibrosis. We examined liver and intestinal damage in Tlr7-/- mice to determine the role of TLR7 in ALD pathogenesis. In an alcoholic hepatitis (AH) mouse model, hepatic steatosis, injury, and inflammation were induced by chronic binge ethanol feeding in mice, and Tlr7 deficiency exacerbated these effects. Because these results demonstrated that endogenous TLR7 signaling activation is protective in the AH mouse model, we hypothesized that TLR7 activation may be an effective therapeutic strategy for ALD. Therefore, we investigated the therapeutic effect of TLR7 agonistic agent, 1Z1, in the AH mouse model. Oral administration of 1Z1 was well tolerated and prevented intestinal barrier disruption and bacterial translocation, which thus suppressed ethanol-induced hepatic injury, steatosis, and inflammation. Furthermore, 1Z1 treatment up-regulated the expression of antimicrobial peptides, Reg3b and Reg3g, in the intestinal epithelium, which modulated the microbiome by decreasing and increasing the amount of Bacteroides and Lactobacillus, respectively. Additionally, 1Z1 up-regulated intestinal interleukin (IL)-22 expression. IL-22 deficiency abolished the protective effects of 1Z1 in ethanol-induced liver and intestinal damage, suggesting intestinal IL-22 as a crucial mediator for 1Z1-mediated protection in the AH mouse model. Collectively, our results indicate that TLR7 signaling exerts protective effects in the AH mouse model and that a TLR7 ligand, 1Z1, holds therapeutic potential for the treatment of AH.}, } @article {pmid33442763, year = {2021}, author = {Mutnale, MC and Reddy, GS and Vasudevan, K}, title = {Bacterial Community in the Skin Microbiome of Frogs in a Coldspot of Chytridiomycosis Infection.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33442763}, issn = {1432-184X}, support = {BSC0207//Council of Scientific and Industrial Research, India/ ; }, abstract = {Chytridiomycosis is a fungal disease caused by the pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), which has caused declines in amphibian populations worldwide. Asia is considered as a coldspot of infection, since adult frogs are less susceptible to Bd-induced mortality or morbidity. Using the next-generation sequencing approach, we assessed the cutaneous bacterial community composition and presence of anti-Bd bacteria in six frog species from India using DNA isolated from skin swabs. All the six frog species sampled were tested using nested PCR and found Bd negative. We found a total of 551 OTUs on frog skin, of which the bacterial phyla such as Proteobacteria (56.15% average relative abundance) was dominated followed by Actinobacteria (21.98% average relative abundance) and Firmicutes (13.7% average relative abundance). The contribution of Proteobacteria in the anti-Bd community was highest and represented by 175 OTUs. Overall, the anti-Bd bacterial community dominated (51.7% anti-Bd OTUs) the skin microbiome of the frogs. The study highlights the putative role of frog skin microbiome in affording resistance to Bd infections in coldspots of infection.}, } @article {pmid33442705, year = {2021}, author = {Romano-Keeler, J and Fiszbein, D and Zhang, J and Horowitz, J and Hayani, K and Buhimschi, I and Lopez, C and Kadhem, Z and Berman, J and Rasamimari, P and Raghavan, A and Pillers, DM and Sun, J}, title = {Center-Based Experiences Implementing Strategies to Reduce Risk of Horizontal Transmission of SARS-Cov-2: Potential for Compromise of Neonatal Microbiome Assemblage.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2021.01.07.21249418}, pmid = {33442705}, abstract = {Perinatal transmission of COVID-19 is poorly understood and many neonatal intensive care units' (NICU) policies minimize mother-infant contact to prevent transmission. We present our unit's approach and ways it may impact neonatal microbiome acquisition. We attended COVID-19 positive mothers' deliveries from March-August 2020. Delayed cord clamping and skin-to-skin were avoided and infants were admitted to the NICU. No parents' visits were allowed and discharge was arranged with COVID-19 negative family members. Maternal breast milk was restricted in the NICU. All twenty-one infants tested negative at 24 and 48 hours and had average hospital stays of nine days. 40% of mothers expressed breastmilk and 30% of infants were discharged with COVID-19 negative caregivers. Extended hospital stays, no skin-to-skin contact, limited maternal milk use, and discharge to caregivers outside primary residences, potentially affect the neonatal microbiome. Future studies are warranted to explore how ours and other centers' similar policies influence this outcome.}, } @article {pmid33442401, year = {2021}, author = {Nie, S and Wang, A and Yuan, Y}, title = {Comparison of clinicopathological parameters, prognosis, micro-ecological environment and metabolic function of Gastric Cancer with or without Fusobacterium sp. Infection.}, journal = {Journal of Cancer}, volume = {12}, number = {4}, pages = {1023-1032}, pmid = {33442401}, issn = {1837-9664}, abstract = {Background: Fusobacterium sp. plays a crucial role in the tumorigenesis and development of gastrointestinal tumors. Our research group previously disclosed that Fusobacterium sp. was more abundant in gastric cancer (GC) tissues than adjacent non-cancerous (NC) tissues. However, Fusobacterium sp. did not exist in all GC tissues and the differentiated features of GC with or without Fusobacterium sp. infection is not clear. Methods: The expression data of 61 GC tissues came from 16S rRNA gene sequencing. Comparison groups were defined based on sOTU at the genus level of Fusobacterium sp., which was performed by the Qiime2 microbiome bioinformatics platform. We used Chi-square and Fisher's exact test to compare clinicopathological parameters, and used Kaplan-Meier analysis, Cox univariate and multivariate analysis to compare prognosis. Micro-ecological environment comparison was characterized by 16S rRNA gene sequencing, and the metabolic function prediction was applied by PICRUSt2. Results of microbial diversity, differential enrichment genus and metabolic function in GC with or without Fusobacterium sp. infection was validated with 229 GC tissues downloaded from an independent cohort in ENA database (PRJNA428883). Results: The infection rate of Fusobacterium sp. in 61 GC tissues was 52.46% and elderly GC patients were more prone to Fusobacterium sp. infection. GC patients infected with Fusobacterium sp. were more likely to have tumor-infiltrating lymphocytes and p53 expression. The microbial diversity and microbial structure showed significant differences between two GC tissue groups with 42 differential enrichment genera. The metabolic function of Fusobacterium sp.-positive GC tissues was related to the biosynthesis of lysine, peptidoglycan, and tRNA. The differences in microbial structure, the existence of some differential enrichment genera and the metabolic function of Fusobacterium sp.-positive GC tissues, were then validated by 229 GC tissues of an independent cohort. Conclusions: Fusobacterium sp. infection can affect the phenotypic characteristics, micro-ecological environment, and metabolic functions of GC, which may provide a basis for further exploring the relationship between Fusobacterium sp. infection and carcinogenesis of GC.}, } @article {pmid33442384, year = {2020}, author = {Xu, H and Cao, J and Li, X and Lu, X and Xia, Y and Fan, D and Zhao, H and Ju, D and Xiao, C}, title = {Regional Differences in the Gut Microbiota and Gut-Associated Immunologic Factors in the Ileum and Cecum of Rats With Collagen-Induced Arthritis.}, journal = {Frontiers in pharmacology}, volume = {11}, number = {}, pages = {587534}, pmid = {33442384}, issn = {1663-9812}, abstract = {Rheumatoid arthritis (RA) is a common autoimmune disease characterized by chronic inflammation and a multifactorial etiology. We previously showed that gut microbiota dysbiosis in the rat ileum is involved in the development of collagen-induced arthritis (CIA). The gut microbiota in the distinct gastrointestinal tract (GIT) plays region-specific roles, but information on the different roles of the microbiota in distinct GIT compartments of CIA rats is limited. This study aimed to evaluate the region-specific differences in the gut microbial communities and certain gut-associated immunologic factors in the ileum and cecum of CIA rats. Ileal and cecal digesta were collected from CIA and control rats for microbiome analysis. We determined the microbial richness, diversity and taxa as well as the expression of interleukin (IL)-1β and IL-17A in the epithelium and lamina propria of the ileum and cecum mucosal layers. The CIA-induced microbiota alterations in the ileum differed from those in the cecum. The ileal microbiota were more markedly influenced in CIA, as revealed by sharp reductions in the abundances of the families Enterococcaceae, Lactobacillaceae and Streptococcaceae and the genera Lactobacillus and Lactococcus. Moreover, significant increases in IL-1β, and IL-17A mRNA expression were detected in only the ileal epithelium and lamina propria of the mucosal layer. Therefore, the microbial characteristics in the ileum were consistent with the immune-mediated inflammatory features of CIA, suggesting that the ileal microbiota might better represent the CIA-induced inflammatory responses than the cecal microbiota and that these responses might partially impact the progression of RA by regulating intestinal mucosal immunity.}, } @article {pmid33442010, year = {2021}, author = {Stower, H}, title = {Microbiome transplant-induced response to immunotherapy.}, journal = {Nature medicine}, volume = {27}, number = {1}, pages = {21}, doi = {10.1038/s41591-020-01220-6}, pmid = {33442010}, issn = {1546-170X}, } @article {pmid33441939, year = {2021}, author = {Gopinath, D and Menon, RK and Wie, CC and Banerjee, M and Panda, S and Mandal, D and Behera, PK and Roychoudhury, S and Kheur, S and Botelho, MG and Johnson, NW}, title = {Differences in the bacteriome of swab, saliva, and tissue biopsies in oral cancer.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1181}, pmid = {33441939}, issn = {2045-2322}, abstract = {Microbial dysbiosis has been implicated in the pathogenesis of oral cancer. We analyzed the compositional and metabolic profile of the bacteriome in three specific niches in oral cancer patients along with controls using 16SrRNA sequencing (Illumina Miseq) and DADA2 software. We found major differences between patients and control subjects. Bacterial communities associated with the tumor surface and deep paired tumor tissue differed significantly. Tumor surfaces carried elevated abundances of taxa belonging to genera Porphyromonas, Enterobacteriae, Neisseria, Streptococcus and Fusobacteria, whereas Prevotella, Treponema, Sphingomonas, Meiothermus and Mycoplasma genera were significantly more abundant in deep tissue. The most abundant microbial metabolic pathways were those related to fatty-acid biosynthesis, carbon metabolism and amino-acid metabolism on the tumor surface: carbohydrate metabolism and organic polymer degradation were elevated in tumor tissues. The bacteriome of saliva from patients with oral cancer differed significantly from paired tumor tissue in terms of community structure, however remained similar at taxonomic and metabolic levels except for elevated abundances of Streptococcus, Lactobacillus and Bacteroides, and acetoin-biosynthesis, respectively. These shifts to a pro-inflammatory profile are consistent with other studies suggesting oncogenic properties. Importantly, selection of the principal source of microbial DNA is key to ensure reliable, reproducible and comparable results in microbiome studies.}, } @article {pmid33441919, year = {2021}, author = {Al Kawas, S and Al-Marzooq, F and Rahman, B and Shearston, JA and Saad, H and Benzina, D and Weitzman, M}, title = {The impact of smoking different tobacco types on the subgingival microbiome and periodontal health: a pilot study.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1113}, pmid = {33441919}, issn = {2045-2322}, support = {AJF2018014//Al Jalila Foundation/ ; NIH/NIEHS 1R21ES026996-01A1/NH/NIH HHS/United States ; }, abstract = {Smoking is a risk factor for periodontal disease, and a cause of oral microbiome dysbiosis. While this has been evaluated for traditional cigarette smoking, there is limited research on the effect of other tobacco types on the oral microbiome. This study investigates subgingival microbiome composition in smokers of different tobacco types and their effect on periodontal health. Subgingival plaques were collected from 40 individuals, including smokers of either cigarettes, medwakh, or shisha, and non-smokers seeking dental treatment at the University Dental Hospital in Sharjah, United Arab Emirates. The entire (~ 1500 bp) 16S rRNA bacterial gene was fully amplified and sequenced using Oxford Nanopore technology. Subjects were compared for the relative abundance and diversity of subgingival microbiota, considering smoking and periodontal condition. The relative abundances of several pathogens were significantly higher among smokers, such as Prevotella denticola and Treponema sp. OMZ 838 in medwakh smokers, Streptococcus mutans and Veillonella dispar in cigarette smokers, Streptococcus sanguinis and Tannerella forsythia in shisha smokers. Subgingival microbiome of smokers was altered even in subjects with no or mild periodontitis, probably making them more prone to severe periodontal diseases. Microbiome profiling can be a useful tool for periodontal risk assessment. Further studies are recommended to investigate the impact of tobacco cessation on periodontal disease progression and oral microbiome.}, } @article {pmid33441848, year = {2021}, author = {Góngora, E and Elliott, KH and Whyte, L}, title = {Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia).}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1200}, pmid = {33441848}, issn = {2045-2322}, support = {Discovery Grant 241061//Natural Sciences and Engineering Research Council of Canada/ ; Discovery Grant 74221//Natural Sciences and Engineering Research Council of Canada/ ; Arctic Ecology//Canada Research Chairs/ ; Polar Microbiology//Canada Research Chairs/ ; Northern Contaminants Program//Indigenous and Northern Affairs Canada/ ; }, abstract = {The role of the gut microbiome is increasingly being recognized by health scientists and veterinarians, yet its role in wild animals remains understudied. Variations in the gut microbiome could be the result of differential diets among individuals, such as variation between sexes, across seasons, or across reproductive stages. We evaluated the hypothesis that diet alters the avian gut microbiome using stable isotope analysis (SIA) and 16S rRNA gene sequencing. We present the first description of the thick-billed murre (Uria lomvia) fecal microbiome. The murre microbiome was dominated by bacteria from the genus Catellicoccus, ubiquitous in the guts of many seabirds. Microbiome variation was explained by murre diet in terms of proportion of littoral carbon, trophic position, and sulfur isotopes, especially for the classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Alphaproteobacteria, and Gammaproteobacteria. We also observed differences in the abundance of bacterial genera such as Catellicoccus and Cetobacterium between sexes and reproductive stages. These results are in accordance with behavioural observations of changes in diet between sexes and across the reproductive season. We concluded that the observed variation in the gut microbiome may be caused by individual prey specialization and may also be reinforced by sexual and reproductive stage differences in diet.}, } @article {pmid33441819, year = {2021}, author = {Zarantoniello, M and Randazzo, B and Nozzi, V and Truzzi, C and Giorgini, E and Cardinaletti, G and Freddi, L and Ratti, S and Girolametti, F and Osimani, A and Notarstefano, V and Milanović, V and Riolo, P and Isidoro, N and Tulli, F and Gioacchini, G and Olivotto, I}, title = {Physiological responses of Siberian sturgeon (Acipenser baerii) juveniles fed on full-fat insect-based diet in an aquaponic system.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1057}, pmid = {33441819}, issn = {2045-2322}, support = {NUTRIFISH project N° 2017.0571//Fondazione Cassa di Risparmio di Verona Vicenza Belluno e Ancona/ ; }, abstract = {Over the last years, the potential use of Black Soldier Fly meal (BSF) as a new and sustainable aquafeed ingredient has been largely explored in several fish species. However, only fragmentary information is available about the use of BSF meal-based diets in sturgeon nutrition. In consideration of a circular economy concept and a more sustainable aquaculture development, the present research represents the first comprehensive multidisciplinary study on the physiological effects of a BSF diet during sturgeon culture in an aquaponic system. Siberian sturgeon (Acipenser baerii) juveniles were fed over a 60-days feeding trial on a control diet (Hi0) and a diet containing 50% of full-fat BSF meal respect to fish meal (Hi50). Physiological responses of fish were investigated using several analytical approaches, such as gas chromatography-mass spectrometry, histology, Fourier Transformed Infrared Spectroscopy (FTIR), microbiome sequencing and Real-time PCR. While aquaponic systems performed optimally during the trial, Hi50 group fish showed lower diet acceptance that resulted in growth and survival reduction, a decrease in hepatic lipids and glycogen content (FTIR), a higher hepatic hsp70.1 gene expression and a worsening in gut histological morphometric parameters. The low feed acceptance showed by Hi50 group sturgeon highlighted the necessity to improve the palatability of BSF-based diet designed for sturgeon culture.}, } @article {pmid33441754, year = {2021}, author = {Imahashi, M and Ode, H and Kobayashi, A and Nemoto, M and Matsuda, M and Hashiba, C and Hamano, A and Nakata, Y and Mori, M and Seko, K and Nakahata, M and Kogure, A and Tanaka, Y and Sugiura, W and Yokomaku, Y and Iwatani, Y}, title = {Impact of long-term antiretroviral therapy on gut and oral microbiotas in HIV-1-infected patients.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {960}, pmid = {33441754}, issn = {2045-2322}, support = {18kk0205011h0203//Japan Agency for Medical Research and Development/ ; }, abstract = {In HIV-1-infected patients, antiretroviral therapy (ART) is a key factor that may impact commensal microbiota and cause the emergence of side effects. However, it is not fully understood how long-term ART regimens have diverse impacts on the microbial compositions over time. Here, we performed 16S ribosomal RNA gene sequencing of the fecal and salivary microbiomes in patients under different long-term ART. We found that ART, especially conventional nucleotide/nucleoside reverse transcriptase inhibitor (NRTI)-based ART, has remarkable impacts on fecal microbial diversity: decreased α-diversity and increased ß-diversity over time. In contrast, dynamic diversity changes in the salivary microbiome were not observed. Comparative analysis of bacterial genus compositions showed a propensity for Prevotella-enriched and Bacteroides-poor gut microbiotas in patients with ART over time. In addition, we observed a gradual reduction in Bacteroides but drastic increases in Succinivibrio and/or Megasphaera under conventional ART. These results suggest that ART, especially NRTI-based ART, has more suppressive impacts on microbiota composition and diversity in the gut than in the mouth, which potentially causes intestinal dysbiosis in patients. Therefore, NRTI-sparing ART, especially integrase strand transfer inhibitor (INSTI)- and/or non-nucleotide reverse transcriptase inhibitor (NNRTI)-containing regimens, might alleviate the burden of intestinal dysbiosis in HIV-1-infected patients under long-term ART.}, } @article {pmid33441710, year = {2021}, author = {Relvas, M and Regueira-Iglesias, A and Balsa-Castro, C and Salazar, F and Pacheco, JJ and Cabral, C and Henriques, C and Tomás, I}, title = {Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {929}, pmid = {33441710}, issn = {2045-2322}, support = {MVOS2016//CESPU, Gandra, Paredes, Portugal/ ; MVOS-PT-IINFACTS-2019//CESPU, Gandra, Paredes, Portugal/ ; ISCIII/PI17/01722//Instituto de Salud Carlos III and co-financed by FEDER, Madrid, Spain/ ; }, abstract = {The present study used 16S rRNA gene amplicon sequencing to assess the impact on salivary microbiome of different grades of dental and periodontal disease and the combination of both (hereinafter referred to as oral disease), in terms of bacterial diversity, co-occurrence network patterns and predictive models. Our scale of overall oral health was used to produce a convenience sample of 81 patients from 270 who were initially recruited. Saliva samples were collected from each participant. Sequencing was performed in Illumina MiSeq with 2 × 300 bp reads, while the raw reads were processed according to the Mothur pipeline. The statistical analysis of the 16S rDNA sequencing data at the species level was conducted using the phyloseq, DESeq2, Microbiome, SpiecEasi, igraph, MixOmics packages. The simultaneous presence of dental and periodontal pathology has a potentiating effect on the richness and diversity of the salivary microbiota. The structure of the bacterial community in oral health differs from that present in dental, periodontal or oral disease, especially in high grades. Supragingival dental parameters influence the microbiota's abundance more than subgingival periodontal parameters, with the former making a greater contribution to the impact that oral health has on the salivary microbiome. The possible keystone OTUs are different in the oral health and disease, and even these vary between dental and periodontal disease: half of them belongs to the core microbiome and are independent of the abundance parameters. The salivary microbiome, involving a considerable number of OTUs, shows an excellent discriminatory potential for distinguishing different grades of dental, periodontal or oral disease; considering the number of predictive OTUs, the best model is that which predicts the combined dental and periodontal status.}, } @article {pmid33441592, year = {2021}, author = {Jo, R and Yama, K and Aita, Y and Tsutsumi, K and Ishihara, C and Maruyama, M and Takeda, K and Nishinaga, E and Shibasaki, KI and Morishima, S}, title = {Comparison of oral microbiome profiles in 18-month-old infants and their parents.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {861}, pmid = {33441592}, issn = {2045-2322}, abstract = {The onset and progress of dental caries and periodontal disease is associated with the oral microbiome. Therefore, it is important to understand the factors that influence oral microbiome formation. One of the factors that influence oral microbiome formation is the transmission of oral bacteria from parents. However, it remains unclear when the transmission begins, and the difference in contributions of father and mother. Here, we focused on the oral microbiome of 18-month-old infants, at which age deciduous dentition is formed and the oral microbiome is likely to become stable, with that of their parents. We collected saliva from forty 18-month-old infants and their parents and compared the diversity and composition of the microbiome using next-generation sequencing of 16S rRNA genes. The results showed that microbial diversity in infants was significantly lower than that in parents and composition of microbiome were significantly different between infants and parents. Meanwhile, the microbiome of the infants was more similar to that of their mothers than unrelated adults. The bacteria highly shared between infants and parents included not only commensal bacteria but also disease related bacteria. These results suggested that the oral microbiome of the parents influences that of their children aged < 18 months.}, } @article {pmid33441409, year = {2021}, author = {Fishbein, SRS and Hink, T and Reske, KA and Cass, C and Struttmann, E and Iqbal, ZH and Seiler, S and Kwon, JH and Burnham, CA and Dantas, G and Dubberke, ER}, title = {Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33441409}, issn = {2379-5042}, abstract = {Clostridioides difficile infection (CDI) is most commonly diagnosed using nucleic acid amplification tests (NAAT); the low positive predictive value of these assays results in patients colonized with C. difficile unnecessarily receiving CDI treatment antibiotics. The risks and benefits of antibiotic treatment in individuals with such cases are unknown. Fecal samples of NAAT-positive, toxin enzyme immunoassay (EIA)-negative patients were collected before, during, and after randomization to vancomycin (n = 8) or placebo (n = 7). C. difficile and antibiotic-resistant organisms (AROs) were selectively cultured from fecal and environmental samples. Shotgun metagenomics and comparative isolate genomics were used to understand the impact of oral vancomycin on the microbiome and environmental contamination. Overall, 80% of placebo patients and 71% of vancomycin patients were colonized with C. difficile posttreatment. One person randomized to placebo subsequently received treatment for CDI. In the vancomycin-treated group, beta-diversity (P = 0.0059) and macrolide-lincosamide-streptogramin (MLS) resistance genes (P = 0.037) increased after treatment; C. difficile and vancomycin-resistant enterococci (VRE) environmental contamination was found in 53% of patients and 26% of patients, respectively. We found that vancomycin alters the gut microbiota, does not permanently clear C. difficile, and is associated with VRE colonization/environmental contamination. (This study has been registered at ClinicalTrials.gov under registration no. NCT03388268.)IMPORTANCE A gold standard diagnostic for Clostridioides difficile infection (CDI) does not exist. An area of controversy is how to manage patients whose stool tests positive by nucleic acid amplification tests but negative by toxin enzyme immunoassay. Existing data suggest most of these patients do not have CDI, but most are treated with oral vancomycin. Potential benefits to treatment include a decreased risk for adverse outcomes if the patient does have CDI and the potential to decrease C. difficile shedding/transmission. However, oral vancomycin perturbs the intestinal microbiota and promotes antibiotic-resistant organism colonization/transmission. We conducted a double-blinded randomized controlled trial to assess the risk-benefit of oral vancomycin treatment in this population. Oral vancomycin did not result in long-term clearance of C. difficile, perturbed the microbiota, and was associated with colonization/shedding of vancomycin-resistant enterococci. This work underscores the need to better understand this population of patients in the context of C. difficile/ARO-related outcomes and transmission.}, } @article {pmid33441186, year = {2021}, author = {Yoshimatsu, Y and Mikami, Y and Kanai, T}, title = {Bacteriotherapy for inflammatory bowel disease.}, journal = {Inflammation and regeneration}, volume = {41}, number = {1}, pages = {3}, pmid = {33441186}, issn = {1880-9693}, support = {16gm1010003h0001//Japan Agency for Medical Research and Development/ ; 20gm1210001h0002//Japan Agency for Medical Research and Development/ ; NA//the Takeda Science Foundation/ ; NA//the Kanae Foundation for The Promotion of Medical Science/ ; 20H03666//Japan Society for the Promotion of Science/ ; 15H02534//Japan Society for the Promotion of Science/ ; 20H00536//Japan Society for the Promotion of Science/ ; NA//Mishima Kaiun Memorial Foundation/ ; NA//School of Medicine, Keio University/ ; }, abstract = {The number of patients with inflammatory bowel disease is rapidly increasing in developed countries. The main cause of this increase is thought not to be genetic, but secondary to rapidly modernized environmental change. Changes in the environment have been detrimental to enteric probiotics useful for fermentation, inducing an increase in pathobionts that survive by means other than fermentation. This dysregulated microbiota composition, the so-called dysbiosis, is believed to have increased the incidence of inflammatory bowel disease. Bacteriotherapy, a treatment that prophylactically and therapeutically corrects the composition of disturbed intestinal microbiota, is a promising recent development. In fact, fecal microbiome transplantation for recurrent Clostridioides difficile infection in 2013 was a significant contribution for bacteriotherapy. In this paper, we comprehensively review bacteriotherapy in an easy-to-understand format.}, } @article {pmid33441125, year = {2021}, author = {Rafeeq, M and Murad, HAS and Abdallah, HM and El-Halawany, AM}, title = {Protective effect of 6-paradol in acetic acid-induced ulcerative colitis in rats.}, journal = {BMC complementary medicine and therapies}, volume = {21}, number = {1}, pages = {28}, pmid = {33441125}, issn = {2662-7671}, support = {G-128-828-1438//Deanship of Scientific Research, King Abdulaziz University (SA)/ ; }, abstract = {BACKGROUND: Ulcerative colitis is a gut inflammatory disorder due to altered immune response to gut microbiome, with interplay of environmental and genetic factors. TNF-α activates inflammatory response through a cascade of immune responses, augmenting pro-inflammatory mediators and proteases, activating chemotaxis, and infiltration of inflammatory cells, leading to ulceration and haemorrhage through cytotoxic reactive oxygen species. 6-Paradol, a dietary component in several plants belonging to the Zingiberaceae family, has shown anti-inflammatory and antioxidant activities. Current study evaluates the effect of 6-paradol in amelioration of ulcerative colitis in rats for the first time.

METHODS: 6-Paradol (95% purity) was obtained from seeds of Aframomum melegueta. Rats were divided randomly into six groups (n = 8). Group one was administered normal saline; group two was treated with the vehicle only; group three, sulfasalazine 500 mg/kg; and groups four, five, and six, were given 6-paradol (50, 100, 200, respectively) mg/kg orally through gastric gavage for 7 days. Colitis was induced on 4th day by intrarectal administration of 2 ml acetic acid (3%), approximately 3 cm from anal verge. On 8th day, rats were sacrificed, and distal one-third of the colon extending proximally up to 4 cm from anal orifice was taken for biochemical and gross examination. Two centimetres of injured mucosal portion was taken for histopathological investigations. SPSS (ver.26) was used for statistical analysis.

RESULTS: Colonic and serum glutathione (GSH) levels decreased, while colonic and serum malondialdehyde (MDA), colonic myeloperoxidase (MPO) activity, serum interleukin-6 (IL-6), serum tumour necrosis factor-α (TNF-α) levels, and colon weight to length ratio were increased significantly in the colitis untreated group compared to normal control. Treatment with 6-paradol considerably improved all these parameters, especially at a dose of 200 mg/kg (p < 0.001), revealing non-significant differences with sulfasalazine 500 mg/kg and normal control (p = 0.998). Sulfasalazine and 6-paradol in a dose dependent manner also markedly reversed mucosal oedema, atrophy and inflammation, cryptic damage, haemorrhage, and ulceration. There were non-significant differences between low and medium doses and between medium and high doses of 6-paradol for IL-6 and serum MDA levels.

CONCLUSION: 6-Paradol demonstrated protection against acetic acid-induced ulcerative colitis, probably by anti-inflammatory and antioxidant actions.}, } @article {pmid33440387, year = {2021}, author = {Maghfour, J and Olson, J and Conic, RRZ and Mesinkovska, NA}, title = {The Association between Alopecia and Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis.}, journal = {Dermatology (Basel, Switzerland)}, volume = {}, number = {}, pages = {1-14}, doi = {10.1159/000512747}, pmid = {33440387}, issn = {1421-9832}, abstract = {IMPORTANCE: The link between autoimmune gut disorders and different types of hair loss conditions has been recently investigated with an increased interest. With acknowledgement of the connection between immune dysregulation and the gut microbiome, this pathway is now becoming recognized as playing an important role in hair growth. The inflammatory cascade that results from the disruption of gut integrity such as seen in inflammatory bowel diseases (IBD) has been associated with certain types of alopecia.

OBJECTIVE: The aim of this work was to evaluate the association between alopecia and IBD.

EVIDENCE REVIEW: A primary literature search was conducted using the PubMed, Embase, and Web of Science databases to identify articles on co-occurring alopecia and IBD from 1967 to 2020. A total of 79 studies were included in the review. A one-way proportional meta-analysis was performed on 19 of the studies to generate the pooled prevalence of alopecia and IBD.

FINDING: The pooled prevalence of non-scarring alopecia among IBD patients was 1.12% (k = 7, I2 = 98.6%, 95% CI 3.1-39.9); the prevalence of IBD among scarring and non-scarring alopecia was 1.99% (k = 12; I2 = 99%, 95% CI 6.2-34). The prevalence of non-scarring alopecia areata (AA) among IBD was compared to the prevalence of AA in the general population (0.63 vs. 0.1%; p < 0.0001). Similarly, the prevalence of IBD among the scarring and non-scarring alopecia groups was compared to the prevalence of IBD in the general population (1.99 vs. 0.396%; p = 0.0004).

CONCLUSION: IBD and alopecia, particularly AA, appear to be strongly associated. Dermatology patients with alopecia may benefit from screening for IBD.}, } @article {pmid33440172, year = {2021}, author = {Nayak, RR and Alexander, M and Deshpande, I and Stapleton-Gray, K and Rimal, B and Patterson, AD and Ubeda, C and Scher, JU and Turnbaugh, PJ}, title = {Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2020.12.008}, pmid = {33440172}, issn = {1934-6069}, abstract = {Immunomodulatory drugs can inhibit bacterial growth, yet their mechanism of action, spectrum, and clinical relevance remain unknown. Methotrexate (MTX), a first-line rheumatoid arthritis (RA) treatment, inhibits mammalian dihydrofolate reductase (DHFR), but whether it directly impacts gut bacteria is unclear. We show that MTX broadly alters the human gut microbiota. Drug sensitivity varied across strains, but the mechanism of action against DHFR appears conserved between mammalian and bacterial cells. RA patient microbiotas were sensitive to MTX, and changes in gut bacterial taxa and gene family abundance were distinct between responders and non-responders. Transplantation of post-treatment samples into germ-free mice given an inflammatory trigger led to reduced immune activation relative to pre-treatment controls, enabling identification of MTX-modulated bacterial taxa associated with intestinal and splenic immune cells. Thus, conservation in cellular pathways across domains of life can result in broad off-target drug effects on the human gut microbiota with consequences for immune function.}, } @article {pmid33440171, year = {2021}, author = {Tanes, C and Bittinger, K and Gao, Y and Friedman, ES and Nessel, L and Paladhi, UR and Chau, L and Panfen, E and Fischbach, MA and Braun, J and Xavier, RJ and Clish, CB and Li, H and Bushman, FD and Lewis, JD and Wu, GD}, title = {Role of dietary fiber in the recovery of the human gut microbiome and its metabolome.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2020.12.012}, pmid = {33440171}, issn = {1934-6069}, abstract = {Gut microbiota metabolites may be important for host health, yet few studies investigate the correlation between human gut microbiome and production of fecal metabolites and their impact on the plasma metabolome. Since gut microbiota metabolites are influenced by diet, we performed a longitudinal analysis of the impact of three divergent diets, vegan, omnivore, and a synthetic enteral nutrition (EEN) diet lacking fiber, on the human gut microbiome and its metabolome, including after a microbiota depletion intervention. Omnivore and vegan, but not EEN, diets altered fecal amino acid levels by supporting the growth of Firmicutes capable of amino acid metabolism. This correlated with relative abundance of a sizable number of fecal amino acid metabolites, some not previously associated with the gut microbiota. The effect on the plasma metabolome, in contrast, were modest. The impact of diet, particularly fiber, on the human microbiome influences broad classes of metabolites that may modify health.}, } @article {pmid33439976, year = {2021}, author = {Fabusoro, OK and Mejia, LA}, title = {Nutrition in HIV-Infected Infants and Children: Current Knowledge, Existing Challenges, and New Dietary Management Opportunities.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/advances/nmaa163}, pmid = {33439976}, issn = {2156-5376}, abstract = {HIV infection and undernutrition remain significant public health concerns for infants and children. In infants and children under these conditions, undernutrition is one of the leading causes of death. Proper management of nutrition and related nutrition complications in these groups with increased nutrition needs are prominent challenges, particularly in HIV-prevalent poor-resource environments. Several studies support the complexity of the relation between HIV infection, nutrition, and the immune system. These elements interact and create a vicious circle of poor health outcomes. Recent studies on the use of probiotics as a novel approach to manage microbiome imbalance and gut-mucosal impairment in HIV infection are gaining attention. This new strategy could help to manage dysbiosis and gut-mucosal impairment by reducing immune activation, thereby potentially forestalling unwanted health outcomes in children with HIV. However, existing trials on HIV-infected children are still insufficient. There are also conflicting reports on the dosage and effectiveness of single or multiple micronutrient supplementation in the survival of HIV-infected children with severe acute malnutrition. The WHO has published guidelines that include time of initiation of antiretroviral therapy for HIV-pregnant mothers and their HIV-exposed or HIV-infected children, micronutrient supplementation, dietary formulations, prevention, and management of HIV therapy. However, such guidelines need to be reviewed owing to recent advances in the field of nutrition. There is a need for new intervention studies, practical strategies, and evidence-based guidelines to reduce the disease burden, improve adherence to treatment regimen, and enhance the nutrition, health, and well-being of HIV-infected infants and children. This review provides up-to-date scientific information on current knowledge and existing challenges for nutrition therapy in HIV-infected infants and children. Moreover, it presents new research findings that could be incorporated into current guidelines.}, } @article {pmid33439913, year = {2021}, author = {Lee, YT and Mohd Ismail, NI and Wei, LK}, title = {Microbiome and ischemic stroke: A systematic review.}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0245038}, doi = {10.1371/journal.pone.0245038}, pmid = {33439913}, issn = {1932-6203}, abstract = {BACKGROUND: Ischemic stroke is one of the non-communicable diseases that contribute to the significant number of deaths worldwide. However, the relationship between microbiome and ischemic stroke remained unknown. Hence, the objective of this study was to perform systematic review on the relationship between human microbiome and ischemic stroke.

METHODS: A systematic review on ischemic stroke was carried out for all articles obtained from databases until 22nd October 2020. Main findings were extracted from all the eligible studies.

RESULTS: Eighteen eligible studies were included in the systematic review. These studies suggested that aging, inflammation, and different microbial compositions could contribute to ischemic stroke. Phyla Firmicutes and Bacteroidetes also appeared to manipulate post-stroke outcome. The important role of microbiota-derived short-chain fatty acids and trimethylamine N-oxide in ischemic stroke were also highlighted.

CONCLUSIONS: This is the first systematic review that investigates the relationship between microbiome and ischemic stroke. Aging and inflammation contribute to differential microbial compositions and predispose individuals to ischemic stroke.}, } @article {pmid33439113, year = {2021}, author = {Hilgarth, M and Redwitz, J and Ehrmann, MA and Vogel, RF and Jakob, F}, title = {Bombella favorum sp. nov. and Bombella mellum sp. nov., two novel species isolated from the honeycombs of Apis mellifera.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1099/ijsem.0.004633}, pmid = {33439113}, issn = {1466-5034}, abstract = {As part of a study investigating the microbiome of bee hives and honey, two novel strains (TMW 2.1880T and TMW 2.1889T) of acetic acid bacteria were isolated and subsequently taxonomically characterized by a polyphasic approach, which revealed that they cannot be assigned to known species. The isolates are Gram-stain-negative, aerobic, pellicle-forming, catalase-positive and oxidase-negative. Cells of TMW 2.1880T are non-motile, thin/short rods, and cells of TMW 2.1889T are motile and occur as rods and long filaments. Morphological, physiological and phylogenetic analyses revealed a distinct lineage within the genus Bombella. Strain TMW 2.1880T is most closely related to the type strain of Bombella intestini with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 94.16 and 56.3 %, respectively. The genome of TMW 2.1880T has a size of 1.98 Mb and a G+C content of 55.3 mol%. Strain TMW 2.1889T is most closely related to the type strain of Bombella apis with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 85.12 and 29.5 %, respectively. The genome of TMW 2.1889T has a size of 2.07 Mb and a G+C content of 60.4 mol%. Ubiquinone analysis revealed that both strains contained Q-10 as the main respiratory quinone. Major fatty acids for both strains were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8, respectively, and additionally C14 : 0 2-OH only for TMW 2.1880T and C14 : 0 only for TMW 2.1889T. Based on polyphasic evidence, the two isolates from honeycombs of Apis mellifera represent two novel species of the genus Bombella, for which the names Bombella favorum sp. nov and Bombella mellum sp. nov. are proposed. The designated respective type strains are TMW 2.1880T (=LMG 31882T=CECT 30114T) and TMW 2.1889T (=LMG 31883T=CECT 30113T).}, } @article {pmid33439104, year = {2021}, author = {Manandhar, I and Alimadadi, A and Aryal, S and Munroe, PB and Joe, B and Cheng, X}, title = {Gut microbiome-based supervised machine learning for clinical diagnosis of inflammatory bowel diseases.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpgi.00360.2020}, pmid = {33439104}, issn = {1522-1547}, support = {Dean's Postdoctoral to Faculty Fellowship//University of Toledo College of Medicine and Life Sciences/ ; P30 Core Center Pilot Grant//NIDA Center of Excellence in Omics, Systems Genetics, and the Addictome/ ; HL143082//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; }, abstract = {Despite the availability of various diagnostic tests for inflammatory bowel diseases (IBD), misdiagnosis of IBD occurs frequently, and thus there is a clinical need to further improve the diagnosis of IBD. As gut dysbiosis is reported in IBD patients, we hypothesized that supervised machine learning (ML) could be used to analyze gut microbiome data for predictive diagnostics of IBD. To test our hypothesis, fecal 16S metagenomic data of 729 IBD and 700 non-IBD subjects from the American Gut Project were analyzed using five different ML algorithms. Fifty differential bacterial taxa were identified (LEfSe: LDA > 3) between the IBD and non-IBD groups, and ML classifications trained with these taxonomic features using random forest (RF) achieved a testing AUC of ~0.80. Next, we tested if operational taxonomic units (OTUs), instead of bacterial taxa, could be used as ML features for diagnostic classification of IBD. Top 500 high-variance OTUs were used for ML training and an improved testing AUC of ~0.82 (RF) was achieved. Lastly, we tested if supervised ML could be used for differentiating Crohn's disease (CD) and ulcerative colitis (UC). Using 331 CD and 141 UC samples, 117 differential bacterial taxa (LEfSe: LDA > 3) were identified, and the RF model trained with differential taxonomic features or high-variance OTU features achieved a testing AUC > 0.90. In summary, our study demonstrates the promising potential of artificial intelligence via supervised ML modeling for predictive diagnostics of IBD using gut microbiome data.}, } @article {pmid33439103, year = {2021}, author = {Cuna, AC and Morowitz, MJ and Ahmed, I and Umar, S and Sampath, V}, title = {Dynamics of the Preterm Gut Microbiome in Health and Disease.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpgi.00399.2020}, pmid = {33439103}, issn = {1522-1547}, support = {R01DK117296//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; K08DK125735//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; }, abstract = {Advances in metagenomics have allowed a detailed study of the gut microbiome, and its role in human health and disease. Infants born prematurely possess a fragile gut microbial ecosystem that is vulnerable to perturbation. Alterations in the developing gut microbiome in preterm infants are linked to life-threatening diseases such as necrotizing enterocolitis (NEC) and late onset sepsis; and may impact future risk of asthma, atopy, obesity, and psychosocial disease. In this mini review, we summarize recent literature on the origins and patterns of development of the preterm gut microbiome in the perinatal period. The host-microbiome-environmental factors that portend development of dysbiotic intestinal microbial patterns associated with NEC and sepsis are reviewed. Strategies to manipulate the microbiome and mitigate dysbiosis, including the use of probiotics and prebiotics will also be discussed. Finally, we explore the challenges and future directions of gut microbiome research in preterm infants.}, } @article {pmid33438970, year = {2021}, author = {Kollef, MH and Torres, A and Shorr, AF and Martin-Loeches, I and Micek, ST}, title = {Nosocomial Infection.}, journal = {Critical care medicine}, volume = {49}, number = {2}, pages = {169-187}, doi = {10.1097/CCM.0000000000004783}, pmid = {33438970}, issn = {1530-0293}, abstract = {OBJECTIVE: The first 70 years of critical care can be considered a period of "industrial revolution-like" advancement in terms of progressing the understanding and care of critical illness. Unfortunately, like the industrial revolution's impact on the environment, advancing ICU care of increasingly elderly, immunosuppressed, and debilitated individuals has resulted in a greater overall burden and complexity of nosocomial infections within modern ICUs. Given the rapid evolution of nosocomial infections, the authors provide an updated review.

We searched PubMed and OVID for peer-reviewed literature dealing with nosocomial infections in the critically ill, as well as the websites of government agencies involved with the reporting and prevention of nosocomial infections. Search terms included nosocomial infection, antibiotic resistance, microbiome, antibiotics, and intensive care.

Nosocomial infections in the ICU setting are evolving in multiple domains including etiologic pathogens plus novel or emerging pathogens, prevalence, host risk factors, antimicrobial resistance, interactions of the host microbiome with nosocomial infection occurrence, and understanding of pathogenesis and prevention strategies. Increasing virulence and antimicrobial resistance of nosocomial infections mandate increasing efforts toward their prevention.

CONCLUSIONS: Nosocomial infections are an important determinant of outcome for patients in the ICU setting. Systematic research aimed at improving the prevention and treatment of nosocomial infections is still needed.}, } @article {pmid33438892, year = {2021}, author = {Peters, BA and Xue, X and Wang, Z and Usyk, M and Santoro, N and Sharma, A and Anastos, K and Tien, PC and Golub, ET and Weber, KM and Gustafson, D and Kaplan, RC and Burk, R and Qi, Q}, title = {Menopausal status and observed differences in the gut microbiome in women with and without HIV infection.}, journal = {Menopause (New York, N.Y.)}, volume = {Publish Ahead of Print}, number = {}, pages = {}, doi = {10.1097/GME.0000000000001730}, pmid = {33438892}, issn = {1530-0374}, abstract = {OBJECTIVE: Gut microbiota respond to host physiological phenomena, yet little is known regarding shifts in the gut microbiome due to menopausal hormonal and metabolic changes in women. HIV infection impacts menopause and may also cause gut dysbiosis. We therefore sought to determine the association between menopausal status and gut microbiome composition in women with and without HIV.

METHODS: Gut microbiome composition was assessed in stool from 432 women (99 premenopausal HIV+, 71 premenopausal HIV-, 182 postmenopausal HIV+, 80 postmenopausal HIV-) via 16S rRNA gene sequencing. We examined cross-sectional associations of menopause with gut microbiota overall diversity and composition, and taxon and inferred metagenomic pathway abundance. Models were stratified by HIV serostatus and adjusted for age, HIV-related variables, and other potential confounders.

RESULTS: Menopause, ie post- versus premenopausal status, was associated with overall microbial composition only in women with HIV (permutational MANOVA of Jensen Shannon Divergence: P = 0.01). In women with HIV, menopause was associated with enrichment of gram-negative order Enterobacteriales, depletion of highly abundant taxa within Prevotella copri, and alterations in other low-abundance taxa. Additionally, menopause in women with HIV was associated with enrichment of metagenomic pathways related to Enterobacteriales, including degradation of amino acids and phenolic compounds, biosynthesis of enterobactin, and energy metabolism pathways. Menopause-related differences in some low-abundance taxa were also observed in women without HIV.

CONCLUSIONS: A changing gut microbiome may be an overlooked phenomenon of reproductive aging in women with HIV. Longitudinal assessments across all reproductive stages are necessary to confirm these findings and identify health implications.}, } @article {pmid33438345, year = {2021}, author = {Le Poole, IC}, title = {Myron Gordon Award paper: Microbes, T-cell diversity and pigmentation.}, journal = {Pigment cell & melanoma research}, volume = {}, number = {}, pages = {}, doi = {10.1111/pcmr.12957}, pmid = {33438345}, issn = {1755-148X}, abstract = {Melanocytes are static, minimally proliferative cells. This leaves them vulnerable in vitiligo. Yet upon malignant transformation, they form vicious tumors. This profound switch in physiology is accompanied by genetic change, and is driven by environmental factors. If UV exposure in younger years supports malignant transformation and melanoma formation, it can likewise impart mutations on melanocytes that reduce their viability, to initiate vitiligo. A wide variety of microbes can influence these diametrically opposed outcomes before either disease takes hold. These microbes are vehicles of change that we are only beginning to study. Once a genetic modification occurs, there is a wide variety of immune cells ready to respond. Though it does not act alone, the T cell is among the most decisive responders in this process. The same biochemical process that offered the skin protection by producing melanin can become an Achilles heel for the cell when the T cells target melanosomal enzymes or, on occasion, neoantigens. T cells are precise, determined and consequential when they strike. Here we probe the relationship between the microbiome and its metabolites, epithelial integrity, and the activation of T cells that target benign and malignant melanocytes in vitiligo and melanoma.}, } @article {pmid33438331, year = {2021}, author = {Cook, KA and Domissy, A and Simon, RA and White, AA and Modena, BD}, title = {Dysbiosis in aspirin-exacerbated respiratory disease.}, journal = {International forum of allergy & rhinology}, volume = {}, number = {}, pages = {}, doi = {10.1002/alr.22762}, pmid = {33438331}, issn = {2042-6984}, support = {K23 HL144418/HL/NHLBI NIH HHS/United States ; //Scripps Clinic Medical Group/ ; K23 HL144418/HL/NHLBI NIH HHS/United States ; }, } @article {pmid33438150, year = {2021}, author = {Corniello, A and Guida, M and Stellato, L and Trifuoggi, M and Carraturo, F and Del Gaudio, E and Del Giudice, C and Forte, G and Giarra, A and Iorio, M and Marzaioli, F and Toscanesi, M}, title = {Hydrochemical, isotopic and microbiota characterization of telese mineral waters (Southern Italy).}, journal = {Environmental geochemistry and health}, volume = {}, number = {}, pages = {}, pmid = {33438150}, issn = {1573-2983}, abstract = {The study deals with the analyses of springs and wells at the base of Montepugliano Hill that represents the SE edge of the wide carbonate Matese massif (Campania, southern Italy). At the base of the hill, from west to east and for almost one kilometre, cold springs HCO3-Ca type (Grassano springs, ~ 4.5 m3/s; TDS: about 0.45 g/L) pass to hypothermal, HCO3-Ca type, sulphurous and CO2-rich springs (~ 1 m3/s with TDS > 1 g/L). Some of the latter are widely used in Telese Spa and Centro Relax Spa. Chemical and isotopic analyses carried out for this study support the hypothesis that all these waters (mineral and non-mineral) have the same catchment area, which is located in the Matese massif. As regards the sulphurous springs, they receive both meteoric waters infiltration and uprising of deeper waters rich in endogenous CO2 and H2S gases through important faults systems. Far from these faults, the chemistry of groundwater is scarcely (or not at all) affected by these deep fluid enrichment processes. This scheme is very significant; in fact, when very important groundwater resources are present, it is possible to use both mineral waters in Spa and, in areas far from the faults, those not yet mineralized. Finally, at Montepugliano Hill, in the final stage of the flow path, groundwater is also affected by change in the microbiome: this could provide a basis for comparison between various mineral waters.}, } @article {pmid33438074, year = {2021}, author = {Shen, J and Wyness, AJ and Claire, MW and Zerkle, AL}, title = {Spatial Variability of Microbial Communities and Salt Distributions Across a Latitudinal Aridity Gradient in the Atacama Desert.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33438074}, issn = {1432-184X}, support = {678812//H2020 European Research Council/ ; 60501//John Templeton Foundation/ ; 201708060070//Chinese Scholarship Council/ ; }, abstract = {Over the past 150 million years, the Chilean Atacama Desert has been transformed into one of the most inhospitable landscapes by geophysical changes, which makes it an ideal Mars analog that has been explored for decades. However, a heavy rainfall that occurred in the Atacama in 2017 provides a unique opportunity to study the response of resident extremophiles to rapid environmental change associated with excessive water and salt shock. Here we combine mineral/salt composition measurements, amendment cell culture experiments, and next-generation sequencing analyses to study the variations in salts and microbial communities along a latitudinal aridity gradient of the Atacama Desert. In addition, we examine the reshuffling of Atacama microbiomes after the rainfall event. Analysis of microbial community composition revealed that soils within the southern arid desert were consistently dominated by Actinobacteria, Chloroflexi, Proteobacteria, Firmicutes, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Acidobacteria, and Verrucomicrobia. Intriguingly, the hyperarid microbial consortia exhibited a similar pattern to the more southern desert. Salts at the shallow subsurface were dissolved and leached down to a deeper layer, challenging indigenous microorganisms with the increasing osmotic stress. Microbial viability was found to change with aridity and rainfall events. This study sheds light on the structure of xerotolerant, halotolerant, and radioresistant microbiomes from the hyperarid northern desert to the less arid southern transition region, as well as their response to changes in water availability.}, } @article {pmid33437992, year = {2021}, author = {Lim, MY and Hong, S and Kim, JH and Nam, YD}, title = {Association between Gut Microbiome and Frailty in the Older Adult Population in Korea.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {}, number = {}, pages = {}, doi = {10.1093/gerona/glaa319}, pmid = {33437992}, issn = {1758-535X}, abstract = {Frailty is a common geriatric syndrome associated with the risk of adverse health outcomes. Recently, two key pathophysiological characteristics of frailty, altered energy metabolism and dysregulated immunity, have been reported to be associated with gut microbiome dysbiosis, indicating that the gut microbiome plays a role in frailty. However, few studies have directly examined the relationship between the gut microbiome and frailty. Here, we investigated the association of frailty measures with the gut microbiome using 16S rRNA gene sequencing data obtained from the fecal samples of 176 Korean older adults. Overall frailty was scored using the Korean Frailty Index (FI). Grip strength and Geriatric Depression Scale (GDS) scores were used as physical and mental frailty measures, respectively. In contrast to age, metabolic, and inflammatory biomarkers, the frailty measures were associated with inter-individual variations in microbial composition (false discovery rate [FDR] < 0.2). Both FI and GDS scores were negatively associated with microbial diversity (FDR < 0.2). Frailty measures showed distinct associations with specific microbial taxa and metabolic functions. Particularly, the Bacteroides enterotype was found only in subjects categorized in the frail group. Moreover, we observed that the abundance of beneficial taxa, such as Prevotella copri and Coprococcus eutactus, was reduced in frailer individuals, whereas that of detrimental taxa, such as Bacteroides fragilis and Clostridium hathewayi, was increased (FDR < 0.2). Our findings suggest that the gut microbiome can be used an indicator of an increased risk of frailty or a target for improving health in frail older adults.}, } @article {pmid33437563, year = {2021}, author = {Pabbathi, NPP and Velidandi, A and Tavarna, T and Gupta, S and Raj, RS and Gandam, PK and Baadhe, RR}, title = {Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review.}, journal = {Biomass conversion and biorefinery}, volume = {}, number = {}, pages = {1-28}, pmid = {33437563}, issn = {2190-6815}, abstract = {As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.}, } @article {pmid33437414, year = {2021}, author = {Kuthyar, S and Kowalewski, MM and Roellig, DM and Mallott, EK and Zeng, Y and Gillespie, TR and Amato, KR}, title = {Effects of anthropogenic habitat disturbance and Giardia duodenalis infection on a sentinel species' gut bacteria.}, journal = {Ecology and evolution}, volume = {11}, number = {1}, pages = {45-57}, pmid = {33437414}, issn = {2045-7758}, abstract = {Habitat disturbance, a common consequence of anthropogenic land use practices, creates human-animal interfaces where humans, wildlife, and domestic species can interact. These altered habitats can influence host-microbe dynamics, leading to potential downstream effects on host physiology and health. Here, we explored the effect of ecological overlap with humans and domestic species and infection with the protozoan parasite Giardia duodenalis on the bacteria of black and gold howler monkeys (Alouatta caraya), a key sentinel species, in northeastern Argentina. Fecal samples were screened for Giardia duodenalis infection using a nested PCR reaction, and the gut bacterial community was characterized using 16S rRNA gene amplicon sequencing. Habitat type was correlated with variation in A. caraya gut bacterial community composition but did not affect gut bacterial diversity. Giardia presence did not have a universal effect on A. caraya gut bacteria across habitats, perhaps due to the high infection prevalence across all habitats. However, some bacterial taxa were found to vary with Giardia infection. While A. caraya's behavioral plasticity and dietary flexibility allow them to exploit a range of habitat conditions, habitats are generally becoming more anthropogenically disturbed and, thus, less hospitable. Alterations in gut bacterial community dynamics are one possible indicator of negative health outcomes for A. caraya in these environments, since changes in host-microbe relationships due to stressors from habitat disturbance may lead to negative repercussions for host health. These dynamics are likely relevant for understanding organism responses to environmental change in other mammals.}, } @article {pmid33437187, year = {2020}, author = {Siwicka-Gieroba, D and Czarko-Wicha, K}, title = {Lung microbiome - a modern knowledge.}, journal = {Central-European journal of immunology}, volume = {45}, number = {3}, pages = {342-345}, pmid = {33437187}, issn = {1426-3912}, abstract = {Recent studies have reported that commensal microorganisms are not just "passive occupants" but may play a crucial role in the immune system activation. It is well-known that in critically ill patients, the microbiome is modified and may be associated with the development of immunosuppression in sepsis, contributing to the development of acute renal injury, cardiovascular diseases, or more importantly, respiratory system disturbances. The conviction of lung sterility has gone down in history. The presence of characteristic gut microbiome, such as Bacteroidetes and Enterobacteriaceae, was demonstrated in lungs of critically ill patients. This bacteria's translocation, especially in ischemia-reperfusion injury, results in increased concentration of inflammation response markers and may play a pivotal role in the pathogenesis of respiratory system disturbances, including acute respiratory distress syndrome. Recent studies have shown that ischemia-reperfusion injury is often observed in intensive care units (ICUs) and predispose to microbiome disturbances that are strictly connected with immune system activation and epithelial damage. Potential effects of dysbiosis treatment are under highly activated investigation. Therefore, it is possible that microbiota-targeted therapy may constitute the future therapeutic path in ICUs.}, } @article {pmid33437021, year = {2021}, author = {de Sousa Lopes, L and Mendes, LW and Antunes, JEL and de Souza Oliveira, LM and Melo, VMM and de Araujo Pereira, AP and da Costa, AF and de Paula Oliveira, J and Martínez, CR and Figueiredo, MDVB and Araujo, ASF}, title = {Distinct bacterial community structure and composition along different cowpea producing ecoregions in Northeastern Brazil.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {831}, pmid = {33437021}, issn = {2045-2322}, abstract = {Soil microbial communities represent the largest biodiversity on Earth, holding an important role in promoting plant growth and productivity. However, the knowledge about how soil factors modulate the bacteria community structure and distribution in tropical regions remain poorly understood, mainly in different cowpea producing ecoregions belonging to Northeastern Brazil. This study addressed the bacterial community along three different ecoregions (Mata, Sertão, and Agreste) through the16S rRNA gene sequencing. The results showed that soil factors, such as Al3+, sand, Na+, cation exchange excel, and total organic C, influenced the bacterial community and could be a predictor of the distinct performance of cowpea production. Also, the bacterial community changed between different ecoregions, and some keystone groups related to plant-growth promotion, such as Bradyrhizobium, Bacillales, Rhizobiales, and Solibacillus, were correlated to cowpea yield, so revealing that the soil microbiome has a primordial role in plant productivity. Here, we provide evidence that bacterial groups related to nutrient cycling can help us to increase cowpea efficiency and we suggest that a better microbiome knowledge can contribute to improving the agricultural performance.}, } @article {pmid33436896, year = {2021}, author = {Funosas, G and Triadó-Margarit, X and Castro, F and Villafuerte, R and Delibes-Mateos, M and Rouco, C and Casamayor, EO}, title = {Individual fate and gut microbiome composition in the European wild rabbit (Oryctolagus cuniculus).}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {766}, pmid = {33436896}, issn = {2045-2322}, support = {CGL2013-43197-R//Agencia Estatal de Investigación/ ; INTERACTOMA RTI2018-101205-B-I00//Agencia Estatal de Investigación/ ; }, abstract = {Studies connecting microbiome composition and functional performance in wildlife have received little attention and understanding their connections with wildlife physical condition are sorely needed. We studied the variation in gut microbiota (hard fecal pellets) between allopatric subspecies of the European wild rabbit in wild populations and in captured individuals studied under captivity. We evaluated the influence of environmental and host-specific factors. The microbiome of wild rabbit populations reduced its heterogeneity under controlled conditions. None of the host-specific factors tested correlated with the microbiota composition. We only observed significant intra-group dispersion for the age factor. The most diverse microbiomes were rich in Ruminococcaceae potentially holding an enriched functional profile with dominance of cellulases and xylanases, and suggesting higher efficiency in the digestion of fiber-rich food. Conversely, low diversity gut microbiomes showed dominance of Enterobacteriaceae potentially rich in amylases. We preliminary noticed geographical variations in field populations with higher dominance of Ruminococcaceae in south-western than in north-eastern Spain. Spatial differences appeared not to be subspecies driven, since they were lost in captivity, but environmentally driven, although differences in social structure and behavior may also play a role that deserve further investigations. A marginally significant relationship between the Ruminococcaceae/Enterobacteriaceae ratio and potential life expectancy was observed in captive rabbits. We hypothesize that the gut microbiome may determine the efficiency of feeding resource exploitation, and can also be a potential proxy for life expectancy, with potential applications for the management of declining wild herbivorous populations. Such hypotheses remain to be explored in the future.}, } @article {pmid33436882, year = {2021}, author = {Moustafa, MAM and Chel, HM and Thu, MJ and Bawm, S and Htun, LL and Win, MM and Oo, ZM and Ohsawa, N and Lahdenperä, M and Mohamed, WMA and Ito, K and Nonaka, N and Nakao, R and Katakura, K}, title = {Anthropogenic interferences lead to gut microbiome dysbiosis in Asian elephants and may alter adaptation processes to surrounding environments.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {741}, pmid = {33436882}, issn = {2045-2322}, support = {19F19097//Japan Society for the Promotion of Science/ ; 15H05633//Japan Society for the Promotion of Science/ ; 16H06429//Japan Society for the Promotion of Science/ ; 16K21723//Japan Society for the Promotion of Science/ ; 16H06431//Japan Society for the Promotion of Science/ ; 19H03118//Japan Society for the Promotion of Science/ ; 19F19097//Japan Society for the Promotion of Science/ ; 17H04638//Japan Society for the Promotion of Science/ ; }, abstract = {Human activities interfere with wild animals and lead to the loss of many animal populations. Therefore, efforts have been made to understand how wildlife can rebound from anthropogenic disturbances. An essential mechanism to adapt to environmental and social changes is the fluctuations in the host gut microbiome. Here we give a comprehensive description of anthropogenically induced microbiome alterations in Asian elephants (n = 30). We detected gut microbial changes due to overseas translocation, captivity and deworming. We found that microbes belonging to Planococcaceae had the highest contribution in the microbiome alterations after translocation, while Clostridiaceae, Spirochaetaceae and Bacteroidia were the most affected after captivity. However, deworming significantly changed the abundance of Flavobacteriaceae, Sphingobacteriaceae, Xanthomonadaceae, Weeksellaceae and Burkholderiaceae. These findings may provide fundamental ideas to help guide the preservation tactics and probiotic replacement therapies of a dysbiosed gut microbiome in Asian elephants. More generally, these results show the severity of anthropogenic activities at the level of gut microbiome, altering the adaptation processes to new environments and the subsequent capability to maintain normal physiological processes in animals.}, } @article {pmid33436774, year = {2021}, author = {Likhitrattanapisal, S and Siriarchawatana, P and Seesang, M and Chunhametha, S and Boonsin, W and Phithakrotchanakoon, C and Kitikhun, S and Eurwilaichitr, L and Ingsriswang, S}, title = {Uncovering multi-faceted taxonomic and functional diversity of soil bacteriomes in tropical Southeast Asian countries.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {582}, pmid = {33436774}, issn = {2045-2322}, abstract = {Environmental microbiomes encompass massive biodiversity and genetic information with a wide-ranging potential for industrial and agricultural applications. Knowledge of the relationship between microbiomes and environmental factors is crucial for translating that information into practical uses. In this study, the integrated data of Southeast Asian soil bacteriomes were used as models to assess the variation in taxonomic and functional diversity of bacterial communities. Our results demonstrated that there were differences in soil bacteriomes across different geographic locality with different soil characteristics: soil class and pH level. Such differences were observed in taxonomic diversity, interspecific association patterns, and functional diversity of soil bacteriomes. The bacterial-mediated biogeochemical cycles of nitrogen, sulfur, carbon, and phosphorus illustrated the functional relationship of soil bacteriome and soil characteristics, as well as an influence from bacterial interspecific interaction. The insights from this study reveal the importance of microbiome data integration for future microbiome research.}, } @article {pmid33436707, year = {2021}, author = {Stinson, LF and Ma, J and Rea, A and Dymock, M and Geddes, DT}, title = {Centrifugation does not remove bacteria from the fat fraction of human milk.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {572}, pmid = {33436707}, issn = {2045-2322}, abstract = {Analysis of the human milk microbiome is complicated by the presence of a variable quantity of fat. The fat fraction of human milk is typically discarded prior to analysis. It is assumed that all cells are pelleted out of human milk by high speed centrifugation; however, studies of bovine milk have reported that bacteria may remain trapped within the fat fraction. Here, the bacterial DNA profiles of the fat fraction and cell pellet of human milk (n = 10) were analysed. Human and bacterial DNA was consistently recovered from the fat fraction of human milk (average of 12.4% and 32.7%, respectively). Staphylococcus epidermidis was significantly more abundant in the cell pellet compared to the fat fraction (P = 0.038), and three low-abundance species (< 5% relative abundance) were recovered from one fraction only. However, inclusion of fat reduced the efficiency of DNA extraction by 39%. Culture-based methods were used to quantify the distribution of an exogenously added strain of Staphylococcus aureus in human milk fractions. S. aureus was consistently recovered from the fat fraction (average 28.9%). Bacterial DNA profiles generated from skim milk or cell pellets are not representative of the entire human milk microbiome. These data have critical implications for the design of future work in this field.}, } @article {pmid33436518, year = {2021}, author = {Panpetch, W and Kullapanich, C and Dang, CP and Visitchanakun, P and Saisorn, W and Wongphoom, J and Wannigama, DL and Thim-Uam, A and Patarakul, K and Somboonna, N and Tumwasorn, S and Leelahavanichkul, A}, title = {Candida Administration Worsens Uremia-Induced Gut Leakage in Bilateral Nephrectomy Mice, an Impact of Gut Fungi and Organismal Molecules in Uremia.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33436518}, issn = {2379-5077}, abstract = {The impact of gut fungi and (1→3)-β-d-glucan (BG), a major fungal cell wall component, on uremia was explored by Candida albicans oral administration in bilateral nephrectomy (BiNx) mice because of the prominence of C. albicans in the human intestine but not in mice. As such, BiNx with Candida administration (BiNx-Candida) enhanced intestinal injury (colon cytokines and apoptosis), gut leakage (fluorescein isothiocyanate [FITC]-dextran assay, endotoxemia, serum BG, and bacteremia), systemic inflammation, and liver injury at 48 h postsurgery compared with non-Candida BiNx mice. Interestingly, uremia-induced enterocyte apoptosis was severe enough for gut translocation of viable bacteria, as indicated by culture positivity for bacteria in blood, mesenteric lymph nodes (MLNs), and other organs, which was more severe in BiNx-Candida than in non-Candida BiNx mice. Candida induced alterations in the gut microbiota of BiNx mice as indicated by (i) the higher fungal burdens in the feces of BiNx-Candida mice than in sham-Candida mice by culture methods and (ii) increased Bacteroides with decreased Firmicutes and reduced bacterial diversity in the feces of BiNx-Candida mice compared with non-Candida BiNx mice by fecal microbiome analysis. In addition, lipopolysaccharide plus BG (LPS+BG), compared with each molecule alone, induced high supernatant cytokine levels, which were enhanced by uremic mouse serum in both hepatocytes (HepG2 cells) and macrophages (RAW264.7 cells). Moreover, LPS+BG, but not each molecule alone, reduced the glycolysis capacity and mitochondrial function in HepG2 cells as determined by extracellular flux analysis. Additionally, a probiotic, Lactobacillus rhamnosus L34 (L34), attenuated disease severity only in BiNx-Candida mice but not in non-Candida BiNx mice, as indicated by liver injury and serum cytokines through the attenuation of gut leakage, the fecal abundance of fungi, and fecal bacterial diversity but not fecal Gram-negative bacteria. In conclusion, Candida enhanced BiNx severity through the worsening of gut leakage and microbiota alterations that resulted in bacteremia, endotoxemia, and glucanemia.IMPORTANCE The impact of fungi in the intestine on acute uremia was demonstrated by the oral administration of Candida albicans in mice with the removal of both kidneys. Because fungi in the mouse intestine are less abundant than in humans, a Candida-administered mouse model has more resemblance to patient conditions. Accordingly, acute uremia, without Candida, induced intestinal mucosal injury, which resulted in the translocation of endotoxin, a major molecule of gut bacteria, from the intestine into blood circulation. In acute uremia with Candida, intestinal injury was more severe due to fungi and the alteration in intestinal bacteria (increased Bacteroides with decreased Firmicutes), leading to the gut translocation of both endotoxin from gut bacteria and (1→3)-β-d-glucan from Candida, which synergistically enhanced systemic inflammation in acute uremia. Both pathogen-associated molecules were delivered to the liver and induced hepatocyte inflammatory responses with a reduced energy production capacity, resulting in acute uremia-induced liver injury. In addition, Lactobacillus rhamnosus attenuated intestinal injury through reduced gut Candida and improved intestinal bacterial conditions.}, } @article {pmid33436515, year = {2021}, author = {Tláskal, V and Brabcová, V and Větrovský, T and Jomura, M and López-Mondéjar, R and Oliveira Monteiro, LM and Saraiva, JP and Human, ZR and Cajthaml, T and Nunes da Rocha, U and Baldrian, P}, title = {Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33436515}, issn = {2379-5077}, abstract = {Forests accumulate and store large amounts of carbon (C), and a substantial fraction of this stock is contained in deadwood. This transient pool is subject to decomposition by deadwood-associated organisms, and in this process it contributes to CO2 emissions. Although fungi and bacteria are known to colonize deadwood, little is known about the microbial processes that mediate carbon and nitrogen (N) cycling in deadwood. In this study, using a combination of metagenomics, metatranscriptomics, and nutrient flux measurements, we demonstrate that the decomposition of deadwood reflects the complementary roles played by fungi and bacteria. Fungi were found to dominate the decomposition of deadwood and particularly its recalcitrant fractions, while several bacterial taxa participate in N accumulation in deadwood through N fixation, being dependent on fungal activity with respect to deadwood colonization and C supply. Conversely, bacterial N fixation helps to decrease the constraints of deadwood decomposition for fungi. Both the CO2 efflux and N accumulation that are a result of a joint action of deadwood bacteria and fungi may be significant for nutrient cycling at ecosystem levels. Especially in boreal forests with low N stocks, deadwood retention may help to improve the nutritional status and fertility of soils.IMPORTANCE Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers. The present paradigm is that fungi accomplish degradation while commensalist bacteria exploit the products of fungal extracellular enzymatic cleavage, but this assumption was never backed by the analysis of microbial roles in deadwood. This study clearly identifies the roles of fungi and bacteria in the microbiome and demonstrates the importance of bacteria and their N fixation for the nutrient balance in deadwood as well as fluxes at the ecosystem level. Deadwood decomposition is shown as a process where fungi and bacteria play defined, complementary roles.}, } @article {pmid33436514, year = {2021}, author = {Fagorzi, C and Bacci, G and Huang, R and Cangioli, L and Checcucci, A and Fini, M and Perrin, E and Natali, C and diCenzo, GC and Mengoni, A}, title = {Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33436514}, issn = {2379-5077}, abstract = {Rhizobia are ecologically important, facultative plant-symbiotic microbes. In nature, there is a large variability in the association of rhizobial strains and host plants of the same species. Here, we evaluated whether plant and rhizobial genotypes influence the initial transcriptional response of rhizobium following perception of a host plant. RNA sequencing of the model rhizobium Sinorhizobium meliloti exposed to root exudates or luteolin (an inducer of nod genes, involved in the early steps of symbiotic interaction) was performed on a combination of three S. meliloti strains and three alfalfa varieties as host plants. The response to root exudates involved hundreds of changes in the rhizobium transcriptome. Of the differentially expressed genes, 35% were influenced by the strain genotype, 16% were influenced by the plant genotype, and 29% were influenced by strain-by-host plant genotype interactions. We also examined the response of a hybrid S. meliloti strain in which the symbiotic megaplasmid (∼20% of the genome) was mobilized between two of the above-mentioned strains. Dozens of genes were upregulated in the hybrid strain, indicative of nonadditive variation in the transcriptome. In conclusion, this study demonstrated that transcriptional responses of rhizobia upon perception of legumes are influenced by the genotypes of both symbiotic partners and their interaction, suggesting a wide spectrum of genetic determinants involved in the phenotypic variation of plant-rhizobium symbiosis.IMPORTANCE A sustainable way for meeting the need of an increased global food demand should be based on a holobiont perspective, viewing crop plants as intimately associated with their microbiome, which helps improve plant nutrition, tolerance to pests, and adverse climate conditions. However, the genetic repertoire needed for efficient association with plants by the microbial symbionts is still poorly understood. The rhizobia are an exemplary model of facultative plant symbiotic microbes. Here, we evaluated whether genotype-by-genotype interactions could be identified in the initial transcriptional response of rhizobium perception of a host plant. We performed an RNA sequencing study to analyze the transcriptomes of different rhizobial strains elicited by root exudates of three alfalfa varieties as a proxy of an early step of the symbiotic interaction. The results indicated strain- and plant variety-dependent variability in the observed transcriptional changes, providing fundamentally novel insights into the genetic basis of rhizobium-plant interactions. Our results provide genetic insights and perspective to aid in the exploitation of natural rhizobium variation for improvement of legume growth in agricultural ecosystems.}, } @article {pmid33436510, year = {2021}, author = {He, JW and Zhou, XJ and Li, YF and Wang, YN and Liu, LJ and Shi, SF and Xin, XH and Li, RS and Falchi, M and Lv, JC and Zhang, H}, title = {Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33436510}, issn = {2379-5077}, abstract = {The gut microbiota has been implicated in immunoglobin A nephropathy (IgAN) because the intestinal immune response is assumed to be one of the disease triggers. Since the microbial composition is heritable, we hypothesize that genetic variants controlling gut microbiota composition may be associated with susceptibility to IgAN or clinical phenotypes. A total of 175 gut-microbiome-associated genetic variants were retrieved from the Genome-Wide Association Study (GWAS) Catalog. Genetic associations were examined in 1,511 patients with IgAN and 4,469 controls. Subphenotype associations and microbiome annotations were undertaken for a better understanding of how genes shaped phenotypes. Likely candidate microbes suggested in genetic associations were validated using 16S rRNA gene sequencing in two independent data sets with 119 patients with IgAN and 45 controls in total. Nine genetic variants were associated with susceptibility to IgAN. Risk genotypes of LYZL1 were associated with higher serum levels of galactose-deficient IgA1 (Gd-IgA1). Other significant findings included the associations between the risk genotype of SIPA1L3 and early age at onset, PLTP and worse kidney function, and AL365503.1 and more severe hematuria. Besides, risk genotypes of LYZL1 and SIPA1L3 were associated with decreased abundances of Dialister and Bacilli, respectively. Risk genotypes of PLTP and AL365503.1 were associated with increased abundances of Erysipelotrichaceae and Lachnobacterium, respectively. 16S data validated a decreased tendency for Dialister and an increased tendency for Erysipelotrichaceae in IgAN. In this pilot study, our results provided preliminary evidence that the gut microbiota in IgAN was affected by host genetics and shed new light on candidate bacteria for future pathogenesis studies.IMPORTANCE The gut microbiota and host genetics are implicated in the pathogenesis of IgAN. Recent studies have confirmed that microbial compositions are heritable (microbiome quantitative trait loci [QTL]). The relationship between host genetics and the microbiota and the role of the microbiota in IgAN are unclear. We retrieved the GWAS Catalog and associated microbiome QTL in IgAN, observing that nine genetic variants were associated with IgAN susceptibility and some clinical phenotypes. In a consistent way, the decreased abundance of Dialister was associated with higher serum levels of Gd-IgA1, and 16S rRNA gene analysis confirmed the decreased abundance of Dialister in IgAN. These data provided preliminary evidence that the gut microbiota in IgAN was affected by host genetics, which is a new strategy for future pathogenesis and intervention studies.}, } @article {pmid33436440, year = {2021}, author = {Griesenauer, B and González-Beiras, C and Fortney, KR and Lin, H and Gao, X and Godornes, C and Nelson, DE and Katz, BP and Lukehart, SA and Mitjà, O and Dong, Q and Spinola, SM}, title = {Streptococcus pyogenes Is Associated with Idiopathic Cutaneous Ulcers in Children on a Yaws-Endemic Island.}, journal = {mBio}, volume = {12}, number = {1}, pages = {}, pmid = {33436440}, issn = {2150-7511}, abstract = {Exudative cutaneous ulcers (CU) in yaws-endemic areas are associated with Treponema pallidum subsp. pertenue (TP) and Haemophilus ducreyi (HD), but one-third of CU cases are idiopathic (IU). Using mass drug administration (MDA) of azithromycin, a yaws eradication campaign on Lihir Island in Papua New Guinea reduced but failed to eradicate yaws; IU rates remained constant throughout the campaign. To identify potential etiologies of IU, we obtained swabs of CU lesions (n = 279) and of the skin of asymptomatic controls (AC; n = 233) from the Lihir Island cohort and characterized their microbiomes using a metagenomics approach. CU bacterial communities were less diverse than those of the AC. Using real-time multiplex PCR with pathogen-specific primers, we separated CU specimens into HD-positive (HD+), TP+, HD+TP+, and IU groups. Each CU subgroup formed a distinct bacterial community, defined by the species detected and/or the relative abundances of species within each group. Streptococcus pyogenes was the most abundant organism in IU (22.65%) and was enriched in IU compared to other ulcer groups. Follow-up samples (n = 31) were obtained from nonhealed ulcers; the average relative abundance of S. pyogenes was 30.11% in not improved ulcers and 0.88% in improved ulcers, suggesting that S. pyogenes in the not improved ulcers may be azithromycin resistant. Catonella morbi was enriched in IU that lacked S. pyogenes As some S. pyogenes and TP strains are macrolide resistant, penicillin may be the drug of choice for CU azithromycin treatment failures. Our study will aid in the design of diagnostic tests and selective therapies for CU.IMPORTANCE Cutaneous ulcers (CU) affect approximately 100,000 children in the tropics each year. While two-thirds of CU are caused by Treponema pallidum subspecies pertenue and Haemophilus ducreyi, the cause(s) of the remaining one-third is unknown. Given the failure of mass drug administration of azithromycin to eradicate CU, the World Health Organization recently proposed an integrated disease management strategy to control CU. Success of this strategy requires determining the unknown cause(s) of CU. By using 16S rRNA gene sequencing of swabs obtained from CU and the skin of asymptomatic children, we identified another possible cause of skin ulcers, Streptococcus pyogenes Although S. pyogenes is known to cause impetigo and cellulitis, this is the first report implicating the organism as a causal agent of CU. Inclusion of S. pyogenes into the integrated disease management plan will improve diagnostic testing and treatment of this painful and debilitating disease of children and strengthen elimination efforts.}, } @article {pmid33436437, year = {2021}, author = {Amenyogbe, N and Dimitriu, P and Smolen, KK and Brown, EM and Shannon, CP and Tebbutt, SJ and Cooper, PJ and Marchant, A and Goetghebuer, T and Esser, M and Finlay, BB and Kollmann, TR and Mohn, WW}, title = {Biogeography of the Relationship between the Child Gut Microbiome and Innate Immune System.}, journal = {mBio}, volume = {12}, number = {1}, pages = {}, pmid = {33436437}, issn = {2150-7511}, abstract = {The gut microbiome is a well-recognized modulator of host immunity, and its compositions differ between geographically separated human populations. Systemic innate immune responses to microbial derivatives also differ between geographically distinct human populations. However, the potential role of the microbiome in mediating geographically varied immune responses is unexplored. We here applied 16S amplicon sequencing to profile the stool microbiome and, in parallel, measured whole-blood innate immune cytokine responses to several pattern recognition receptor (PRR) agonists among 2-year-old children across biogeographically diverse settings. Microbiomes differed mainly between high- and low-resource environments and were not strongly associated with other demographic factors. We found strong correlations between responses to Toll-like receptor 2 (TLR2) and relative abundances of Bacteroides and Prevotella populations, shared among Canadian and Ecuadorean children. Additional correlations between responses to TLR2 and bacterial populations were specific to individual geographic cohorts. As a proof of concept, we gavaged germfree mice with human donor stools and found murine splenocyte responses to TLR stimulation were consistent with responses of the corresponding human donor populations. This study identified differences in immune responses correlating to gut microbiomes across biogeographically diverse settings and evaluated biological plausibility using a mouse model. This insight paves the way to guide optimization of population-specific interventions aimed to improve child health outcomes.IMPORTANCE Both the gut microbiome and innate immunity are known to differ across biogeographically diverse human populations. The gut microbiome has been shown to directly influence systemic immunity in animal models. With this, modulation of the gut microbiome represents an attractive avenue to improve child health outcomes associated with altered immunity using population-specific approaches. However, there are very scarce data available to determine which members of the gut microbiome are associated with specific immune responses and how these differ around the world, creating a substantial barrier to rationally designing such interventions. This study addressed this knowledge gap by identifying relationships between distinct bacterial taxa and cytokine responses to specific microbial agonists across highly diverse settings. Furthermore, we provide evidence that immunomodulatory effects of region-specific stool microbiomes can be partially recapitulated in germfree mice. This is an important contribution toward improving global child health by targeting the gut microbiome.}, } @article {pmid33436328, year = {2021}, author = {Hussein, AA and Elsayed, AS and Durrani, M and Jing, Z and Iqbal, U and Gomez, EC and Singh, PK and Liu, S and Smith, G and Tang, L and Guru, KA}, title = {Investigating the association between the urinary microbiome and bladder cancer: An exploratory study.}, journal = {Urologic oncology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.urolonc.2020.12.011}, pmid = {33436328}, issn = {1873-2496}, abstract = {INTRODUCTION: We sought to investigate the association between the urinary microbiome and bladder cancer, including the difference between nonmuscle-invasive (NMIBC) and muscle-invasive (MIBC) bladder cancer, and Bacillus Calmette Guerin (BCG) responsive vs. BCG-refractory NMIBC.

METHODS: Urine specimens were collected from consecutive patients with bladder cancer and healthy volunteers. Urine samples were analyzed using 16S rRNA sequencing to identify and compare any present bacteria. Alteration in the urinary microbiome was described in terms of alpha (diversity of populations within a sample) and beta diversities (differences between populations among different samples). Analyses were corrected for age, sex, method of sample preservation, and method of collection (mid-stream catch vs. catheterized urine).

RESULTS: Fifty-three samples (43 patients with bladder cancer, and 10 controls) were included. For bladder cancer patients, mean age was 70 years, 7 (16%) were females; and 29 (67%) had NMIBC. Among patients with NMIBC, 11 (38%) patients received BCG, 6 of which had recurrence or progression after a median follow up of 13 months. Comparing the microbiome of bladder cancer patients vs. healthy controls, beta-diversity was significantly different, with Actinomyces, Achromobacter, Brevibacterium, and Brucella significantly more abundant in urine samples of bladder cancer patients. Comparing NMIBC and MIBC, Hemophilus and Veillonella were significantly more abundant in urine of MIBC patients, while Cupriavidus was significantly more abundant in NMIBC patients. Among NMIBC patients, Serratia and Brochothrix, Negativicoccus, Escherichia-Shigella, and Pseudomonas were significantly more abundant in patients who responded to BCG in comparison to those who did not.

CONCLUSION: Urinary microbiome varied between patients with bladder cancer and healthy controls. Moreover, urinary microbial profiles differed among patient with NMIBC vs. MIBC, and among BCG responsive vs. BCG refractory NMIBC.}, } @article {pmid33436217, year = {2021}, author = {Elshahed, MS and Miron, A and Aprotosoaie, AC and Farag, MA}, title = {Pectin in diet: Interactions with the human microbiome, role in gut homeostasis, and nutrient-drug interactions.}, journal = {Carbohydrate polymers}, volume = {255}, number = {}, pages = {117388}, doi = {10.1016/j.carbpol.2020.117388}, pmid = {33436217}, issn = {1879-1344}, abstract = {Pectins are a part of daily diet as well as food additives that are indigestible polysaccharides by human enzymes, however, they can be easily degraded by gut bacteria with the production of short chain fatty acids (SCFAs). Knowledge of pectin gut homeostasis and further how pectin affect gut bacterial communities is insufficient and limited. This review focuses on providing the whole story of how pectin functions as prebiotics in the gut. Understanding the interplay between functional and immunological responses inside animal or human gut as influenced by pectin in diets is provided. The interaction between pectin and gut microbiota is presented from both sides, in terms of how pectin affects gut microbiome and or the fermentation products produced in response by gut bacteria. This knowledge can be used to define preferred dietary pectins, targeting beneficial bacteria, and favoring balanced microbiota communities in the gut to maximize pectins' health benefits.}, } @article {pmid33436213, year = {2021}, author = {Hövels, M and Kosciow, K and Deppenmeier, U}, title = {Characterization of a novel endo-levanase from Azotobacter chroococcum DSM 2286 and its application for the production of prebiotic fructooligosaccharides.}, journal = {Carbohydrate polymers}, volume = {255}, number = {}, pages = {117384}, doi = {10.1016/j.carbpol.2020.117384}, pmid = {33436213}, issn = {1879-1344}, abstract = {Prebiotics are known for their ability to modulate the composition of the human microbiome and mediate health-promoting benefits. Endo-levanases, which hydrolyze levan into short-chain FOS, could be used for the production of levan-based prebiotics. The novel endo-levanase (LevB2286) from Azotobacter chroococcum DSM 2286, combines an exceptionally high specific activity with advantageous hydrolytic properties. Starting from levan isolated from Timothy grass, LevB2286 produced FOS ranging from DP 2 - 8. In contrast to endo-levanases described in the literature, LevB2286 formed minor amounts of fructose and levanbiose, even with greatly extended incubation. The combined activity of LevB2286 and the levansucrase LevS1417 from Gluconobacter japonicus LMG 1417 led to a one-step synthesis of levan-type FOS from sucrose. 387.4 ± 17.3 g L-1 FOS were produced within 48 h by the production strategy based on crude cell extract of recombinant Escherichia coli expressing levS1417 and levB2286 simultaneously.}, } @article {pmid33436102, year = {2021}, author = {Yan, Z and He, F and Xiao, F and He, H and Li, D and Cong, L and Lin, L and Zhu, H and Wu, Y and Yan, R and Li, X and Shan, H}, title = {A semi-tryptic peptide centric metaproteomic mining approach and its potential utility in capturing signatures of gut microbial proteolysis.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {12}, pmid = {33436102}, issn = {2049-2618}, support = {31900070//National Natural Science Foundation of China/ ; 81473281//National Natural Science Foundation of China/ ; 2019A1515011771//Guangdong Basic and Applied Basic Research Foundation/ ; 0098/2019/A2//Science and Technology Development Fund of Macau SAR/ ; }, abstract = {BACKGROUND: Proteolysis regulation allows gut microbes to respond rapidly to dynamic intestinal environments by fast degradation of misfolded proteins and activation of regulatory proteins. However, alterations of gut microbial proteolytic signatures under complex disease status such as inflammatory bowel disease (IBD, including Crohn's disease (CD) and ulcerative colitis (UC)), have not been investigated. Metaproteomics holds the potential to investigate gut microbial proteolysis because semi-tryptic peptides mainly derive from endogenous proteolysis.

RESULTS: We have developed a semi-tryptic peptide centric metaproteomic mining approach to obtain a snapshot of human gut microbial proteolysis signatures. This approach employed a comprehensive meta-database, two-step multiengine database search, and datasets with high-resolution fragmentation spectra to increase the confidence of semi-tryptic peptide identification. The approach was validated by discovering altered proteolysis signatures of Escherichia coli heat shock response. Utilizing two published large-scale metaproteomics datasets containing 623 metaproteomes from 447 fecal and 176 mucosal luminal interface (MLI) samples from IBD patients and healthy individuals, we obtain potential signatures of altered gut microbial proteolysis at taxonomic, functional, and cleavage site motif levels. The functional alterations mainly involved microbial carbohydrate transport and metabolism, oxidative stress, cell motility, protein synthesis, and maturation. Altered microbial proteolysis signatures of CD and UC mainly occurred in terminal ileum and descending colon, respectively. Microbial proteolysis patterns exhibited low correlations with β-diversity and moderate correlations with microbial protease and chaperones levels, respectively. Human protease inhibitors and immunoglobulins were mainly negatively associated with microbial proteolysis patterns, probably because of the inhibitory effects of these host factors on gut microbial proteolysis events.

CONCLUSIONS: This semi-tryptic peptide centric mining strategy offers a label-free approach to discover signatures of in vivo gut microbial proteolysis events if experimental conditions are well controlled. It can also capture in vitro proteolysis signatures to facilitate the evaluation and optimization of experimental conditions. Our findings highlight the complex and diverse proteolytic events of gut microbiome, providing a unique layer of information beyond taxonomic and proteomic abundance. Video abstract.}, } @article {pmid33436100, year = {2021}, author = {Silverstein, RB and Mysorekar, IU}, title = {Group therapy on in utero colonization: seeking common truths and a way forward.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {7}, pmid = {33436100}, issn = {2049-2618}, support = {R01HD091218//National Institutes for Health/ National Institute for Child Health and Development/ ; uSTAR fellowship//MARC/ ; }, abstract = {The human microbiome refers to the genetic composition of microorganisms in a particular location in the human body. Emerging evidence over the past many years suggests that the microbiome constitute drivers of human fate almost at par with our genome and epigenome. It is now well accepted after decades of disbelief that a broad understanding of human development, health, physiology, and disease requires understanding of the microbiome along with the genome and epigenome. We are learning daily of the interdependent relationships between microbiome/microbiota and immune responses, mood, cancer progression, response to therapies, aging, obesity, antibiotic usage, and overusage and much more. The next frontier in microbiome field is understanding when does this influence begin? Does the human microbiome initiate at the time of birth or are developing human fetuses already primed with microbes and their products in utero. In this commentary, we reflect on evidence gathered thus far on this question and identify the unknown common truths. We present a way forward to continue understanding our microbial colleagues and our interwoven fates.}, } @article {pmid33436099, year = {2021}, author = {de Goffau, MC and Charnock-Jones, DS and Smith, GCS and Parkhill, J}, title = {Batch effects account for the main findings of an in utero human intestinal bacterial colonization study.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {6}, pmid = {33436099}, issn = {2049-2618}, abstract = {A recent study by Rackaityte et al. reported evidence for a low level of bacterial colonization, specifically of Micrococcus luteus, in the intestine of second trimester human fetuses. We have re-analyzed their sequence data and identified a batch effect which violates the underlying assumptions of the bioinformatic method used for contamination removal. This batch effect resulted in Micrococcus not being identified as a contaminant in the original work and being falsely assigned to the fetal samples. We further provide evidence that the micrographs presented by Rackaityte et al. are unlikely to show Micrococci or other bacteria as the size of the particles shown exceeds that of related bacterial cells. Finally, phylogenetic analysis showed that the microbes cultured from the fetal samples differed significantly from those detected by sequencing. Overall, our findings show that the presence of Micrococcus in the fetal gut is not supported by the primary sequence data. Our findings underline important aspects of the nature of contamination for both sequencing and culture approaches in microbiome studies and the appropriate use of automated contamination identification tools.}, } @article {pmid33436098, year = {2021}, author = {Blaser, MJ and Devkota, S and McCoy, KD and Relman, DA and Yassour, M and Young, VB}, title = {Lessons learned from the prenatal microbiome controversy.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {8}, pmid = {33436098}, issn = {2049-2618}, abstract = {For more than a century, the prenatal environment was considered sterile. Over the last few years, findings obtained with next-generation sequencing approaches from samples of the placenta, the amniotic fluid, meconium, and even fetal tissues have challenged the dogma of a sterile womb, and additional reports have emerged that used culture, microscopy, and quantitative PCR to support the presence of a low-biomass microbial community at prenatal sites. Given the substantial implications of prenatal exposure to microbes for the development and health of the host, the findings have gathered substantial interest from academics, high impact journals, the public press, and funding agencies. However, an increasing number of studies have challenged the prenatal microbiome identifying contamination as a major issue, and scientists that remained skeptical have pointed to inconsistencies with in utero colonization, the impact of c-sections on early microbiome assembly, and the ability to generate germ-free mammals. A lively academic controversy has emerged on the existence of the wider importance of prenatal microbial communities. Microbiome has asked experts to discuss these issues and provide their thoughts on the implications. To allow for a broader perspective of this discussion, we have specifically selected scientists, who have a long-standing expertise in microbiome sciences but who have not directly been involved in the debate so far.}, } @article {pmid33436093, year = {2021}, author = {Walter, J and Hornef, MW}, title = {A philosophical perspective on the prenatal in utero microbiome debate.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {5}, pmid = {33436093}, issn = {2049-2618}, abstract = {Within the last 6 years, a research field has emerged that focuses on the characterization of microbial communities in the prenatal intrauterine environment of humans and their putative role in human health. However, there is considerable controversy around the existence of such microbial populations. The often contentious debate is primarily focused on technical aspects of the research, such as difficulties to assure aseptic sampling and to differentiate legitimate signals in the data from contamination. Although such discussions are clearly important, we feel that the problems with the prenatal microbiome field go deeper. In this commentary, we apply a philosophical framework to evaluate the foundations, experimental approaches, and interpretations used by scientists on both sides of the debate. We argue that the evidence for a "sterile womb" is based on a scientific approach that aligns well with important principles of the philosophy of science as genuine tests of the hypothesis and multiple angles of explanatory considerations were applied. In contrast, research in support of the "in utero colonization hypothesis" is solely based on descriptive verifications that do not provide explanatory insight, which weakens the evidence for a prenatal intrauterine microbiome. We propose that a reflection on philosophical principles can inform not only the debate on the prenatal intrauterine microbiome but also other disciplines that attempt to study low-biomass microbial communities.}, } @article {pmid33436081, year = {2021}, author = {Fricke, WF and Ravel, J}, title = {Microbiome or no microbiome: are we looking at the prenatal environment through the right lens?.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {9}, pmid = {33436081}, issn = {2049-2618}, } @article {pmid33436075, year = {2021}, author = {Wang, Y and Wan, X and Wu, X and Zhang, C and Liu, J and Hou, S}, title = {Eubacterium rectale contributes to colorectal cancer initiation via promoting colitis.}, journal = {Gut pathogens}, volume = {13}, number = {1}, pages = {2}, pmid = {33436075}, issn = {1757-4749}, support = {81972826//Natural Science Foundation of China/ ; 63191440//Fundamental Research Funds for the Central Universities, Nankai University/ ; }, abstract = {BACKGROUND: Inflammatory bowel disease caused by microbial dysbiosis is an important factor contributing to colorectal cancer (CRC) initiation. The 'driver-passenger' model in human gut microbial dysbiosis suggests that 'driver' bacteria may colonize with low relative abundance on tumor site but persistently induce chronic change in normal intestinal epithelium and initiate CRC. They are gradually replaced by 'passenger' bacteria later on, due to their low adaptability to the on-tumor site niche.

RESULTS: To reveal site-specific bacterial taxon markers in CRC patients, we analyzed the gut mucosal microbiome of 75 paired samples of on-tumor and tumor-adjacent sites, 75 off-tumor sites, and 26 healthy controls. Linear discriminant analysis of relative abundance profiles revealed unique bacterial taxon distribution correlated with specific tumor sites, with Eubacterium having the distribution characteristic of potential driver bacteria. We further show that Eubacterium rectale endotoxin activates the transcription factor NF-κΒ, which regulates multiple aspects of innate and adaptive immune responses in normal colon epithelial cells. Unlike the 'passenger' bacterium Fusobacterium nucleatum, E. rectale promotes dextran sodium sulfate-induced colitis in Balb/c mice.

CONCLUSIONS: Our findings reveal that E. rectale functions as a 'driver' bacterium and contributes to cancer initiation via promoting inflammation.}, } @article {pmid33436067, year = {2021}, author = {Yeung, M and Saingam, P and Xu, Y and Xi, J}, title = {Low-dosage ozonation in gas-phase biofilter promotes community diversity and robustness.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {14}, pmid = {33436067}, issn = {2049-2618}, support = {52070113//National Natural Science Foundation of China/ ; 2011ZX07301-003//Major Science and Technology Program for Water Pollution Control and Treatment (CN)/ ; }, abstract = {BACKGROUND: The ozonation of biofilters is known to alleviate clogging and pressure drop issues while maintaining removal performances in biofiltration systems treating gaseous volatile organic compounds (VOCs). The effects of ozone on the biofilter microbiome in terms of biodiversity, community structure, metabolic abilities, and dominant taxa correlated with performance remain largely unknown.

METHODS: This study investigated two biofilters treating high-concentration toluene operating in parallel, with one acting as control and the other exposed to low-dosage (200 mg/m3) ozonation. The microbial community diversity, metabolic rates of different carbon sources, functional predictions, and microbial co-occurrence networks of both communities were examined.

RESULTS: Consistently higher biodiversity of over 30% was observed in the microbiome after ozonation, with increased overall metabolic abilities for amino acids and carboxylic acids. The relative abundance of species with reported stress-tolerant and biofilm-forming abilities significantly increased, with a consortium of changes in predicted biological pathways, including shifts in degradation pathways of intermediate compounds, while the correlation of top ASVs and genus with performance indicators showed diversifications in microbiota responsible for toluene degradation. A co-occurrence network of the community showed a decrease in average path distance and average betweenness with ozonation.

CONCLUSION: Major degrading species highly correlated with performance shifted after ozonation. Increases in microbial biodiversity, coupled with improvements in metabolizing performances of multiple carbon sources including organic acids could explain the consistent performance commonly seen in the ozonation of biofilters despite the decrease in biomass, while avoiding acid buildup in long-term operation. The increased presence of stress-tolerant microbes in the microbiome coupled with the decentralization of the co-occurrence network suggest that ozonation could not only ameliorate clogging issues but also provide a microbiome more robust to loading shock seen in full-scale biofilters. Video abstract.}, } @article {pmid33436066, year = {2021}, author = {Chen, C and Niu, M and Pan, J and Du, N and Liu, S and Li, H and He, Q and Mao, J and Duan, Y and Du, Y}, title = {Bacteroides, butyric acid and t10,c12-CLA changes in colorectal adenomatous polyp patients.}, journal = {Gut pathogens}, volume = {13}, number = {1}, pages = {1}, pmid = {33436066}, issn = {1757-4749}, support = {81960382//National Natural Science Foundation of China/ ; 2018FA043//Natural Science Foundation of Yunnan Province/ ; 2017FE467 (-173)//Joint special fund for applied basic research in Yunnan Province/ ; 2019FE001 (-060)//Joint special fund for applied basic research in Yunnan Province/ ; }, abstract = {BACKGROUND: Colorectal adenomatous polyps (CAPs) are considered precancerous lesions of colorectal cancer (CRC). The gut microbiota participates in the process of digestion and, in the process, produces metabolites, mainly short-chain fatty acids (SCFAs), secondary bile acids and conjugated linoleic acid (CLA). This study aimed to investigate the gut microbiota constituents and metabolites in the faeces of CAP patients to identify microbiota or metabolites that can be used as sensitive biological predictors and to provide a theoretical basis for the clinical treatment of CAPs.

METHODS: 16S rRNA sequence analysis was used to detect microbial changes in the faeces of CAP patients. qPCR analysis was used to evaluate the ability of the microbiota to produce metabolites, and the contents of metabolites in faeces were detected by ion chromatography and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS).

RESULTS: Based on the detection of the gut microbiota, patients with CAPs had increased abundances of Bacteroides and Citrobacter, and the abundances of Weissella and Lactobacillus were decreased. We also explored gene expression, and the abundance of butyrate-producing bacterial genes was significantly increased in the faeces of CAP patients, but those of secondary bile acid-producing and CLA-producing bacterial genes showed no differences in faecal samples. The acetic acid and butyric acid contents were increased in the faeces of the CAP group, and the healthy control group had higher t10,c12-CLA contents.

CONCLUSION: The gut microbiota analysis results, assessed in faeces, showed that Bacteroides and Citrobacter were positively correlated with CAPs, which indicated that changes in specific genera might be detrimental to intestinal health. In addition, t10,c12-CLA played an important role in protecting the intestine.}, } @article {pmid33436010, year = {2021}, author = {Liu, J and Liu, C and Yue, J}, title = {Radiotherapy and the gut microbiome: facts and fiction.}, journal = {Radiation oncology (London, England)}, volume = {16}, number = {1}, pages = {9}, pmid = {33436010}, issn = {1748-717X}, support = {81871895//National Natural Science Foundation of China/ ; 2019RC003//Young Taishan Scholars and Academic Promotion Program of Shandong First Medical University/ ; }, abstract = {An ever-growing body of evidence has linked the gut microbiome with both the effectiveness and the toxicity of cancer therapies. Radiotherapy is an effective way to treat tumors, although large variations exist among patients in tumor radio-responsiveness and in the incidence and severity of radiotherapy-induced side effects. Relatively little is known about whether and how the microbiome regulates the response to radiotherapy. Gut microbiota may be an important player in modulating "hot" versus "cold" tumor microenvironment, ultimately affecting treatment efficacy. The interaction of the gut microbiome and radiotherapy is a bidirectional function, in that radiotherapy can disrupt the microbiome and those disruptions can influence the effectiveness of the anticancer treatments. Limited data have shown that interactions between the radiation and the microbiome can have positive effects on oncotherapy. On the other hand, exposure to ionizing radiation leads to changes in the gut microbiome that contribute to radiation enteropathy. The gut microbiome can influence radiation-induced gastrointestinal mucositis through two mechanisms including translocation and dysbiosis. We propose that the gut microbiome can be modified to maximize the response to treatment and minimize adverse effects through the use of personalized probiotics, prebiotics, or fecal microbial transplantation. 16S rRNA sequencing is the most commonly used approach to investigate distribution and diversity of gut microbiome between individuals though it only identifies bacteria level other than strain level. The functional gut microbiome can be studied using methods involving metagenomics, metatranscriptomics, metaproteomics, as well as metabolomics. Multiple '-omic' approaches can be applied simultaneously to the same sample to obtain integrated results. That said, challenges and remaining unknowns in the future that persist at this time include the mechanisms by which the gut microbiome affects radiosensitivity, interactions between the gut microbiome and combination treatments, the role of the gut microbiome with regard to predictive and prognostic biomarkers, the need for multi "-omic" approach for in-depth exploration of functional changes and their effects on host-microbiome interactions, and interactions between gut microbiome, microbial metabolites and immune microenvironment.}, } @article {pmid33435920, year = {2021}, author = {Butler, ÉM and Reynolds, AJ and Derraik, JGB and Wilson, BC and Cutfield, WS and Grigg, CP}, title = {The views of pregnant women in New Zealand on vaginal seeding: a mixed-methods study.}, journal = {BMC pregnancy and childbirth}, volume = {21}, number = {1}, pages = {49}, pmid = {33435920}, issn = {1471-2393}, abstract = {BACKGROUND: Vaginal seeding is the administration of maternal vaginal bacteria to babies following birth by caesarean section (CS), intended to mimic the microbial exposure that occurs during vaginal birth. Appropriate development of the infant gut microbiome assists early immune development and might help reduce the risk of certain health conditions later in life, such as obesity and asthma. We aimed to explore the views of pregnant women on this practice.

METHODS: We conducted a sequential mixed-methods study on the views of pregnant women in New Zealand (NZ) on vaginal seeding. Phase one: brief semi-structured interviews with pregnant women participating in a clinical trial of vaginal seeding (n = 15); and phase two: online questionnaire of pregnant women throughout NZ (not in the trial) (n = 264). Reflexive thematic analysis was applied to interview and open-ended questionnaire data. Closed-ended questionnaire responses were analysed using descriptive statistics.

RESULTS: Six themes were produced through analysis of the open-ended data: "seeding replicates a natural process", "microbiome is in the media", "seeding may have potential benefits", "seeking validation by a maternity caregiver", "seeding could help reduce CS guilt", and "the unknowns of seeding". The idea that vaginal seeding replicates a natural process was suggested by some as an explanation to help overcome any initial negative perceptions of it. Many considered vaginal seeding to have potential benefit for the gut microbiome, while comparatively fewer considered it to be potentially beneficial for specific conditions such as obesity. Just under 30% of questionnaire respondents (n = 78; 29.5%) had prior knowledge of vaginal seeding, while most (n = 133; 82.6%) had an initially positive or neutral reaction to it. Few respondents changed their initial views on the practice after reading provided evidence-based information (n = 60; 22.7%), but of those who did, most became more positive (n = 51; 86.4%).

CONCLUSIONS: Given its apparent acceptability, and if shown to be safe and effective for the prevention of early childhood obesity, vaginal seeding could be a non-stigmatising approach to prevention of this condition among children born by CS. Our findings also highlight the importance of lead maternity carers in NZ remaining current in their knowledge of vaginal seeding research.}, } @article {pmid33435848, year = {2021}, author = {Sanders, D and Grunden, A and Dunn, RR}, title = {A review of clothing microbiology: the history of clothing and the role of microbes in textiles.}, journal = {Biology letters}, volume = {17}, number = {1}, pages = {20200700}, doi = {10.1098/rsbl.2020.0700}, pmid = {33435848}, issn = {1744-957X}, abstract = {Humans have worn clothing for thousands of years, and since its invention, clothing has evolved from its simple utilitarian function for survival to become an integral part of society. While much consideration has been given to the broad environmental impacts of the textile and laundering industries, little is known about the impact wearing clothing has had on the human microbiome, particularly that of the skin, despite our long history with clothing. This review discusses the history of clothing and the evolution of textiles, what is and is not known about microbial persistence on and degradation of various fibres, and what opportunities for the industrial and environmental application of clothing microbiology exist for the future.}, } @article {pmid33435575, year = {2021}, author = {Landlinger, C and Tisakova, L and Oberbauer, V and Schwebs, T and Muhammad, A and Latka, A and Van Simaey, L and Vaneechoutte, M and Guschin, A and Resch, G and Swidsinski, S and Swidsinski, A and Corsini, L}, title = {Engineered Phage Endolysin Eliminates Gardnerella Biofilm without Damaging Beneficial Bacteria in Bacterial Vaginosis Ex Vivo.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, doi = {10.3390/pathogens10010054}, pmid = {33435575}, issn = {2076-0817}, support = {876839//Österreichische Forschungsförderungsgesellschaft/ ; }, abstract = {Bacterial vaginosis is characterized by an imbalance of the vaginal microbiome and a characteristic biofilm formed on the vaginal epithelium, which is initiated and dominated by Gardnerella bacteria, and is frequently refractory to antibiotic treatment. We investigated endolysins of the type 1,4-beta-N-acetylmuramidase encoded on Gardnerella prophages as an alternative treatment. When recombinantly expressed, these proteins demonstrated strong bactericidal activity against four different Gardnerella species. By domain shuffling, we generated several engineered endolysins with 10-fold higher bactericidal activity than any wild-type enzyme. When tested against a panel of 20 Gardnerella strains, the most active endolysin, called PM-477, showed minimum inhibitory concentrations of 0.13-8 µg/mL. PM-477 had no effect on beneficial lactobacilli or other species of vaginal bacteria. Furthermore, the efficacy of PM-477 was tested by fluorescence in situ hybridization on vaginal samples of fifteen patients with either first time or recurring bacterial vaginosis. In thirteen cases, PM-477 killed the Gardnerella bacteria and physically dissolved the biofilms without affecting the remaining vaginal microbiome. The high selectivity and effectiveness in eliminating Gardnerella, both in cultures of isolated strains as well as in clinically derived samples of natural polymicrobial biofilms, makes PM-477 a promising alternative to antibiotics for the treatment of bacterial vaginosis, especially in patients with frequent recurrence.}, } @article {pmid33435398, year = {2021}, author = {Juste Contin Gomes, M and Stampini Duarte Martino, H and Tako, E}, title = {Effects of Iron and Zinc Biofortified Foods on Gut Microbiota In Vivo (Gallus gallus): A Systematic Review.}, journal = {Nutrients}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/nu13010189}, pmid = {33435398}, issn = {2072-6643}, abstract = {Dietary iron and zinc deficiencies are a global health concern. Bacteria that colonize the gastrointestinal tract depend on minerals to maintain their activities; thus, recent evidence suggests that biofortified foods can modulate the host's beneficial bacterial taxa. The current review analyzed the research data that linked between iron and zinc biofortified foods and gut microbiota modulation. The data analysis was based on the PRISMA guidelines and the data search was performed at PubMed, Web of Science, Science Direct, and Scopus databases for experimental studies published from January 2010 until December 2020. The five selected studies were conducted in an experimental in vivo model (Gallus gallus). The identified and discussed research showed positive effects of biofortified foods on the composition and function of the gut microbiota. Further, an increase in short chain fatty acids producing bacterial populations as Lactobacillus and Ruminococcus, and a decrease in potentially pathogenic bacteria as Streptococcus, Escherichia, and Enterobacter was identified due to the consumption of biofortified foods. In conclusion, biofortified foods may contribute to improved gut health without increasing the colonization of pathogenic bacteria. The dietary inclusion of approximately 50% of iron/zinc biofortified foods has a significant beneficial effect on the gut microbiota. Additional studies in humans and animal models are warranted to further establish the suggested effects on the intestinal microbiome. PROSPERO (CRD42020184221).}, } @article {pmid33435303, year = {2021}, author = {Mahapatro, M and Erkert, L and Becker, C}, title = {Cytokine-Mediated Crosstalk between Immune Cells and Epithelial Cells in the Gut.}, journal = {Cells}, volume = {10}, number = {1}, pages = {}, doi = {10.3390/cells10010111}, pmid = {33435303}, issn = {2073-4409}, support = {TRR241 (A03)//University Erlangen-Nuremberg/ ; C05//SFB1181/ ; }, abstract = {Cytokines are small proteins that are secreted by a vast majority of cell types in the gut. They not only establish cell-to-cell interactions and facilitate cellular signaling, but also regulate both innate and adaptive immune responses, thereby playing a central role in genetic, inflammatory, and infectious diseases of the gut. Both, immune cells and gut epithelial cells, play important roles in intestinal disease development. The epithelium is located in between the mucosal immune system and the gut microbiome. It not only establishes an efficient barrier against gut microbes, but it also signals information from the gut lumen and its composition to the immune cell compartment. Communication across the epithelial cell layer also occurs in the other direction. Intestinal epithelial cells respond to immune cell cytokines and their response influences and shapes the microbial community within the gut lumen. Thus, the epithelium should be seen as a translator or a moderator between the microbiota and the mucosal immune system. Proper communication across the epithelium seems to be a key to gut homeostasis. Indeed, current genome-wide association studies for intestinal disorders have identified several disease susceptibility loci, which map cytokine signatures and their related signaling genes. A thorough understanding of this tightly regulated cytokine signaling network is crucial. The main objective of this review was to shed light on how cytokines can orchestrate epithelial functions such as proliferation, cell death, permeability, microbe interaction, and barrier maintenance, thereby safeguarding host health. In addition, cytokine-mediated therapy for inflammation and cancer are discussed.}, } @article {pmid33435275, year = {2021}, author = {Mannaa, M and Seo, YS}, title = {Plants under the Attack of Allies: Moving towards the Plant Pathobiome Paradigm.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, doi = {10.3390/plants10010125}, pmid = {33435275}, issn = {2223-7747}, abstract = {Plants are functional macrobes living in a close association with diverse communities of microbes and viruses as complex systems that continuously interact with the surrounding environment. The microbiota within the plant holobiont serves various essential and beneficial roles, such as in plant growth at different stages, starting from seed germination. Meanwhile, pathogenic microbes-differentiated from the rest of the plant microbiome based on their ability to damage the plant tissues through transient blooming under specific conditions-are also a part of the plant microbiome. Recent advances in multi-omics have furthered our understanding of the structure and functions of plant-associated microbes, and a pathobiome paradigm has emerged as a set of organisms (i.e., complex eukaryotic, microbial, and viral communities) within the plant's biotic environment which interact with the host to deteriorate its health status. Recent studies have demonstrated that the one pathogen-one disease hypothesis is insufficient to describe the disease process in many cases, particularly when complex organismic communities are involved. The present review discusses the plant holobiont and covers the steady transition of plant pathology from the one pathogen-one disease hypothesis to the pathobiome paradigm. Moreover, previous reports on model plant diseases, in which more than one pathogen or co-operative interaction amongst pathogenic microbes is implicated, are reviewed and discussed.}, } @article {pmid33434516, year = {2020}, author = {Chaudhari, SN and Luo, JN and Harris, DA and Aliakbarian, H and Yao, L and Paik, D and Subramaniam, R and Adhikari, AA and Vernon, AH and Kiliç, A and Weiss, ST and Huh, JR and Sheu, EG and Devlin, AS}, title = {A microbial metabolite remodels the gut-liver axis following bariatric surgery.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2020.12.004}, pmid = {33434516}, issn = {1934-6069}, abstract = {Bariatric surgery is the most effective treatment for type 2 diabetes and is associated with changes in gut metabolites. Previous work uncovered a gut-restricted TGR5 agonist with anti-diabetic properties-cholic acid-7-sulfate (CA7S)-that is elevated following sleeve gastrectomy (SG). Here, we elucidate a microbiome-dependent pathway by which SG increases CA7S production. We show that a microbial metabolite, lithocholic acid (LCA), is increased in murine portal veins post-SG and by activating the vitamin D receptor, induces hepatic mSult2A1/hSULT2A expression to drive CA7S production. An SG-induced shift in the microbiome increases gut expression of the bile acid transporters Asbt and Ostα, which in turn facilitate selective transport of LCA across the gut epithelium. Cecal microbiota transplant from SG animals is sufficient to recreate the pathway in germ-free (GF) animals. Activation of this gut-liver pathway leads to CA7S synthesis and GLP-1 secretion, causally connecting a microbial metabolite with the improvement of diabetic phenotypes.}, } @article {pmid33434506, year = {2021}, author = {Seguin-Orlando, A and Donat, R and Der Sarkissian, C and Southon, J and Thèves, C and Manen, C and Tchérémissinoff, Y and Crubézy, E and Shapiro, B and Deleuze, JF and Dalén, L and Guilaine, J and Orlando, L}, title = {Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2020.12.015}, pmid = {33434506}, issn = {1879-0445}, abstract = {The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe.1 These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes2,3 into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry.4-8 This transition is documented through extensive ancient genomic data from present-day Britain,9,10 Ireland,11,12 Iberia,13 Mediterranean islands,14,15 and Germany.8 It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63),8,9,16 with the exception of one Late Neolithic genome sequenced at 0.05× coverage.16 This leaves the key transitional period covering ∼3,400-2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400-1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale.}, } @article {pmid33434463, year = {2021}, author = {O'Brien, AM and Jack, CN and Friesen, ML and Frederickson, ME}, title = {Whose trait is it anyways? Coevolution of joint phenotypes and genetic architecture in mutualisms.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1942}, pages = {20202483}, doi = {10.1098/rspb.2020.2483}, pmid = {33434463}, issn = {1471-2954}, abstract = {Evolutionary biologists typically envision a trait's genetic basis and fitness effects occurring within a single species. However, traits can be determined by and have fitness consequences for interacting species, thus evolving in multiple genomes. This is especially likely in mutualisms, where species exchange fitness benefits and can associate over long periods of time. Partners may experience evolutionary conflict over the value of a multi-genomic trait, but such conflicts may be ameliorated by mutualism's positive fitness feedbacks. Here, we develop a simulation model of a host-microbe mutualism to explore the evolution of a multi-genomic trait. Coevolutionary outcomes depend on whether hosts and microbes have similar or different optimal trait values, strengths of selection and fitness feedbacks. We show that genome-wide association studies can map joint traits to loci in multiple genomes and describe how fitness conflict and fitness feedback generate different multi-genomic architectures with distinct signals around segregating loci. Partner fitnesses can be positively correlated even when partners are in conflict over the value of a multi-genomic trait, and conflict can generate strong mutualistic dependency. While fitness alignment facilitates rapid adaptation to a new optimum, conflict maintains genetic variation and evolvability, with implications for applied microbiome science.}, } @article {pmid33434392, year = {2021}, author = {Onwuliri, V and Agbakoba, NR and Anukam, KC}, title = {Topical cream containing live lactobacilli decreases malodour-producing bacteria and downregulates genes encoding PLP-dependent enzymes on the axillary skin microbiome of healthy adult Nigerians.}, journal = {Journal of cosmetic dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jocd.13949}, pmid = {33434392}, issn = {1473-2165}, abstract = {BACKGROUND: Clinical data exist that supports the utility of topical probiotics for certain dermatological diseases such as atopic dermatitis, acne, and psoriasis. However, there is paucity of data on the use of live lactobacilli to control axillary malodour. The objective of this study was to determine whether application of topical oil-based cream containing live Lactobacilli could decrease malodour-producing bacteria in the axilla of healthy subjects.

METHODS: Twenty-five adult volunteers comprising 12 males and 13 females provided informed consent. Axillary skin swabs were collected before and after 14 days application of topical cream containing live Lactobacillus pentosus KCA1. Bacterial DNA was extracted and V4 region of the 16S rRNA were amplified and sequenced in a pair-end configuration on the Illumina MiSeq platform rendering 2 x 150 bp sequences. Microbial taxonomy to species level was generated using the Greengenes database. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biologically and statistically significant differences in relative abundance.

RESULTS: Actinobacteria decreased from 70% to 24%, Firmicutes increased from 26.6% to 73.9% among the female participants. In males, Actinobacteria decreased from 65% to 38%, while Firmicutes increased from 24% to 57%. Corynebacterium decreased from 62.91% to 36.63%, while Lactobacillus increased from 0.06% to 23.11%. In males, unliked females, there were reduction of Staphylococcus species associated with malodour, notably Staphylococcus hominis, Staphylococcus haemolyticus, and Staphylococcus lugdunensis. Bacterial functional gene- Pyridoxal protein dependent enzymes involved in biotransformation of malodor precursor to volatile thioalcohols were down-regulated.

CONCLUSIONS: Application of Lactobacillus pentosus KCA1 cream led to a significant decrease in the relative abundance of odour-producing Corynebacterium species in both female and male subjects. Some species associated with malodour especially Corynebacterium striatum, Corynebacterium jeikeium, Corynebacterium tuberculostearicum, Staphylococcus hominis decreased by 96%, 73%, 7% and 20.8% respectively in males.}, } @article {pmid33434389, year = {2021}, author = {Garber, JM and Hennet, T and Szymanski, CM}, title = {Significance of fucose in intestinal health and disease.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.14681}, pmid = {33434389}, issn = {1365-2958}, abstract = {The deoxy hexose sugar L-fucose is important for many biological processes within the human body and the associated microbiota. This carbohydrate is abundant in host gut mucosal surfaces, numerous microbial cell surface structures, and some dietary carbohydrates. Fucosylated oligosaccharides facilitate the establishment of a healthy microbiota and provide protection from infection. However, there are instances where pathogens can also exploit these fucosylated structures to cause infection. Furthermore, deficiencies in host fucosylation are associated with specific disease outcomes. This review focuses on our current understanding of the impact of fucosylation within the mucosal environment of the gastrointestinal tract with a specific emphasis on the mediatory effects in host-microbe interactions.}, } @article {pmid33434310, year = {2021}, author = {Costa, CPS and Silva, MA and Neto, LGL and Valois, EM and Monteiro-Neto, V and Souza, SFC}, title = {Is there bacterial infection in intact crowns teeth and pulp necrosis of sickle-cell anaemia patients? A case series study nested in a cohort.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.13476}, pmid = {33434310}, issn = {1365-2591}, abstract = {AIM: To evaluate the presence of bacteria in permanent teeth with intact crowns (without caries, periodontal disease, or dental trauma) in sickle cell anaemia patients (HbSS genotype) by analyzing their clinical, imaging, and microbiological parameters.

METHODOLOGY: This is a case series study nested in a cohort. In the first follow-up of this cohort study (Costa et al. 2013), ten HbSS patients with at least one tooth with intact crown and clinically diagnosed with pulp necrosis, by pulse oximetry adapted for dentistry and a cold sensitivity test (n = 27 teeth), were selected. Changes in the pulp chamber, root, and periodontal ligament were identified in the tomographic analysis. Bacterial culture, staining for live and dead bacteria, and real-time polymerase chain reaction with 16S rRNA primers were used to identify the presence of bacteria. Culture sample collection was performed immediately after access to the pulp chamber. The microbiome was analyzed with a MiSeq sequencer (Illumina, San Diego, CA).

RESULTS: The diagnosis of pulp necrosis was clinically confirmed in 82% (22/27) of the teeth. The amount of bacterial load identified was less than 100 copies/μL in 23% (5/22) of the teeth with intact crowns and pulp necrosis. Thirteen bacterial species were identified that are commonly found in urinary tract infection, septicemia, and infective endocarditis. Only one of these species, Granulicatella adjacens, has also be found in primary endodontic infections.

CONCLUSION: Prospective clinical, imaging and microbiological analyses suggest that pulp necrosis of teeth with intact crowns from HbSS patients is not caused by the presence of bacteria.}, } @article {pmid33434009, year = {2021}, author = {Brandon, AM and Garcia, AM and Khlystov, NA and Wu, WM and Criddle, CS}, title = {Enhanced Bioavailability and Microbial Biodegradation of Polystyrene in an Enrichment Derived from the Gut Microbiome of Tenebrio molitor (Mealworm Larvae).}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.0c04952}, pmid = {33434009}, issn = {1520-5851}, abstract = {As the global threat of plastic pollution has grown in scale and urgency, so have efforts to find sustainable and efficient solutions. Research conducted over the past few years has identified gut environments within insect larvae, including Tenebrio molitor (yellow mealworms), as microenvironments uniquely suited to rapid plastic biodegradation. However, there is currently limited understanding of how the insect host and its gut microbiome collaborate to create an environment conducive to plastic biodegradation. In this work, we provide evidence that T. molitor secretes one or more emulsifying factor(s) (30-100 kDa) that mediate plastic bioavailability. We also demonstrate that the insect gut microbiome secretes factor(s) (<30 kDa) that enhance respiration on polystyrene (PS). We apply these insights to culture PS-fed gut microbiome enrichments, with elevated rates of respiration and degradation compared to the unenriched gut microbiome. Within the enrichment, we identified eight unique gut microorganisms associated with PS biodegradation including Citrobacter freundii, Serratia marcescens, and Klebsiella aerogenes. Our results demonstrate that both the mealworm itself and its gut microbiome contribute to accelerated plastic biodegradation. This work provides new insights into insect-mediated mechanisms of plastic degradation and potential strategies for cultivation of plastic-degrading microorganisms in future investigations and scale-up.}, } @article {pmid33433826, year = {2021}, author = {Chatkin, J and Correa, L and Santos, U}, title = {External Environmental Pollution as a Risk Factor for Asthma.}, journal = {Clinical reviews in allergy & immunology}, volume = {}, number = {}, pages = {}, pmid = {33433826}, issn = {1559-0267}, abstract = {Air pollution is a worrisome risk factor for global morbidity and mortality and plays a special role in many respiratory conditions. It contributes to around 8 million deaths/year, with outdoor exposure being responsible for more than 4.2 million deaths throughout the world, while more than 3.8 million die from situations related to indoor pollution. Pollutant agents induce several respiratory symptoms. In addition, there is a clear interference in numerous asthma outcomes, such as incidence, prevalence, hospital admission, visits to emergency departments, mortality, and asthma attacks, among others. The particulate matter group of pollutants includes coarse particles/PM10, fine particles/PM2.5, and ultrafine particles/PM0.1. The gaseous components include ground-level ozone, nitrogen dioxide, sulfur dioxide, and carbon monoxide. The timing, load, and route of allergen exposure are other items affecting allergic disease phenotypes. The complex interaction between pollutant exposures and human host factors has an implication in the development and rise of asthma as a public health problem. However, there are hiatuses in the understanding of the pathways in this disease. The routes through which pollutants induce asthma are multiple, and include the epigenetic changes that occur in the respiratory tract microbiome, oxidative stress, and immune dysregulation. In addition, the expansion of the modern Westernized lifestyle, which is characterized by intense urbanization and more time spent indoors, resulted in greater exposure to polluted air. Another point to consider is the different role of the environment according to age groups. Children growing up in economically disadvantaged neighborhoods suffer more important negative health impacts. This narrative review highlights the principal polluting agents, their sources of emission, epidemiological findings, and mechanistic evidence that links environmental exposures to asthma.}, } @article {pmid33433815, year = {2021}, author = {Chan, AP and Namjoshi, SS and Jardack, PM and Maloney, L and Ardjmand, A and Jackson, NN and Martin, MG}, title = {Long-Term Dietary Changes in Subjects with Glucose Galactose Malabsorption Secondary to Biallelic Mutations of SLC5A1.}, journal = {Digestive diseases and sciences}, volume = {}, number = {}, pages = {}, pmid = {33433815}, issn = {1573-2568}, support = {UL1TR001881/TR/NCATS NIH HHS/United States ; RC2 DK118640/DK/NIDDK NIH HHS/United States ; }, abstract = {BACKGROUND: Glucose galactose malabsorption (GGM) is a congenital diarrheal disorder of intestinal Na+/glucose cotransport (SGLT1/SLC5A1). The required glucose and galactose-restricted diet has been well described in infancy, but long-term nutrition follow-up is limited.

AIM: To perform a comprehensive nutritional assessment on a cohort of patients with GGM to gain insights into the consumption patterns within the population.

METHODS: A cross-sectional study examining dietary intake of a GGM cohort using prospective food records. The calories and nutrients of all foods, beverages, and condiments were analyzed with descriptive statistics and compared to intake patterns of age- and sex-matched NHANES groups.

RESULTS: The six patients were 0.7-26 years old. Whole foods and vegetable fats were major parts of the diet, while dairy and added sweeteners were restricted. Compared to typical US intakes, mean macronutrient distribution was 88th percentile from fat, 18th percentile from carbohydrates, and 78th percentile from protein. Fructose consumption, as a proportion of total sugar intake, decreased with age, from 86.1 to 50.4%. Meanwhile, glucose consumption increased with age, from 13.8 to 48.6% of sugar intake. However, the actual amount of glucose consumed remained low, equivalent to 4th percentile of US consumption level. Galactose intake was marginal throughout life.

CONCLUSIONS: A GGM diet is a high-fat and high-protein/low-carbohydrate diet that is rich in fruits and vegetables but limited in dairy and added sugar. Relatively less fructose but more glucose is incorporated into the diet with age. Future studies should investigate the effects of the GGM diet on gut microbiome and long-term health.}, } @article {pmid33433585, year = {2021}, author = {Jang, K and Purvis, JM and Kim, SW}, title = {Dose-response and functional role of whey permeate as a source of lactose and milk oligosaccharides on intestinal health and growth of nursery pigs.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skab008}, pmid = {33433585}, issn = {1525-3163}, abstract = {Two experiments were conducted to evaluate dose-response and supplemental effects of whey permeate on growth performance and intestinal health of nursery pigs. In Exp. 1, 1,080 pigs weaned at 6.24 kg body weight (BW) were allotted to 5 treatments (8 pens/treatment) with increasing levels of whey permeate in 3 phases (from 10 to 30%, 3 to 23%, and 0 to 9% for phase 1, 2, and 3, respectively) fed until 11 kg BW and then fed a common phase 4 diet (0% whey permeate) until 25 kg BW in a 48 d feeding trial. Feed intake and BW were measured at the end of each phase. In Exp. 2, 1,200 nursery pigs at 7.50 kg BW were allotted to 6 treatments (10 pens/treatment) with increasing levels of whey permeate from 0 to 18.75% fed until 11 kg BW. Feed intake and BW were measured during 11 d. Six pigs per treatment (1 per pens) were euthanized to collect the jejunum to evaluate tumor necrosis factor alpha, interleukin-8 (IL-8), transforming growth factor beta 1, mucin 2, histomorphology, digestive enzyme activity, crypt cell proliferation rate, and jejunal mucosa-associated microbiota. Data were analyzed using contrasts in the MIXED procedure and a broken-line analysis using the NLIN procedure of SAS. In Exp. 1, increasing whey permeate had quadratic effect (P < 0.05) on feed efficiency (G:F; maximum: 1.35 at 18.3%) in phase 1. Increasing whey permeate linearly increased (P < 0.05) average daily gain (ADG; 292 to 327 g/d) and G:F (0.96 to 1.04) of pigs in phase 2. In Exp. 2, increasing whey permeate linearly increased (P < 0.05) ADG (349 to 414 g/d) and G:F (0.78 to 0.85), and linearly increased (P < 0.05) crypt cell proliferation rate (27.8 to 37.0%). The breakpoint from a broken-line analysis was obtained at 13.6% whey permeate for maximal G:F. Increasing whey permeate tended to change IL-8 (quadratic, P = 0.052; maximum: 223 pg/mg at 10.9%), to decrease Firmicutes:Bacteroidetes (P = 0.073, 1.59 to 1.13), increase (P = 0.089) Bifidobacteriaceae (0.73 to 1.11%), and to decrease Enterobacteriaceae (P = 0.091, 1.04 to 0.52%) and Stretococcaceae (P = 0.094, 1.50 to 0.71%) in the jejunal mucosa. In conclusion, dietary inclusion of whey permeate increased growth of nursery pigs from 7 to 11 kg BW. Pigs grew most efficiently with 13.6% whey permeate. Improvement in growth performance partly attributed from stimulating intestinal immune response and enterocyte proliferation with positive changes in jejunal mucosa-associated microbiota in nursery pigs.}, } @article {pmid33433346, year = {2020}, author = {Almeida, AR and Domingues, I and Henriques, I}, title = {Zebrafish and water microbiome recovery after oxytetracycline exposure.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {272}, number = {}, pages = {116371}, doi = {10.1016/j.envpol.2020.116371}, pmid = {33433346}, issn = {1873-6424}, abstract = {Oxytetracycline (OTC) is a broad-spectrum antibiotic widely used in aquaculture, resulting in contamination of aquatic environments. In a previous study, we observed significant effects of OTC sublethal concentrations in zebrafish, its microbiome and the water bacterial community. Here we assessed the extent to which these effects are reversible after a recovery period. Zebrafish adults were exposed to OTC (10,000 μg/L) via water exposure. Effects were analyzed at 5 days (5 dE) and 2 months (2 mE) of exposure and recovery was assessed at 5 days (5dPE) and 1 month (1mPE) after exposure Impacts were observed in fish energetic reserves and in fish and water microbiomes structure, being significant even at 5 dE. At energetic reserves level, the effect in cellular energy allocation (CEA) was dependent on the exposure time: initially CEA increased while after 2 mE CEA decreased. At microbiome level, diversity was not affected but the richness of the water microbiome significantly decreased at 2 mE. Regarding the post-exposure period, at CEA level, organisms seem to recover. In water and gut microbiomes OTC effects were also attenuated after exposure ceases, indicating a recovery. Even so, the structure of water exposed community remained significantly different towards the control, while richness of this community significantly increased at 1mPE. During exposure the relative abundance of 11 and 16 genera was significantly affected in the gut and water microbiomes, respectively, though these numbers decreased to 4 and 8 genera in the post-exposure period. At functional level during exposure 12 and 13 pathways were predicted to be affected in zebrafish gut and water microbiomes respectively, while post-exposure few pathways remained significantly affected. Hence, our results suggest a recovery of the fish fitness as well as of the water and intestine microbiomes after exposure ceases. Even so, some of the effects caused by OTC remain significant after this recovery period.}, } @article {pmid33433023, year = {2021}, author = {Chan, CWH and Leung, TF and Choi, KC and Tsui, SKW and Wong, CL and Chow, KM and Chan, JYW}, title = {Association of early-life gut microbiome and lifestyle factors in the development of eczema in Hong Kong infants.}, journal = {Experimental dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/exd.14280}, pmid = {33433023}, issn = {1600-0625}, abstract = {Childhood eczema is common but its prevalence is variable in different regions of the world. In this study, we explore the associations of various risk factors such as the microbiome, environment, lifestyle, diet and maternal stress with the development of eczema among infants in Hong Kong. Upon enrolment in the study, the infants' parents provided demographic data by self-reporting. At enrolment and 1 year after birth, the infants' allergic conditions, lifestyles and dietary factors and the degree of maternal stress were assessed using various questionnaires. The infants' gut microbiomes were analysed by 16S RNA sequencing, and the longitudinal changes in various bacterial strains were compared between control and eczema-affected groups. Multivariate analyses (after adjustment for other significant factors) revealed that the changes in the abundance of Hungatella hathewayi in the gut were significantly associated with the development of eczema (p = 0.005). In conclusion, the increased abundance of Hungatella hathewayi was associated with an increased risk of developing eczema by 1 year of age. This study thus explored the potential risk factors for the development of eczema in Hong Kong infants, and sheds light on the possible association between early-life gut microbiome and other environmental factors.}, } @article {pmid33432923, year = {2021}, author = {Tyagi, AM and Darby, TM and Hsu, E and Yu, M and Pal, S and Dar, H and Li, JY and Adams, J and Jones, RM and Pacifici, R}, title = {The gut microbiota is a transmissible determinant of skeletal maturation.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33432923}, issn = {2050-084X}, support = {DK112946/NH/NIH HHS/United States ; DK108842/NH/NIH HHS/United States ; RR028009/NH/NIH HHS/United States ; DK098391/NH/NIH HHS/United States ; }, abstract = {Genetic factors account for the majority of the variance of human bone mass, but the contribution of non-genetic factors remains largely unknown. By utilizing maternal/offspring transmission, cohabitation, or fecal material transplantation (FMT) studies, we investigated the influence of the gut microbiome on skeletal maturation. We show that the gut microbiome is a communicable regulator of bone structure and turnover in mice. In addition, we found that the acquisition of a specific bacterial strain, segmented filamentous bacteria (SFB), a gut microbe that induces intestinal Th17 cell expansion, was sufficient to negatively impact skeletal maturation. These findings have significant translational implications, as the identification of methods or timing of microbiome transfer may lead to the development of bacteriotherapeutic interventions to optimize skeletal maturation in humans. Moreover, the transfer of SFB-like microbes capable of triggering the expansion of human Th17 cells during therapeutic FMT procedures could lead to significant bone loss in fecal material recipients.}, } @article {pmid33432778, year = {2021}, author = {Hariharan, R and Mousa, A and de Courten, B}, title = {Influence of AMY1A copy number variations on obesity and other cardiometabolic risk factors: A review of the evidence.}, journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity}, volume = {}, number = {}, pages = {}, doi = {10.1111/obr.13205}, pmid = {33432778}, issn = {1467-789X}, abstract = {The rising incidence of obesity and type 2 diabetes is contributing to the escalating burden of disease globally. These metabolic disorders are closely linked with diet and in particular with carbohydrate consumption; hence, it is important to understand the underlying mechanisms that influence carbohydrate metabolism. Amylase, the enzyme responsible for the digestion of starch, is coded by the genes AMY1A, AMY1B, and AMY1C (salivary amylase) and AMY2A and AMY2B (pancreatic amylase). Previous studies demonstrate wide variations in AMY1A copy numbers, which can be attributed to several genetic, nutritional, and geographical diversities seen in populations globally. Current literature suggests that AMY1A copy number variations are important in obesity and other cardiometabolic disorders through their effects on glucose and lipid homeostasis, inflammatory markers, and the gut microbiome. This review synthesizes the available evidence to improve understanding of the role of AMY1A in obesity and related cardiometabolic risk factors and disorders including insulin resistance and type 2 diabetes, cardiovascular risk and inflammation, and the gut microbiome.}, } @article {pmid33432727, year = {2021}, author = {Camarena-Pozos, DA and Flores-Núñez, VM and López, MG and Partida-Martínez, LP}, title = {Fungal volatiles emitted by members of the microbiome of desert plants are diverse and capable of promoting plant growth.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15395}, pmid = {33432727}, issn = {1462-2920}, abstract = {Fungi represent a group of eukaryotic microorganisms that are an important part of the plant microbiome. They produce a vast array of metabolites, including fungal volatile organic compounds (fVOCs). However, the diversity and biological activities of fVOCs emitted by the mycobiota of plants native to arid and semi-arid environments remains under-explored. We characterized the chemical diversity of fVOCs produced by 22 representative members of the microbiome of agaves and cacti using SPME-GC-MS. We further tested the effects of pure compounds on the growth and development of Arabidopsis thaliana and host plants. Members of the Sordariomycetes (9 strains), Eurotiomycetes (3), Dothideomycetes (8), Saccharomycetes (1) and Mucoromycetes (1) were included in our study. We identified 94 fungal organic volatiles classified in nine chemical classes. Terpenes showed the greatest chemical diversity, followed by alcohols and aliphatic compounds. We discovered that camphene and benzyl benzoate, together with the widely distributed and already tested benzyl alcohol, 2-phenylethyl alcohol and 3-methyl-1-butanol, improved plant growth and development of A. thaliana, Agave tequilana and Agave salmiana. Our studies on the fungal VOCs from desert plants underscore an untapped chemical diversity with promising biotechnological applications. This article is protected by copyright. All rights reserved.}, } @article {pmid33432685, year = {2021}, author = {Neu, AT and Hughes, IV and Allen, EE and Roy, K}, title = {Decade-scale stability and change in a marine bivalve microbiome.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15796}, pmid = {33432685}, issn = {1365-294X}, abstract = {Predicting how populations and communities of organisms will respond to anthropogenic change is of paramount concern in ecology today. For communities of microorganisms, however, these predictions remain challenging, primarily due to data limitations. Information about long-term dynamics of host-associated microbial communities, in particular, are lacking. In this study, we use well-preserved and freshly collected samples of soft tissue from a marine bivalve host, Donax gouldii, at a single site to quantify the diversity and composition of its microbiome over a decadal timescale. Site-level measurements of temperature, salinity and chlorophyll a allowed us to test how the microbiome of this species responded to two natural experiments - a seasonal increase in temperature and a phytoplankton bloom. Our results show that ethanol-preserved tissue can provide high-resolution information about temporal trends in compositions of host-associated microbial communities. Specifically, we found that the richness of amplicon sequence variants (ASVs) associated with D. gouldii did not change significantly over time despite increases in water temperature (+1.6°C due to seasonal change) and chlorophyll a concentration (more than nine-fold). The phylogenetic composition of the communities, on the other hand, varied significantly between all collection years, with only six ASVs persisting over our sampling period. Overall, these results suggest that the diversity of microbial taxa associated with D. gouldii has remained stable over time and in response to seasonal environmental change over the course of more than a decade, but such stability is underlain by substantial turnover in the composition of the microbiome.}, } @article {pmid33432580, year = {2021}, author = {Yamane, K and Nakamura, H and Hamasaki, M and Minei, Y and Aibara, N and Shimizu, T and Kawakami, A and Nakashima, M and Kuroda, N and Ohyama, K}, title = {Immune complexome analysis reveals the presence of immune complexes and identifies disease-specific immune complex antigens in saliva samples from patients with Sjögren's syndrome.}, journal = {Clinical and experimental immunology}, volume = {}, number = {}, pages = {}, doi = {10.1111/cei.13574}, pmid = {33432580}, issn = {1365-2249}, abstract = {Sjögren's syndrome (SS) is a chronic autoimmune disease that mainly damages the salivary and lacrimal glands. Immune complex (IC) formation triggers local inflammation through IC deposition and decreased antigen function. Some ICs can leak from the lesion and into the saliva but no salivary ICs have been reported to date. We used immune complexome analysis to comprehensively identify antigens incorporated into IC (IC-antigens) in saliva samples from patients with SS (n=9) or with xerostomia (n=7). Neutrophil defensin 1 (67%), small proline-rich protein 2D (67%), myeloperoxidase (44%), neutrophil elastase (44%), cathepsin G (33%), nuclear mitotic apparatus 1 (33%) and phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit gamma (33%) were identified as new IC-antigens specifically and frequently detected in the saliva of SS patients. Of these, neutrophil defensin 1, myeloperoxidase, neutrophil elastase and cathepsin G are neutrophil intracellular proteins, which suggests that repeated destruction of neutrophils due to abnormal autoimmunity may be involved in the pathogenesis of SS. We also analyzed serum samples from three SS patients. There was little overlap of IC-antigens between two of the samples (less than 30% of the IC-antigens in the saliva samples), suggesting that many ICs are formed locally and independently of the circulation. In addition, we found that four SS-specific salivary antigens show sequence homology with several proteins of oral microbiomes but no antigen has homology with Epstein-Barr virus proteins. The homology between some IC-antigens and oral microbiome proteins may indicate the impact of oral infection on local autoimmunity through molecular mimicry theory.}, } @article {pmid33432577, year = {2021}, author = {Wood, HL and Acharjee, A and Pearce, H and Quraishi, MN and Powell, RM and Rossiter, AE and Beggs, AD and Ewer, AK and Moss, P and Toldi, G}, title = {Breastfeeding promotes early neonatal regulatory T cell expansion and immune tolerance of non-inherited maternal antigens.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.14736}, pmid = {33432577}, issn = {1398-9995}, abstract = {BACKGROUND: Breastfeeding is associated with long-term health benefits, such as a lower incidence of childhood infections, asthma, obesity and autoimmune disorders. However, little is known regarding how the maternal and neonatal immune systems interact after parturition when the neonate receives nutrition from maternal breastmilk.

METHODS: We undertook a comparative analysis of immune repertoire and function at birth and 3 weeks of age in a cohort of 38 term neonates born by caesarean section grouped according to feeding method (breastmilk versus formula). We used flow cytometry to study the immune phenotype in neonatal and maternal blood samples and mixed lymphocyte reactions to establish the proliferation response of neonatal versus maternal lymphocytes and vice versa. The microbiome of neonatal stool samples was also investigated using 16S rRNA sequencing.

RESULTS: We show that the proportion of regulatory T cells (Tregs) increases in this period and is nearly two-fold higher in exclusively breastfed neonates compared to those who received formula milk only. Moreover, breastfed neonates show a specific and Treg-dependent reduction in proliferative T cell responses to non-inherited maternal antigens (NIMA), associated with a reduction in inflammatory cytokine production. We also observed the enrichment of short chain fatty acid producing taxa (Veillonella and Gemella) in stool samples of exclusively breastfed neonates.

CONCLUSIONS: These data indicate that exposure of the neonate to maternal cells through breastfeeding acts to drive the maturation of Tregs and 'tolerizes' the neonate towards NIMA.}, } @article {pmid33432532, year = {2021}, author = {Nunn, KL and Witkin, SS and Schneider, GM and Boester, A and Nasioudis, D and Minis, E and Gliniewicz, K and Forney, LJ}, title = {Changes in the Vaginal Microbiome during the Pregnancy to Postpartum Transition.}, journal = {Reproductive sciences (Thousand Oaks, Calif.)}, volume = {}, number = {}, pages = {}, pmid = {33432532}, issn = {1933-7205}, abstract = {Substantial changes in the composition of the vaginal microbiome occur following the end of pregnancy. To identify potential drivers of microbiome changes in individual women during the pregnancy to postpartum transition, we evaluated vaginal samples from 48 pregnant women during their first and third trimesters and postpartum. We determined the species composition of vaginal communities and the vaginal fluid levels of compounds involved in mediating changes in host physiology and the immune system at each time point. We used linear mixed-effects models to characterize associations. Consistent with previous reports, but with a larger sample size, a US population, and variations in the dominant bacteria, the vaginal microbiome was found to be more diverse during the postpartum period. There was a lower abundance of Lactobacillus and significantly higher proportions of Streptococcus anginosus and Prevotella bivia. Moreover, we uniquely demonstrated that postpartum vaginal secretions were also altered postpartum. There were elevated levels of hyaluronan and Hsp70 and decreased levels of the D- and L-lactic acid isomers. We posit that these variations are consequences of alterations in the vagina after delivery that profoundly alter the host environment and, thus, lead to changes in the capability of different bacterial species to survive and proliferate.}, } @article {pmid33432373, year = {2021}, author = {Malakar, D and Sarathbabu, S and Borah, P and Kumar, NS}, title = {Fish gill microbiome from India's largest Brahmaputra River-a trans-border biodiversity hotspot region.}, journal = {Environmental monitoring and assessment}, volume = {193}, number = {2}, pages = {56}, doi = {10.1007/s10661-021-08847-z}, pmid = {33432373}, issn = {1573-2959}, support = {No. BT/BI/12/060/2012//Department of Biotechnology, Government of India/ ; }, mesh = {Animals ; Biodiversity ; Environmental Monitoring ; Gills ; India ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Rivers ; }, abstract = {In this study, we sequenced the V3-V4 region of 16S rRNA gene amplicon using paired-end Illumina HiSeq to study the bacterial community in the gills of fish from the bank of the trans-border river of Brahmaputra, Northeast India. Metagenome data consisted of 278,784 reads, 248-bp length, and 56.48% GC content with 85% sequence having a Phred score Q = 30. Community metagenomics revealed a total of 631 genera belonging to 22 different phyla, dominated by Proteobacteria (118,222 features), Firmicutes (101,043 features), Actinobacteria (34,189 features), Bacteroidetes (17,977 features), and Cyanobacteria (2730 features). The bacterial community identified was composed of both pathogenic zoonotic and non-harmful groups. The pathway or functional analysis of the fish gill microbiome exhibited 21 different pathways which also included the pathogenic-related functions. Our data detected a wide group of bacterial communities that will be useful in further isolating and characterizing the pathogenic bacteria from the fish and also to understand the bacterial association in highly consumed fish.}, } @article {pmid33432310, year = {2021}, author = {Guo, L and Xiao, P and Zhang, X and Yang, Y and Yang, M and Wang, T and Lu, H and Tian, H and Wang, H and Liu, J}, title = {Inulin ameliorates schizophrenia via modulation of the gut microbiota and anti-inflammation in mice.}, journal = {Food & function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d0fo02778b}, pmid = {33432310}, issn = {2042-650X}, abstract = {The microbiome-gut-brain (MGB) axis, which regulates neurological and cognitive functions, plays an essential role in schizophrenia (SCZ) progression. Dietary inulin could be a novel strategy for the treatment of SCZ due to its modulating effects on the gut microbiota. In this study, the effects of inulin on mice with SCZ were studied. As indicated by the behavioural tests, expression of neurotransmitters, inflammatory indicators, and brain morphology, inulin administration ameliorated aberrant behaviours (locomotor hypoactivity, anxiety disorders and depressive behaviours, and impaired learning and spatial recognition memory) and effectively reduced neuroinflammation and neuronal damage. In addition, inulin improved intestinal integrity and permeability, as indicated by the elevated expression of tight junction proteins (p < 0.05). The results of 16S rRNA sequencing and analysis showed that inulin increased the abundance of Lactobacillus and Bifidobacterium, which were negatively correlated with 5-hydroxytryptamine and inflammatory cytokines and positively correlated with brain-derived neurotrophic factor (BDNF). Inulin caused a reduction in Akkermansia that was positively correlated with inflammatory cytokines and negatively correlated with BDNF. These results suggested that dietary inulin modulated the gut microbiota and exerted anti-inflammatory effects in mice though the MGB axis, which further ameliorated SCZ. Therefore, the results of this study provide a potential explanation for inulin intervention in the treatment of SCZ.}, } @article {pmid33432175, year = {2021}, author = {Asnicar, F and Berry, SE and Valdes, AM and Nguyen, LH and Piccinno, G and Drew, DA and Leeming, E and Gibson, R and Le Roy, C and Khatib, HA and Francis, L and Mazidi, M and Mompeo, O and Valles-Colomer, M and Tett, A and Beghini, F and Dubois, L and Bazzani, D and Thomas, AM and Mirzayi, C and Khleborodova, A and Oh, S and Hine, R and Bonnett, C and Capdevila, J and Danzanvilliers, S and Giordano, F and Geistlinger, L and Waldron, L and Davies, R and Hadjigeorgiou, G and Wolf, J and Ordovás, JM and Gardner, C and Franks, PW and Chan, AT and Huttenhower, C and Spector, TD and Segata, N}, title = {Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {33432175}, issn = {1546-170X}, abstract = {The gut microbiome is shaped by diet and influences host metabolism; however, these links are complex and can be unique to each individual. We performed deep metagenomic sequencing of 1,203 gut microbiomes from 1,098 individuals enrolled in the Personalised Responses to Dietary Composition Trial (PREDICT 1) study, whose detailed long-term diet information, as well as hundreds of fasting and same-meal postprandial cardiometabolic blood marker measurements were available. We found many significant associations between microbes and specific nutrients, foods, food groups and general dietary indices, which were driven especially by the presence and diversity of healthy and plant-based foods. Microbial biomarkers of obesity were reproducible across external publicly available cohorts and in agreement with circulating blood metabolites that are indicators of cardiovascular disease risk. While some microbes, such as Prevotella copri and Blastocystis spp., were indicators of favorable postprandial glucose metabolism, overall microbiome composition was predictive for a large panel of cardiometabolic blood markers including fasting and postprandial glycemic, lipemic and inflammatory indices. The panel of intestinal species associated with healthy dietary habits overlapped with those associated with favorable cardiometabolic and postprandial markers, indicating that our large-scale resource can potentially stratify the gut microbiome into generalizable health levels in individuals without clinically manifest disease.}, } @article {pmid33432149, year = {2021}, author = {Lee, SH and Cho, SY and Yoon, Y and Park, C and Sohn, J and Jeong, JJ and Jeon, BN and Jang, M and An, C and Lee, S and Kim, YY and Kim, G and Kim, S and Kim, Y and Lee, GB and Lee, EJ and Kim, SG and Kim, HS and Kim, Y and Kim, H and Yang, HS and Kim, S and Kim, S and Chung, H and Moon, MH and Nam, MH and Kwon, JY and Won, S and Park, JS and Weinstock, GM and Lee, C and Yoon, KW and Park, H}, title = {Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {33432149}, issn = {2058-5276}, support = {10067758//Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)/ ; NRF-2018M3A9F3056902//National Research Foundation of Korea (NRF)/ ; 2018R1C1B6005768//National Research Foundation of Korea (NRF)/ ; NRF-2018R1A2A1A05019794//National Research Foundation of Korea (NRF)/ ; 2015K1A4A3047851//National Research Foundation of Korea (NRF)/ ; 2017R1C1B2011196//National Research Foundation of Korea (NRF)/ ; NRF-2017M3A9F304636//National Research Foundation of Korea (NRF)/ ; 2017-2019//Ewha Womans University (Ewha)/ ; HI17C1076//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; NCC-1911267//National Cancer Center (NCC)/ ; GIST Research Institute (GRI)//Gwangju Institute of Science and Technology (GIST)/ ; }, abstract = {The gut microbiome can influence the development of tumours and the efficacy of cancer therapeutics1-5; however, the multi-omics characteristics of antitumour bacterial strains have not been fully elucidated. In this study, we integrated metagenomics, genomics and transcriptomics of bacteria, and analyses of mouse intestinal transcriptome and serum metabolome data to reveal an additional mechanism by which bacteria determine the efficacy of cancer therapeutics. In gut microbiome analyses of 96 samples from patients with non-small-cell lung cancer, Bifidobacterium bifidum was abundant in patients responsive to therapy. However, when we treated syngeneic mouse tumours with commercial strains of B. bifidum to establish relevance for potential therapeutic uses, only specific B. bifidum strains reduced tumour burden synergistically with PD-1 blockade or oxaliplatin treatment by eliciting an antitumour host immune response. In mice, these strains induced tuning of the immunological background by potentiating the production of interferon-γ, probably through the enhanced biosynthesis of immune-stimulating molecules and metabolites.}, } @article {pmid33432015, year = {2021}, author = {Debesa-Tur, G and Pérez-Brocal, V and Ruiz-Ruiz, S and Castillejo, A and Latorre, A and Soto, JL and Moya, A}, title = {Metagenomic analysis of formalin-fixed paraffin-embedded tumor and normal mucosa reveals differences in the microbiome of colorectal cancer patients.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {391}, pmid = {33432015}, issn = {2045-2322}, support = {AECC 2017-1485//Fundación Científica Asociación Española Contra el Cáncer/ ; AECC 2017-1485//Fundación Científica Asociación Española Contra el Cáncer/ ; AECC 2017-1485//Fundación Científica Asociación Española Contra el Cáncer/ ; AECC 2017-1485//Fundación Científica Asociación Española Contra el Cáncer/ ; }, abstract = {An increased risk of developing colorectal cancer (CRC) and other types of tumor is associated to Lynch syndrome (LS), an inherited condition caused by germline mutations in mismatch repair genes. We selected a cohort of LS patients that had developed CRC and had undergone surgical resection. Formalin-fixed paraffin embedded (FFPE) tissue blocks from matched colorectal and normal mucosa were used for genomic DNA extraction with a commercial kit and sequenced by high-throughput sequencing. A metagenomic approach enabled the taxonomic and functional identification of the microbial community and associated genes detected in the specimens. Slightly lower taxonomic diversity was observed in the tumor compared to the non-tumor tissue. Furthermore, the most remarkable differences between tumors and healthy tissue was the significant increase in the genus Fusobacterium in the former, in particular the species F. nucleatum, as well as Camplylobacter or Bacteroides fragilis, in accordance with previous studies of CRC. However, unlike prior studies, the present work is not based on directed detection by qPCR but instead uses a metagenomic approach to retrieve the whole bacterial community, and addresses the additional difficulty of using long-term stored FFPE samples.}, } @article {pmid33431988, year = {2021}, author = {Jin, X and Zhang, Y and Celniker, SE and Xia, Y and Mao, JH and Snijders, AM and Chang, H}, title = {Gut microbiome partially mediates and coordinates the effects of genetics on anxiety-like behavior in Collaborative Cross mice.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {270}, pmid = {33431988}, issn = {2045-2322}, support = {81961128022//National Natural Science Foundation of China/ ; DE AC02-05CH11231//Laboratory Directed Research and Development/ ; DE AC02-05CH11231//Laboratory Directed Research and Development/ ; R01ES031322/ES/NIEHS NIH HHS/United States ; R01CA184476/CA/NCI NIH HHS/United States ; }, abstract = {Growing evidence suggests that the gut microbiome (GM) plays a critical role in health and disease. However, the contribution of GM to psychiatric disorders, especially anxiety, remains unclear. We used the Collaborative Cross (CC) mouse population-based model to identify anxiety associated host genetic and GM factors. Anxiety-like behavior of 445 mice across 30 CC strains was measured using the light/dark box assay and documented by video. A custom tracking system was developed to quantify seven anxiety-related phenotypes based on video. Mice were assigned to a low or high anxiety group by consensus clustering using seven anxiety-related phenotypes. Genome-wide association analysis (GWAS) identified 141 genes (264 SNPs) significantly enriched for anxiety and depression related functions. In the same CC cohort, we measured GM composition and identified five families that differ between high and low anxiety mice. Anxiety level was predicted with 79% accuracy and an AUC of 0.81. Mediation analyses revealed that the genetic contribution to anxiety was partially mediated by the GM. Our findings indicate that GM partially mediates and coordinates the effects of genetics on anxiety.}, } @article {pmid33431904, year = {2021}, author = {Murphy, KM and Edwards, J and Louie, KB and Bowen, BP and Sundaresan, V and Northen, TR and Zerbe, P}, title = {Bioactive diterpenoids impact the composition of the root-associated microbiome in maize (Zea mays).}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {333}, pmid = {33431904}, issn = {2045-2322}, support = {Graduate Research Fellowship Program//National Science Foundation/ ; 1758976//National Science Foundation/ ; 2019-67011-29544//USDA NIFA/ ; DE-AC02-05CH11231//DOE Joint Genome Institute/ ; DE-AC02-05CH11231//Lawrence Berkeley National Laboratory/ ; }, abstract = {Plants deploy both primary and species-specific, specialized metabolites to communicate with other organisms and adapt to environmental challenges, including interactions with soil-dwelling microbial communities. However, the role of specialized metabolites in modulating plant-microbiome interactions often remains elusive. In this study, we report that maize (Zea mays) diterpenoid metabolites with known antifungal bioactivities also influence rhizosphere bacterial communities. Metabolite profiling showed that dolabralexins, antibiotic diterpenoids that are highly abundant in roots of some maize varieties, can be exuded from the roots. Comparative 16S rRNA gene sequencing determined the bacterial community composition of the maize mutant Zman2 (anther ear 2), which is deficient in dolabralexins and closely related bioactive kauralexin diterpenoids. The Zman2 rhizosphere microbiome differed significantly from the wild-type sibling with the most significant changes observed for Alphaproteobacteria of the order Sphingomonadales. Metabolomics analyses support that these differences are attributed to the diterpenoid deficiency of the Zman2 mutant, rather than other large-scale metabolome alterations. Together, these findings support physiological functions of maize diterpenoids beyond known chemical defenses, including the assembly of the rhizosphere microbiome.}, } @article {pmid33431800, year = {2021}, author = {Mocking, RJT and Naviaux, JC and Li, K and Wang, L and Monk, JM and Bright, AT and Figueroa, CA and Schene, AH and Ruhé, HG and Assies, J and Naviaux, RK}, title = {Metabolic features of recurrent major depressive disorder in remission, and the risk of future recurrence.}, journal = {Translational psychiatry}, volume = {11}, number = {1}, pages = {37}, pmid = {33431800}, issn = {2158-3188}, abstract = {Recurrent major depressive disorder (rMDD) is a relapsing-remitting disease with high morbidity and a 5-year risk of recurrence of up to 80%. This was a prospective pilot study to examine the potential diagnostic and prognostic value of targeted plasma metabolomics in the care of patients with rMDD in remission. We used an established LC-MS/MS platform to measure 399 metabolites in 68 subjects with rMDD (n = 45 females and 23 males) in antidepressant-free remission and 59 age- and sex-matched controls (n = 40 females and 19 males). Patients were then followed prospectively for 2.5 years. Metabolomics explained up to 43% of the phenotypic variance. The strongest biomarkers were gender specific. 80% of the metabolic predictors of recurrence in both males and females belonged to 6 pathways: (1) phospholipids, (2) sphingomyelins, (3) glycosphingolipids, (4) eicosanoids, (5) microbiome, and (6) purines. These changes traced to altered mitochondrial regulation of cellular redox, signaling, energy, and lipid metabolism. Metabolomics identified a chemical endophenotype that could be used to stratify rrMDD patients at greatest risk for recurrence with an accuracy over 0.90 (95%CI = 0.69-1.0). Power calculations suggest that a validation study of at least 198 females and 198 males (99 cases and 99 controls each) will be needed to confirm these results. Although a small study, these results are the first to show the potential utility of metabolomics in assisting with the important clinical challenge of prospectively identifying the patients at greatest risk of recurrence of a depressive episode and those who are at lower risk.}, } @article {pmid33431595, year = {2021}, author = {McNamara, MP and Singleton, JM and Cadney, MD and Ruegger, PM and Borneman, J and Garland, T}, title = {Early-life effects of juvenile Western diet and exercise on adult gut microbiome composition in mice.}, journal = {The Journal of experimental biology}, volume = {}, number = {}, pages = {}, doi = {10.1242/jeb.239699}, pmid = {33431595}, issn = {1477-9145}, abstract = {Alterations to the gut microbiome caused by changes in diet, consumption of antibiotics, etc., can affect host function. Moreover, perturbation of the microbiome during critical developmental periods potentially have long-lasting impacts on hosts. Using four selectively bred High Runner and four non-selected Control lines of mice, we examined the effects of early-life diet and exercise manipulations on the adult microbiome by sequencing the hypervariable Internal Transcribed Spacer region of the bacterial gut community. Mice from High Runner lines run ∼3-fold more on wheels than do Controls, and have several other phenotypic differences (e.g., higher food consumption and body temperature) that could alter the microbiome, either acutely or in terms of coevolution. Males from generation 76 were given wheels and/or Western diet from weaning until sexual maturity at 6 weeks of age, then housed individually without wheels on standard diet until 14 weeks of age, when fecal samples were taken. Juvenile Western diet reduced bacterial richness and diversity after the 8-week washout period (equivalent to ∼6 human years). We also found interactive effects of genetic linetype, juvenile diet, and/or juvenile exercise on microbiome composition and diversity. Microbial community structure clustered significantly in relation to both linetype and diet. Western diet also reduced the relative abundance of Muribaculum intestinale These results constitute one of the first reports of juvenile diet having long-lasting effects on the adult microbiome after a substantial washout period. Moreover, we found interactive effects of diet with early-life exercise exposure, and a dependence of these effects on genetic background.}, } @article {pmid33431578, year = {2021}, author = {Yeoh, YK and Zuo, T and Lui, GC and Zhang, F and Liu, Q and Li, AY and Chung, AC and Cheung, CP and Tso, EY and Fung, KS and Chan, V and Ling, L and Joynt, G and Hui, DS and Chow, KM and Ng, SSS and Li, TC and Ng, RW and Yip, TC and Wong, GL and Chan, FK and Wong, CK and Chan, PK and Ng, SC}, title = {Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19.}, journal = {Gut}, volume = {}, number = {}, pages = {}, pmid = {33431578}, issn = {1468-3288}, abstract = {OBJECTIVE: Although COVID-19 is primarily a respiratory illness, there is mounting evidence suggesting that the GI tract is involved in this disease. We investigated whether the gut microbiome is linked to disease severity in patients with COVID-19, and whether perturbations in microbiome composition, if any, resolve with clearance of the SARS-CoV-2 virus.

METHODS: In this two-hospital cohort study, we obtained blood, stool and patient records from 100 patients with laboratory-confirmed SARS-CoV-2 infection. Serial stool samples were collected from 27 of the 100 patients up to 30 days after clearance of SARS-CoV-2. Gut microbiome compositions were characterised by shotgun sequencing total DNA extracted from stools. Concentrations of inflammatory cytokines and blood markers were measured from plasma.

RESULTS: Gut microbiome composition was significantly altered in patients with COVID-19 compared with non-COVID-19 individuals irrespective of whether patients had received medication (p<0.01). Several gut commensals with known immunomodulatory potential such as Faecalibacterium prausnitzii, Eubacterium rectale and bifidobacteria were underrepresented in patients and remained low in samples collected up to 30 days after disease resolution. Moreover, this perturbed composition exhibited stratification with disease severity concordant with elevated concentrations of inflammatory cytokines and blood markers such as C reactive protein, lactate dehydrogenase, aspartate aminotransferase and gamma-glutamyl transferase.

CONCLUSION: Associations between gut microbiota composition, levels of cytokines and inflammatory markers in patients with COVID-19 suggest that the gut microbiome is involved in the magnitude of COVID-19 severity possibly via modulating host immune responses. Furthermore, the gut microbiota dysbiosis after disease resolution could contribute to persistent symptoms, highlighting a need to understand how gut microorganisms are involved in inflammation and COVID-19.}, } @article {pmid33431308, year = {2021}, author = {Frey, DL and Boutin, S and Dittrich, SA and Graeber, SY and Stahl, M and Wege, S and Herth, FJF and Sommerburg, O and Schultz, C and Mall, MA and Dalpke, AH}, title = {Relationship between airway dysbiosis, inflammation and lung function in adults with cystic fibrosis.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2020.12.022}, pmid = {33431308}, issn = {1873-5010}, abstract = {Airway dysbiosis has been associated with lung disease severity in patients with cystic fibrosis (CF). However, the relationship between dysbiosis, airway inflammation and lung function impairement remains poorly understood. The aim of this study was therefore to determine how the structure of the sputum microbiota, airway inflammation markers and spirometry are related in patients with CF. Sputum samples were collected from 106 CF patients between 12 and 72 years. These were analyzed by 16S rRNA gene amplicon sequencing. Moreover, levels of pro-inflammatory cytokines (IL-1β, IL-8, IL-6 and TNF-α) and Neutrophil elastase (NE) were determined. The relationship between the microbiota, inflammation markers and forced expiratory volume in one second percent predicted (FEV1% predicted) was evaluated by multi-parameter analysis. The microbiota α-diversity correlated inverse with inflammation markers IL-1β, IL-8, TNF-α, NE and positively with FEV1% predicted. Patients could be divided into 7 clusters based on their microbiota structure. The most diverse cluster was defined by oropharyngeal-like flora (OF) while the others were characterized by the dominance of a single pathogen. Patients with the diverse OF microbiota cluster had lower sputum inflammatory markers and higher FEV1% predicted compared to patients with a pathogen-dominated microbiota including Pseudomonas aeruginosa. Our results suggest that the diversity of the airway microbiota is an important biomarker of the severity of airway inflammation linking dysbiosis to lung function decline in patients with CF.}, } @article {pmid33431167, year = {2021}, author = {Jain, T and Dudeja, V}, title = {Neoadjuvant therapy alters the biliary microbiome in PDAC.}, journal = {American journal of surgery}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.amjsurg.2020.12.050}, pmid = {33431167}, issn = {1879-1883}, } @article {pmid33431022, year = {2021}, author = {Zhao, J and Zhang, Z and Zhang, S and Page, G and Jaworski, NW}, title = {The role of lactose in weanling pig nutrition: a literature and meta-analysis review.}, journal = {Journal of animal science and biotechnology}, volume = {12}, number = {1}, pages = {10}, pmid = {33431022}, issn = {1674-9782}, abstract = {Lactose plays a crucial role in the growth performance of pigs at weaning because it is a palatable and easily digestible energy source that eases the transition from milk to solid feed. However, the digestibility of lactose declines after weaning due to a reduction in endogenous lactase activity in piglets. As a result, some lactose may be fermented in the gastrointestinal tract of pigs. Fermentation of lactose by intestinal microbiota yields lactic acid and volatile fatty acids, which may positively regulate the intestinal environment and microbiome, resulting in improved gastrointestinal health of weanling pigs. We hypothesize that the prebiotic effect of lactose may play a larger role in weanling pig nutrition as the global feed industry strives to reduce antibiotic usage and pharmacological levels of zinc oxide and supra-nutritional levels of copper. Evidence presented in this review indicates that high dietary lactose improves growth performance of piglets, as well as the growth of beneficial bacteria, particularly Lactobacillus, with the positive effects being more pronounced in the first 2 weeks after weaning. However, the risk of post-weaning diarrhea may increase as pigs get older due to reduced lactase activity, high dietary lactose concentrations, and larger feed intakes, all of which may lead to excessive lactose fermentation in the intestine of the pig. Therefore, dietary lactose levels exert different effects on growth performance and gastrointestinal physiological functions in different feeding phases of weanling pigs. However, no formal recommendation of lactose for weanling pigs has been reported. A meta-analysis approach was used to determine that diets fed to swine should include 20%, 15%, and 0 lactose from d 0-7, d 7-14, and d 14-35 post-weaning, respectively. However, sustainable swine production demands that economics must also be taken into account as lactose and lactose containing ingredients are expensive. Therefore, alternatives to lactose, so called "lactose equivalents" have also been studied in an effort to decrease feed cost while maintaining piglet performance with lower dietary lactose inclusions. In summary, the present review investigated dose-response effects of dietary lactose supplementation to exert positive responses and begin to elucidate its mechanisms of action in post-weaning pig diets. The results may help to replace some or all lactose in the diet of weanling pigs, while improving production economics given the high cost of lactose and availability in some swine production markets.}, } @article {pmid33430915, year = {2021}, author = {Maes, M and Higginson, E and Pereira-Dias, J and Curran, MD and Parmar, S and Khokhar, F and Cuchet-Lourenço, D and Lux, J and Sharma-Hajela, S and Ravenhill, B and Hamed, I and Heales, L and Mahroof, R and Solderholm, A and Forrest, S and Sridhar, S and Brown, NM and Baker, S and Navapurkar, V and Dougan, G and Bartholdson Scott, J and Conway Morris, A}, title = {Ventilator-associated pneumonia in critically ill patients with COVID-19.}, journal = {Critical care (London, England)}, volume = {25}, number = {1}, pages = {25}, pmid = {33430915}, issn = {1466-609X}, support = {WT 2055214/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; Cambridge BRC grant//National Institute for Health Research/International ; }, abstract = {BACKGROUND: Pandemic COVID-19 caused by the coronavirus SARS-CoV-2 has a high incidence of patients with severe acute respiratory syndrome (SARS). Many of these patients require admission to an intensive care unit (ICU) for invasive ventilation and are at significant risk of developing a secondary, ventilator-associated pneumonia (VAP).

OBJECTIVES: To study the incidence of VAP and bacterial lung microbiome composition of ventilated COVID-19 and non-COVID-19 patients.

METHODS: In this retrospective observational study, we compared the incidence of VAP and secondary infections using a combination of microbial culture and a TaqMan multi-pathogen array. In addition, we determined the lung microbiome composition using 16S RNA analysis in a subset of samples. The study involved 81 COVID-19 and 144 non-COVID-19 patients receiving invasive ventilation in a single University teaching hospital between March 15th 2020 and August 30th 2020.

RESULTS: COVID-19 patients were significantly more likely to develop VAP than patients without COVID (Cox proportional hazard ratio 2.01 95% CI 1.14-3.54, p = 0.0015) with an incidence density of 28/1000 ventilator days versus 13/1000 for patients without COVID (p = 0.009). Although the distribution of organisms causing VAP was similar between the two groups, and the pulmonary microbiome was similar, we identified 3 cases of invasive aspergillosis amongst the patients with COVID-19 but none in the non-COVID-19 cohort. Herpesvirade activation was also numerically more frequent amongst patients with COVID-19.

CONCLUSION: COVID-19 is associated with an increased risk of VAP, which is not fully explained by the prolonged duration of ventilation. The pulmonary dysbiosis caused by COVID-19, and the causative organisms of secondary pneumonia observed are similar to that seen in critically ill patients ventilated for other reasons.}, } @article {pmid33430766, year = {2021}, author = {Wolf, PG and Devendran, S and Doden, HL and Ly, LK and Moore, T and Takei, H and Nittono, H and Murai, T and Kurosawa, T and Chlipala, GE and Green, SJ and Kakiyama, G and Kashyap, P and McCracken, VJ and Gaskins, HR and Gillevet, PM and Ridlon, JM}, title = {Berberine alters gut microbial function through modulation of bile acids.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {24}, pmid = {33430766}, issn = {1471-2180}, support = {Hatch ILLU-538-916//Department of Animal Sciences, University of Illinois at Urbana-Champaign (US)/ ; RB18068//University of Illinois/ ; 1RO1 CA204808-01//Foundation for the National Institutes of Health/ ; 1RO1 CA204808-01//Foundation for the National Institutes of Health/ ; R01CA179243//Foundation for the National Institutes of Health/ ; Fire Grant//College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign/ ; Fire Grant//College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign/ ; Young Investigators Grant for Probiotic Research//Danone/ ; Graduate Research Fellowship//National Science Foundation (US)/ ; T32CA057699//National Cancer Institute (US)/ ; }, abstract = {BACKGROUND: Berberine (BBR) is a plant-based nutraceutical that has been used for millennia to treat diarrheal infections and in contemporary medicine to improve patient lipid profiles. Reduction in lipids, particularly cholesterol, is achieved partly through up-regulation of bile acid synthesis and excretion into the gastrointestinal tract (GI). The efficacy of BBR is also thought to be dependent on structural and functional alterations of the gut microbiome. However, knowledge of the effects of BBR on gut microbiome communities is currently lacking. Distinguishing indirect effects of BBR on bacteria through altered bile acid profiles is particularly important in understanding how dietary nutraceuticals alter the microbiome.

RESULTS: Germfree mice were colonized with a defined minimal gut bacterial consortium capable of functional bile acid metabolism (Bacteroides vulgatus, Bacteroides uniformis, Parabacteroides distasonis, Bilophila wadsworthia, Clostridium hylemonae, Clostridium hiranonis, Blautia producta; B4PC2). Multi-omics (bile acid metabolomics, 16S rDNA sequencing, cecal metatranscriptomics) were performed in order to provide a simple in vivo model from which to identify network-based correlations between bile acids and bacterial transcripts in the presence and absence of dietary BBR. Significant alterations in network topology and connectivity in function were observed, despite similarity in gut microbial alpha diversity (P = 0.30) and beta-diversity (P = 0.123) between control and BBR treatment. BBR increased cecal bile acid concentrations, (P < 0.05), most notably deoxycholic acid (DCA) (P < 0.001). Overall, analysis of transcriptomes and correlation networks indicates both bacterial species-specific responses to BBR, as well as functional commonalities among species, such as up-regulation of Na+/H+ antiporter, cell wall synthesis/repair, carbohydrate metabolism and amino acid metabolism. Bile acid concentrations in the GI tract increased significantly during BBR treatment and developed extensive correlation networks with expressed genes in the B4PC2 community.

CONCLUSIONS: This work has important implications for interpreting the effects of BBR on structure and function of the complex gut microbiome, which may lead to targeted pharmaceutical interventions aimed to achieve the positive physiological effects previously observed with BBR supplementation.}, } @article {pmid33430702, year = {2021}, author = {Wang, Y and Gao, X and Zhang, X and Xiao, F and Hu, H and Li, X and Dong, F and Sun, M and Xiao, Y and Ge, T and Li, D and Yu, G and Liu, Z and Zhang, T}, title = {Microbial and metabolic features associated with outcome of infliximab therapy in pediatric Crohn's disease.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-18}, doi = {10.1080/19490976.2020.1865708}, pmid = {33430702}, issn = {1949-0984}, abstract = {Gut microbial dysbiosis and altered metabonomics have been implicated in the pathogenesis of Crohn's disease (CD). The aim of our study was to characterize the gut microbiome structure and metabolic activities in pediatric CD patients with different clinical outcomes after infliximab (IFX) therapy. Fecal samples were collected from 20 healthy children and 29 newly diagnosed pediatric CD patients. 16S rRNA/ITS2 gene sequencing and targeted metabolomics analysis were applied to profile the gut bacterial microbiome, mycobiome, and metabolome, respectively. Pediatric CD patients exhibited lower relative abundances of short-chain fatty acids (SCFAs)-producing bacteria including Faecalibacterium, Clostridium clusters IV and XIVb, Roseburia, and Ruminococcus, which were correlated with reduced fecal levels of SCFAs. Decreased unconjugated bile acids (BAs) pool size and a lower unconjugated/conjugated BAs ratio were associated with reduced relative abundances of Bifidobacterium and Clostridium clusters IV and XIVb which contain bile salt hydrolases (BSH) genes. IFX treatment enriched the BSH-producing bacteria in CD subjects, which may explain a decreased level of conjugated BAs and an increase in unconjugated BAs as well as the unconjugated/conjugated BAs ratio. Furthermore, a sustained response (SR) of IFX therapy was associated with higher abundances of Methylobacterium, Sphingomonas, Staphylococcus, and Streptococcus, and higher fecal concentrations of amino acids, including L-aspartic acid, linoleic acid, and L-lactic acid at baseline. Our study suggests that the effects of IFX might be partially mediated by enriching bacteria taxa that producing SCFAs and BSH thereby inhibiting inflammation and restoring the BA metabolism. Some fecal bacteria and metabolites may be predictive of outcomes of IFX therapy for pediatric CD patients.}, } @article {pmid33430247, year = {2021}, author = {Bulteel, L and Houwenhuyse, S and Declerck, SAJ and Decaestecker, E}, title = {The Role of Microbiome and Genotype in Daphnia magna upon Parasite Re-Exposure.}, journal = {Genes}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/genes12010070}, pmid = {33430247}, issn = {2073-4425}, support = {G092619N//FWO/ ; G06216N//FWO/ ; C16/17/002//KU Leuven/ ; }, abstract = {Recently, it has been shown that the community of gut microorganisms plays a crucial role in host performance with respect to parasite tolerance. Knowledge, however, is lacking on the role of the gut microbiome in mediating host tolerance after parasite re-exposure, especially considering multiple parasite infections. We here aimed to fill this knowledge gap by studying the role of the gut microbiome on tolerance in Daphnia magna upon multiple parasite species re-exposure. Additionally, we investigated the role of the host genotype in the interaction between the gut microbiome and the host phenotypic performance. A microbiome transplant experiment was performed in which three germ-free D. magna genotypes were exposed to a gut microbial inoculum and a parasite community treatment. The gut microbiome inocula were pre-exposed to the same parasite communities or a control treatment. Daphnia performance was monitored, and amplicon sequencing was performed to characterize the gut microbial community. Our experimental results showed that the gut microbiome plays no role in Daphnia tolerance upon parasite re-exposure. We did, however, find a main effect of the gut microbiome on Daphnia body size reflecting parasite specific responses. Our results also showed that it is rather the Daphnia genotype, and not the gut microbiome, that affected parasite-induced host mortality. Additionally, we found a role of the genotype in structuring the gut microbial community, both in alpha diversity as in the microbial composition.}, } @article {pmid33429936, year = {2021}, author = {Barandouzi, ZA and Lee, J and Maas, K and Starkweather, AR and Cong, XS}, title = {Altered Gut Microbiota in Irritable Bowel Syndrome and Its Association with Food Components.}, journal = {Journal of personalized medicine}, volume = {11}, number = {1}, pages = {}, doi = {10.3390/jpm11010035}, pmid = {33429936}, issn = {2075-4426}, support = {P20 NR016605-01/NH/NIH HHS/United States ; 10042//American Nurses Foundation/ ; }, abstract = {The interplay between diet and gut microbiota has gained interest as a potential contributor in pathophysiology of irritable bowel syndrome (IBS). The purpose of this study was to compare food components and gut microbiota patterns between IBS patients and healthy controls (HC) as well as to explore the associations of food components and microbiota profiles. A cross-sectional study was conducted with 80 young adults with IBS and 21 HC recruited. The food frequency questionnaire was used to measure food components. Fecal samples were collected and profiled by 16S rRNA Illumina sequencing. Food components were similar in both IBS and HC groups, except in caffeine consumption. Higher alpha diversity indices and altered gut microbiota were observed in IBS compared to the HC. A negative correlation existed between total observed species and caffeine intake in the HC, and a positive correlation between alpha diversity indices and dietary fiber in the IBS group. Higher alpha diversity and gut microbiota alteration were found in IBS people who consumed caffeine more than 400 mg/d. Moreover, high microbial diversity and alteration of gut microbiota composition in IBS people with high caffeine consumption may be a clue toward the effects of caffeine on the gut microbiome pattern, which warrants further study.}, } @article {pmid33429452, year = {2021}, author = {Hild, B and Heinzow, HS and Schmidt, HH and Maschmeier, M}, title = {Bile Acids in Control of the Gut-Liver-Axis.}, journal = {Zeitschrift fur Gastroenterologie}, volume = {59}, number = {1}, pages = {63-68}, doi = {10.1055/a-1330-9644}, pmid = {33429452}, issn = {1439-7803}, abstract = {The liver and gut share an intimate relationship whose communication relies heavily on metabolites, among which bile acids play a major role. Beyond their function as emulsifiers, bile acids have been recognized for their influence on metabolism of glucose and lipids as well as for their impact on immune responses. Therefore, changes to the composition of the bile acid pool can be consequential to liver and to gut physiology. By metabolizing primary bile acids to secondary bile acids, the bacterial gut microbiome modifies how bile acids exert influence. An altered ratio of secondary to primary bile acids is found to be substantial in many studies. Thus, disease pathogenesis and progression could be changed by gut microbiome modification which influences the bile acid pool.}, } @article {pmid33429063, year = {2021}, author = {Smits, MM and Fluitman, KS and Herrema, H and Davids, M and Kramer, MHH and Groen, AK and Belzer, C and de Vos, WM and Cahen, DL and Nieuwdorp, M and van Raalte, DH}, title = {Liraglutide and sitagliptin have no effect on intestinal microbiota composition: A 12-week randomized placebo-controlled trial in adults with type 2 diabetes.}, journal = {Diabetes & metabolism}, volume = {}, number = {}, pages = {101223}, doi = {10.1016/j.diabet.2021.101223}, pmid = {33429063}, issn = {1878-1780}, abstract = {AIM: Preclinical data suggest that treatment with either glucagon-like peptide (GLP)-1 receptor agonists or dipeptidyl peptidase (DPP)-4 inhibitors could change the intestinal microbiome and thereby contribute to their beneficial (cardio)metabolic effects. Therefore, our study aimed to investigate the effects of these agents on microbiota composition in adults with type 2 diabetes (T2D).

METHODS: A total of 51 adults with T2D (mean ± SD: age 62.8 ± 6.9 years, BMI 31.8 ± 4.1 kg/m2, HbA1c 7.3 ± 0.6%) treated with metformin and/or sulphonylureas were included in the 12-week randomized, double-blind trial. Patients were given the GLP-1 receptor agonist liraglutide (1.8 mg sc) or the DPP-4 inhibitor sitagliptin (100 mg), or matching placebos, once daily for 12 weeks. Faecal samples were collected at baseline and at 12 weeks after the start of the intervention. Microbiota analyses were performed by 16S rRNA gene-sequencing analysis. Bile acids were measured in faeces and plasma.

RESULTS: Liraglutide decreased HbA1c by 1.3% (95% CI: -1.7 to -0.9) and tended to reduce body weight (-1.7 kg, 95% CI: -3.6 to 0.3), but increased faecal secondary bile acid deoxycholic acid. Sitagliptin lowered HbA1c by 0.8% (95% CI: -1.4 to -0.4) while body weight remained stable (-0.8 kg, 95% CI: -2.7 to 1.0), but increased faecal levels of cholic acid, chenodeoxycholic acid and ursodeoxycholic acid. However, neither liraglutide nor sitagliptin affected either alpha or beta diversity of the intestinal microbiota, nor were changes in microbial composition related to clinical parameters.

CONCLUSION: These data suggest that the beneficial effects of liraglutide and sitagliptin on glucose metabolism, body weight and bile acids, when used as add-on therapies to metformin or sulphonylureas, are not linked to changes in the intestinal microbiota (NCT01744236).}, } @article {pmid33428723, year = {2021}, author = {Laursen, MF and Bahl, MI and Licht, TR}, title = {Settlers of our inner surface - Factors shaping the gut microbiota from birth to toddlerhood.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuab001}, pmid = {33428723}, issn = {1574-6976}, abstract = {During the first three years of life, the microbial ecosystem within the human gut undergoes a process that is unlike what happens in this ecosystem at any other time of our life. This period in time is considered a highly important developmental window, where the gut microbiota is much less resilient and much more responsive to external and environmental factors than seen in the adult gut. While advanced bioinformatics and clinical correlation studies have received extensive focus within studies of the human microbiome, basic microbial growth physiology has attracted much less attention, although it plays a pivotal role to understand the developing gut microbiota during early life. In this review, we will thus take a microbial ecology perspective on the analysis of factors that influence the temporal development of the infant gut microbiota. Such factors include sources of microbes that seed the intestinal environment, physico-chemical (abiotic) conditions influencing microbial growth, and the availability of nutrients needed by the intestinal microbes.}, } @article {pmid33428498, year = {2021}, author = {Koidl, L and Untersmayr, E}, title = {The clinical implications of the microbiome in the development of allergy diseases.}, journal = {Expert review of clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1080/1744666X.2021.1874353}, pmid = {33428498}, issn = {1744-8409}, abstract = {INTRODUCTION: A substantial number of patients worldwide is affected by allergies. Emerging evidence suggests that the individual microbial composition might contribute to the development of allergies or might even protect from allergic diseases.

AREAS COVERED: This review provides a detailed summary regarding available knowledge on the composition of a healthy human microbiome at allergy relevant body sites. It highlights factors influencing the microbiota composition. Furthermore, recent findings on the mutual interaction of the microbiota with the innate and adaptive immune system are reported. In the final part, this knowledge is combined to discuss microbial implications for food allergy, allergic asthma, allergic rhinitis and skin allergies. Literature for this review was gathered by searching PubMed and Google Scholar databases between October and December 2020.

EXPERT OPINION: Due to the highly individual composition, it is currently not possible to define the characteristics of a site-specific microbiome in health and disease. Mainly effects of bacterial communities have been investigated, while fungal or viral influences are not yet well understood. The communication between microbial communities found in different organs impact on allergy development. Thus, a personalized approach is essential to beneficially influence these complex interactions and to modulate the host specific microbiota in allergies.}, } @article {pmid33428274, year = {2021}, author = {Schäbitz, A and Eyerich, K and Garzorz-Stark, N}, title = {So close, and yet so far away: The dichotomy of the specific immune response and inflammation in psoriasis and atopic dermatitis.}, journal = {Journal of internal medicine}, volume = {}, number = {}, pages = {}, doi = {10.1111/joim.13235}, pmid = {33428274}, issn = {1365-2796}, support = {IMCIS ERC STG676858//H2020 European Research Council/ ; }, abstract = {Characterization of the complex interplay between cytokines, chemokines and microorganisms has led to a better understanding of the pathogenesis of both psoriasis and AD and resulted in new therapeutics targeting distinct immune responses. Psoriasis and AD share many characteristics: they are highly prevalent, chronic, cause primarily skin inflammation, but are associated with comorbidities, and come with a devastating quality of life due to itch and stigmatization. However, the pathogenesis of psoriasis and AD is opposing - psoriasis is dominated by a Th17 immune response that causes neutrophil migration, induction of innate immunity and exaggerated epithelial metabolism. Leading cytokines of this Th17 immune response are IL-17A and F, IL-22 and TNF-a. AD is characterized by Th2 immunity characterized by the signature cytokines IL-4 and IL-13 leading to an impaired epidermal barrier, dampened innate immunity and eosinophil migration. This review compares genetics, microbiome and T-cell infiltrate and resulting epithelial response in psoriasis and AD. Whilst the antagonistic course of psoriasis and AD is confirmed by response to specific biologics targeting the key cytokines of inflammation in psoriasis and AD, respectively, clinically overlapping phenotypes are challenging in our daily clinical practice. We conclude this review by summarizing what is known about these mixed phenotypes and how the identification of clinically relevant endotypes and molecular-driven decision-making is the next step in the field of dermato-immunology.}, } @article {pmid33428153, year = {2021}, author = {Zhao, W and Ren, Z and Luo, Y and Cheng, J and Wang, J and Wang, Y and Yang, Z and Yao, X and Zhong, Z and Yang, W and Wu, X}, title = {Metagenomics analysis of the gut microbiome in healthy and bacterial pneumonia forest musk deer.}, journal = {Genes & genomics}, volume = {}, number = {}, pages = {}, pmid = {33428153}, issn = {2092-9293}, support = {2020JDZH0024//The Science and Technology Achievements Transfer Project in 2020 from Scientific Research Institutions of Science and Technology Department of Sichuan Province, Sichuan, China/ ; }, abstract = {BACKGROUND: The forest musk deer (FMD, Moschus berezovskii) is an threatened species in China. Bacterial pneumonia was found to seriously restrict the development of FMD captive breeding. Historical evidence has demonstrated the relationship between immune system and intestinal Lactobacillus in FMD.

OBJECTIVE: We sought to elucidate the differences in the gut microbiota of healthy and bacterial pneumonia FMD.

METHODS: The bacterial pneumonia FMD was demonstrated by bacterial and pathological diagnosis, and the gut microbiome of healthy and bacterial pneumonia FMD was sequenced and analysed.

RESULTS: There are three pathogens (Pseudomonas aeruginosa, Streptococcus equinus and Trueperella pyogenes) isolated from the bacterial pneumonia FMD individuals. Compared with the healthy group, the abundance of Firmicutes and Proteobacteria in the pneumonia group was changed, and a high level of Proteobacteria was found in the pneumonia group. In addition, a higher abundance of Acinetobacter (p = 0.01) was observed in the population of the pneumonia group compared with the healthy group. Several potentially harmful bacteria and disease-related KEGG subsystems were only found in the gut of the bacterial pneumonia group. Analysis of KEGG revealed that many genes related to type IV secretion system, type IV pilus, lipopolysaccharide export system, HTH-type transcriptional regulator/antitoxin MqsA, and ArsR family transcriptional regulator were significantly enriched in the metagenome of the bacterial pneumonia FMD.

CONCLUSION: Our results demonstrated that the gut microbiome was significantly altered in the bacterial pneumonia group. Overall, our research improves the understanding of the potential role of the gut microbiota in the FMD bacterial pneumonia.}, } @article {pmid33427793, year = {2021}, author = {Jain, V and Alexander, EC and Burford, C and Verma, A and Dhawan, A}, title = {Gut Microbiome: A Potential Modifiable Risk Factor in Biliary Atresia.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {72}, number = {2}, pages = {184-193}, doi = {10.1097/MPG.0000000000002973}, pmid = {33427793}, issn = {1536-4801}, abstract = {ABSTRACT: Biliary atresia (BA) is a fibro-obliterative condition of the biliary tree, presenting in infancy. The bilioenteric conduit formed at Kasai portoenterostomy (KPE), achieves restoration of bile flow in approximately 60% of infants. Even if the operation is successful, cirrhosis and its associated complications are, however, common. BA remains the leading cause for liver transplantation (LT) in children. Antibiotic, choleretic, and steroid therapy post-KPE have not convincingly reduced LT rates. Advances in molecular technology have enabled characterisation of the encoded genes of the gut microbiota (gut microbiome). The gut microbiome plays an important role in host metabolism, nutrition, and immune function, with alterations in its diversity and/or composition, known as dysbiosis, being described in disease states, including liver disease. Liver-gut microbiome exploration in adulthood largely focuses on nonalcoholic liver disease, cirrhosis (mainly alcohol- or viral-based aetiology) and cholestatic liver diseases (eg, primary sclerosing cholangitis), with microbial signatures correlating to disease severity. Investigation of the gut microbiota in BA had been limited to culture-based methodology, but molecular studies are emerging, and although in their infancy, highlight a potential pathogenic role for Enterobacteriaceae and Streptococcus, and a potential beneficial role for Bifidobacteria. Bacterial translocation, and the production of gut microbiome-derived metabolites, are key host-microbiome-mechanistic pathways in liver disease pathogenesis. Microbiome-targeted therapeutics for liver disease are in development, with faecal microbiota transplantation showing promise in cirrhosis. Could the gut microbiome be a novel modifiable risk factor in BA, reducing the need for LT?}, } @article {pmid33427531, year = {2021}, author = {Khanna, S}, title = {Advances in Clostridioides difficile therapeutics.}, journal = {Expert review of anti-infective therapy}, volume = {}, number = {}, pages = {}, doi = {10.1080/14787210.2021.1874919}, pmid = {33427531}, issn = {1744-8336}, } @article {pmid33427409, year = {2021}, author = {Abdelfattah, A and Wisniewski, M and Schena, L and Tack, AJM}, title = {Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15392}, pmid = {33427409}, issn = {1462-2920}, abstract = {While the environment is considered the primary origin of the plant microbiome, the potential role of seeds as a source of transmitting microorganisms has not received much attention. Here we tested the hypothesis that the plant microbiome is partially inherited through vertical transmission. An experimental culturing device was constructed to grow oak seedlings in a microbe-free environment while keeping belowground and aboveground tissues separated. The microbial communities associated with the acorn's embryo and pericarp and the developing seeding's phyllosphere and root systems were analyzed using amplicon sequencing of fungal ITS and bacterial 16S rDNA. Results showed that the seed microbiome is diverse and non-randomly distributed within an acorn. The microbial composition of the phyllosphere was diverse and strongly resembled the composition found in the embryo, whereas the roots and pericarp each had a less diverse and distinct microbial community. Our findings demonstrate a high level of microbial diversity and spatial partitioning of the fungal and bacterial community within both seed and seedling, indicating inheritance, niche differentiation, and divergent transmission routes for the establishment of root and phyllosphere communities. This article is protected by copyright. All rights reserved.}, } @article {pmid33427228, year = {2021}, author = {Schmid, E and Eick, S and Sculean, A and Salvi, GE}, title = {Peri-Implant Diseases: Characteristics of the Microbiota and of the Host Response in Humans - A Narrative Review.}, journal = {Monographs in oral science}, volume = {29}, number = {}, pages = {98-104}, doi = {10.1159/000510186}, pmid = {33427228}, issn = {1662-3843}, mesh = {Bacteria ; *Dental Implants/adverse effects ; Humans ; *Microbiota ; *Peri-Implantitis/etiology ; *Stomatitis/etiology ; }, abstract = {The present narrative review provides a summary of the temporal and spatial reactions of the oral microbiome to the placement of a dental implant into the oral cavity, depicting the most important interactions between the oral microbiota and the host response involved in the development of peri-implant infections in humans (i.e., peri-implant mucositis and peri-implantitis). Starting with the formation of a pellicle to acute and rampant peri-implant inflammation, a number of steps, including biofilm formation, aggressive bacterial invasion, and host defense mechanisms, are involved. Better understanding of the factors related to the host response and changes in the composition of microbiota has led to the development of novel treatment modalities. Finally, a short outlook into the future is provided.}, } @article {pmid33427220, year = {2021}, author = {Astasov-Frauenhoffer, M and Kulik, EM}, title = {Cariogenic Biofilms and Caries from Birth to Old Age.}, journal = {Monographs in oral science}, volume = {29}, number = {}, pages = {53-64}, doi = {10.1159/000510200}, pmid = {33427220}, issn = {1662-3843}, mesh = {Biofilms ; Child ; *Dental Caries ; Dentition, Permanent ; Humans ; *Microbiota ; Saliva ; }, abstract = {Caries is a complex microbial disease characterized by a multifactorial etiology. The disease is driven by cariogenic microbiota that metabolize dietary carbohydrates into acids, creating prolonged periods of low pH on the biofilm surrounding the teeth, which will result in loss of calcium from the teeth leading to carious lesions. Caries remains a major public health problem globally, ranking first for the decay of permanent teeth (2.3 billion people) and 12th for deciduous teeth (560 million children) according to the Global Burden of Disease study by the WHO in 2015. Different factors play a role in the development of the disease: (i) individual factors such as tooth morphology, saliva, and the oral microbiome, (ii) behavioral factors such as frequency and amount of fermentable carbohydrates in the host's diet and overall oral hygiene, and (iii) socioeconomic status and host genetics as well as modifying factors such as fluoride. Various models exist which explain the transition from a health-compatible oral microbiota to a cariogenic microbiota. Longitudinal studies may increase our knowledge of the oral microbial compositions in different age groups by analyzing the temporal sequence leading to carious lesions. Understanding the factors which control microbial colonization early in life as well as the keystone species that should be present or absent may provide us with strategies for the acquisition and maintenance of a health-promoting oral microbiome. Thus, the importance lies in understanding caries etiology to improve strategies for diagnosis, risk assessment, prevention, and (operative) treatment.}, } @article {pmid33427218, year = {2021}, author = {Müller, LK and Jungbauer, G and Jungbauer, R and Wolf, M and Deschner, J}, title = {Biofilm and Orthodontic Therapy.}, journal = {Monographs in oral science}, volume = {29}, number = {}, pages = {201-213}, doi = {10.1159/000510193}, pmid = {33427218}, issn = {1662-3843}, mesh = {Biofilms ; *Dental Caries/therapy ; *Gingivitis ; Humans ; Orthodontic Appliances/adverse effects ; Streptococcus mutans ; }, abstract = {Dental biofilms can cause major oral diseases like gingivitis, periodontitis, and caries. Orthodontic appliances promote supra- and subgingival biofilm accumulation, alter the oral microbiome, and hamper oral hygiene. Orthodontic treatment can be associated with adverse effects, such as enamel decalcification, gingivitis, and periodontal disease. The aim of this review is to summarize the changes in supra- and subgingival biofilm and periodontal tissues during and after orthodontic treatment. Studies have reported elevated levels of Streptococcus mutans and periodontopathogenic bacteria in patients undergoing orthodontic treatment. In general, the microbial changes and periodontal parameters decreased to pretreatment levels after appliance removal. Nevertheless, some adverse effects associated with orthodontic treatment are not reversible, such as enamel decalcifications caused by metabolic products of high levels of cariogenic bacteria. The evidence suggests that the roughness and constituents of the orthodontic materials influence the bacterial colonization. Therefore, several antibacterial orthodontic bonding systems, which show antibacterial effects in vitro, have been developed. The importance of adequate oral hygiene should be emphasized to all orthodontic patients. They should be frequently reminded and motivated to obtain a good oral hygiene. The evidence from the current literature suggests the safest way for orthodontic treatment in periodontally diseased patients may be after successful completion of the periodontal therapy. However, the exact time point needs to be better clarified in future studies.}, } @article {pmid33426773, year = {2021}, author = {Soelberg, KK and Datcu, R and Jørgensen, CAB and Faber, C and Wied, J and Fuursted, K and Justesen, US}, title = {A case report describing Candida albicans endophthalmitis demonstrated by 16S/18S microbiome sequencing.}, journal = {Acta ophthalmologica}, volume = {}, number = {}, pages = {}, doi = {10.1111/aos.14740}, pmid = {33426773}, issn = {1755-3768}, } @article {pmid33426540, year = {2020}, author = {Jonscher, KR and Abrams, J and Friedman, JE}, title = {Maternal Diet Alters Trained Immunity in the Pathogenesis of Pediatric NAFLD.}, journal = {Journal of cellular immunology}, volume = {2}, number = {6}, pages = {315-325}, pmid = {33426540}, issn = {2689-2812}, support = {R01 DK121951/DK/NIDDK NIH HHS/United States ; R24 DK090964/DK/NIDDK NIH HHS/United States ; R56 DK114711/DK/NIDDK NIH HHS/United States ; }, abstract = {Pediatric nonalcoholic fatty liver disease (NAFLD) affects 1 in 10 children in the US, increases risk of cirrhosis and transplantation in early adulthood, and shortens lifespan, even after transplantation. Exposure to maternal obesity and/or a diet high in fat, sugar and cholesterol is strongly associated with development of NAFLD in offspring. However, mechanisms by which "priming" of the immune system in early life increases susceptibility to NAFLD are poorly understood. Recent studies have focused on the role "non-reparative" macrophages play in accelerating inflammatory signals promoting fibrogenesis. In this Commentary, we review evidence that the pioneering gut bacteria colonizing the infant intestinal tract remodel the naïve immune system in the offspring. Epigenetic changes in hematopoietic stem and progenitor cells, induced by exposure to an obesogenic diet in utero, may skew lineage commitment of myeloid cells during gestation. Further, microbial dysbiosis in neonatal life contributes to training innate immune cell responsiveness in the gut, bone marrow, and liver, leading to developmental programming of pediatric NAFLD. Comprehensive understanding of how different gut bacteria and their byproducts shape development of the early innate immune system and microbiome will uncover early interventions to prevent NAFLD pathophysiology.}, } @article {pmid33426525, year = {2020}, author = {Ribeiro, MF and Santos, AA and Afonso, MB and Rodrigues, PM and Sá Santos, S and Castro, RE and Rodrigues, CMP and Solá, S}, title = {Diet-dependent gut microbiota impacts on adult neurogenesis through mitochondrial stress modulation.}, journal = {Brain communications}, volume = {2}, number = {2}, pages = {fcaa165}, pmid = {33426525}, issn = {2632-1297}, abstract = {The influence of dietary factors on brain health and mental function is becoming increasingly recognized. Similarly, mounting evidence supports a role for gut microbiota in modulating central nervous system function and behaviour. Still, the molecular mechanisms responsible for the impact of diet and associated microbiome in adult neurodegeneration are still largely unclear. In this study, we aimed to investigate whether and how changes in diet-associated microbiome and its metabolites impact on adult neurogenesis. Mice were fed a high-fat, choline-deficient diet, developing obesity and several features of the metabolic syndrome, including non-alcoholic steatohepatitis. Strikingly, our results showed, for the first time, that animals fed with this specific diet display premature increased neurogenesis, possibly exhausting the available neural stem cell pool for long-term neurogenesis processes. The high-fat, choline-deficient diet further induced neuroinflammation, oxidative stress, synaptic loss and cell death in different regions of the brain. Notably, this diet-favoured gut dysbiosis in the small intestine and cecum, up-regulating metabolic pathways of short-chain fatty acids, such as propionate and butyrate and significantly increasing propionate levels in the liver. By dissecting the effect of these two specific short-chain fatty acids in vitro, we were able to show that propionate and butyrate enhance mitochondrial biogenesis and promote early neurogenic differentiation of neural stem cells through reactive oxygen species- and extracellular signal-regulated kinases 1/2-dependent mechanism. More importantly, neurogenic niches of high-fat, choline-deficient-fed mice showed increased expression of mitochondrial biogenesis markers, and decreased mitochondrial reactive oxygen species scavengers, corroborating the involvement of this mitochondrial stress-dependent pathway in mediating changes of adult neurogenesis by diet. Altogether, our results highlight a mitochondria-dependent pathway as a novel mediator of the gut microbiota-brain axis upon dietary influences.}, } @article {pmid33426512, year = {2021}, author = {Perera, D and Kleinstein, SE and Hanson, B and Hasturk, H and Eveloff, R and Freire, M and Ramsey, M}, title = {Impaired host response and the presence of Acinetobacter baumannii in the serum microbiome of type-II diabetic patients.}, journal = {iScience}, volume = {24}, number = {1}, pages = {101941}, pmid = {33426512}, issn = {2589-0042}, abstract = {Type II diabetes (T2D) affects over 10% of the US population and is a growing disease worldwide that manifests with numerous comorbidities and defects in inflammation. This dysbiotic host response allows for infection of the host by numerous microorganisms. In the course of T2D disease, individuals can develop chronic infections including foot ulcers and periodontitis, which lead to further complications and opportunistic infections in multiple body sites. In this study, we investigated the serum of healthy subjects and patients with T2D with (T2DP) or without periodontitis for both microbiome signatures in addition to cytokine profiles. Surprisingly, we detected the presence of Acinetobacter baumanii in the serum of 23% individuals with T2D/T2DP tested. In T2DP, IL-1β, TNF-α, MCP-1, IL-6, IL-8, and IFN-γ were significantly elevated in ABC-positive subjects. As an emerging pathogen, A. baumanii infection represents a risk for impaired inflammation and the development of comorbidities in subjects with T2D.}, } @article {pmid33426367, year = {2021}, author = {Bannerman, CA and Douchant, K and Sheth, PM and Ghasemlou, N}, title = {The gut-brain axis and beyond: Microbiome control of spinal cord injury pain in humans and rodents.}, journal = {Neurobiology of pain (Cambridge, Mass.)}, volume = {9}, number = {}, pages = {100059}, pmid = {33426367}, issn = {2452-073X}, abstract = {Spinal cord injury (SCI) is a devastating injury to the central nervous system in which 60 to 80% of patients experience chronic pain. Unfortunately, this pain is notoriously difficult to treat, with few effective options currently available. Patients are also commonly faced with various compounding injuries and medical challenges, often requiring frequent hospitalization and antibiotic treatment. Change in the gut microbiome from the "normal" state to one of imbalance, referred to as gut dysbiosis, has been found in both patients and rodent models following SCI. Similarities exist in the bacterial changes observed after SCI and other diseases with chronic pain as an outcome. These changes cause a shift in the regulation of inflammation, causing immune cell activation and secretion of inflammatory mediators that likely contribute to the generation/maintenance of SCI pain. Therefore, correcting gut dysbiosis may be used as a tool towards providing patients with effective pain management and improved quality of life.}, } @article {pmid33425978, year = {2020}, author = {Shah, S and Brown, PDS and Mayengbam, S and Gänzle, MG and Wang, W and Mu, C and Lettrari, S and Bertagnolli, C and Shearer, J}, title = {Metabolic and Gut Microbiota Responses to Sourdough Pasta Consumption in Overweight and Obese Adults.}, journal = {Frontiers in nutrition}, volume = {7}, number = {}, pages = {615003}, pmid = {33425978}, issn = {2296-861X}, abstract = {Increasing consumer interest in fermented products has driven the emergence of a number of novel foods including shelf-stable sourdough pasta. This study comprehensively examined the impact of fermentation on the microbial composition of the culture, pasta, its subsequent effects on glycemic responses and gut microbiota in overweight men and women (>25 kg/m2) compared to a conventional, non-fermented pasta. Two, randomized crossover trials were performed. Study A examined acute feeding responses to each product wherein fasted participants completed a meal tolerance test comprised of 75 g of conventional or sourdough pasta to examine glycemic responses. Results showed enhanced gastric emptying with sourdough, but no difference in overall blood glucose, insulin or satiety hormone responses between the treatments. Study B consisted of three standard oral glucose tolerance tests as well as fecal collection for sequencing at baseline and following each pasta intervention (150 g or 2 serving/d for 5 days) followed by a 2-week washout period. Results showed no differential impact of either pasta treatment on glucose tolerance. Analysis of fecal bacterial and fungal (mycobiome) microbiota showed no change at the individual species or genus levels. However, fungi were adaptive following chronic pasta consumption with decreases in alpha diversity of fungi following sourdough, but not conventional pasta. This was accompanied by reductions in total fecal short chain fatty acid concentrations. In conclusion, sourdough fermentation did not change the overall glycemic properties of the pasta, incretin responses or bacterial gut microbiota, but appears to impact microbiome fungal community structure with chronic consumption.}, } @article {pmid33425970, year = {2020}, author = {Chen, B and Liu, S and Feng, D and Xiao, L and Yang, T and Li, T and Sun, W and Chen, J}, title = {Vitamin A Deficiency in the Early-Life Periods Alters a Diversity of the Colonic Mucosal Microbiota in Rats.}, journal = {Frontiers in nutrition}, volume = {7}, number = {}, pages = {580780}, pmid = {33425970}, issn = {2296-861X}, abstract = {Vitamin A deficiency (VAD) remains a public health issue worldwide, affecting pregnant women and children. The early-life microbiota is a potentially effective intervention target for modulating immune and metabolic development of the host. This paper investigates the effects of VAD during different life periods on the structure of the colonic mucosa microbiota in adolescent rats. The results showed that the concentrations of serum retinol were > ~1.05 μmol/L in maternal VA normal (VAN)rats and < 0.7 μmol/L in maternal VAD rats, while the serum retinol levels were higher than 0.7 μmol/L in the pups of the VAN group and below 0.5 μmol/L in the pups of the VAD group. Compared to the offspring persistent with VAN from embryonic stage (group A), all the remaining groups exhibited an increased ratio of Firmicutes/Bacteroidetes abundance. A metagenome analysis (LEfSe) and a differentially abundant features approach using Metastats for genus abundances revealed that Diaphorobacter and Psychrobacter were increased in the offspring persistent with VAD from embryonic stage (group B);Bifidobacterium was decreased and Staphylococcus was increased in the offspring with VAD after weaning (group C); Propionibacterium and Enterobacter were increased significantly in the offspring with VAD during gestation(group E); and Ochrobactrum was increased in group B and the offspring with VAD during gestation and lactation(group D). Faecalibacterium abundance was significantly and positively related to serum retinol levels, while that of Staphylococcus was significantly and negatively correlated with serum retinol levels. VAD in different life periods can alter the gut microbiome in rats, but VAD in the early-life periods (especially gestation and/or lactation) leads to a diversity of the colonic mucosal microbiota in adolescent rats as well as an imbalance of the ratio between Firmicutes and Bacteroidetes. The early-life period may become a time window of VA intervention to improve intestinal microbiota caused by VA deficiency, but the specific mechanism requires more in-depth research.}, } @article {pmid33425781, year = {2020}, author = {Komatsu, K and Shiba, T and Takeuchi, Y and Watanabe, T and Koyanagi, T and Nemoto, T and Shimogishi, M and Shibasaki, M and Katagiri, S and Kasugai, S and Iwata, T}, title = {Discriminating Microbial Community Structure Between Peri-Implantitis and Periodontitis With Integrated Metagenomic, Metatranscriptomic, and Network Analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {596490}, pmid = {33425781}, issn = {2235-2988}, abstract = {Peri-implantitis and periodontitis are both polymicrobial diseases induced by subgingival plaque accumulation, with some differing clinical features. Studies on the microbial and gene transcription activity of peri-implantitis microbiota are limited. This study aimed to verify the hypothesis that disease-specific microbial and gene transcription activity lead to disease-specific clinical features, using an integrated metagenomic, metatranscriptomic, and network analysis. Metagenomic data in peri-implantitis and periodontitis were obtained from the same 21 subjects and metatranscriptomic data from 12 subjects were obtained from a database. The microbial co-occurrence network based on metagenomic analysis had more diverse species taxa and correlations than the network based on the metatranscriptomic analysis. Solobacterium moorei and Prevotella denticola had high activity and were core species taxa specific to peri-implantitis in the co-occurrence network. Moreover, the activity of plasmin receptor/glyceraldehyde-3-phosphate dehydrogenase genes was higher in peri-implantitis. These activity differences may increase complexity in the peri-implantitis microbiome and distinguish clinical symptoms of the two diseases. These findings should help in exploring a novel biomarker that assist in the diagnosis and preventive treatment design of peri-implantitis.}, } @article {pmid33425774, year = {2020}, author = {Campbell, PM and Humphreys, GJ and Summers, AM and Konkel, JE and Knight, CG and Augustine, T and McBain, AJ}, title = {Does the Microbiome Affect the Outcome of Renal Transplantation?.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {558644}, pmid = {33425774}, issn = {2235-2988}, abstract = {The role of the human microbiome in health and disease is becoming increasingly apparent. Emerging evidence suggests that the microbiome is affected by solid organ transplantation. Kidney transplantation is the gold standard treatment for End-Stage Renal Disease (ESRD), the advanced stage of Chronic Kidney Disease (CKD). The question of how ESRD and transplantation affect the microbiome and vice versa includes how the microbiome is affected by increased concentrations of toxins such as urea and creatinine (which are elevated in ESRD), whether restoration of renal function following transplantation alters the composition of the microbiome, and the impact of lifelong administration of immunosuppressive drugs on the microbiome. Changes in microbiome composition and activity have been reported in ESRD and in therapeutic immunosuppression, but the effect on the outcome of transplantation is not well-understood. Here, we consider the current evidence that changes in kidney function and immunosuppression following transplantation influence the oral, gut, and urinary microbiomes in kidney transplant patients. The potential for changes in these microbiomes to lead to disease, systemic inflammation, or rejection of the organ itself is discussed, along with the possibility that restoration of kidney function might re-establish orthobiosis.}, } @article {pmid33425458, year = {2021}, author = {Cao, L and Yang, L and Swanson, CS and Li, S and He, Q}, title = {Comparative analysis of impact of human occupancy on indoor microbiomes.}, journal = {Frontiers of environmental science & engineering}, volume = {15}, number = {5}, pages = {89}, pmid = {33425458}, issn = {2095-2201}, abstract = {Educational facilities serve as community hubs and consequently hotspots for exposure to pathogenic microorganisms. Therefore, it is of critical importance to understand processes shaping the indoor microbiomes in educational facilities to protect public health by reducing potential exposure risks of students and the broader community. In this study, the indoor surface bacterial microbiomes were characterized in two multifunctional university buildings with contrasting levels of human occupancy, of which one was recently constructed with minimal human occupancy while the other had been in full operation for six years. Higher levels of human occupancy in the older building were shown to result in greater microbial abundance in the indoor environment and greater proportion of the indoor surface bacterial microbiomes contributed from human-associated microbiota, particularly the skin microbiota. It was further revealed that human-associated microbiota had greater influence on the indoor surface bacterial microbiomes in areas of high occupancy than areas of low occupancy. Consistent with minimal impact from human occupancy in a new construction, the indoor microbiomes in the new building exhibited significantly lower influence from human-associated microbiota than in the older building, with microbial taxa originating from soil and plants representing the dominant constituents of the indoor surface bacterial microbiomes. In contrast, microbial taxa in the older building with extensive human occupancy were represented by constituents of the human microbiota, likely from occupants. These findings provide insights into processes shaping the indoor microbiomes which will aid the development of effective strategies to control microbial exposure risks of occupants in educational facilities.}, } @article {pmid33425362, year = {2021}, author = {Baindara, P and Chakraborty, R and Holliday, ZM and Mandal, SM and Schrum, AG}, title = {Oral probiotics in COVID-19: connecting the gut-lung axis to viral pathogenesis, inflammation, secondary infection, and clinical trials.}, journal = {New microbes and new infections}, volume = {}, number = {}, pages = {100837}, doi = {10.1016/j.nmni.2021.100837}, pmid = {33425362}, issn = {2052-2975}, abstract = {Defined as helpful live bacteria that can provide medical advantages to the host when administered in tolerable amounts, oral probiotics might be worth considering as a possible preventive or therapeutic modality to mitigate Coronavirus disease 2019 (COVID-19) symptom severity. This hypothesis stems from an emerging understanding of the gut-lung axis wherein probiotic microbial species in the digestive tract can influence systemic immunity, lung immunity, and possibly viral pathogenesis and secondary infection co-morbidities. We review the principles underlying the gut-lung axis, examples of probiotic-associated antiviral activities, and current clinical trials in COVID-19 based on oral probiotics.}, } @article {pmid33425246, year = {2021}, author = {Engevik, AC and Engevik, MA}, title = {Exploring the impact of intestinal ion transport on the gut microbiota.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {134-144}, pmid = {33425246}, issn = {2001-0370}, abstract = {The gut microbiota and the host are intimately connected. The host physiology dictates the intestinal environment through regulation of pH, ion concentration, mucus production, etc., all of which exerts a selective pressure on the gut microbiota. Since different regions of the gastrointestinal tract are characterized by their own physicochemical conditions, distinct microbial communities are present in these locations. While it is widely accepted that the intestinal microbiome influences the host (tight junctions, cytokine/immune responses, diarrhea, etc.), the reciprocal interaction of the host on the microbiome is under-explored. This review aims to address these gaps in knowledge by focusing on how the host intestinal ion transport influences the luminal environment and thereby modulates the gut microbiota composition.}, } @article {pmid33425245, year = {2021}, author = {Lopez Leyva, L and Brereton, NJB and Koski, KG}, title = {Emerging frontiers in human milk microbiome research and suggested primers for 16S rRNA gene analysis.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {121-133}, pmid = {33425245}, issn = {2001-0370}, abstract = {Human milk is the ideal food for infants due to its unique nutritional and immune properties, and more recently human milk has also been recognized as an important source of bacteria for infants. However, a substantial amount of fundamental human milk microbiome information remains unclear, such as the origin, composition and function of the community and its members. There is emerging evidence to suggest that the diversity and composition of the milk microbiome might differ between lactation stages, due to maternal factors and diet, agrarian and urban lifestyles, and geographical location. The evolution of the methods used for studying milk microbiota, transitioning from culture dependent-approaches to include culture-independent approaches, has had an impact on findings and, in particular, primer selection within 16S rRNA gene barcoding studies have led to discrepancies in observed microbiota communities. Here, the current state-of-the-art is reviewed and emerging frontiers essential to improving our understanding of the human milk microbiome are considered.}, } @article {pmid33425244, year = {2021}, author = {Hao, X and Zhu, J and Rensing, C and Liu, Y and Gao, S and Chen, W and Huang, Q and Liu, YR}, title = {Recent advances in exploring the heavy metal(loid) resistant microbiome.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {94-109}, pmid = {33425244}, issn = {2001-0370}, abstract = {Heavy metal(loid)s exert selective pressure on microbial communities and evolution of metal resistance determinants. Despite increasing knowledge concerning the impact of metal pollution on microbial community and ecological function, it is still a challenge to identify a consistent pattern of microbial community composition along gradients of elevated metal(loid)s in natural environments. Further, our current knowledge of the microbial metal resistome at the community level has been lagging behind compared to the state-of-the-art genetic profiling of bacterial metal resistance mechanisms in a pure culture system. This review provides an overview of the core metal resistant microbiome, development of metal resistance strategies, and potential factors driving the diversity and distribution of metal resistance determinants in natural environments. The impacts of biotic factors regulating the bacterial metal resistome are highlighted. We finally discuss the advances in multiple technologies, research challenges, and future directions to better understand the interface of the environmental microbiome with the metal resistome. This review aims to highlight the diversity and wide distribution of heavy metal(loid)s and their corresponding resistance determinants, helping to better understand the resistance strategy at the community level.}, } @article {pmid33424865, year = {2020}, author = {Li, JJ and Yi, S and Wei, L}, title = {Ocular Microbiota and Intraocular Inflammation.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {609765}, pmid = {33424865}, issn = {1664-3224}, abstract = {The term ocular microbiota refers to all types of commensal and pathogenic microorganisms present on or in the eye. The ocular surface is continuously exposed to the environment and harbors various commensals. Commensal microbes have been demonstrated to regulate host metabolism, development of immune system, and host defense against pathogen invasion. An unbalanced microbiota could lead to pathogenic microbial overgrowth and cause local or systemic inflammation. The specific antigens that irritate the deleterious immune responses in various inflammatory eye diseases remain obscure, while recent evidence implies a microbial etiology of these illnesses. The purpose of this review is to provide an overview of the literature on ocular microbiota and the role of commensal microbes in several eye diseases. In addition, this review will also discuss the interaction between microbial pathogens and host factors involved in intraocular inflammation, and evaluate therapeutic potential of targeting ocular microbiota to treat intraocular inflammation.}, } @article {pmid33424849, year = {2020}, author = {Crossland, RE and Perutelli, F and Bogunia-Kubik, K and Mooney, N and Milutin Gašperov, N and Pučić-Baković, M and Greinix, H and Weber, D and Holler, E and Pulanić, D and Wolff, D and Dickinson, AM and Inngjerdingen, M and Grce, M}, title = {Potential Novel Biomarkers in Chronic Graft-Versus-Host Disease.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {602547}, pmid = {33424849}, issn = {1664-3224}, abstract = {Prognostic, diagnostic or predictive biomarkers are urgently needed for assessment of chronic graft-versus-host disease (cGvHD), a major risk for patients undergoing allogeneic hematopoietic stem cell transplantation. The main goal of this review generated within the COST Action EUROGRAFT "Integrated European Network on Chronic Graft Versus Host Disease" was to identify potential novel biomarkers for cGvHD besides the widely accepted molecular and cellular biomarkers. Thus, the focus was on cellular biomarkers, alloantibodies, glycomics, endothelial derived particles, extracellular vesicles, microbiome, epigenetic and neurologic changes in cGvHD patients. Both host-reactive antibodies in general, and particularly alloantibodies have been associated with cGvHD and require further consideration. Glycans attached to IgG modulate its activity and represent a promising predictive and/or stratification biomarker for cGVHD. Furthermore, epigenetic changes such as microRNAs and DNA methylation represent potential biomarkers for monitoring cGvHD patients and novel targets for developing new treatment approaches. Finally, the microbiome likely affects the pathophysiology of cGvHD; bacterial strains as well as microbial metabolites could display potential biomarkers for dysbiosis and risk for the development of cGvHD. In summary, although there are no validated biomarkers currently available for clinical use to better inform on the diagnosis, prognosis or prediction of outcome for cGvHD, many novel sources of potential markers have shown promise and warrant further investigation using well characterized, multi-center patient cohorts.}, } @article {pmid33424820, year = {2020}, author = {de Assis Lage, CF and Räisänen, SE and Melgar, A and Nedelkov, K and Chen, X and Oh, J and Fetter, ME and Indugu, N and Bender, JS and Vecchiarelli, B and Hennessy, ML and Pitta, D and Hristov, AN}, title = {Comparison of Two Sampling Techniques for Evaluating Ruminal Fermentation and Microbiota in the Planktonic Phase of Rumen Digesta in Dairy Cows.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {618032}, pmid = {33424820}, issn = {1664-302X}, abstract = {The objective of this experiment was to compare ruminal fluid samples collected through rumen cannula (RC) or using an oral stomach tube (ST) for measurement of ruminal fermentation and microbiota variables. Six ruminally cannulated lactating Holstein cows fed a standard diet were used in the study. Rumen samples were collected at 0, 2, 4, 6, 8, and 12 h after the morning feeding on two consecutive days using both RC and ST techniques. Samples were filtered through two layers of cheesecloth and the filtered ruminal fluid was used for further analysis. Compared with RC, ST samples had 7% greater pH; however, the pattern in pH change after feeding was similar between sampling methods. Total volatile fatty acids (VFA), acetate and propionate concentrations in ruminal fluid were on average 23% lower for ST compared with RC. There were no differences between RC and ST in VFA molar proportions (except for isobutyrate), ammonia and dissolved hydrogen (dH2) concentrations, or total protozoa counts, and there were no interactions between sampling technique and time of sampling. Bacterial ASV richness was higher in ST compared with RC samples; however, no differences were observed for Shannon diversity. Based on Permanova analysis, bacterial community composition was influenced by sampling method and there was an interaction between sampling method and time of sampling. A core microbiota comprised of Prevotella, S24-7, unclassified Bacteroidales and unclassified Clostridiales, Butyrivibrio, unclassified Lachnospiraceae, unclassified Ruminococcaceae, Ruminococcus, and Sharpea was present in both ST and RC samples, although their relative abundance varied and was influenced by an interaction between sampling time and sampling method. Overall, our results suggest that ruminal fluid samples collected using ST (at 180 to 200 cm depth) are not representative of rumen pH, absolute values of VFA concentrations, or bacterial communities >2 h post-feeding when compared to samples of ruminal fluid collected using RC. However, ST can be a feasible sampling technique if the purpose is to study molar proportions of VFA, protozoa counts, dH2, and ammonia concentrations.}, } @article {pmid33424800, year = {2020}, author = {Zhang, R and Zhang, J and Dang, W and Irwin, DM and Wang, Z and Zhang, S}, title = {Unveiling the Biogeography and Potential Functions of the Intestinal Digesta- and Mucosa-Associated Microbiome of Donkeys.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {596882}, pmid = {33424800}, issn = {1664-302X}, abstract = {The intestinal microbial composition and metabolic functions under normal physiological conditions in the donkey are crucial for health and production performance. However, compared with other animal species, limited information is currently available regarding the intestinal microbiota of donkeys. In the present study, we characterized the biogeography and potential functions of the intestinal digesta- and mucosa-associated microbiota of different segments of the intestine (jejunum, ileum, cecum, and colon) in the donkey, focusing on the differences in the microbial communities between the small and large intestine. Our results show that, Firmicutes and Bacteroidetes dominate in both the digesta- and mucosa-associated microbiota in different intestinal locations of the donkey. Starch-degrading and acid-producing (butyrate and lactate) microbiota, such as Lactobacillus and Sarcina, were more enriched in the small intestine, while the fiber- and mucin-degrading bacteria, such as Akkermansia, were more enriched in the large intestine. Furthermore, metabolic functions in membrane transport and lipid metabolism were more enriched in the small intestine, while functions for energy metabolism, metabolism of cofactors and vitamins, amino acid metabolism were more enriched in the large intestine. In addition, the microbial composition and functions in the digesta-associated microbiota among intestinal locations differed greatly, while the mucosal differences were smaller, suggesting a more stable and consistent role in the different intestinal locations. This study provides us with new information on the microbial differences between the small and large intestines of the donkey and the synergistic effects of the intestinal microbiota with host functions, which may improve our understanding the evolution of the equine digestive system and contribute to the healthy and efficient breeding of donkeys.}, } @article {pmid33424792, year = {2020}, author = {Huyben, D and Roehe, BK and Bekaert, M and Ruyter, B and Glencross, B}, title = {Dietary Lipid:Protein Ratio and n-3 Long-Chain Polyunsaturated Fatty Acids Alters the Gut Microbiome of Atlantic Salmon Under Hypoxic and Normoxic Conditions.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {589898}, pmid = {33424792}, issn = {1664-302X}, abstract = {Researchers have adjusted dietary lipid:protein ratios and n-3 long-chain polyunsaturated fatty acids (LC-PUFA) to optimize the growth performance of Atlantic salmon. However, dietary impacts on the gut microbiome are lacking, especially under varying environmental conditions. To examine this response, post-smolt salmon (184 ± 5 g) were fed diets with lipid:protein ratios considered low (180, 570 g/kg) and high (230, 460 g/kg) along with low and high levels of n-3 LC-PUFA (7 or 14 g/kg) while fish were reared under low and high levels of dissolved oxygen (6.7 or 8.0 mg/L). At day 0, 35 and 116, digesta in the distal intestine were collected and analyzed for viable counts and 16S ribosomal RNA (rRNA) genes (V4 region) using Illumina MiSeq. The reduction in oxygen had negligible effects, except on viable plate counts of total bacteria and an initial effect on beta-diversity. In contrast, the high lipid (HL) diets had an increased alpha-diversity (e.g., Shannon and Chao-1) at day 0 and day 35 whereas high n-3 diets suppressed these indices at day 116. Generally, a reduction in alpha-diversity was observed over time and an interaction between lipid:protein ratio x n-3 was found. Between diets, beta-diversity and phyla abundance were similar as both Proteobacteria (44%) and Firmicutes (21%) dominated. However, at the genus level Aliivibrio, Streptococcus, Weissella, and Lactobacillus, were associated with low lipid (LL) diets while the high lipid diets were associated with less abundant bacteria, e.g., Chromohalobacter. At day 116, the relative abundance of the Tenericutes phylum increased 10-fold (36%). Fish fed the high lipid diet with high n-3 had reduced alpha-diversity, lowest abundance of lactic acid bacteria, and highest abundance of Mycoplasma, which may indicate a less healthy gut microbiome. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis revealed that saturated and unsaturated fatty acid biosynthesis pathways were several folds higher in fish fed the high lipid diet, possibly to compensate for the lack of dietary n-3. In summary, our results show that the viable plate counts, alpha-diversity, beta-diversity, and predictive function of gut bacteria in Atlantic salmon post-smolts are influenced by dietary lipid:protein ratio and n-3 LC-PUFA over several time points with little effect by dissolved oxygen.}, } @article {pmid33424783, year = {2020}, author = {Song, J and Li, Q and Everaert, N and Liu, R and Zheng, M and Zhao, G and Wen, J}, title = {Dietary Inulin Supplementation Modulates Short-Chain Fatty Acid Levels and Cecum Microbiota Composition and Function in Chickens Infected With Salmonella.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {584380}, pmid = {33424783}, issn = {1664-302X}, abstract = {The current study investigated the effects of inulin on the gut microbiota, microbiome functions, and short-chain fatty acids (SCFAs) levels in specific pathogen-free (SPF) chickens infected with Salmonella enteritidis (SE). SPF Arbor Acres chickens (n = 240, 1-day-old) were divided into four groups: a control group (CON) fed a basal diet without inulin supplementation or SE infection, and three groups fed a basal diet supplemented with inulin 0, 0.5, and 1% (SE, 0.5%InSE, 1%InSE, respectively) up to 28-days-old, followed by SE challenge at 28 days of age. Cecal SCFA contents and microbiome composition and function were analyzed at 1-day post-infection. The results showed that SE infection significantly decreased cecal butyrate concentrations compared with the CON group (p < 0.05), while inulin supplementation reversed these changes compared with the SE group (p < 0.05). Inulin supplementation at 1% significantly increased the abundances of Lactobacillus and Streptococcus, and significantly decreased the abundances of Subdoligranulum and Sellimonas compared with the SE group (p < 0.05). The functional profiles of microbial communities based on metagenomic sequencing analysis showed that SE infection significantly increased the abundances of pathways related to carbohydrate metabolism, amino acid metabolism, energy metabolism, metabolism of cofactors and vitamins, and glycan biosynthesis and metabolism (p < 0.05), and significantly decreased the abundances of pathways related to nucleotide metabolism, translation, and replication and repair compared with the CON group (p < 0.05), and these effects were reversed by inulin supplementation (0.5 and 1%) (p < 0.05). In conclusion, inulin modulated the dysbiosis induced by SE infection via affecting SCFA metabolism and microbial functional profiles.}, } @article {pmid33424068, year = {2020}, author = {Sakowski, EG and Wommack, KE and Polson, SW}, title = {Oyster Calcifying Fluid Harbors Persistent and Dynamic Autochthonous Bacterial Populations That May Aid in Shell Formation.}, journal = {Marine ecology progress series}, volume = {653}, number = {}, pages = {57-75}, pmid = {33424068}, issn = {0171-8630}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; }, abstract = {The eastern oyster (Crassostrea virginica) is a keystone species in estuarine environments but faces threats to shell formation associated with warming temperatures and acidification. Extrapallial fluid (EF), which is responsible for shell formation, harbors diverse and abundant microbial communities. Commensal microbial communities are vital to host health and fitness, yet long-term studies investigating temporal responses of the EF microbiome and its function in oyster fitness are lacking. In this study, bacterial communities of oyster EF and the water column were characterized monthly from October 2010 to September 2011. We investigated the selection, composition, and dynamics of resident and transient community members, evaluated the impact of temperature on EF microbial communities, and examined the functional role of the EF microbiome. Oyster EF communities were significantly different from the water column and were enriched for several taxa, including the Deltaproteobacteria, Epsilonproteobacteria, and Gammaproteobacteria. Overall, 94 resident members were identified in oyster EF. These members were persistent and abundant, comprising on average 33% of EF communities. Resident EF communities formed high-temperature and low-temperature groups and were more abundant overall at colder temperatures. Oyster EF resident communities were predicted to be enriched for dissimilatory nitrate reduction, nitrogen fixation, nitrification, and sulfite reductase genes. Sulfate and nitrate reduction may have a synergistic effect on calcium carbonate precipitation and indirectly aid in shell formation. Therefore, the potential role of the oyster EF microbiome in shell formation warrants further investigation as oysters and other shellfish face the future impacts of ocean warming and acidification.}, } @article {pmid33424043, year = {2021}, author = {Yu, L}, title = {Restoring Good Health in Elderly with Diverse Gut Microbiome and Food Intake Restriction to Combat COVID-19.}, journal = {Indian journal of microbiology}, volume = {}, number = {}, pages = {1-4}, pmid = {33424043}, issn = {0046-8991}, abstract = {COVID-19 continues to be an ongoing global threat. The elderly with underlying health conditions like cardiovascular and lung diseases, diabetes, obesity, are the most vulnerable to this disease. Curing the pre-existing health conditions will greatly increase a person's resilience to COVID-19 and lower the death rate of the old people. Digestion and immunity form an integrated nutrition acquisition process, especially in obtaining essential amino acids and essential fatty acids from living microbial cells. A mature strong immunity coupled with gut dysbiosis in adults is the main cause of nutritional disorders like morbid obesity, diabetes mellitus, cardiovascular and pulmonary diseases. Nutrition disorders in return worsen dysbiosis. Human microbiome has an intrinsic duality. While a diverse microbiome provides a full spectrum of essential nutrients to our body, nutrition disorders fuel overgrowth of microbiota (dysbiosis) at many sites on or inside our body, and are the main causes of chronic inflammation at these sites. In the case of COVID-19, nutritional disorder impairs the immunity, causes hyperinflammation, and leads to the protracted overload of cytokines by the immune system, i.e., the cytokine storm. Autophagy induced by restrictive eating is an ideal inhibitor of microbiota overgrowth, as autophagy deprives microbiota of excessive nutrition for replication. Autophagy also attenuates inflammation. Therefore, as a precaution, the author suggests restoring good health in the elderly with the support from a diverse gut microbiome and daily regular food intake restriction, so as to lower the risk of developing into severe case even if they are infected by COVID-19.}, } @article {pmid33423868, year = {2020}, author = {Saji, N and Murotani, K and Hisada, T and Tsuduki, T and Sugimoto, T and Kimura, A and Niida, S and Toba, K and Sakurai, T}, title = {The Association between Cerebral Small Vessel Disease and the Gut Microbiome: A Cross-Sectional Analysis.}, journal = {Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association}, volume = {}, number = {}, pages = {105568}, doi = {10.1016/j.jstrokecerebrovasdis.2020.105568}, pmid = {33423868}, issn = {1532-8511}, abstract = {BACKGROUND: Recent studies have demonstrated an association between the gut microbiome and cognitive function. However, the associations between the gut microbiome and brain parenchyma damage, and their underlying mechanisms, remain unclear.

MATERIALS AND METHODS: We performed a cross-sectional sub-analysis using data from our prospective cohort study to determine the association between the gut microbiome and cerebral small vessel disease (SVD). We assessed patient demographics, risk factors, cognitive function, brain imaging, voxel-based specific regional analysis system for Alzheimer's Disease (VSRAD, indicating brain atrophy), and the gut microbiome as indicated by enterotypes and faecal microbiome metabolites. We then analysed the associations between total SVD scores, cognitive function, and the gut microbiome.

RESULTS: We analysed data from 87 patients without dementia or a history of stroke, 64 of whom exhibited mild cognitive impairment. Higher total SVD scores were associated with cognitive decline and behavioural and psychological symptoms. Compared with all other patients, patients with enterotype I (Bacteroides >30%) were more likely to have cognitive decline (median scores: Mini-Mental State Examination, 25 vs. 27, P = 0.047; Clinical Dementia Rating-Sum of Boxes, 1.5 vs. 0.5, P = 0.002) and present with cerebral SVD and high VSRAD scores (1.01 vs. 0.57, P = 0.012). Furthermore, faecal metabolites were significantly higher in patients with higher total SVD scores compared with those with lower scores. Multivariable logistic regression analyses indicated that certain gut microbiomes may double the risk of white matter hyperintensity.

CONCLUSIONS: The gut microbiome is associated with cerebral SVD.}, } @article {pmid33423845, year = {2021}, author = {Lam, SY and Radjabzadeh, D and Eppinga, H and Nossent, YRA and van der Zee, HH and Kraaij, R and Konstantinov, SR and Fuhler, GM and Prens, EP and Thio, HB and Peppelenbosch, MP}, title = {A microbiome study to explore the gut-skin axis in hidradenitis suppurativa.}, journal = {Journal of dermatological science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jdermsci.2020.12.008}, pmid = {33423845}, issn = {1873-569X}, } @article {pmid33423794, year = {2020}, author = {Burris, AD and Pizzarello, C and Järvinen, KM}, title = {Immunologic components in human milk and allergic diseases with focus on food allergy.}, journal = {Seminars in perinatology}, volume = {}, number = {}, pages = {151386}, doi = {10.1016/j.semperi.2020.151386}, pmid = {33423794}, issn = {1558-075X}, abstract = {Human milk contains a wide range of immunomodulatory factors, including immunoglobulins, human milk oligosaccharides, cytokines, microbiome, innate factors and food antigens. Maternal diet can influence the content of human milk as it is well-established that dietary antigens can be secreted in human milk after maternal consumption, but whether these dietary antigens promote tolerance or sensitization in the infant is a subject of debate. This review summarizes the current literature on these immunologically active factors in human milk, including the microbiome, innate factors, and maternal diet-derived dietary antigens in the context of development of allergic diseases, with the focus on food allergy.}, } @article {pmid33423574, year = {2021}, author = {Heimisdottir, LH and Lin, BM and Cho, H and Orlenko, A and Ribeiro, AA and Simon-Soro, A and Roach, J and Shungin, D and Ginnis, J and Simancas-Pallares, MA and Spangler, HD and Zandoná, AGF and Wright, JT and Ramamoorthy, P and Moore, JH and Koo, H and Wu, D and Divaris, K}, title = {Metabolomics Insights in Early Childhood Caries.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {22034520982963}, doi = {10.1177/0022034520982963}, pmid = {33423574}, issn = {1544-0591}, abstract = {Dental caries is characterized by a dysbiotic shift at the biofilm-tooth surface interface, yet comprehensive biochemical characterizations of the biofilm are scant. We used metabolomics to identify biochemical features of the supragingival biofilm associated with early childhood caries (ECC) prevalence and severity. The study's analytical sample comprised 289 children ages 3 to 5 (51% with ECC) who attended public preschools in North Carolina and were enrolled in a community-based cross-sectional study of early childhood oral health. Clinical examinations were conducted by calibrated examiners in community locations using International Caries Detection and Classification System (ICDAS) criteria. Supragingival plaque collected from the facial/buccal surfaces of all primary teeth in the upper-left quadrant was analyzed using ultra-performance liquid chromatography-tandem mass spectrometry. Associations between individual metabolites and 18 clinical traits (based on different ECC definitions and sets of tooth surfaces) were quantified using Brownian distance correlations (dCor) and linear regression modeling of log2-transformed values, applying a false discovery rate multiple testing correction. A tree-based pipeline optimization tool (TPOT)-machine learning process was used to identify the best-fitting ECC classification metabolite model. There were 503 named metabolites identified, including microbial, host, and exogenous biochemicals. Most significant ECC-metabolite associations were positive (i.e., upregulations/enrichments). The localized ECC case definition (ICDAS ≥1 caries experience within the surfaces from which plaque was collected) had the strongest correlation with the metabolome (dCor P = 8 × 10-3). Sixteen metabolites were significantly associated with ECC after multiple testing correction, including fucose (P = 3.0 × 10-6) and N-acetylneuraminate (p = 6.8 × 10-6) with higher ECC prevalence, as well as catechin (P = 4.7 × 10-6) and epicatechin (P = 2.9 × 10-6) with lower. Catechin, epicatechin, imidazole propionate, fucose, 9,10-DiHOME, and N-acetylneuraminate were among the top 15 metabolites in terms of ECC classification importance in the automated TPOT model. These supragingival biofilm metabolite findings provide novel insights in ECC biology and can serve as the basis for the development of measures of disease activity or risk assessment.}, } @article {pmid33423388, year = {2021}, author = {Belančić, A and Kresović, A and Troskot Dijan, M}, title = {Glucagon-like peptide-1 receptor agonists in the era of COVID-19: Friend or foe?.}, journal = {Clinical obesity}, volume = {}, number = {}, pages = {e12439}, doi = {10.1111/cob.12439}, pmid = {33423388}, issn = {1758-8111}, abstract = {The aim of the present manuscript is to discuss on potential pros and cons of glucagon-like peptide-1 receptor agonists (GLP-1RAs) as glucose-lowering agents during COVID-19 pandemic, and what is more to evaluate them as potential candidates for the treatment of patients, affected by COVID-19 infection, with or even without diabetes mellitus type 2. Besides being important glucose-lowering agents, GLP-1RAs pose promising anti-inflammatory and anti-obesogenic properties, pulmonary protective effects, as well as beneficial impact on gut microbiome composition. Hence, taking everything previously mentioned into consideration, GLP-1RAs seem to be potential candidates for the treatment of patients, affected by COVID-19 infection, with or even without type 2 diabetes mellitus, as well as excellent antidiabetic (glucose-lowering) agents during COVID-19 pandemic times.}, } @article {pmid33422791, year = {2020}, author = {Rico, JL and Reardon, KF and De Long, SK}, title = {Inoculum microbiome composition impacts fatty acid product profile from cellulosic feedstock.}, journal = {Bioresource technology}, volume = {323}, number = {}, pages = {124532}, doi = {10.1016/j.biortech.2020.124532}, pmid = {33422791}, issn = {1873-2976}, abstract = {Conversion of organic wastes to fatty acids rather than methane through anaerobic digestion-based technologies has considerable promise. However, the relationships between microbiome structure and fatty acids produced from cellulosic feedstocks are not well understood. This study investigated the nature of those relationships for anaerobic digester sludge, bison rumen, and cattle rumen inocula grown on cellulose. Acetic acid production was highest in anaerobic sludge reactors, while propionic acid production was highest in cattle rumen reactors. Butyric and pentanoic acid were produced at the highest rates in bison rumen before Day 5. Reactor microbiomes remained distinct, despite identical operating conditions. Novel associations linked Alistipes with butyric acid production and Eubacterium nodatum and Clostridiales bacterium with pentanoic acid production. This study provides new insights into the ability of microbiomes to convert cellulose to different fatty acid mixtures and adds impetus for the rewiring of anaerobic digestion to generate high-value products.}, } @article {pmid33422623, year = {2021}, author = {Pineider, J and Reisch, J and Harris-Tryon, T and Savory, S}, title = {Knowledge and attitude towards the human microbiome: a single-center cross-sectional survey.}, journal = {Journal of the American Academy of Dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaad.2020.12.078}, pmid = {33422623}, issn = {1097-6787}, } @article {pmid33422152, year = {2021}, author = {Gardiner, LJ and Haiminen, N and Utro, F and Parida, L and Seabolt, E and Krishna, R and Kaufman, JH}, title = {Re-purposing software for functional characterization of the microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {4}, pmid = {33422152}, issn = {2049-2618}, support = {STFC Hartree Centre's Innovation Return on Research programme//Department for Business, Energy and Industrial Strategy/ ; }, abstract = {BACKGROUND: Widespread bioinformatic resource development generates a constantly evolving and abundant landscape of workflows and software. For analysis of the microbiome, workflows typically begin with taxonomic classification of the microorganisms that are present in a given environment. Additional investigation is then required to uncover the functionality of the microbial community, in order to characterize its currently or potentially active biological processes. Such functional analysis of metagenomic data can be computationally demanding for high-throughput sequencing experiments. Instead, we can directly compare sequencing reads to a functionally annotated database. However, since reads frequently match multiple sequences equally well, analyses benefit from a hierarchical annotation tree, e.g. for taxonomic classification where reads are assigned to the lowest taxonomic unit.

RESULTS: To facilitate functional microbiome analysis, we re-purpose well-known taxonomic classification tools to allow us to perform direct functional sequencing read classification with the added benefit of a functional hierarchy. To enable this, we develop and present a tree-shaped functional hierarchy representing the molecular function subset of the Gene Ontology annotation structure. We use this functional hierarchy to replace the standard phylogenetic taxonomy used by the classification tools and assign query sequences accurately to the lowest possible molecular function in the tree. We demonstrate this with simulated and experimental datasets, where we reveal new biological insights.

CONCLUSIONS: We demonstrate that improved functional classification of metagenomic sequencing reads is possible by re-purposing a range of taxonomic classification tools that are already well-established, in conjunction with either protein or nucleotide reference databases. We leverage the advances in speed, accuracy and efficiency that have been made for taxonomic classification and translate these benefits for the rapid functional classification of microbiomes. While we focus on a specific set of commonly used methods, the functional annotation approach has broad applicability across other sequence classification tools. We hope that re-purposing becomes a routine consideration during bioinformatic resource development. Video abstract.}, } @article {pmid33422110, year = {2021}, author = {Dwyer, Z and Chaiquin, M and Landrigan, J and Ayoub, K and Shail, P and Rocha, J and Childers, CL and Storey, KB and Philpott, DJ and Sun, H and Hayley, S}, title = {The impact of dextran sodium sulphate and probiotic pre-treatment in a murine model of Parkinson's disease.}, journal = {Journal of neuroinflammation}, volume = {18}, number = {1}, pages = {20}, pmid = {33422110}, issn = {1742-2094}, abstract = {BACKGROUND: Recent work has established that Parkinson's disease (PD) patients have an altered gut microbiome, along with signs of intestinal inflammation. This could help explain the high degree of gastric disturbances in PD patients, as well as potentially be linked to the migration of peripheral inflammatory factors into the brain. To our knowledge, this is the first study to examine microbiome alteration prior to the induction of a PD murine model.

METHODS: We presently assessed whether pre-treatment with the probiotic, VSL #3, or the inflammatory inducer, dextran sodium sulphate (DSS), would influence the PD-like pathology provoked by a dual hit toxin model using lipopolysaccharide (LPS) and paraquat exposure.

RESULTS: While VSL #3 has been reported to have anti-inflammatory effects, DSS is often used as a model of colitis because of the gut inflammation and the breach of the intestinal barrier that it induces. We found that VSL#3 did not have any significant effects (beyond a blunting of LPS paraquat-induced weight loss). However, the DSS treatment caused marked changes in the gut microbiome and was also associated with augmented behavioral and inflammatory outcomes. In fact, DSS markedly increased taxa belonging to the Bacteroidaceae and Porphyromonadaceae families but reduced those from Rikencellaceae and S24-7, as well as provoking colonic pro-inflammatory cytokine expression, consistent with an inflamed gut. The DSS also increased the impact of LPS plus paraquat upon microglial morphology, along with circulating lipocalin-2 (neutrophil marker) and IL-6. Yet, neither DSS nor VSL#3 influenced the loss of substantia nigra dopamine neurons or the astrocytic and cytoskeleton remodeling protein changes that were provoked by the LPS followed by paraquat treatment.

CONCLUSIONS: These data suggest that disruption of the intestinal integrity and the associated microbiome can interact with systemic inflammatory events to promote widespread brain-gut changes that could be relevant for PD and at the very least, suggestive of novel neuro-immune communication.}, } @article {pmid33421868, year = {2020}, author = {Chen, YH and Xue, F and Yu, SF and Li, XS and Liu, L and Jia, YY and Yan, WJ and Tan, QR and Wang, HN and Peng, ZW}, title = {Gut microbiota dysbiosis in depressed women: The association of symptom severity and microbiota function.}, journal = {Journal of affective disorders}, volume = {282}, number = {}, pages = {391-400}, doi = {10.1016/j.jad.2020.12.143}, pmid = {33421868}, issn = {1573-2517}, abstract = {BACKGROUND: The association between abnormal gut microbiome composition and depression is well established. However, the composition and functional capacity of the gut microbiota regarding depressed women has been poorly addressed.

METHODS: Stool samples from 62 female patients with major depressive disorder (MDD) and 46 healthy controls (Con) were analyzed by 16S rRNA gene sequencing; Twenty fecal samples from the patient group and 21 fecal samples from the Con group were further analyzed by shotgun metagenomic sequencing. Psychiatric symptoms and psychological, social, and professional functioning was also assessed.

RESULTS: Phylum Bacteroidetes, proteobaeteria, and Fusobacteria were greatly enriched in patients with MDD, while the Firmicutes and Actinobacteria phyla were consistently higher in Con. Notably, 18 microbial markers were identified on a random forest model and achieve an area under the curve of 0.92 between patients with MDD and the Con group. Forty-five species and their associated function were identified with statistically significant differences between patients with MDD and the Con group.

LIMITATIONS: The number of recruited samples, especially samples enrolled for shotgun metagenomic sequencing was relatively small, and the stool samples were collected only at baseline, making it difficult to establish a causal association between changes in gut microbiota compositions and disease remission.

CONCLUSIONS: This study characterizes the gut microbiota and their related function in female MDD. The gut microbiota-based biomarkers may be helpful in diagnosis and the altered gut microbial metabolites may contribute to the pathogenesis of MDD in women, representing potential microbial targets.}, } @article {pmid33421678, year = {2021}, author = {Corduneanu, A and Mihalca, AD and Sándor, AD and Hornok, S and Malmberg, M and Viso, NP and Bongcam-Rudloff, E}, title = {The heart microbiome of insectivorous bats from Central and South Eastern Europe.}, journal = {Comparative immunology, microbiology and infectious diseases}, volume = {75}, number = {}, pages = {101605}, doi = {10.1016/j.cimid.2020.101605}, pmid = {33421678}, issn = {1878-1667}, abstract = {Host associated microbiome not only may affect the individual health-status or provide insights into the species- or group specific bacterial communities but may act as early warning signs in the assessment of zoonotic reservoirs, offering clues to predict, prevent and control possible episodes of emerging zoonoses. Bats may be carriers and reservoirs of multiple pathogens such as viruses, bacteria and parasites, showing in the same time robust immunity against many of them. The microbiota plays a fundamental role on the induction, training and function of the host immune system and the immune system has largely evolved in order to maintain the symbiotic relationship of the host with these diverse microbes. Thus, expanding our knowledge on bat-associated microbiome it can be usefully in understanding bats' outstanding immune capacities. The aim of this study was to investigate the presence of different bacterial communities in heart tissue of insectivorous bats, Nyctalus noctula, Pipistrellus pipistrellus and Rhinoplophus hipposideros, from Central and Eastern Europe using high-throughput sequencing of variable regions of the 16S rRNA. In addition, species-specific PCRs were used to validate the presence of the vector-borne pathogens Bartonella spp. and Rickettsia spp. In this study we identified a wide variety of bacterial groups, with the most abundant phyla being Proteobacteria and Firmicutes. The results showed that at individual level, the year or location had no effect on the diversity and composition of the microbiome, however host species determined both structure and abundance of the bacterial community. We report the presence of vector-borne bacteria Bartonella spp. in samples of N. noctula and indications of Rickettsia spp. in R. hipposideros. Our results provide a first insight into the bacterial community found in heart tissue of bats from Central and South Eastern Europe.}, } @article {pmid33421657, year = {2021}, author = {Chumponsuk, T and Gruneck, L and Gentekaki, E and Jitprasertwong, P and Kullawong, N and Nakayama, J and Popluechai, S}, title = {The salivary microbiota of Thai adults with metabolic disorders and association with diet.}, journal = {Archives of oral biology}, volume = {122}, number = {}, pages = {105036}, doi = {10.1016/j.archoralbio.2020.105036}, pmid = {33421657}, issn = {1879-1506}, abstract = {OBJECTIVE: This study aimed to investigate abundance of specific bacterial taxa in the saliva of 105 Thai adults with different BMI (lean, overweight, and obese) and T2DM subjects using qPCR targeting the 16S rRNA gene of various bacteria taxa.

DESIGN: We employed qPCR targeting 16S rRNA genes to explore the bacterial profiles and abundances in the saliva of Thai adult subjects with different BMI and T2DM. Multivariate statistical analyses (multiple factor analysis (MFA) and sparse Partial Least Squares Discriminant Analysis (sPLS-DA) were performed to assess the associations of salivary bacteria with diet, blood profile, gender, age, and use of antibiotics.

RESULTS: We found that abundance profiles of the examined salivary bacteria were similar across the four groups. When diet, blood profile, and gender, age, and use of antibiotics were considered, significant differences were noted between subgroups. A positive correlation was also found between consumption of carbonate soft drinks and Bacteroidetes, Gamma-proteobacteria, Veillonella, Fusobacterium and Fusobacterium nucleatum.

CONCLUSIONS: This is the first study demonstrating the relative abundance of salivary bacteria in adult Thai subjects with different levels of BMI and T2DM. Regardless of the similar pattern of bacterial profiles across groups, sPLS-DA analysis highlighted the influence of host variables (gender, age, and use of antibiotics) on the abundance of salivary microbiota. Our findings pave the way for further hypothesis testing to gain insight into the association between host factors and salivary microbiome.}, } @article {pmid33421519, year = {2021}, author = {Khalili, H and Axelrad, JE and Roelstraete, B and Olén, O and D'Amato, M and Ludvigsson, JF}, title = {Gastrointestinal Infection and Risk of Microscopic Colitis: A Nationwide Case-Control Study in Sweden.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2021.01.004}, pmid = {33421519}, issn = {1528-0012}, abstract = {BACKGROUND AND AIMS: Gastrointestinal infections have been linked to changes in the composition and function of gut microbiome and development of inflammatory bowel diseases. We therefore sought to examine the relationship between gastroenteritis and risk of microscopic colitis (MC).

METHODS: We conducted a case-control study of all adult MC patients diagnosed between 1990-2016 in Sweden matched to up to 5 general population controls according to age, sex, calendar year, and county. Cases of MC were identified using SNOMED codes from the ESPRESSO study, a cohort of gastrointestinal pathology reports from all 28 pathology centers in Sweden. We used logistic regression modeling to estimate adjusted odds ratios (aORs) and 95% CIs.

RESULTS: Through December of 2016, we matched 13,468 MC cases to 64,479 controls. The prevalence of previous diagnosed gastrointestinal infection was 7.5% among MC patients which was significantly higher than in controls (3.0%, Pcomparison <0.001). After adjustment, gastroenteritis was associated with an increased risk of MC (aOR 2.63; 95%CI=2.42-2.85). Among specific pathogens, Clostridioides difficile (aOR 4.39, 95%CI=3.42-5.63), Norovirus (aOR 2.87, 95%CI=1.66-4.87) and Escherichia species (aOR 3.82, 95%CI=1.22-11.58) but not Salmonella species were associated with an increased risk of MC. The association between gastrointestinal infections and risk of MC was stronger for collagenous subtype (aOR 3.23, 95% CI 2.81-3.70) as compared to lymphocytic colitis (aOR = 2.51, 95% CI 2.28-2.76, Pheterogeneity = 0.005). The associations remained significant after adjustment for immune-mediated conditions and polypharmacy and when compared to unaffected siblings.

CONCLUSION: In a nationwide study, we found that gastrointestinal infection, particularly Clostridioides difficile is associated with an increased risk of subsequent MC.}, } @article {pmid33421237, year = {2021}, author = {Cheema, AS and Lai, CT and Dymock, M and Rae, A and Geddes, DT and Payne, MS and Stinson, LF}, title = {Impact of expression mode and timing of sample collection, relative to milk ejection, on human milk bacterial DNA profiles.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.14998}, pmid = {33421237}, issn = {1365-2672}, abstract = {AIM: To investigate the impact of expression mode: electric breast pump or hand expression, and timing of sample collection: pre- and post-milk ejection on human milk bacterial DNA profiles.

METHODS AND RESULTS: Three human milk samples from the same breast were collected from 30 breastfeeding mothers: a pre-milk ejection pump-expressed sample (pre-pump), a post-milk ejection pump-expressed sample (post-pump), and a post-milk ejection hand-expressed sample (post-hand). Full-length 16S rRNA gene sequencing was used to assess milk bacterial DNA profiles. Bacterial profiles did not differ significantly based on mode of expression nor timing of sample collection. No significant differences were detected in the relative abundance of any OTUs based on expression condition (pre-pump/ post-pump and post-pump/post-hand) with univariate linear mixed-effects regression analyses (all p-values >0.01; α = 0.01). Similarly, no difference in richness was observed between sample types (number of observed OTUs: post-pump/post-hand P = 0.13; pre-pump/post-pump P = 0. 45).

CONCLUSION: Bacterial DNA profiles of human milk did not differ according to either expression method or timing of sample collection.

Hand or pump expression can be utilized to collect samples for microbiome studies. This has implications for the design of future human milk microbiome studies.}, } @article {pmid33421158, year = {2021}, author = {Caraceni, P and Vargas, V and Solà, E and Alessandria, C and de Wit, K and Trebicka, J and Angeli, P and Mookerjee, RP and Durand, F and Pose, E and Krag, A and Bajaj, JS and Beuers, U and Ginès, P}, title = {The use of Rifaximin in Patients with Cirrhosis.}, journal = {Hepatology (Baltimore, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1002/hep.31708}, pmid = {33421158}, issn = {1527-3350}, abstract = {Rifaximin is an oral non-systemic antibiotic, with minimal gastrointestinal absorption and broad-spectrum antibacterial activity covering both grampositive and gramnegative organisms. Rifaximin is currently worldwide used in patients with cirrhosis for preventing recurrent hepatic encephalopathy because its efficacy and safety has been proved by large randomized clinical trials. In the last decade, experimental and clinical evidence suggest that rifaximin could have other beneficial effects on the course of cirrhosis by modulating the gut microbiome and affecting the gut-liver axis, which, in turn, can interfere with major events of the pathophysiological cascade underlying decompensated cirrhosis, such as systemic inflammatory syndrome, portal hypertension, and bacterial infections. However, the use of rifaximin for prevention or treatment of other complications, including spontaneous bacterial peritonitis or other bacterial infections, is not accepted as evidence by clinical trials is still very weak. The present review deals in the first part with the potential impact of rifaximin on pathogenic mechanisms in liver diseases, whereas, in the second part, its clinical effects are critically discussed. It clearly emerges that, due to its potential activity on multiple pathogenic events, the efficacy of rifaximin in the prevention or management of complications other than hepatic encephalopathy deserves to be investigated extensively. The results of double-blinded, adequately powered randomized clinical trials assessing the effect of rifaximin, alone or in combination with other drugs, on hard clinical endpoints, such as decompensation of cirrhosis, acute-on-chronic liver failure and mortality, are therefore eagerly awaited.}, } @article {pmid33421139, year = {2021}, author = {Hernandez, CE and Granados, L}, title = {Quality differentiation of cocoa beans, implications for geographical indications.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.11077}, pmid = {33421139}, issn = {1097-0010}, abstract = {Geographical Indications (GIs) may stimulate collective actions of governance for quality control, trade, marketing as well as innovation based on the use of local resources and regional biodiversity. Cocoa production, however, dominated by small family agriculture in tropical regions, has rarely made use of such strategies. This review aimed at understanding major research interests and emerging technologies helpful for the origin differentiation of cocoa quality. Results from literature search and cited references of publications on cocoa research were imported into VOSviewer for data analysis, which aided to visualize major research hotpots. Co-occurrence analysis yielded major research clusters which guided the discussion of this review. It was observed a consensus recognizing cocoa quality resulting from the interaction of genotype, fermentation variables, and geographical origin. A classic view of cocoa genetics based on the dichotomy of "fine versus bulk", has been reexamined by a broader perspective of human selection and cocoa genotype evolution. This new approach to cocoa genetic diversity, altogether with the understanding of complex microbiome interactions through fermentation, as well as quality reproducibility challenged by geographical conditions, have demonstrated the importance of terroir in the production of special attributes. Cocoa growing communities around the tropics have been clearly enabled by new omics and chemometrics to systematize producing conditions and practices in the designation of specifications for the differentiation of origin quality. This article is protected by copyright. All rights reserved.}, } @article {pmid33420910, year = {2021}, author = {García Hernández, E and Berg, MP and Van Oosten, AR and Smit, C and Falcão Salles, J}, title = {Linking Bacterial Communities Associated with the Environment and the Ecosystem Engineer Orchestia gammarellus at Contrasting Salt Marsh Elevations.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33420910}, issn = {1432-184X}, support = {484425//Consejo Nacional de Ciencia y Tecnología/ ; ALWOP.219.00179028//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {The digestive tract of animals harbors microbiota important for the host's fitness and performance. The interaction between digestive tract bacteria and soil animal hosts is still poorly explored despite the importance of soil fauna for ecosystem processes. In this study, we investigated the interactions between the bacterial communities from the digestive tract of the litter-feeding, semi-terrestrial crustacean Orchestia gammarellus and those obtained from the environment; these organisms thrive in, i.e., soil and plant litter from salt marshes. We hypothesized that elevation is an important driver of soil and litter bacterial communities, which indirectly (via ingested soil and litter bacteria) influences the bacterial communities in the digestive tract of O. gammarellus. Indeed, our results revealed that elevation modulated soil and litter bacterial community composition along with soil organic matter content and the C:N ratio. Soil and plant litter differed in alpha diversity indexes (richness and diversity), and in the case of plant litter, both indexes increased with elevation. In contrast, elevation did not affect the composition of bacterial communities associated with O. gammarellus' digestive tract, suggesting selection by the host, despite the fact that a large component of the bacterial community was also detected in external sources. Importantly, Ca. Bacilloplasma and Vibrio were highly prevalent and abundant in the host. The taxonomic comparison of Ca. Bacilloplasma amplicon sequence variants across the host at different elevations suggested a phylogenetic divergence due to host habitat (i.e., marine or semi-terrestrial), thus supporting their potential functional role in the animal physiology. Our study sheds light on the influence of the environment on soil animal-bacteria interactions and provides insights into the resilience of the O. gammarellus-associated bacteria to increased flooding frequency.}, } @article {pmid33420624, year = {2021}, author = {Eraqi, WA and ElRakaiby, MT and Megahed, SA and Yousef, NH and Elshahed, MS and Yassin, AS}, title = {Spatiotemporal Analysis of the Water and Sediment Nile Microbial Community Along an Urban Metropolis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33420624}, issn = {1432-184X}, support = {2016423//National Science Foundation/ ; 3046//Academy of Scientific Research and Technology/ ; }, abstract = {Assessing microbial identity, diversity, and community structure could be a valuable tool for monitoring the impact of xenobiotics and anthropogenic inputs in rivers, especially in urban and industrial settings. Here, we characterize the Nile River microbial community in water and sediments in summer and winter at five locations that span its natural flow through the Cairo metropolis. 16S rRNA gene datasets were analyzed to identify the role played by sample type (sediment versus water), season, and location in shaping the community, as well as to predict functional potential of the Nile River microbiome. Microbial communities were mostly influenced by sampling type (sediments versus water), while seasonal effects were only observed in water samples. Spatial differences did not represent a significant factor in shaping the community in either summer or winter seasons. Proteobacteria was the most abundant phylum in both water and sediment samples, with the order Betaproteobacteriales being the abundant one. Chloroflexi and Bacteroidetes were also prevalent in sediment samples, while Cyanobacteria and Actinobacteria were abundant in water samples. The linear discriminative analysis effect size (LEfSe) identified the cyanobacterial genus Cyanobium PCC-6307 as the main variable between summer and winter water. Sequences representing human and animal potential pathogens, as well as toxin-producing Cyanobacteria, were identified in low abundance within the Nile microbiome. Functionally predicted metabolic pathways predicted the presence of antibiotic biosynthesis, as well as aerobic xenobiotic degradation pathways in the river microbiome.}, } @article {pmid33420408, year = {2021}, author = {Palladino, G and Morozzi, P and Biagi, E and Brattich, E and Turroni, S and Rampelli, S and Tositti, L and Candela, M}, title = {Particulate matter emission sources and meteorological parameters combine to shape the airborne bacteria communities in the Ligurian coast, Italy.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {175}, pmid = {33420408}, issn = {2045-2322}, abstract = {Aim of the present study is to explore how the chemical composition of particulate matter (PM) and meteorological conditions combine in shaping the air microbiome in Savona (Italy), a medium-size, heavily inhabited urban settlement, hosting a wide range of industrial activities. In particular, the air microbiome and PM10 were monitored over six months in 2012. During that time, the air microbiome was highly dynamic, fluctuating between different compositional states, likely resulting from the aerosolization of different microbiomes emission sources. According to our findings, this dynamic process depends on the combination of local meteorological parameters and particle emission sources, which may affect the prevalent aerosolized microbiomes, thus representing further fundamental tools for source apportionment in a holistic approach encompassing chemical as well as microbiological pollution. In particular, we showed that, in the investigated area, industrial emissions and winds blowing from the inlands combine with an airborne microbiome which include faecal microbiomes components, suggesting multiple citizens' exposure to both chemicals and microorganisms of faecal origin, as related to landscape exploitation and population density. In conclusion, our findings support the need to include monitoring of the air microbiome compositional structure as a relevant factor for the final assessment of local air quality.}, } @article {pmid33420219, year = {2021}, author = {Kawar, N and Park, SG and Schwartz, JL and Callahan, N and Obrez, A and Yang, B and Chen, Z and Adami, GR}, title = {Salivary microbiome with gastroesophageal reflux disease and treatment.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {188}, pmid = {33420219}, issn = {2045-2322}, abstract = {The effect of oral microbial composition on periodontal health and on systemic health has been, and is being established. The oral microbiome, in turn, can be altered by local and systemic diseases and conditions. Gastroesophageal reflux disease (GERD), has been associated with increased acidity in the oral cavity resulting in dental erosion, and controversially a reduced risk of periodontal disease. We hypothesized that presence of GERD was linked to a modified microbial profile in untreated GERD patients and that the use of proton pump inhibitor (PPI) drugs: potent disruptors of gut microbiome, in GERD patients might result in a salivary microbiome that is further distinct. Untreated GERD patients showed multiple differences in salivary microbiome as compared to healthy controls. Taxa found at lower levels related to the presence of GERD not treated by PPI included: Prevotella melaninogenica, Prevotella pallens, Leptotrichia, and Solobacterium moorei and thirteen others. In contrast, GERD patients chronically using PPI showed minimal differences in salivary taxa compared to healthy controls not using PPI.}, } @article {pmid33420159, year = {2021}, author = {Virdee, MS and Saini, N and Kay, CD and Neilson, AP and Kwan, STC and Helfrich, KK and Mooney, SM and Smith, SM}, title = {An enriched biosignature of gut microbiota-dependent metabolites characterizes maternal plasma in a mouse model of fetal alcohol spectrum disorder.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {248}, pmid = {33420159}, issn = {2045-2322}, support = {R01 AA011085/AA/NIAAA NIH HHS/United States ; F32 AA027121/NH/NIH HHS/United States ; T32 DK007686/NH/NIH HHS/United States ; R01 AA011085/NH/NIH HHS/United States ; T32 DK007686/DK/NIDDK NIH HHS/United States ; R01 AA022999/AA/NIAAA NIH HHS/United States ; pilot project grant//UNC Nutrition Research Institute/ ; F32 AA027121/AA/NIAAA NIH HHS/United States ; }, abstract = {Prenatal alcohol exposure (PAE) causes permanent cognitive disability. The enteric microbiome generates microbial-dependent products (MDPs) that may contribute to disorders including autism, depression, and anxiety; it is unknown whether similar alterations occur in PAE. Using a mouse PAE model, we performed untargeted metabolome analyses upon the maternal-fetal dyad at gestational day 17.5. Hierarchical clustering by principal component analysis and Pearson's correlation of maternal plasma (813 metabolites) both identified MDPs as significant predictors for PAE. The majority were phenolic acids enriched in PAE. Correlational network analyses revealed that alcohol altered plasma MDP-metabolite relationships, and alcohol-exposed maternal plasma was characterized by a subnetwork dominated by phenolic acids. Twenty-nine MDPs were detected in fetal liver and sixteen in fetal brain, where their impact is unknown. Several of these, including 4-ethylphenylsulfate, oxindole, indolepropionate, p-cresol sulfate, catechol sulfate, and salicylate, are implicated in other neurological disorders. We conclude that MDPs constitute a characteristic biosignature that distinguishes PAE. These MDPs are abundant in human plasma, where they influence physiology and disease. Their altered abundance here may reflect alcohol's known effects on microbiota composition and gut permeability. We propose that the maternal microbiome and its MDPs are a previously unrecognized influence upon the pathologies that typify PAE.}, } @article {pmid33420074, year = {2021}, author = {Behary, J and Amorim, N and Jiang, XT and Raposo, A and Gong, L and McGovern, E and Ibrahim, R and Chu, F and Stephens, C and Jebeili, H and Fragomeli, V and Koay, YC and Jackson, M and O'Sullivan, J and Weltman, M and McCaughan, G and El-Omar, E and Zekry, A}, title = {Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {187}, pmid = {33420074}, issn = {2041-1723}, abstract = {The gut microbiota is reported to modulate the immune response in hepatocellular carcinoma (HCC). Here, we employ metagenomic and metabolomic studies to characterise gut microbiota in patients with non-alcoholic fatty liver disease (NAFLD) related cirrhosis, with or without HCC, and evaluate its effect on the peripheral immune response in an ex vivo model. We find that dysbiosis characterises the microbiota of patients with NAFLD-cirrhosis, with compositional and functional shifts occurring with HCC development. Gene function of the microbiota in NAFLD-HCC supports short chain fatty acid production, and this is confirmed by metabolomic studies. Ex vivo studies show that bacterial extracts from the NAFLD-HCC microbiota, but not from the control groups, elicit a T cell immunosuppressive phenotype, characterised by expansion of regulatory T cells and attenuation of CD8 + T cells. Our study suggest that the gut microbiota in NAFLD-HCC is characterised by a distinctive microbiome/metabolomic profile, and can modulate the peripheral immune response.}, } @article {pmid33419736, year = {2021}, author = {Shore, A and Day, RD and Stewart, JA and Burge, CA}, title = {Dichotomy between regulation of coral bacterial communities and calcification physiology under ocean acidification conditions.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02189-20}, pmid = {33419736}, issn = {1098-5336}, abstract = {Ocean acidification (OA) threatens the growth and function of coral reef ecosystems. A key component to coral health is the microbiome, but little is known about the impact of OA on coral microbiomes. A submarine CO2 vent at Maug Island in the Northern Marianas Islands provides a natural pH gradient to investigate coral responses to long-term OA conditions. Three coral species (Pocillopora eydouxi, Porites lobata, and Porites rus) were sampled from three sites where mean seawater pH is 8.04, 7.98, and 7.94. We characterized coral bacterial communities (using 16S rRNA gene sequencing) and determined pH of the extracellular calcifying fluid (ECF) (using skeletal boron isotopes) across the seawater pH gradient. Bacterial communities of both Porites species stabilized (decreases in community dispersion) with decreased seawater pH, coupled with large increases in the abundance of Endozoicomonas, an endosymbiont. P. lobata experienced a significant decrease in ECF pH near the vent, whereas P. rus experienced a trending decrease in ECF pH near the vent. By contrast, Pocillopora exhibited bacterial community destabilization (increases in community dispersion), with significant decreases in Endozoicomonas abundance, while its ECF pH remained unchanged across the pH gradient. Our study shows that OA has multiple consequences on Endozoicomonas abundance and suggests that Endozoicomonas abundance may be an indicator of coral response to OA. We reveal an interesting dichotomy between two facets of coral physiology (regulation of bacterial communities and regulation of calcification), highlighting the importance of multidisciplinary approaches to understanding coral health and function in a changing ocean.IMPORTANCEOcean acidification (OA) is a consequence of anthropogenic CO2 emissions that is negatively impacting marine ecosystems such as coral reefs. OA affects many aspects of coral physiology, including growth (i.e. calcification) and disrupting associated bacterial communities. Coral-associated bacteria are important for host health, but it remains unclear how coral-associated bacterial communities will respond to future OA conditions. We document changes in coral-associated bacterial communities and changes to calcification physiology with long-term exposure to decreases in seawater pH that are environmentally relevant under mid-range IPCC emission scenarios (0.1 pH units). We also find species-specific responses that may reflect different responses to long-term OA. In Pocillopora, calcification physiology was highly regulated despite changing seawater conditions. In Porites spp., changes in bacterial communities do not reflect a breakdown of coral-bacterial symbiosis. Insights into calcification and host-microbe interactions are critical to predicting the health and function of different coral taxa to future OA conditions.}, } @article {pmid33419590, year = {2021}, author = {Malmuthuge, N and Guan, LL}, title = {Noncoding RNAs: Regulatory Molecules of Host-Microbiome Crosstalk.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2020.12.003}, pmid = {33419590}, issn = {1878-4380}, abstract = {Recent emerging evidence has revealed that regulatory noncoding RNAs (microRNAs, circular RNAs) modulate host-microbe interactions and they have been proposed as potential biomarkers of the host's response to microbiome-linked pathologies such as cancers, obesity, and neurodegenerative diseases. Interactions between microRNAs and circular RNAs, however, increase the complexity of the mechanisms that modulate host-microbe interactions. Current knowledge on these noncoding RNAs (ncRNAs) is mainly generated from well controlled germ-free or knockout (small) animal models. Application of such knowledge to effective modulation outcomes in humans (and livestock) is challenging due to the complex nature of microbiome-linked pathologies in larger outbred animals that constantly interact with the changing environment. This review critically discusses the findings of regulatory noncoding RNAs and their roles in microbiome-linked pathologies in small and large animals and provides insights on their roles as potential therapeutic agents to improve human (and livestock) health.}, } @article {pmid33419468, year = {2021}, author = {Daniel, S and Phillippi, D and Schneider, LJ and Nguyen, KN and Mirpuri, J and Lund, AK}, title = {Exposure to diesel exhaust particles results in altered lung microbial profiles, associated with increased reactive oxygen species/reactive nitrogen species and inflammation, in C57Bl/6 wildtype mice on a high-fat diet.}, journal = {Particle and fibre toxicology}, volume = {18}, number = {1}, pages = {3}, pmid = {33419468}, issn = {1743-8977}, support = {R15ES026795/ES/NIEHS NIH HHS/United States ; }, abstract = {BACKGROUND: Exposure to traffic-generated emissions is associated with the development and exacerbation of inflammatory lung disorders such as chronic obstructive pulmonary disorder (COPD) and idiopathic pulmonary fibrosis (IPF). Although many lung diseases show an expansion of Proteobacteria, the role of traffic-generated particulate matter pollutants on the lung microbiota has not been well-characterized. Thus, we investigated the hypothesis that exposure to diesel exhaust particles (DEP) can alter commensal lung microbiota, thereby promoting alterations in the lung's immune and inflammatory responses. We aimed to understand whether diet might also contribute to the alteration of the commensal lung microbiome, either alone or related to exposure. To do this, we used male C57Bl/6 mice (4-6-week-old) on either regular chow (LF) or high-fat (HF) diet (45% kcal fat), randomly assigned to be exposed via oropharyngeal aspiration to 35 μg DEP, suspended in 35 μl 0.9% sterile saline or sterile saline only (control) twice a week for 30 days. A separate group of study animals on the HF diet was concurrently treated with 0.3 g/day of Winclove Ecologic® Barrier probiotics in their drinking water throughout the study.

RESULTS: Our results show that DEP-exposure increases lung tumor necrosis factor (TNF)-α, interleukin (IL)-10, Toll-like receptor (TLR)-2, TLR-4, and the nuclear factor kappa B (NF-κB) histologically and by RT-qPCR, as well as Immunoglobulin A (IgA) and Immunoglobulin G (IgG) in the bronchoalveolar lavage fluid (BALF), as quantified by ELISA. We also observed an increase in macrophage infiltration and peroxynitrite, a marker of reactive oxygen species (ROS) + reactive nitrogen species (RNS), immunofluorescence staining in the lungs of DEP-exposed and HF-diet animals, which was further exacerbated by concurrent DEP-exposure and HF-diet consumption. Histological examinations revealed enhanced inflammation and collagen deposition in the lungs DEP-exposed mice, regardless of diet. We observed an expansion of Proteobacteria, by qPCR of bacterial 16S rRNA, in the BALF of DEP-exposed mice on the HF diet, which was diminished with probiotic-treatment.

CONCLUSIONS: Our findings suggest that exposure to DEP causes persistent and sustained inflammation and bacterial alterations in a ROS-RNS mediated fashion, which is exacerbated by concurrent consumption of an HF diet.}, } @article {pmid33419429, year = {2021}, author = {Cholewińska, P and Górniak, W and Wojnarowski, K}, title = {Impact of selected environmental factors on microbiome of the digestive tract of ruminants.}, journal = {BMC veterinary research}, volume = {17}, number = {1}, pages = {25}, pmid = {33419429}, issn = {1746-6148}, abstract = {Ruminants are an important part of world animal production. The main factors affecting their production rates are age, diet, physiological condition and welfare. Disorders related to low level of welfare can significantly affect the microbiological composition of the digestive system, which is essential to maintain high production rates. The microbiology of the ruminant gastrointestinal tract may be significantly affected by inappropriate keeping system (especially in juveniles), psychological stress (e.g. transport), or heat stress. This results in an increased risk of metabolic diseases, reduced fertility and systemic diseases. Therefore, the paper focuses on selected disorders i.e., aforementioned inappropriate maintenance system, psychological stress, heat stress and their effects on the microbiome of the digestive system.}, } @article {pmid33419388, year = {2021}, author = {Tong, AZ and Liu, W and Liu, Q and Xia, GQ and Zhu, JY}, title = {Diversity and composition of the Panax ginseng rhizosphere microbiome in various cultivation modesand ages.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {18}, pmid = {33419388}, issn = {1471-2180}, abstract = {BACKGROUND: Continuous cropping of ginseng (Panax ginseng Meyer) cultivated in farmland for an extended period gives rise to soil-borne disease. The change in soil microbial composition is a major cause of soil-borne diseases and an obstacle to continuous cropping. The impact of cultivation modes and ages on the diversity and composition of the P. ginseng rhizosphere microbial community and technology suitable for cropping P. ginseng in farmland are still being explored.

METHODS: Amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions were analyzed for microbial community composition and diversity.

RESULTS: The obtained sequencing data were reasonable for estimating soil microbial diversity. We observed significant variations in richness, diversity, and relative abundances of microbial taxa between farmland, deforestation field, and different cultivation years. The bacterial communities of LCK (forest soil where P. ginseng was not grown) had a much higher richness and diversity than those in NCK (farmland soil where P. ginseng was not grown). The increase in cultivation years of P. ginseng in farmland and deforestation field significantly changed the diversity of soil microbial communities. In addition, the accumulation of P. ginseng soil-borne pathogens (Monographella cucumerina, Ilyonectria mors-panacis, I. robusta, Fusarium solani, and Nectria ramulariae) varied with the cropping age of P. ginseng.

CONCLUSION: Soil microbial diversity and function were significantly poorer in farmland than in the deforestation field and were affected by P. ginseng planting years. The abundance of common soil-borne pathogens of P. ginseng increased with the cultivation age and led to an imbalance in the microbial community.}, } @article {pmid33419357, year = {2020}, author = {Ravegnini, G and Fosso, B and Saverio, VD and Sammarini, G and Zanotti, F and Rossi, G and Ricci, M and D'Amico, F and Valori, G and Ioli, A and Turroni, S and Brigidi, P and Hrelia, P and Angelini, S}, title = {Gastric Adenocarcinomas and Signet-Ring Cell Carcinoma: Unraveling Gastric Cancer Complexity through Microbiome Analysis-Deepening Heterogeneity for a Personalized Therapy.}, journal = {International journal of molecular sciences}, volume = {21}, number = {24}, pages = {}, pmid = {33419357}, issn = {1422-0067}, abstract = {Gastric cancer (GC) is the fifth most prevalent cancer worldwide and the third leading cause of global cancer mortality. With the advances of the omic studies, a heterogeneous GC landscape has been revealed, with significant molecular diversity. Given the multifaceted nature of GC, identification of different patient subsets with prognostic and/or predictive outcomes is a key aspect to allow tailoring of specific treatments. Recently, the involvement of the microbiota in gastric carcinogenesis has been described. To deepen this aspect, we compared microbiota composition in signet-ring cell carcinoma (SRCC) and adenocarcinoma (ADC), two distinct GC subtypes. To this purpose, 10 ADC and 10 SRCC and their paired non-tumor (PNT) counterparts were evaluated for microbiota composition through 16S rRNA analysis. Weighted and unweighted UniFrac and Bray-Curtis dissimilarity showed significant community-level separation between ADC and SRCC. Through the LEfSe (linear discriminant analysis coupled with effect size) tool, we identified potential microbial biomarkers associated with GC subtypes. In particular, SRCCs were significantly enriched in the phyla Fusobacteria, Bacteroidetes, Patescibacteria, whereas in the ADC type, Proteobacteria and Acidobacteria phyla were found. Overall, our data add new insights into GC heterogeneity and may contribute to deepening the GC classification.}, } @article {pmid33419325, year = {2020}, author = {Ilich, JZ}, title = {Nutritional and Behavioral Approaches to Body Composition and Low-Grade Chronic Inflammation Management for Older Adults in the Ordinary and COVID-19 Times.}, journal = {Nutrients}, volume = {12}, number = {12}, pages = {}, pmid = {33419325}, issn = {2072-6643}, mesh = {Adiposity/physiology ; Aged ; Aging ; *Body Composition ; Bone Diseases, Metabolic/complications ; COVID-19/*complications ; Diet/standards ; Food Supply ; Humans ; Inflammation/*complications/*therapy ; Malnutrition ; *Nutritional Status ; *SARS-CoV-2 ; Sarcopenia/complications ; Syndrome ; }, abstract = {As more insight is gained into personalized health care, the importance of personalized nutritional and behavioral approaches is even more relevant in the COVID-19 era, in addition to the need for further elucidation regarding several diseases/conditions. One of these concerning body composition (in this context; bone, lean and adipose tissue) is osteosarcopenic adiposity (OSA) syndrome. OSA occurs most often with aging, but also in cases of some chronic diseases and is exacerbated with the presence of low-grade chronic inflammation (LGCI). OSA has been associated with poor nutrition, metabolic disorders and diminished functional abilities. This paper addresses various influences on OSA and LGCI, as well as their mutual action on each other, and provides nutritional and behavioral approaches which could be personalized to help with either preventing or managing OSA and LGCI in general, and specifically in the time of the COVID-19 pandemic. Addressed in more detail are nutritional recommendations for and roles of macro- and micronutrients and bioactive food components; the microbiome; and optimal physical activity regimens. Other issues, such as food insecurity and nutritional inadequacy, circadian misalignment and shift workers are addressed as well. Since there is still a lack of longer-term primary studies in COVID-19 patients (either acute or recovered) and interventions for OSA improvement, this discussion is based on the existing knowledge, scientific hypotheses and observations derived from similar conditions or studies just being published at the time of this writing.}, } @article {pmid33419265, year = {2020}, author = {Wu, PH and Liu, PY and Chiu, YW and Hung, WC and Lin, YT and Lin, TY and Hung, SC and Delicano, RA and Kuo, MC and Wu, CY}, title = {Comparative Gut Microbiome Differences between Ferric Citrate and Calcium Carbonate Phosphate Binders in Patients with End-Stage Kidney Disease.}, journal = {Microorganisms}, volume = {8}, number = {12}, pages = {}, pmid = {33419265}, issn = {2076-2607}, support = {MOST 105-2628-B-037-005-MY2//Ministry of Science and Technology, Taiwan/ ; MOST 106-2314-B-037-054//Ministry of Science and Technology, Taiwan/ ; MOST 107-2314-B-037-104//Ministry of Science and Technology, Taiwan/ ; KMUH104-4M05//Kaohsiung Medical University Chung-Ho Memorial Hospital/ ; KMUH105-5R15//Kaohsiung Medical University Chung-Ho Memorial Hospital/ ; KMUH106-6R17//Kaohsiung Medical University Chung-Ho Memorial Hospital/ ; KMU-Q108024//Kaohsiung Medical University/ ; KMU-TP104PR25//Kaohsiung Medical University/ ; KMU-TP104PR26//Kaohsiung Medical University/ ; }, abstract = {Gut dysbiosis in patients with chronic kidney disease (CKD) may induce chronic inflammation and increase morbidity. Phosphate-binding agents, generally used in patients with CKD, may potentially change the composition of the gut microbiota. This study aimed to compare the microbiota composition in hemodialysis patients treated with ferric citrate or calcium carbonate. The stool microbiota was investigated in hemodialysis patients treated with ferric citrate (n = 8) and calcium carbonate (n = 46) using 16S rRNA gene amplicon sequencing profiling using linear discriminant analysis of effect size. Further predictive functional profiling of microbial communities was obtained with Tax4Fun in R. Hemodialysis patients treated with calcium carbonate had a significantly reduced microbial species diversity (Shannon index and Simpson index) and an increased microbial alteration ratio compared with patients treated with ferric citrate. A distinct microbial community structure was found in patients treated with ferric citrate, with an increased abundance of the Bacteroidetes phylum and a decreased abundance of the phylum Firmicutes. Members of the order Lactobacillales were enriched in patients treated with calcium carbonate, whereas taxa of the genera Ruminococcaceae UCG-004, Flavonifractor, and Cronobacter were enriched in patients treated with ferric citrate phosphate binder. In conclusion, Ferric citrate therapy results in a more diverse microbiome community compared to calcium carbonate therapy in hemodialysis patients with phosphate binder treatment. The gut microbiome reflects the phosphate binder choice in hemodialysis patients, further affecting the physiological environment in the gastrointestinal tract.}, } @article {pmid33419054, year = {2021}, author = {Fernández, L and Castro, I and Arroyo, R and Alba, C and Beltrán, D and Rodríguez, JM}, title = {Application of Ligilactobacillus salivarius CECT5713 to Achieve Term Pregnancies in Women with Repetitive Abortion or Infertility of Unknown Origin by Microbiological and Immunological Modulation of the Vaginal Ecosystem.}, journal = {Nutrients}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/nu13010162}, pmid = {33419054}, issn = {2072-6643}, support = {Research contrat//Biosearch Life/ ; }, abstract = {In this study, the cervicovaginal environment of women with reproductive failure (repetitive abortion, infertility of unknown origin) was assessed and compared to that of healthy fertile women. Subsequently, the ability of Ligilactobacillus salivarius CECT5713 to increase pregnancy rates in women with reproductive failure was evaluated. Vaginal pH and Nugent score were higher in women with reproductive failure than in fertile women. The opposite was observed regarding the immune factors TGF-β 1, TFG-β 2, and VEFG. Lactobacilli were detected at a higher frequency and concentration in fertile women than in women with repetitive abortion or infertility. The metataxonomic study revealed that vaginal samples from fertile women were characterized by the high abundance of Lactobacillus sequences, while DNA from this genus was practically absent in one third of samples from women with reproductive failure. Daily oral administration of L. salivarius CECT5713 (~9 log10 CFU/day) to women with reproductive failure for a maximum of 6 months resulted in an overall successful pregnancy rate of 56%. The probiotic intervention modified key microbiological, biochemical, and immunological parameters in women who got pregnant. In conclusion, L. salivarius CECT5713 has proved to be a good candidate to improve reproductive success in women with reproductive failure.}, } @article {pmid33418488, year = {2020}, author = {Iyama, S and Tatsumi, H and Shiraishi, T and Yoshida, M and Tatekoshi, A and Endo, A and Ishige, T and Shiwa, Y and Ibata, S and Goto, A and Nagashima, K and Horiguchi, H and Fujita, C and Ikeda, H and Takada, K and Nobuoka, T and Kamihara, Y and Kikuchi, S and Sato, T and Ohnishi, H and Yokota, SI and Kobune, M}, title = {Possible clinical outcomes using early enteral nutrition in individuals with allogeneic hematopoietic stem cell transplantation: A single-center retrospective study.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {83}, number = {}, pages = {111093}, doi = {10.1016/j.nut.2020.111093}, pmid = {33418488}, issn = {1873-1244}, abstract = {OBJECTIVES: Intensive nutritional support during allogeneic hematopoietic stem cell transplantation (allo-HSCT) yields improved clinical outcomes. However, the clinical implications of early enteral nutrition (EN) in allo-HSCT remain unclear. This retrospective study was conducted to determine the significance of early EN in individuals who underwent allo-HSCT, and the association between early nutritional intervention and clinical outcomes, including the status of the intestinal microbiome.

METHODS: Thirty-one participants received EN before conditioning. The intestinal microbiota was examined by meta 16S rRNA gene sequencing of fecal samples.

RESULTS: The median body mass variation was only -0.35 kg on day 60. The probability of 2-y overall survival was 61.1%. The cumulative incidence of treatment-related mortality was 17.4%, and those of acute graft-versus-host disease were 32.3% (grades II-IV) and 3.2% (grades III-IV). Chronic graft-versus-host disease was observed in four participants. Dysbiosis of the intestines and acute graft-versus-host disease occurred simultaneously, and Enterococcus species were abundant.

CONCLUSIONS: Our results suggest that early nutritional support can improve the outcomes for individuals who have undergone allo-HSCT and can maintain homeostasis of their intestinal microbiome. Future prospective clinical trials are required to elucidate the role of EN in allo-HSCT and the association between the intestinal microbiome and EN.}, } @article {pmid33418307, year = {2021}, author = {Lee, JG and Lee, YR and Lee, AR and Park, CH and Han, DS and Eun, CS}, title = {Role of the global gut microbial community in the development of colitis-associated cancer in a murine model.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {135}, number = {}, pages = {111206}, doi = {10.1016/j.biopha.2020.111206}, pmid = {33418307}, issn = {1950-6007}, abstract = {The gut microbiota has been implicated in the development of colitis-associated cancer (CAC). We investigated how the gut microbiota affects the development of CAC when the composition of the microbial community is altered by the administration of various antibiotics in a murine model. C57BL/6 mice were given intraperitoneal injection of 12.5 mg/kg azoxymethane (AOM), followed by two rounds of 2.0 % dextran sodium sulfate (DSS) exposure. Antibiotics, including ampicillin, neomycin, metronidazole, and/or vancomycin, were administered 14 days prior to AOM injection until the end of the experiment. High-throughput sequencing of mice feces was conducted to evaluate alterations of the gut microbiota. Tumorigenesis and inflammation were most markedly suppressed in the mice treated with an antibiotic cocktail therapy consisting of ampicillin, neomycin, metronidazole, and vancomycin. Individual antibiotic treatments had different effects on tumorigenesis and inflammation. Metronidazole attenuated both tumorigenesis and inflammation. Neomycin suppressed tumorigenesis but did not alleviate inflammation. Ampicillin and vancomycin did not significantly attenuate either tumorigenesis or inflammation. Antimicrobial therapy differentially altered the diversity and composition of the gut microbiota depending on antibiotic type. The phyla Proteobacteria and Tenericutes were positively correlated with tumor burden. Colon tumorigenesis was attenuated through various antibiotics in the AOM/DSS-induced CAC model. Individual antibiotics differentially altered the gut microbial composition and showed different effects on tumor suppression; however, the degree of tumor suppression was less pronounced than that relative to the antibiotic cocktail therapy, suggesting that the global gut microbial community plays an important role in the development of CAC.}, } @article {pmid33418277, year = {2021}, author = {Yu, Q and Jobin, C and Thomas, RM}, title = {Implications of the microbiome in the development and treatment of pancreatic cancer: Thinking outside of the box by looking inside the gut.}, journal = {Neoplasia (New York, N.Y.)}, volume = {23}, number = {2}, pages = {246-256}, doi = {10.1016/j.neo.2020.12.008}, pmid = {33418277}, issn = {1476-5586}, abstract = {Pancreatic ductal adenocarcinoma is the third leading cause of cancer-related death in the United States. As one of the most lethal cancer types, the prognosis for patients diagnosed with pancreatic cancer remains dismal and novel investigations are urgently needed. Evidence for an association of microbes with pancreatic cancer risk, development, treatment response, and post-treatment survivorship is rapidly developing. Herein, we provide an overview on the role of the microbiome as it relates to the natural history of pancreatic cancer, including host immune interactions, alterations in metabolism, direct carcinogenic effect, and its role in treatment response.}, } @article {pmid33418265, year = {2020}, author = {Knisz, J and Shetty, P and Wirth, R and Maróti, G and Karches, T and Dalkó, I and Bálint, M and Vadkerti, E and Bíró, T}, title = {Genome-level insights into the operation of an on-site biological wastewater treatment unit reveal the importance of storage time.}, journal = {The Science of the total environment}, volume = {766}, number = {}, pages = {144425}, doi = {10.1016/j.scitotenv.2020.144425}, pmid = {33418265}, issn = {1879-1026}, abstract = {On-site wastewater treatment systems are gaining popularity in areas where centralized wastewater treatment is not available. In the current case study a domestic activated sludge system was investigated, where treated effluent was stored in a short-term (1 week turn-over time) and a long-term (over 2-3 months) storage tank and was then used for irrigation. This design provided a unique opportunity to assess the chemical and microbial changes of the effluent upon storage. Long-term storage greatly improved both the chemical quality and the degradation efficiency of most organic micropollutants examined, including petroleum hydrocarbons and the pesticide diethyltoluamide. Taxonomic profile of the core microbiome of the effluent was also influenced upon storage. Relative abundance values of the members of Azoarcus and Thauera genera, which are important in degrading polycyclic aromatic hydrocarbons compounds, clearly indicated the biodegrading activity of these microbes across samples. The abundance of xenobiotics degradation functions correlated with the observed organic micropollutant degradation values indicating efficient microbial decomposition of these contaminants. Functions related to infectious diseases also had the highest abundance in the short-term storage tank corresponding well with the relative abundance of indicator organisms and implying to the significance of storage time in the elimination of pathogens. Based on these results, small, on-site wastewater treatment systems could benefit from long-term storage of wastewater effluent.}, } @article {pmid33417973, year = {2021}, author = {Rani, L and Mondal, AC}, title = {Unravelling the role of gut microbiota in Parkinson's disease progression: Pathogenic and therapeutic implications.}, journal = {Neuroscience research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.neures.2021.01.001}, pmid = {33417973}, issn = {1872-8111}, abstract = {In recent years, researchers have shown interest in bi-directional interaction between the brain and gut, called "gut-brain axis". Emerging pieces of evidence indicate that disturbances in this axis is found to be associated with the Parkinson's disease (PD). Several clinical investigations revealed the crucial role of gut microbiota in the pathogenesis of PD. It has been suggested that aggregation of misfolded protein α-syn, the neuropathological hallmark of PD, might begin in gut and propagates to the CNS via vagus nerve and olfactory bulb. Emerging evidences also suggest that initiation and progression of PD may be due to inflammation originating from gut. It has been shown that microbial gut dysbiosis causes the production of various pathogenic microbial metabolites which elevates pro-inflammatory environment in the gut that promotes neuroinflammation in the CNS. These observations raise the intriguing question - how gut microbial dysbiosis could contribute to PD progression. In this context, various microbiota-targeted therapies are under consideration that can re-establish the intestinal homeostasis which may have greater promise in the prevention and treatment of PD. This review focuses on the role of the gut microbiota in the initiation, progression of PD and current therapeutic intervention to deplete the severity of the disease.}, } @article {pmid33417698, year = {2021}, author = {Moossavi, S and Fontes, ME and Rossi, L and Fusch, G and Surette, MG and Azad, MB}, title = {Capturing the diversity of the human milk microbiota through culture-enriched molecular profiling: a feasibility study.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnab001}, pmid = {33417698}, issn = {1574-6968}, abstract = {Previous human milk studies have confirmed the existence of a highly diverse bacterial community using culture-independent and targeted culture-dependent techniques. However, culture-enriched molecular profiling of milk microbiota has not been done. Additionally, the impact of storage conditions and milk fractionation on microbiota composition is not understood. In this feasibility study, we optimised and applied culture-enriched molecular profiling to study culturable milk microbiota in eight milk samples collected from mothers of infants admitted to a neonatal intensive care unit. Fresh samples were immediately plated or stored at -80°C for two weeks (short-term frozen). Long-term samples were stored at -20°C for more than six months. Samples were cultured using 10 different culture media and incubated both aerobically and anaerobically. We successfully isolated major milk bacteria including Streptococcus, Staphylococcus, and Bifidobacterium from fresh milk samples, but were unable to culture any bacteria from the long-term frozen samples. Short-term freezing shifted the composition of viable milk bacteria from the original composition in fresh samples. Nevertheless, the inter-individual variability of milk microbiota composition was observed even after short-term storage. There was no major difference in the overall milk microbiota composition between milk fractions in this feasibility study. This is among the first studies on culture-enriched molecular profiling of the milk microbiota demonstrating the effect of storage and fractionation on milk microbiota composition.}, } @article {pmid33416892, year = {2021}, author = {Fontana, L and Ghezzi, L and Cross, AH and Piccio, L}, title = {Effects of dietary restriction on neuroinflammation in neurodegenerative diseases.}, journal = {The Journal of experimental medicine}, volume = {218}, number = {2}, pages = {}, pmid = {33416892}, issn = {1540-9538}, support = {R01 NS102633/NS/NINDS NIH HHS/United States ; }, abstract = {Recent and accumulating work in experimental animal models and humans shows that diet has a much more pervasive and prominent role than previously thought in modulating neuroinflammatory and neurodegenerative mechanisms leading to some of the most common chronic central nervous system (CNS) diseases. Chronic or intermittent food restriction has profound effects in shaping brain and peripheral metabolism, immunity, and gut microbiome biology. Interactions among calorie intake, meal frequency, diet quality, and the gut microbiome modulate specific metabolic and molecular pathways that regulate cellular, tissue, and organ homeostasis as well as inflammation during normal brain aging and CNS neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and multiple sclerosis, among others. This review discusses these findings and their potential application to the prevention and treatment of CNS neuroinflammatory diseases and the promotion of healthy brain aging.}, } @article {pmid33416850, year = {2021}, author = {Ma, Y and Jiang, H}, title = {NinimHMDA: Neural integration of neighborhood information on a multiplex heterogeneous network for multiple types of human Microbe-Disease association.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaa1080}, pmid = {33416850}, issn = {1367-4811}, abstract = {MOTIVATION: Many computational methods have been recently proposed to identify differentially abundant microbes related to a single disease; however, few studies have focused on large-scale microbe-disease association prediction using existing experimentally verified associations. This area has critical meanings. For example, it can help to rank and select potential candidate microbes for different diseases at-scale for downstream lab validation experiments and it utilizes existing evidence instead of the microbiome abundance data which usually costs money and time to generate.

RESULTS: We construct a multiplex heterogeneous network (MHEN) using human microbe-disease association database, Disbiome, and other prior biological databases, and define the large-scale human microbe-disease association prediction as link prediction problems on MHEN. We develop an end-to-end graph convolutional neural network-based mining model NinimHMDA which can not only integrate different prior biological knowledge but also predict different types of microbe-disease associations (e.g. a microbe may be reduced or elevated under the impact of a disease) using one-time model training. To the best of our knowledge, this is the first method that targets on predicting different association types between microbes and diseases. Results from large-scale cross validation and case studies show that our model is highly competitive compared to other commonly used approaches.

AVAILABILITY: The codes are available at Github https://github.com/yuanjing-ma/NinimHMDA.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid33416489, year = {2021}, author = {Jiang, Y and Yuan, Z and Shen, Y and Rosa, BA and Martin, J and Cao, S and Zhou, Y and Mitreva, M and Cao, J}, title = {Alteration of the fecal microbiota in Chinese patients with Schistosoma japonicum infection.}, journal = {Parasite (Paris, France)}, volume = {28}, number = {}, pages = {1}, pmid = {33416489}, issn = {1776-1042}, abstract = {Schistosoma japonicum infection causes pathological injury to the host. Multiple studies have shown that intestinal helminth infection causes dysbiosis for the gut microbial community and impacts host immunology. However, the effect of acute S. japonicum infection on the gut microbiome structure (abundance and diversity) is still unclear. We collected fecal samples from healthy and infected patients from a single hospital in Hunan Province, China. The bacterial community was analyzed using 16S ribosomal RNA gene sequencing of the V4 hypervariable region using the HiSeq platform. Compared with healthy subjects, infected patients exhibited an increase in relative abundance of the TM7 phylum. At the genus level, there were seven differentially abundant genera between groups. The most significant finding was a Bacteroides enterotype in patients with acute schistosomiasis. These results suggest that S. japonicum infection has a significant effect on microbiome composition characterized by a higher abundance of the TM7 phylum and development of a Bacteroides enterotype.}, } @article {pmid33416261, year = {2021}, author = {Mendonça Gorgulho, C and Krishnamurthy, A and Lanzi, A and Galon, J and Housseau, F and Kaneno, R and Lotze, MT}, title = {Gutting it Out: Developing Effective Immunotherapies for Patients With Colorectal Cancer.}, journal = {Journal of immunotherapy (Hagerstown, Md. : 1997)}, volume = {Publish Ahead of Print}, number = {}, pages = {}, doi = {10.1097/CJI.0000000000000357}, pmid = {33416261}, issn = {1537-4513}, abstract = {Risk factors for colorectal cancer (CRC) include proinflammatory diets, sedentary habits, and obesity, in addition to genetic syndromes that predispose individuals to this disease. Current treatment relies on surgical excision and cytotoxic chemotherapies. There has been a renewed interest in immunotherapy as a treatment option for CRC given the success in melanoma and microsatellite instable (MSI) CRC. Immunotherapy with checkpoint inhibitors only plays a role in the 4%-6% of patients with MSIhigh tumors and even within this subpopulation, response rates can vary from 30% to 50%. Most patients with CRC do not respond to this modality of treatment, even though colorectal tumors are frequently infiltrated with T cells. Tumor cells limit apoptosis and survive following intensive chemotherapy leading to drug resistance and induction of autophagy. Pharmacological or molecular inhibition of autophagy improves the efficacy of cytotoxic chemotherapy in murine models. The microbiome clearly plays an etiologic role, in some or most colon tumors, realized by elegant findings in murine models and now investigated in human clinical trials. Recent results have suggested that cancer vaccines may be beneficial, perhaps best as preventive strategies. The search for therapies that can be combined with current approaches to increase their efficacy, and new knowledge of the biology of CRC are pivotal to improve the care of patients suffering from this disease. Here, we review the basic immunobiology of CRC, current "state-of-the-art" immunotherapies and define those areas with greatest therapeutic promise for the future.}, } @article {pmid33415370, year = {2021}, author = {Gasz, NE and Geary, MJ and Doggett, SL and Harvey, ML}, title = {Bacterial association observations in Lucilia sericata and Lucilia cuprina organs through 16S rRNA gene sequencing.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {33415370}, issn = {1432-0614}, abstract = {Blowfly (Diptera: Calliphoridae) species Lucilia sericata (Meigen) and related species Lucilia cuprina (Wiedmann) are important agricultural pests, assist in forensic fields and also have a therapeutic role in medicine. Both species (though predominantly L. sericata) are utilised in a clinical setting for maggot debridement therapy (MDT) where the larvae ingest necrotic tissue and bacteria from non-healing wounds. Conversely, larvae of L. cuprina feed invasively, as major initiators of sheep myiasis in Australia, New Zealand, and the UK, among other regions. Both species exhibit larval and adult interactions with bacterially rich environments, but the significance of this in the composition of their microbiome has yet to be considered. This study utilised dissected samples of digestive and reproductive organs from both disinfected and non-disinfected adults and larvae of both species for bacterial DNA extraction, followed by 16S rRNA gene sequencing. Sequencing data indicated unsurprisingly that digestive tracts of both genders and female salivary glands from all non-disinfected samples carry the most concentrated amounts of bacteria. Genera Pseudomonas and Corynebacterium were also highly represented within all organs and species analysed. Comparison of bait lures to sample sequence read output of insect specimens showed no correlation with genera such as Pseudomonas present in insects, while absent from wild bait, and in reduced amounts from fleece bait profiles. With this information, future work can focus on key organs such as the spermathecae and salivary glands, while also providing the potential to identify the role these bacteria may play in the blowfly life cycle. KEY POINTS: Genera Pseudomonas appears consistently in the microbiome of Lucilia species. Female spermathecae and salivary glands show the highest microbial diversity. Bacterial profiles of L. sericata and L. cuprina have similar composition.}, } @article {pmid33415132, year = {2020}, author = {Pilla, R and Law, TH and Pan, Y and Zanghi, BM and Li, Q and Want, EJ and Lidbury, JA and Steiner, JM and Suchodolski, JS and Volk, HA}, title = {The Effects of a Ketogenic Medium-Chain Triglyceride Diet on the Feces in Dogs With Idiopathic Epilepsy.}, journal = {Frontiers in veterinary science}, volume = {7}, number = {}, pages = {541547}, pmid = {33415132}, issn = {2297-1769}, abstract = {Consumption of diets containing medium chain triglycerides have been shown to confer neuroprotective and behavior modulating effects. We aimed to identify metabolic and microbiome perturbations in feces that are associated with consumption of a medium chain triglyceride ketogenic diet (MCT-KD) in dogs with idiopathic epilepsy. We used 16S rRNA gene sequencing to generate microbiome profiles and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) to generate lipidomic profiles of canine feces. We made comparisons between the MCT-KD, standardized placebo diet and baseline pre-trial diet phases. Consumption of the MCT-KD resulted in a significant increase in the species richness (α-diversity) of bacterial communities found in the feces when compared to the baseline diet. However, phylogenetical diversity between samples (beta-diversity) was not affected by diet. An unnamed Bacteroidaceae species within genus 5-7N15 was identified by LEfSe as a potential biomarker associated with consumption of the MCT-KD, showing an increased abundance (p = 0.005, q = 0.230) during consumption of MCT-KD. In addition, unclassified members of families Erysipelotrichaceae (p = 0.013, q = 0.335) and Fusobacteriaceae (p = 0.022, q = 0.358) were significantly increased during MCT-KD consumption compared to baseline. Blautia sp. and Megamonas sp. instead were decreased during consumption of either placebo or MCT-KD (p = 0.045, q = 0.449, and p = 0.039, q = 0.449, respectively). Bacteroidaceae, including genus 5-7N15, have previously been associated with non-aggressive behavior in dogs. In addition, 5-7N15 is correlated in humans with Akkermansia, a genus known to be involved in the neuroprotective effect of ketogenic diets in mice models of seizures. Five metabolite features, tentatively identified as long chain triglycerides, were significantly higher after consumption of the placebo diet, but no unique features were identified after consumption of the MCT-KD. The data presented in this study highlight significant changes shown in both the fecal microbiome and lipidome as a result of consumption of the MCT-KD. Elucidating the global canine gut response to MCT consumption will improve our understanding of the potential mechanisms which confer anti-seizure and behavior modulating effects. Further studies should aim to characterize the gut microbiome of both dogs with epilepsy and healthy controls.}, } @article {pmid33414773, year = {2020}, author = {Lu, Z and Xu, Z and Kong, L and Shen, H and Aschenbach, JR}, title = {Functional Changes of the Community of Microbes With Ni-Dependent Enzyme Genes Accompany Adaptation of the Ruminal Microbiome to Urea-Supplemented Diets.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {596681}, pmid = {33414773}, issn = {1664-302X}, abstract = {Urea is an inexpensive non-protein nitrogen source commonly supplemented to the diets of ruminants. It is cleaved to ammonia by bacterial ureases, which require Ni as a catalyst for ureolysis. The key event in the changes of the ruminal microbiome after urea supplementation remains unknown. We have therefore investigated changes in the ruminal microbiome and its community with Ni-dependent enzyme genes following urea supplementation and analyzed the associations of rumen environmental factors, including fermentation variables and Ni concentrations, with the compositional and functional changes of these communities. We found that urea supplementation increased urease activity and the concentrations of ammonia and Ni, and tended to increase concentrations of short chain fatty acids and acetate, whereas it decreased rumen pH and the L-/D-lactate ratio. With standards for genome completeness >60% and strain heterogeneity <10%, 20 bacterial species containing five Ni-dependent enzyme genes were detected in the metagenome sequences. For the five Ni-dependent enzyme genes, urea supplementation increased the relative abundances of genes of urease and acetyl-CoA synthase, whereas it decreased the relative abundances of genes of glyoxalase I, [NiFe]-hydrogenase, and lactate racemase. For the 20 microbes with Ni-dependent enzyme genes, urea supplementation increased the relative abundances of five bacteria exhibiting high capacities for the utilization of hemicellulose and pectin for butyrate and fatty acid biosynthesis. For the ruminal microbiome, urea supplementation increased the metagenomic capacities for hemicellulose and pectin degradation, butyrate generation, fatty acid biosynthesis, and carbon fixation, whereas it decreased the metagenomic capacities for starch degradation, propionate generation, and sulfur and nitrogen metabolism. Constrained correspondence analysis identified rumen ammonia and Ni concentrations as likely driving factors in the reshaping of the ruminal microbiome and, together with pH, of the community of microbes with Ni-dependent enzyme genes. Thus, the functional change of the latter community is probably an important event in the adaptation of the ruminal microbiome to urea-supplemented diets. This result provides a new perspective for the understanding of the effects of urea supplementation on rumen fermentation.}, } @article {pmid33414326, year = {2021}, author = {Amanbayeva, M and Anarkulova, E and Bogoyavlenskiy, A and Alexyuk, M and Imangazy, A and Berezin, V}, title = {Metagenomic Exploration of Atelerix albiventris Gut Microbiome.}, journal = {Microbiology resource announcements}, volume = {10}, number = {1}, pages = {}, pmid = {33414326}, issn = {2576-098X}, abstract = {Here, we report the metagenomic analysis of the gut of Atelerix albiventris, an animal typically kept as a pet in Kazakhstan. In this case, shotgun metagenomic sequencing of the RNA and DNA viral community was performed.}, } @article {pmid33414318, year = {2021}, author = {Babalola, OO and Omotayo, OP and Igiehon, NO}, title = {Survey of Maize Rhizosphere Microbiome Using Shotgun Metagenomics.}, journal = {Microbiology resource announcements}, volume = {10}, number = {1}, pages = {}, pmid = {33414318}, issn = {2576-098X}, abstract = {Several processes which occur in the rhizosphere make it a vital region in plant development. However, studies that examine rhizosphere microbiomes and their functional potentials remain scarce. Shotgun metagenomics was employed here to evaluate the functional potentials of the maize rhizosphere microbiome of farms in two South African provinces.}, } @article {pmid33414033, year = {2020}, author = {Fuhri Snethlage, CM and Nieuwdorp, M and Hanssen, NMJ}, title = {Faecal microbiota transplantation in endocrine diseases and obesity.}, journal = {Best practice & research. Clinical endocrinology & metabolism}, volume = {}, number = {}, pages = {101483}, doi = {10.1016/j.beem.2020.101483}, pmid = {33414033}, issn = {1878-1594}, abstract = {The prevalence of type 1 (T1D) and type 2 diabetes mellitus (T2D) has greatly increased worldwide over the last century. Although the exact pathophysiology of both these conditions is distinct and still largely unknown, T1D as well as T2D, have been linked to distinct perturbations of the gut microbiome. Faecal microbiota transplantation (FMT) is a potent, and if performed well, a safe method to modulate the composition of the gut microbiome and thus positively influences the course of these hyperglycaemic conditions in humans. In this review, we provide an overview of how FMT is commonly performed and summarise how this procedure may reduce the insulin-resistance driving T2D, and the underlying auto-immunity driving T1D. Insights derived from FMT studies in T1D and T2D may help identify beneficial microbiota and associated metabolites that may serve as future treatments for these conditions.}, } @article {pmid33413501, year = {2021}, author = {Kong, L and Chen, J and Ji, X and Qin, Q and Yang, H and Liu, D and Li, D and Sun, M}, title = {Alcoholic fatty liver disease inhibited the co-expression of Fmo5 and PPARα to activate the NF-κB signaling pathway, thereby reducing liver injury via inducing gut microbiota disturbance.}, journal = {Journal of experimental & clinical cancer research : CR}, volume = {40}, number = {1}, pages = {18}, pmid = {33413501}, issn = {1756-9966}, support = {YYYJK201814//Basic research project of Henan Academy of Medical and Pharmaceutical/ ; }, abstract = {BACKGROUND: Alcohol-induced intestinal dysbiosis disrupts and inflammatory responses are essential in the development of alcoholic fatty liver disease (AFLD). Here, we investigated the effects of Fmo5 on changes in enteric microbiome composition in a model of AFLD and dissected the pathogenic role of Fmo5 in AFLD-induced liver pathology.

METHODS: The expression profile data of GSE8006 and GSE40334 datasets were downloaded from the GEO database. The WGCNA approach allowed us to investigate the AFLD-correlated module. DEGs were used to perform KEGG pathway enrichment analyses. Four PPI networks were constructed using the STRING database and visualized using Cytoscape software. The Cytohubba plug-in was used to identify the hub genes. Western blot and immunohistochemistry assays were used to detect protein expression. ELISA assay was used to detect the levels of serum inflammatory cytokines. Lipid droplets in the cytoplasm were observed using Oil Red O staining. Apoptosis was detected using a TUNEL assay and flow cytometry analysis. ROS levels were detected using flow cytometry analysis. Nuclear translocation of NF-κB p65 was observed using immunofluorescence staining. Co-immunoprecipitation was used to detect the co-expression of PPARα and Fmo5 in L02 cells. 16S rDNA sequencing defined the bacterial communities in mice with AFLD.

RESULTS: Fmo5 is a key DEG and is closely associated with the gut microbiota and PPAR signaling pathway. Gut microbiome function in AFLD was significantly related to the PPAR signaling pathway. AFLD induced shifts in various bacterial phyla in the cecum, including a reduction in Bacteroidetes and increased Firmicutes. Fmo5 and PPARα co-expression in cell and animal models with AFLD, which decreased significantly. Silencing of Fmo5 and PPARα aggravated the functions of AFLD inducing apoptosis and inflammatory response, promoting liver injury, and activating the NF-κB signaling pathway in vivo and in vitro. The NF-κB inhibitor abolished the functions of silencing of Fmo5 and PPARα promoting AFLD-induced apoptosis, inflammatory response, and liver injury.

CONCLUSION: Our data indicated that the co-expression of Fmo5 and PPARα was involved in AFLD-related gut microbiota composition and alleviated AFLD-induced liver injury, apoptosis, and inflammatory response by inhibiting the nuclear translocation of NF-κB p65 to inhibit the NF-κB signaling pathway.}, } @article {pmid33413361, year = {2021}, author = {Ye, X and Zhou, L and Zhang, Y and Xue, S and Gan, QF and Fang, S}, title = {Effect of host breeds on gut microbiome and serum metabolome in meat rabbits.}, journal = {BMC veterinary research}, volume = {17}, number = {1}, pages = {24}, pmid = {33413361}, issn = {1746-6148}, abstract = {BACKGROUND: Gut microbial compositional and functional variation can affect health and production performance of farm animals. Analysing metabolites in biological samples provides information on the basic mechanisms that affect the well-being and production traits in farm animals. However, the extent to which host breeds affect the gut microbiome and serum metabolome in meat rabbits is still unknown. In this study, the differences in phylogenetic composition and functional capacities of gut microbiota in two commercial rabbit breeds Elco and Ira were determined by 16S rRNA gene and metagenomic sequencing. The alternations in serum metabolome in the two rabbit breeds were detected using ultra-performance liquid chromatography system coupled with quadrupole time of flight mass spectrometry (UPLC-QTOFMS).

RESULTS: Sequencing results revealed that there were significant differences in the gut microbiota of the two breeds studied, suggesting that host breeds affect structure and diversity of gut microbiota. Numerous breed-associated microorganisms were identified at different taxonomic levels and most microbial taxa belonged to the families Lachnospiraceae and Ruminococcaceae. In particular, several short-chain fatty acids (SCFAs) producing species including Coprococcus comes, Ruminococcus faecis, Ruminococcus callidus, and Lachnospiraceae bacterium NK4A136 could be considered as biomarkers for improving the health and production performance in meat rabbits. Additionally, gut microbial functional capacities related to bacterial chemotaxis, ABC transporters, and metabolism of different carbohydrates, amino acids, and lipids varied greatly between rabbit breeds. Several fatty acids, amino acids, and organic acids in the serum were identified as breed-associated, where certain metabolites could be regarded as biomarkers correlated with the well-being and production traits of meat rabbits. Correlation analysis between breed-associated microbial species and serum metabolites revealed significant co-variations, indicating the existence of cross-talk among host-gut microbiome-serum metabolome.

CONCLUSIONS: Our study provides insight into how gut microbiome and serum metabolome of meat rabbits are affected by host breeds and uncovers potential biomarkers important for breed improvement of meat rabbits.}, } @article {pmid33413128, year = {2021}, author = {Mustafa, GR and Li, C and Zhao, S and Jin, L and He, X and Shabbir, MZ and He, Y and Li, T and Deng, W and Xu, L and Xiong, Y and Zhang, G and Zhang, H and Huang, Y and Zou, L}, title = {Metagenomic analysis revealed a wide distribution of antibiotic resistance genes and biosynthesis of antibiotics in the gut of giant pandas.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {15}, pmid = {33413128}, issn = {1471-2180}, support = {KLSFGAGP2020.003//Key Laboratory of SFGA on Conservation Biology of Rare Animals in the Giant Panda National Park (CCRCGP)/ ; No. 2017115//State Forestry Administration/ ; GH201709//International Cooperation project of giant panda/ ; }, abstract = {BACKGROUND: The gut microbiome is essential for the host's health and serves as an essential reservoir of antibiotic resistance genes (ARGs). We investigated the effects of different factors, including the dietary shifts and age, on the functional characteristics of the giant panda's gut microbiome (GPs) through shotgun metagenome sequencing. We explored the association between gut bacterial genera and ARGs within the gut based on network analysis.

RESULTS: Fecal samples (n=60) from captive juvenile, adult, and geriatric GPs were processed, and variations were identified in the gut microbiome according to different ages, the abundance of novel ARGs and the biosynthesis of antibiotics. Among 667 ARGs identified, nine from the top ten ARGs had a higher abundance in juveniles. For 102 ARGs against bacteria, a co-occurrence pattern revealed a positive association for predominant ARGs with Streptococcus. A comparative KEGG pathways analysis revealed an abundant biosynthesis of antibiotics among three different groups of GPs, where it was more significantly observed in the juvenile group. A co-occurrence pattern further revealed a positive association for the top ten ARGs, biosynthesis of antibiotics, and metabolic pathways.

CONCLUSION: Gut of GPs serve as a reservoir for novel ARGs and biosynthesis of antibiotics. Dietary changes and age may influence the gut microbiome's functional characteristics; however, it needs further studies to ascertain the study outcomes.}, } @article {pmid33413098, year = {2021}, author = {Li, Y and Xu, Z and Liu, H}, title = {Nutrient-imbalanced conditions shift the interplay between zooplankton and gut microbiota.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {37}, pmid = {33413098}, issn = {1471-2164}, abstract = {BACKGROUND: Nutrient stoichiometry of phytoplankton frequently changes with aquatic ambient nutrient concentrations, which is mainly influenced by anthropogenic water treatment and the ecosystem dynamics. Consequently, the stoichiometry of phytoplankton can markedly alter the metabolism and growth of zooplankton. However, the effects of nutrient-imbalanced prey on the interplay between zooplankton and their gut microbiota remain unknown. Using metatranscriptome, a 16 s rRNA amplicon-based neutral community model (NCM) and experimental validation, we investigated the interactions between Daphnia magna and its gut microbiota in a nutrient-imbalanced algal diet.

RESULTS: Our results showed that in nutrient-depleted water, the nutrient-enriched zooplankton gut stimulated the accumulation of microbial polyphosphate in fecal pellets under phosphorus limitation and the microbial assimilation of ammonia under nitrogen limitation. Compared with the nutrient replete group, both N and P limitation markedly promoted the gene expression of the gut microbiome for organic matter degradation but repressed that for anaerobic metabolisms. In the nutrient limited diet, the gut microbial community exhibited a higher fit to NCM (R2 = 0.624 and 0.781, for N- and P-limitation, respectively) when compared with the Control group (R2 = 0.542), suggesting increased ambient-gut exchange process favored by compensatory feeding. Further, an additional axenic grazing experiment revealed that the growth of D. magna can still benefit from gut microbiota under a nutrient-imbalanced diet.

CONCLUSIONS: Together, these results demonstrated that under a nutrient-imbalanced diet, the microbes not only benefit themselves by absorbing excess nutrients inside the zooplankton gut but also help zooplankton to survive during nutrient limitation.}, } @article {pmid33412999, year = {2021}, author = {Liu, Z and Mao, X and Dan, Z and Pei, Y and Xu, R and Guo, M and Liu, K and Zhang, F and Chen, J and Su, C and Zhuang, Y and Tang, J and Xia, Y and Qin, L and Hu, Z and Liu, X}, title = {Gene variations in autism spectrum disorder are associated with alteration of gut microbiota, metabolites and cytokines.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-16}, doi = {10.1080/19490976.2020.1854967}, pmid = {33412999}, issn = {1949-0984}, abstract = {The genetic variations and dysbiosis of gut microbiota are associated with ASD. However, the role of the microbiota in the etiology of ASD in terms of host genetic susceptibility remains unclear. This study aims to systematically explore the interplay between host genetic variation and gut microbiota in ASD children. Whole-exon sequencing was applied to 26 ASD children and 26 matched controls to identify the single nucleotide variations (SNVs) in ASD. Our previous study revealed alteration in gut microbiota and disorder of metabolism activity in ASD for this cohort. Systematic bioinformatic analyses were further performed to identify associations between SNVs and gut microbiota, as well as their metabolites. The ASD SNVs were significantly enriched in genes associated with innate immune response, protein glycosylation process, and retrograde axonal transport. These SNVs were also correlated with the microbiome composition and a broad aspect of microbial functions, especially metabolism. Additionally, the abundance of metabolites involved in the metabolic network of neurotransmitters was inferred to be causally related to specific SNVs and microbes. Furthermore, our data suggested that the interaction of host genetics and gut microbes may play a crucial role in the immune and metabolism homeostasis of ASD. This study may provide valuable clues to investigate the interaction of host genetic variations and gut microbiota in the pathogenesis of ASD.}, } @article {pmid33412949, year = {2021}, author = {Chang, CC and Hayase, E and Jenq, RR}, title = {The role of microbiota in allogeneic hematopoietic stem cell transplantation.}, journal = {Expert opinion on biological therapy}, volume = {}, number = {}, pages = {}, doi = {10.1080/14712598.2021.1872541}, pmid = {33412949}, issn = {1744-7682}, abstract = {INTRODUCTION: : Allogeneic hematopoietic stem cell transplantation (Allo-HSCT) is commonly performed to treat a variety of benign and malignant hematological diseases. Acute graft-versus-host disease (GVHD) is a major life-threatening complication that often occurs following allo-HSCT. Recently, improvements in methods to characterize the microbiota have led to a greater appreciation for how frequently and profoundly an alteration in microbial composition, or dysbiosis, can occur in allo-HSCT recipients to better decipher the complex interplay of between microbiota and allo-HSCT outcomes.

AREAS COVERED: : This article reviews the current knowledge of the microbiota's impact on allo-HSCT outcomes, including effects of microbiota-derived metabolites, and crosstalk between commensals and the allogeneic immune response. This article also summarizes the effects of HSCT and transplant-related procedures on microbiota, and recent developments in interventional strategies.

EXPERT OPINION: : A growing body of literature indicate that the composition of the intestinal microbiota can function as a predictive biomarker for the risk and severity of acute GVHD, as well as overall survival, in patients undergoing allo-HSCT. Mechanisms underpinning this associations, however, are not well-understood, and clinical strategies that modulate the microbiome to improve outcomes have yet to be fully developed. There is an unmet need to determine mechanisms to improve the efficacy of allo-HSCT.}, } @article {pmid33412896, year = {2021}, author = {Kamp, KJ and Plantinga, AM and Cain, KC and Burr, RL and Barney, P and Jarrett, M and Luna, RA and Savidge, T and Shulman, R and Heitkemper, MM}, title = {A Comprehensive Self-Management Program With Diet Education Does Not Alter Microbiome Characteristics in Women With Irritable Bowel Syndrome.}, journal = {Biological research for nursing}, volume = {}, number = {}, pages = {1099800420984543}, doi = {10.1177/1099800420984543}, pmid = {33412896}, issn = {1552-4175}, abstract = {BACKGROUND AND PURPOSE: Changes in diet and lifestyle factors are frequently recommended for persons with irritable bowel syndrome (IBS). It is unknown whether these recommendations alter the gut microbiome and/or whether baseline microbiome predicts improvement in symptoms and quality of life following treatment. Therefore, the purpose of this study was to explore if baseline gut microbiome composition predicted response to a Comprehensive Self-Management (CSM) intervention and if the intervention resulted in a different gut microbiome composition compared to usual care.

METHODS: Individuals aged 18-70 years with IBS symptoms ≥6 months were recruited using convenience sampling. Individuals were excluded if medication use or comorbidities would influence symptoms or microbiome. Participants completed a baseline assessment and were randomized into the eight-session CSM intervention which included dietary education and cognitive behavioral therapy versus usual care. Questionnaires included demographics, quality of life, and symptom diaries. Fecal samples were collected at baseline and 3-month post-randomization for 16S rRNA-based microbiome analysis.

RESULTS: Within the CSM intervention group (n = 30), Shannon diversity, richness, and beta diversity measures at baseline did not predict benefit from the CSM intervention at 3 months, as measured by change in abdominal pain and quality of life. Based on both alpha and beta diversity, the change from baseline to follow-up microbiome bacterial taxa did not differ between CSM (n = 25) and usual care (n = 25).

CONCLUSIONS AND INFERENCES: Baseline microbiome does not predict symptom improvement with CSM intervention. We do not find evidence that the CSM intervention influences gut microbiome diversity or composition over the course of 3 months.}, } @article {pmid33412751, year = {2020}, author = {Kim, S and Kim, DH and Lee, W and Lee, YM and Choi, SY and Han, K}, title = {The nature of triple-negative breast cancer classification and antitumoral strategies.}, journal = {Genomics & informatics}, volume = {18}, number = {4}, pages = {e35}, doi = {10.5808/GI.2020.18.4.e35}, pmid = {33412751}, issn = {1598-866X}, support = {2019R1A6C1010033//Korea Basic Science Institute/ ; //Ministry of Education/ ; }, abstract = {Identifying the patterns of gene expression in breast cancers is essential to understanding their pathophysiology and developing anticancer drugs. Breast cancer is a heterogeneous disease with different subtypes determined by distinct biological features. Luminal breast cancer is characterized by a relatively high expression of estrogen receptor (ER) and progesterone receptor (PR) genes, which are expressed in breast luminal cells. In ~25% of invasive breast cancers, human epidermal growth factor receptor 2 (HER2) is overexpressed; these cancers are categorized as the HER2 type. Triple-negative breast cancer (TNBC), in which the cancer cells do not express ER/PR or HER2, shows highly aggressive clinical outcomes. TNBC can be further classified into specific subtypes according to genomic mutations and cancer immunogenicity. Herein, we discuss the brief history of TNBC classification and its implications for promising treatments.}, } @article {pmid33411981, year = {2021}, author = {Wellhöner, F and Döscher, N and Woelfl, F and Vital, M and Plumeier, I and Kahl, S and Potthoff, A and Manns, MP and Pieper, DH and Cornberg, M and Wedemeyer, H and Heidrich, B}, title = {Eradication of chronic HCV infection: improvement of dysbiosis only in patients without liver cirrhosis.}, journal = {Hepatology (Baltimore, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1002/hep.31700}, pmid = {33411981}, issn = {1527-3350}, abstract = {It is well accepted that liver diseases and their outcomes are associated with intestinal microbiota but causality is difficult to establish. The intestinal microbiota is altered in patients with hepatitis C. As chronic HCV infection can now be cured in almost all patients, it is an ideal model to study the influence of liver disease on the microbiota. We aimed to analyze prospectively the changes in the gut microbiome in patients who received direct acting antivirals (DAA) and achieved sustained virological response (SVR). Amplicon sequencing of the V1-V2 region in the 16S rRNA gene was performed in stool samples of patients with chronic hepatitis C. Patients in the treatment group received direct acting antivirals (n=65) whereas in the control group no DAA were given (n=33). Only patients achieving SVR were included. The alpha diversity increased numerical but not significantly from baseline to SVR24/48 (2.784±0.248 vs. 2.846±0.224; p= 0.057). When stratifying for the presence of liver cirrhosis, a significant increase in diversity was only seen in patients without cirrhosis. Differences in the microbial community structure induced by the achievement of SVR were only observed in patients without liver cirrhosis. In patients with liver cirrhosis and in the control group, no significant differences were observed. In conclusion, the achievement of SVR24/48 in patients with chronic HCV was associated with changes in the intestinal microbiota. However, these changes were only seen in patients without liver cirrhosis. A major role of liver remodeling on the intestinal microbiota is indicated by the dynamics of the intestinal microbial community structure depending on the stage of fibrosis in patients resolving chronic hepatitis C.}, } @article {pmid33411719, year = {2021}, author = {Elmassry, MM and Kim, S and Busby, B}, title = {Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes.}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0244876}, doi = {10.1371/journal.pone.0244876}, pmid = {33411719}, issn = {1932-6203}, abstract = {Characterizing the gut microbiota in terms of their capacity to interfere with drug metabolism is necessary to achieve drug efficacy and safety. Although examples of drug-microbiome interactions are well-documented, little has been reported about a computational pipeline for systematically identifying and characterizing bacterial enzymes that process particular classes of drugs. The goal of our study is to develop a computational approach that compiles drugs whose metabolism may be influenced by a particular class of microbial enzymes and that quantifies the variability in the collective level of those enzymes among individuals. The present paper describes this approach, with microbial β-glucuronidases as an example, which break down drug-glucuronide conjugates and reactivate the drugs or their metabolites. We identified 100 medications that may be metabolized by β-glucuronidases from the gut microbiome. These medications included morphine, estrogen, ibuprofen, midazolam, and their structural analogues. The analysis of metagenomic data available through the Sequence Read Archive (SRA) showed that the level of β-glucuronidase in the gut metagenomes was higher in males than in females, which provides a potential explanation for the sex-based differences in efficacy and toxicity for several drugs, reported in previous studies. Our analysis also showed that infant gut metagenomes at birth and 12 months of age have higher levels of β-glucuronidase than the metagenomes of their mothers and the implication of this observed variability was discussed in the context of breastfeeding as well as infant hyperbilirubinemia. Overall, despite important limitations discussed in this paper, our analysis provided useful insights on the role of the human gut metagenome in the variability in drug response among individuals. Importantly, this approach exploits drug and metagenome data available in public databases as well as open-source cheminformatics and bioinformatics tools to predict drug-metagenome interactions.}, } @article {pmid33411382, year = {2021}, author = {Jervis, P and Pintanel, P and Hopkins, K and Wierzbicki, C and Shelton, JMG and Skelly, E and Rosa, GM and Almeida-Reinoso, D and Eugenia-Ordoñez, M and Ron, S and Harrison, X and Merino-Viteri, A and Fisher, MC}, title = {Post-epizootic microbiome associations across communities of neotropical amphibians.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15789}, pmid = {33411382}, issn = {1365-294X}, abstract = {Microbiome-pathogen interactions are increasingly recognised as an important element of host immunity. While these host-level interactions will have consequences for community disease dynamics, the factors which influence host microbiomes at larger scales are poorly understood. We here describe landscape scale pathogen-microbiome associations within the context of post-epizootic amphibian chytridiomycosis, a disease caused by the panzootic chytrid fungus Batrachochytrium dendrobatidis. We undertook a survey of Neotropical amphibians across altitudinal gradients in Ecuador ~30 years following the observed amphibian declines and collected skin swab-samples which were metabarcoded using both fungal (ITS-2) and bacterial (r16S) amplicons. Our data reveals marked variation in patterns of both B. dendrobatidis infection and microbiome structure that are associated with host life history. Stream breeding amphibians were most likely to be infected with B. dendrobatidis. This increased probability of infection was further associated with increased abundance and diversity of non-Batrachochytrium chytrid fungi in the skin and environmental microbiome. We also show that increased alpha diversity and the relative abundance of fungi is lower in the skin microbiome of adult stream amphibians compared to adult pond breeding amphibians, an association not seen for bacteria. Finally, stream tadpoles exhibit lower proportions of predicted protective microbial taxa than pond tadpoles, suggestive of reduced biotic resistance. Our analyses show that host breeding ecology strongly shapes pathogen-microbiome associations at a landscape scale, a trait that may influence resilience in the face of emerging infectious diseases.}, } @article {pmid33410935, year = {2021}, author = {Li, W and Nelson, KE}, title = {Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33410935}, issn = {1432-184X}, abstract = {In recent years, many studies have described the composition and function of the human microbiome at different body sites and suggested a role for the microbiome in various diseases and health conditions. Some studies, using longitudinal samples, have also suggested how the microbiome changes over time due to disease, diet, development, travel, and other environmental factors. However, to date, no study has demonstrated whether the microorganisms established at birth or in early childhood, either transmitted from parents or obtained from the environment, can stay in the human body until adult or senior age. To directly answer this question is difficult, because microbiome samples at childhood and at later adulthood for the same individual will need to be compared and the field is not old enough to have allowed for that type of sample collection. Here, using a metagenomic approach, we analyzed 1004 gut microbiome samples from senior adults (65 ± 7.8 years) from the TwinsUK cohort. Our data indicate that many species in the human gut acquired in early childhood can stay for a lifetime until senior ages. We identified the rare genomic variants (single nucleotide variation and indels) for 27 prevalent species with enough sequencing coverage for confident genomic variant identification. We found that for some species, twin pairs, including both monozygotic (MZ) and dizygotic (DZ) twins, share significantly more rare variants than unrelated subject pairs. But no significant difference is found between MZ and DZ twin pairs. These observations strongly suggest that these species acquired in early childhood remained in these persons until senior adulthood.}, } @article {pmid33410931, year = {2021}, author = {Gomez, JA and Primm, TP}, title = {A Slimy Business: the Future of Fish Skin Microbiome Studies.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33410931}, issn = {1432-184X}, abstract = {Fish skin contains a mucosal microbiome for the largest and oldest group of vertebrates, a location ideal for microbial community ecology and practical applications in agriculture and veterinary medicine. These selective microbiomes are dominated by Proteobacteria, with compositions different from the surrounding water. Core taxa are a small percentage of those present and are currently functionally uncharacterized. Methods for skin sampling, DNA extraction and amplification, and sequence data processing are highly varied across the field, and reanalysis of recent studies using a consistent pipeline revealed that some conclusions did change in statistical significance. Further, the 16S gene sequencing approaches lack quantitation of microbes and copy number adjustment. Thus, consistency in the field is a serious limitation in comparing across studies. The most significant area for future study, requiring metagenomic and metabolomics data, is the biochemical pathways and functions within the microbiome community, the interactions between members, and the resulting effects on fish host health being linked to specific nutrients and microbial species. Genes linked to skin colonization, such as those for attachment or mucin degradation, need to be uncovered and explored. Skin immunity factors need to be directly linked to microbiome composition and individual taxa. The basic foundation has been laid, and many exciting future discoveries remain.}, } @article {pmid33410764, year = {2021}, author = {De Vadder, F and Joly, A and Leulier, F}, title = {Microbial and nutritional influence on endocrine control of growth.}, journal = {Journal of molecular endocrinology}, volume = {}, number = {}, pages = {}, doi = {10.1530/JME-20-0288}, pmid = {33410764}, issn = {1479-6813}, abstract = {The worrying number of children suffering from undernutrition and consequent stunting worldwide makes the understanding of the relationship between nutritional status and postnatal growth crucial. Moreover, it is now well established that undernourished children harbor an altered microbiota, correlating with impaired growth. In this review, we describe how murine models have been used to explore the functional relationships between endocrine regulation of growth, nutrition and gut microbiota. In numerous Mammalian species, postnatal growth is mainly regulated by the conserved GH/IGF-1 somatotropic axis that acts through endocrine and paracrine pathways, notably enabling longitudinal bone growth. Recent studies have demonstrated that the microbiota effects on growth could involve a modulation of GH and IGF-1 circulating levels. Besides, the GH/IGF-1 somatotropic axis may regulate the gut microbiota composition and diversity. Studying the bidirectional relationship between growth hormones and the gut microbiome could therefore help developing microbiota-targeting therapies in order to reduce the long-term consequences of stunting.}, } @article {pmid33409871, year = {2021}, author = {Guo, J and Shao, J and Yang, Y and Niu, X and Liao, J and Zhao, Q and Wang, D and Li, S and Hu, J}, title = {Gut Microbiota in Patients with Polycystic Ovary Syndrome: a Systematic Review.}, journal = {Reproductive sciences (Thousand Oaks, Calif.)}, volume = {}, number = {}, pages = {}, pmid = {33409871}, issn = {1933-7205}, abstract = {Polycystic ovary Syndrome (PCOS) is one of the most popular diseases that cause menstrual dysfunction and infertility in women. Recently, the relationships between the gastrointestinal microbiome and metabolic disorders such as obesity, type 2 diabetes and PCOS have been discovered. However, the association between the gut microbiome and PCOS symptoms has not been well established. We systematically reviewed existing studies comparing gut microbial composition in PCOS and healthy volunteers to explore evidence for this association. A systematic search was carried out in PubMed, Embase, Cochrane Library, and Web of Science from inception to May 26, 2020, for all original cross-sectional, cohort, or case-control studies comparing the fecal microbiomes of patients with PCOS with microbiomes of healthy volunteers (controls). The primary outcomes were differences in specific gut microbes between patients with PCOS and controls. The search identified 256 citations; 10 studies were included. The total population study of these articles consists of 611 participants (including PCOS group and healthy controls group). Among the included 10 studies, nine studies compared α-diversity, and six studies demonstrated that α-diversity has a significant reduction in PCOS patients. Seven of them reported that there was a significant difference of β-diversity composition between healthy controls groups and PCOS patients. The most common bacterial alterations in PCOS patients included Bacteroidaceae, Coprococcus, Bacteroides, Prevotella, Lactobacillus, Parabacteroides, Escherichia/Shigella, and Faecalibacterium prausnitzii. No consensus has emerged from existing human studies of PCOS and gut microbiome concerning which bacterial taxa are most relevant to it. In this systematic review, we identified specific bacteria associated with microbiomes of patients with PCOS vs controls. Higher level of evidence is needed to determine whether these microbes are a product or cause of PCOS.}, } @article {pmid33409849, year = {2021}, author = {Wilson, RL and Hewes, SA and Rajan, A and Lin, SC and Bomidi, C and Iida, T and Estes, MK and Maresso, AW and Grande-Allen, KJ}, title = {A Millifluidic Perfusion Cassette for Studying the Pathogenesis of Enteric Infections Using Ex-Vivo Organoids.}, journal = {Annals of biomedical engineering}, volume = {}, number = {}, pages = {}, pmid = {33409849}, issn = {1573-9686}, support = {U19 AI116497/NH/NIH HHS/United States ; F30 DK108541/NH/NIH HHS/United States ; RP160283//Cancer Prevention and Research Institute of Texas/ ; }, abstract = {To generate physiologically-relevant experimental models, the study of enteric diarrheal diseases is turning increasingly to advanced in vitro models that combine ex vivo, stem cell-derived "organoid" cell lines with bioengineered culture environments that expose them to mechanical stimuli, such as fluid flow. However, such approaches require considerable technical expertise with both microfabrication and organoid culture, and are, therefore, inaccessible to many researchers. For this reason, we have developed a perfusion system that is simple to fabricate, operate, and maintain. Its dimensions approximate the volume and cell culture area of traditional 96-well plates and allow the incorporation of fastidious primary, stem cell-derived cell lines with only minimal adaptation of their established culture techniques. We show that infections with enteroaggregative E. coli and norovirus, common causes of infectious diarrhea, in the system display important differences from static models, and in some ways better recreate the pathophysiology of in vivo infections. Furthermore, commensal strains of bacteria can be added alongside the pathogens to simulate the effects of a host microbiome on the infectious process. For these reasons, we believe that this perfusion system is a powerful, yet easily accessible tool for studying host-pathogen interactions in the human intestine.}, } @article {pmid33409714, year = {2021}, author = {Cheng, X and Guo, X and Huang, F and Lei, H and Zhou, Q and Song, C}, title = {Effect of different sweeteners on the oral microbiota and immune system of Sprague Dawley rats.}, journal = {AMB Express}, volume = {11}, number = {1}, pages = {8}, pmid = {33409714}, issn = {2191-0855}, support = {0903-00040031//Scientific Research Foundation for Talent Introduction of Southwest Medical University/ ; 0903-00031093//the Science Fund Project of Southwest Medical University/ ; }, abstract = {Sucrose, xylose, and saccharin are commonly used beverage additives and long-term consumption of these compounds inevitably affects the oral immune system and the composition of oral microbiomes. In this study, we used 24 Sprague Dawley rats divided into four groups, i.e., sucrose, saccharin, xylose, or pure water treated over an eight week period to evaluate any changes in the composition, community structure, and function of the oral microbiomes. At the end of the treatment period, we collected oral microbiome samples from each animal and subjected them to high-throughput sequencing. We also used ELISA to determine the concentration of salivary immunoglobulin in these rats to reveal the effect of sweetener on the oral immune system. Sequencing results demonstrated that Firmicutes and Proteobacteria, remained the predominant phyla, but we found that the oral microbial diversity of rats drinking sucrose water was significantly higher than that of the other groups. Our results indicate that drinking water supplemented with sweeteners may influence oral immunity as well as the composition, metabolic function, and diversity of the oral microbiota, thereby disrupting the oral microbiome.}, } @article {pmid33409607, year = {2021}, author = {Song, Y and Mhuantong, W and Liu, SY and Pisutpaisal, N and Wongwilaiwalin, S and Kanokratana, P and Wang, AJ and Jiang, CY and Champreda, V and Qiu, DR and Liu, SJ}, title = {Tropical and temperate wastewater treatment plants assemble different and diverse microbiomes.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {2}, pages = {853-867}, pmid = {33409607}, issn = {1432-0614}, support = {KY201701011//Ministry of Science and Technology of the People's Republic of China/ ; 2019YFA0905500//Ministry of Science and Technology of the People's Republic of China/ ; 2019YFC1905001//Ministry of Science and Technology of China/ ; 153211KYSB20160029//Chinese Academy of Sciences/ ; P-18-52413//Ministry of Science and Technology of Thailand/ ; }, abstract = {The diversity and assembly of activated sludge microbiomes play a key role in the performances of municipal wastewater treatment plants (WWTPs), which are the most widely applied biotechnological process systems. In this study, we investigated the microbiomes of municipal WWTPs in Bangkok, Wuhan, and Beijing that respectively represent tropical, subtropical, and temperate climate regions, and also explored how microbiomes assembled in these municipal WWTPs. Our results showed that the microbiomes from these municipal WWTPs were significantly different. The assembly of microbiomes in municipal WWTPs followed deterministic and stochastic processes governed by geographical location, temperature, and nutrients. We found that both taxonomic and phylogenetic α-diversities of tropical Bangkok municipal WWTPs were the highest and were rich in yet-to-be-identified microbial taxa. Nitrospirae and β-Proteobacteria were more abundant in tropical municipal WWTPs, but did not result in better removal efficiencies of ammonium and total nitrogen. Overall, these results suggest that tropical and temperate municipal WWTPs harbored diverse and unique microbial resources, and the municipal WWTP microbiomes were assembled with different processes. Implications of these findings for designing and running tropical municipal WWTPs were discussed. KEY POINTS: • Six WWTPs of tropical Thailand and subtropical and temperate China were investigated. • Tropical Bangkok WWTPs had more diverse and yet-to-be-identified microbial taxa. • Microbiome assembly processes were associated with geographical location.}, } @article {pmid33409398, year = {2021}, author = {Kwong, EK and Puri, P}, title = {Gut microbiome changes in Nonalcoholic fatty liver disease & alcoholic liver disease.}, journal = {Translational gastroenterology and hepatology}, volume = {6}, number = {}, pages = {3}, pmid = {33409398}, issn = {2415-1289}, support = {K23 AA021179/AA/NIAAA NIH HHS/United States ; }, abstract = {Nonalcoholic fatty liver disease (NAFLD) and alcoholic liver disease (ALD) are some of the most common liver diseases worldwide. The human gut microbiome is dynamic and shifts in bacterial composition have been implicated in many diseases. Studies have shown that there is a shift in bacterial overgrowth favoring pro-inflammatory mediators in patients with advanced disease progression such as cirrhosis. Further investigation demonstrated that the transplantation of gut microbiota from advanced liver disease patients can reproduce severe liver inflammation and injury in mice. Various techniques in manipulating the gut microbiota have been attempted including fecal transplantation and probiotics. This review focuses on the changes in the gut microbiota as well as emerging lines of microbiome work with respect to NAFLD and ALD.}, } @article {pmid33408884, year = {2020}, author = {Jarman, R and Ribeiro-Milograna, S and Kalle, W}, title = {Potential of the Microbiome as a Biomarker for Early Diagnosis and Prognosis of Breast Cancer.}, journal = {Journal of breast cancer}, volume = {23}, number = {6}, pages = {579-587}, pmid = {33408884}, issn = {1738-6756}, abstract = {Breast cancer affects 1 in 8 women globally, and is the leading cause of cancer-related deaths in female patients. The majority of breast cancer cases are of unknown cause; few are linked to genetic predisposition, and some arise sporadically. Finding the cause of these sporadic cases is an important area in cancer research. Investigations into the microbiome show links between microbiome dysbiosis and breast cancer, with possible mechanisms in the association of the microbiome and breast cancer, including estrogen metabolism and the 'oestrobolome,' immune regulation, propensity for obesity, and the regulation of the tumor microenvironment. This paper reviews the literature and discusses the potential implications of links between the microbiome and breast cancer, and concludes that the microbiome may have significant applications as a biomarker for breast cancer diagnosis, prognosis, and management. Further investigation is crucial, since modification of the microbiome can, at the most basic level, be achieved via dietary modification.}, } @article {pmid33408878, year = {2020}, author = {Plyusnin, I and Kant, R and Jääskeläinen, AJ and Sironen, T and Holm, L and Vapalahti, O and Smura, T}, title = {Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types.}, journal = {Virus evolution}, volume = {6}, number = {2}, pages = {veaa091}, pmid = {33408878}, issn = {2057-1577}, abstract = {The study of the microbiome data holds great potential for elucidating the biological and metabolic functioning of living organisms and their role in the environment. Metagenomic analyses have shown that humans, along with for example, domestic animals, wildlife and arthropods, are colonized by an immense community of viruses. The current Coronavirus pandemic (COVID-19) heightens the need to rapidly detect previously unknown viruses in an unbiased way. The increasing availability of metagenomic data in this era of next-generation sequencing (NGS), along with increasingly affordable sequencing technologies, highlight the need for reliable and comprehensive methods to manage such data. In this article, we present a novel bioinformatics pipeline called LAZYPIPE for identifying both previously known and novel viruses in host associated or environmental samples and give examples of virus discovery based on it. LAZYPIPE is a Unix-based pipeline for automated assembling and taxonomic profiling of NGS libraries implemented as a collection of C++, Perl, and R scripts.}, } @article {pmid33408712, year = {2020}, author = {Ray, P and Lakshmanan, V and Labbé, JL and Craven, KD}, title = {Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {622926}, pmid = {33408712}, issn = {1664-302X}, abstract = {Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.}, } @article {pmid33408698, year = {2020}, author = {Vishwakarma, K and Kumar, N and Shandilya, C and Mohapatra, S and Bhayana, S and Varma, A}, title = {Revisiting Plant-Microbe Interactions and Microbial Consortia Application for Enhancing Sustainable Agriculture: A Review.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {560406}, pmid = {33408698}, issn = {1664-302X}, abstract = {The present scenario of agricultural sector is dependent hugely on the use of chemical-based fertilizers and pesticides that impact the nutritional quality, health status, and productivity of the crops. Moreover, continuous release of these chemical inputs causes toxic compounds such as metals to accumulate in the soil and move to the plants with prolonged exposure, which ultimately impact the human health. Hence, it becomes necessary to bring out the alternatives to chemical pesticides/fertilizers for improvement of agricultural outputs. The rhizosphere of plant is an important niche with abundant microorganisms residing in it. They possess the properties of plant growth promotion, disease suppression, removal of toxic compounds, and assimilating nutrients to plants. Utilizing such beneficial microbes for crop productivity presents an efficient way to modulate the crop yield and productivity by maintaining healthy status and quality of the plants through bioformulations. To understand these microbial formulation compositions, it becomes essential to understand the processes going on in the rhizosphere as well as their concrete identification for better utilization of the microbial diversity such as plant growth-promoting bacteria and arbuscular mycorrhizal fungi. Hence, with this background, the present review article highlights the plant microbiome aboveground and belowground, importance of microbial inoculants in various plant species, and their subsequent interactive mechanisms for sustainable agriculture.}, } @article {pmid33408417, year = {2021}, author = {Sanmarco, LM and Wheeler, MA and Gutiérrez-Vázquez, C and Polonio, CM and Linnerbauer, M and Pinho-Ribeiro, FA and Li, Z and Giovannoni, F and Batterman, KV and Scalisi, G and Zandee, SEJ and Heck, ES and Alsuwailm, M and Rosene, DL and Becher, B and Chiu, IM and Prat, A and Quintana, FJ}, title = {Gut-licensed IFNγ+ NK cells drive LAMP1+TRAIL+ anti-inflammatory astrocytes.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {33408417}, issn = {1476-4687}, abstract = {Astrocytes are glial cells that are abundant in the central nervous system (CNS) and that have important homeostatic and disease-promoting functions1. However, little is known about the homeostatic anti-inflammatory activities of astrocytes and their regulation. Here, using high-throughput flow cytometry screening, single-cell RNA sequencing and CRISPR-Cas9-based cell-specific in vivo genetic perturbations in mice, we identify a subset of astrocytes that expresses the lysosomal protein LAMP12 and the death receptor ligand TRAIL3. LAMP1+TRAIL+ astrocytes limit inflammation in the CNS by inducing T cell apoptosis through TRAIL-DR5 signalling. In homeostatic conditions, the expression of TRAIL in astrocytes is driven by interferon-γ (IFNγ) produced by meningeal natural killer (NK) cells, in which IFNγ expression is modulated by the gut microbiome. TRAIL expression in astrocytes is repressed by molecules produced by T cells and microglia in the context of inflammation. Altogether, we show that LAMP1+TRAIL+ astrocytes limit CNS inflammation by inducing T cell apoptosis, and that this astrocyte subset is maintained by meningeal IFNγ+ NK cells that are licensed by the microbiome.}, } @article {pmid33408370, year = {2021}, author = {Bullington, BW and Lee, MH and Mlingi, J and Paul, N and Aristide, C and Fontana, E and Littmann, ER and Mukerebe, C and Shigella, P and Kashangaki, P and Kalluvya, SE and de Dood, CJ and van Dam, GJ and Corstjens, PLAM and Fitzgerald, DW and Pamer, EG and Downs, JA}, title = {Cervicovaginal bacterial communities in reproductive-aged Tanzanian women with Schistosoma mansoni, Schistosoma haematobium, or without schistosome infection.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {33408370}, issn = {1751-7370}, support = {K23 AI110238/AI/NIAID NIH HHS/United States ; K23 AI 110238//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; }, abstract = {Schistosome infection is recognized as a potentially modifiable risk factor for HIV in women by the World Health Organization. Alterations in cervicovaginal bacteria have been associated with HIV acquisition and have not been studied in schistosome infection. We collected cervical swabs from Tanzanian women with and without S. mansoni and S. haematobium to determine effects on cervicovaginal microbiota. Infected women were treated, and follow-up swabs were collected after 3 months. 16S rRNA sequencing was performed on DNA extracted from swabs. We compared 39 women with S. mansoni with 52 uninfected controls, and 16 with S. haematobium with 27 controls. S. mansoni-infected women had increased abundance of Peptostreptococcus (p = 0.026) and presence of Prevotella timonesis (p = 0.048) compared to controls. High-intensity S. haematobium infection was associated with more diverse cervicovaginal bacterial communities than uninfected controls (p = 0.0159). High-intensity S. mansoni infection showed a similar trend (p = 0.154). At follow-up, we observed increased alpha diversity in S. mansoni (2.53 vs. 1.72, p = 0.022) and S. haematobium (2.05 vs. 1.12, p = 0.066) infection groups compared to controls. Modifications in cervicovaginal microbiota, particularly increased diversity and abundance of taxa associated with bacterial vaginosis and HIV (Peptostreptococcus, Prevotella), were associated with schistosome infection.}, } @article {pmid33408369, year = {2021}, author = {Meisner, A and Snoek, BL and Nesme, J and Dent, E and Jacquiod, S and Classen, AT and Priemé, A}, title = {Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {33408369}, issn = {1751-7370}, support = {330-2014-6430//Vetenskapsrådet (Swedish Research Council)/ ; Cofund Project INCA600398//EC | EC Seventh Framework Programm | FP7 People: Marie-Curie Actions (FP7-PEOPLE - Specific Programme "People" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; }, abstract = {Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO2 pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO2 emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO2 production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.}, } @article {pmid33408228, year = {2021}, author = {Renelies-Hamilton, J and Germer, K and Sillam-Dussès, D and Bodawatta, KH and Poulsen, M}, title = {Disentangling the Relative Roles of Vertical Transmission, Subsequent Colonizations, and Diet on Cockroach Microbiome Assembly.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33408228}, issn = {2379-5042}, abstract = {A multitude of factors affect the assemblies of complex microbial communities associated with animal hosts, with implications for community flexibility, resilience, and long-term stability; however, their relative effects have rarely been deduced. Here, we use a tractable lab model to quantify the relative and combined effects of parental transmission (egg case microbiome present/reduced), gut inocula (cockroach versus termite gut provisioned), and varying diets (matched or unmatched with gut inoculum source) on gut microbiota structure of hatchlings of the omnivorous cockroach Shelfordella lateralis using 16S rRNA gene (rDNA) amplicon sequencing. We show that the presence of a preexisting bacterial community via vertical transmission of microbes on egg cases reduces subsequent microbial invasion, suggesting priority effects that allow initial colonizers to take a strong hold and which stabilize the microbiome. However, subsequent inoculation sources more strongly affect ultimate community composition and their ecological networks, with distinct host-taxon-of-origin effects on which bacteria establish. While this is so, communities respond flexibly to specific diets in ways that consequently impact predicted community functions. In conclusion, our findings suggest that inoculations drive communities toward different stable states depending on colonization and extinction events, through ecological host-microbe relations and interactions with other gut bacteria, while diet in parallel shapes the functional capabilities of these microbiomes. These effects may lead to consistent microbial communities that maximize the extended phenotype that the microbiota provides the host, particularly if microbes spend most of their lives in host-associated environments.IMPORTANCE When host fitness is dependent on gut microbiota, microbial community flexibility and reproducibility enhance host fitness by allowing fine-tuned environmental tracking and sufficient stability for host traits to evolve. Our findings lend support to the importance of vertically transmitted early-life microbiota as stabilizers, through interactions with potential colonizers, which may contribute to ensuring that the microbiota aligns within host fitness-enhancing parameters. Subsequent colonizations are driven by microbial composition of the sources available, and we confirm that host-taxon-of-origin affects stable subsequent communities, while communities at the same time retain sufficient flexibility to shift in response to available diets. Microbiome structure is thus the result of the relative impact and combined effects of inocula and fluctuations driven by environment-specific microbial sources and digestive needs. These affect short-term community structure on an ecological time scale but could ultimately shape host species specificities in microbiomes across evolutionary time, if environmental conditions prevail.}, } @article {pmid33408227, year = {2021}, author = {Cole, AL and Sundar, M and Lopez, A and Forsman, A and Yooseph, S and Cole, AM}, title = {Identification of Nasal Gammaproteobacteria with Potent Activity against Staphylococcus aureus: Novel Insights into the "Noncarrier" State.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33408227}, issn = {2379-5042}, abstract = {Staphylococcus aureus nasal carriage provides the bacterial reservoir for opportunistic infection. In comparing the nasal microbiomes of culture-defined persistent S. aureus carriers versus noncarriers, we detected S. aureus DNA in all noses, including those with an established history of S. aureus negativity based on culture. Colonization with Gammaproteobacteria, including Klebsiella aerogenes, Citrobacter koseri, Moraxella lincolnii, and select Acinetobacter spp., was associated with S. aureus noncarriage. We next developed physiological competition assays for testing anti-S. aureus activity of isolated nasal species, utilizing medium modeling the nutrient-limited fluid of the nasal mucosa, polarized primary nasal epithelia, and nasal secretions. K. aerogenes from the nose of an S. aureus noncarrier demonstrated >99% inhibition of S. aureus recovery in all assays, even when S. aureus was coincubated in 9-fold excess. Secreted S. aureus inhibitory proteins from K. aerogenes and M. lincolnii were heat-stable and <30 kDa, fitting the profile of antimicrobial peptides. C. koseri, Acinetobacter haemolyticus, Acinetobacter junii, and Acinetobacter schindleri inhibited S. aureus recovery on nasal epithelia in a contact-dependent manner, while several other species either had no effect or promoted S. aureus growth. Collectively, this project is one of the first to identify resident nasal microbial species that impede S. aureus survival, and it implies that detectable nasal S. aureus results from shifts in microbial community composition.IMPORTANCE Nasal carriage of Staphylococcus aureus is a risk factor for infection, but it is not yet understood why some individuals carry nasal S. aureus persistently, intermittently, or seemingly not at all when tested via culture methods. This study compared the nasal microbiomes of established S. aureus carriers and noncarriers, identified species associated with noncarriage, and tested them for anti-S. aureus activity using assays developed to model the nutrient-limited nasal mucosa. We determined that all nostril swabs contain S. aureus DNA, even swabs from hosts considered to be long-term noncarriers. Select members of the Gammaproteobacteria class were more prevalent in noncarrier than carrier nostrils and demonstrated potent activity against multiple strains of S. aureus The results described here provide a better understanding of how the nasal microbiome controls S. aureus growth and viability and may be useful in the design of improved S. aureus decolonization strategies.}, } @article {pmid33407969, year = {2021}, author = {Carney, MC and Zhan, X and Rangnekar, A and Chroneos, MZ and Craig, SJC and Makova, KD and Paul, IM and Hicks, SD}, title = {Associations between stool micro-transcriptome, gut microbiota, and infant growth.}, journal = {Journal of developmental origins of health and disease}, volume = {}, number = {}, pages = {1-7}, doi = {10.1017/S2040174420001324}, pmid = {33407969}, issn = {2040-1752}, abstract = {Rapid infant growth increases the risk for adult obesity. The gut microbiome is associated with early weight status; however, no study has examined how interactions between microbial and host ribonucleic acid (RNA) expression influence infant growth. We hypothesized that dynamics in infant stool micro-ribonucleic acids (miRNAs) would be associated with both microbial activity and infant growth via putative metabolic targets. Stool was collected twice from 30 full-term infants, at 1 month and again between 6 and 12 months. Stool RNA were measured with high-throughput sequencing and aligned to human and microbial databases. Infant growth was measured by weight-for-length z-score at birth and 12 months. Increased RNA transcriptional activity of Clostridia (R = 0.55; Adj p = 3.7E-2) and Burkholderia (R = -0.820, Adj p = 2.62E-3) were associated with infant growth. Of the 25 human RNAs associated with growth, 16 were miRNAs. The miRNAs demonstrated significant target enrichment (Adj p < 0.05) for four metabolic pathways. There were four associations between growth-related miRNAs and growth-related phyla. We have shown that longitudinal trends in gut microbiota activity and human miRNA levels are associated with infant growth and the metabolic targets of miRNAs suggest these molecules may regulate the biosynthetic landscape of the gut and influence microbial activity.}, } @article {pmid33407877, year = {2021}, author = {Song, M and Yuan, F and Li, X and Ma, X and Yin, X and Rouchka, EC and Zhang, X and Deng, Z and Prough, RA and McClain, CJ}, title = {Analysis of sex differences in dietary copper-fructose interaction-induced alterations of gut microbial activity in relation to hepatic steatosis.}, journal = {Biology of sex differences}, volume = {12}, number = {1}, pages = {3}, pmid = {33407877}, issn = {2042-6410}, support = {P20GM113226/GM/NIGMS NIH HHS/United States ; P30 GM106396/GM/NIGMS NIH HHS/United States ; P20GM103436/GM/NIGMS NIH HHS/United States ; P50AA024337/AA/NIAAA NIH HHS/United States ; U01AA026934/AA/NIAAA NIH HHS/United States ; U01AA026936/AA/NIAAA NIH HHS/United States ; U01AA026980/AA/NIAAA NIH HHS/United States ; R01AA023681/AA/NIAAA NIH HHS/United States ; R21AA025724/AA/NIAAA NIH HHS/United States ; T35ES014559/ES/NIEHS NIH HHS/United States ; R01DK115406/DK/NIDDK NIH HHS/United States ; R21AI128206//National Institute of Allergy and Infectious Diseases/ ; 1I01BX002996//Office of Academic Affiliations, Department of Veterans Affairs/ ; 2019-2020 Pilot Grant//Jewish Heritage Fund for Excellence Pilot Grant Program at the University of Louisville School of Medicine/ ; }, abstract = {BACKGROUND: Inadequate copper intake and increased fructose consumption represent two important nutritional problems in the USA. Dietary copper-fructose interactions alter gut microbial activity and contribute to the development of nonalcoholic fatty liver disease (NAFLD). The aim of this study is to determine whether dietary copper-fructose interactions alter gut microbial activity in a sex-differential manner and whether sex differences in gut microbial activity are associated with sex differences in hepatic steatosis.

METHODS: Male and female weanling Sprague-Dawley (SD) rats were fed ad libitum with an AIN-93G purified rodent diet with defined copper content for 8 weeks. The copper content is 6 mg/kg and 1.5 mg/kg in adequate copper diet (CuA) and marginal copper diet (CuM), respectively. Animals had free access to either deionized water or deionized water containing 10% fructose (F) (w/v) as the only drink during the experiment. Body weight, calorie intake, plasma alanine aminotransferase, aspartate aminotransferase, and liver histology as well as liver triglyceride were evaluated. Fecal microbial contents were analyzed by 16S ribosomal RNA (16S rRNA) sequencing. Fecal and cecal short-chain fatty acids (SCFAs) were determined by gas chromatography-mass spectrometry (GC-MS).

RESULTS: Male and female rats exhibit similar trends of changes in the body weight gain and calorie intake in response to dietary copper and fructose, with a generally higher level in male rats. Several female rats in the CuAF group developed mild steatosis, while no obvious steatosis was observed in male rats fed with CuAF or CuMF diets. Fecal 16S rRNA sequencing analysis revealed distinct alterations of the gut microbiome in male and female rats. Linear discriminant analysis (LDA) effect size (LEfSe) identified sex-specific abundant taxa in different groups. Further, total SCFAs, as well as, butyrate were decreased in a more pronounced manner in female CuMF rats than in male rats. Of note, the decreased SCFAs are concomitant with the reduced SCFA producers, but not correlated to hepatic steatosis.

CONCLUSIONS: Our data demonstrated sex differences in the alterations of gut microbial abundance, activities, and hepatic steatosis in response to dietary copper-fructose interaction in rats. The correlation between sex differences in metabolic phenotypes and alterations of gut microbial activities remains elusive.}, } @article {pmid33407867, year = {2021}, author = {Sloan, MA and Sadlova, J and Lestinova, T and Sanders, MJ and Cotton, JA and Volf, P and Ligoxygakis, P}, title = {The Phlebotomus papatasi systemic transcriptional response to trypanosomatid-contaminated blood does not differ from the non-infected blood meal.}, journal = {Parasites & vectors}, volume = {14}, number = {1}, pages = {15}, pmid = {33407867}, issn = {1756-3305}, support = {31012//H2020 European Research Council/ ; BB/K003569/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: Leishmaniasis, caused by parasites of the genus Leishmania, is a disease that affects up to 8 million people worldwide. Parasites are transmitted to human and animal hosts through the bite of an infected sand fly. Novel strategies for disease control require a better understanding of the key step for transmission, namely the establishment of infection inside the fly.

METHODS: The aim of this work was to identify sand fly systemic transcriptomic signatures associated with Leishmania infection. We used next generation sequencing to describe the transcriptome of whole Phlebotomus papatasi sand flies when fed with blood alone (control) or with blood containing one of three trypanosomatids: Leishmania major, L. donovani and Herpetomonas muscarum, the latter being a parasite not transmitted to humans.

RESULTS: Of the trypanosomatids studied, only L. major was able to successfully establish an infection in the host P. papatasi. However, the transcriptional signatures observed after each parasite-contaminated blood meal were not specific to success or failure of a specific infection and they did not differ from each other. The transcriptional signatures were also indistinguishable after a non-contaminated blood meal.

CONCLUSIONS: The results imply that sand flies perceive Leishmania as just one feature of their microbiome landscape and that any strategy to tackle transmission should focus on the response towards the blood meal rather than parasite establishment. Alternatively, Leishmania could suppress host responses. These results will generate new thinking around the concept of stopping transmission by controlling the parasite inside the insect.}, } @article {pmid33407614, year = {2021}, author = {Chi, H and Cao, W and Zhang, M and Su, D and Yang, H and Li, Z and Li, C and She, X and Wang, K and Gao, X and Ma, K and Zheng, P and Li, X and Cui, B}, title = {Environmental noise stress disturbs commensal microbiota homeostasis and induces oxi-inflammmation and AD-like neuropathology through epithelial barrier disruption in the EOAD mouse model.}, journal = {Journal of neuroinflammation}, volume = {18}, number = {1}, pages = {9}, pmid = {33407614}, issn = {1742-2094}, support = {81673136//National Natural Science Foundation of China/ ; 17JCZDJC34900//Natural Science Foundation of Tianjin City/ ; }, abstract = {BACKGROUND: Both genetic factors and environmental hazards, including environmental noise stress, have been associated with gut microbiome that exacerbates Alzheimer's disease (AD) pathology. However, the role and mechanism of environmental risk factors in early-onset AD (EOAD) pathogenesis remain unclear.

METHODS: The molecular pathways underlying EOAD pathophysiology following environmental noise exposure were evaluated using C57BL/6 wild-type (WT) and APP/PS1 Tg mouse models. The composition differences in intestinal microbiota were analyzed by 16S rRNA sequencing and Tax4Fun to predict the metagenome content from sequencing results. An assessment of the flora dysbiosis-triggered dyshomeostasis of oxi-inflamm-barrier and the effects of the CNS end of the gut-brain axis was conducted to explore the underlying pathological mechanisms.

RESULTS: Both WT and APP/PS1 mice showed a statistically significant relationship between environmental noise and the taxonomic composition of the corresponding gut microbiome. Bacterial-encoded functional categories in noise-exposed WT and APP/PS1 mice included phospholipid and galactose metabolism, oxidative stress, and cell senescence. These alterations corresponded with imbalanced intestinal oxidation and anti-oxidation systems and low-grade systemic inflammation following noise exposure. Mechanistically, axis-series experiments demonstrated that following noise exposure, intestinal and hippocampal tight junction protein levels reduced, whereas serum levels of inflammatory mediator were elevated. Regarding APP/PS1 overexpression, noise-induced abnormalities in the gut-brain axis may contribute to aggravation of neuropathology in the presymptomatic stage of EOAD mice model.

CONCLUSION: Our results demonstrate that noise exposure has deleterious effects on the homeostasis of oxi-inflamm-barrier in the microbiome-gut-brain axis. Therefore, at least in a genetic context, chronic noise may aggravate the progression of EOAD.}, } @article {pmid33407528, year = {2021}, author = {Jiang, S and Lu, S and Chen, X and Li, F and Zhu, C and Zheng, Y and Wang, X and Xu, S}, title = {Dysbiosis of urine microbiota in obstructive urinary retention patients revealed by next-generation sequencing.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {20}, number = {1}, pages = {2}, pmid = {33407528}, issn = {1476-0711}, support = {81700062//National Natural Science Foundation of China/ ; LQ16H010003//Natural Science Foundation of Zhejiang Province (CN)/ ; LY18H030011//Natural Science Foundation of Zhejiang Province (CN)/ ; 2019RC050//Science and Technology Project of Zhejiang Provincial Health Commission/ ; }, abstract = {BACKGROUND: Urinary retention (UR) is a common urinary system disease can be caused by urinary tract obstruction with numerous reasons, however, the role of urine microbes in these disorders is still poorly understood. The aim of this study was to identify the urine microbial features of two common types of obstructive UR, caused by urinary stones or urinary tract tumors, with comparison to healthy controls.

METHODS: Urine samples were collected from a cohort of 32 individuals with stone UR, 25 subjects with tumor UR and 25 healthy controls. The urine microbiome of all samples was analyzed using high-throughput 16S rRNA (16S ribosomal RNA) gene sequencing.

RESULTS: We observed dramatically increased urine microbial richness and diversity in both obstructive UR groups compared to healthy controls. Despite different origins of UR, bacteria such as Pseudomonas, Acinetobacter and Sphingomonas were enriched, while Lactobacillus, Streptococcus, Gardnerella, Prevotella and Atopobium were decreased in both UR groups in comparison with healthy controls, exhibited an approximate urine microbial community and functional characteristics of two types of obstructive UR. Furthermore, disease classifiers were constructed using specific enriched genera in UR, which can distinguish stone UR or tumor UR patients from healthy controls with an accuracy of 92.29% and 97.96%, respectively.

CONCLUSION: We presented comprehensive microbial landscapes of two common types of obstructive urinary retention and demonstrated that urine microbial features of these patients are significantly different from that of healthy people. The urine microbial signatures would shed light on the pathogenesis of these types of urinary retention and might be used as potential classification tools in the future.}, } @article {pmid33407119, year = {2021}, author = {Lu, ZH and Liu, YW and Ji, ZH and Fu, T and Yan, M and Shao, ZJ and Long, Y}, title = {Alterations in the intestinal microbiome and mental health status of workers in an underground tunnel environment.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {7}, pmid = {33407119}, issn = {1471-2180}, support = {81803289//National Natural Science Foundation of China/ ; 81773488//National Natural Science Foundation of China/ ; 2020JM-329//Natural Science Foundation of Shaanxi Province/ ; 18CXZ011//Military Medicine Innovation Fund/ ; 2017ZX10105011//China Special Grant for the Prevention and Control of Infection Diseases/ ; }, abstract = {BACKGROUND: Working in an underground tunnel environment is unavoidable in professions such as miners and tunnel workers, and there is a concern about the health of these workers. Few studies have addressed alterations in the intestinal microbiome of workers within that environment.

RESULTS: Fecal samples were collected from the workers before they entered the tunnel (baseline status, BS) and after they left the tunnel (exposed status, ES), respectively (a time period of 3 weeks between them). We analyzed 16S rRNA sequencing to show the changes in microbial composition and self-evaluation of mental health questionnaire was also performed. The results showed that Shannon and Simpson indices decreased significantly from BS to ES. A higher abundance was found in the phylum Actinobacteria, classes Actinobacteria and Deltaproteobacteria, orders Bifidobacteriales, Coriobacteriales, and Desulfovibrionales, families Bifidobacteriaceae, Peptostreptococcaceae, Coriobacteriaceae, Clostridiaceae_1, Desulfovibrionaceae, Pseudomonadaceae, and Microbacteriaceae, and genera Bifidobacterium, Romboutsia, Clostridium sensu stricto, and Leucobacter in ES, while BS showed greater levels of genera Faecalibacterium and Roseburia. The self-evaluation showed that at least one-half of the tunnel workers experienced one or more symptoms of mental distress (inattention, sleeplessness, loss of appetite, headache or dizziness, irritability) after working in the underground tunnel environment.

CONCLUSIONS: Collectively, the underground tunnel environment led to alterations in the intestinal microbiome, which might be relevant to symptoms of mental distress in underground-tunnel workers.}, } @article {pmid33407112, year = {2021}, author = {Jing, G and Zhang, Y and Cui, W and Liu, L and Xu, J and Su, X}, title = {Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {9}, pmid = {33407112}, issn = {1471-2164}, support = {31771463//National Natural Science Foundation of China (CN)/ ; ZR201807060158//Natural Science Foundation of Shandong Province/ ; 2018M630807//China Postdoctoral Science Foundation/ ; 32070086//National Natural Science Foundation of China/ ; 32000389//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2. However, due to the potential PCR bias and gene profile variation among phylogenetically related genomes, functional profiles predicted from 16S amplicons may deviate from WGS-derived ones, resulting in misleading results.

RESULTS: Here we present Meta-Apo, which greatly reduces or even eliminates such deviation, thus deduces much more consistent diversity patterns between the two approaches. Tests of Meta-Apo on > 5000 16S-rRNA amplicon human microbiome samples from 4 body sites showed the deviation between the two strategies is significantly reduced by using only 15 WGS-amplicon training sample pairs. Moreover, Meta-Apo enables cross-platform functional comparison between WGS and amplicon samples, thus greatly improve 16S-based microbiome diagnosis, e.g. accuracy of gingivitis diagnosis via 16S-derived functional profiles was elevated from 65 to 95% by WGS-based classification. Therefore, with the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun WGS.

CONCLUSIONS: This suggests that large-scale, function-oriented microbiome sequencing projects can probably benefit from the lower cost of 16S-amplicon strategy, without sacrificing the precision in functional reconstruction that otherwise requires WGS. An optimized C++ implementation of Meta-Apo is available on GitHub (https://github.com/qibebt-bioinfo/meta-apo) under a GNU GPL license. It takes the functional profiles of a few paired WGS:16S-amplicon samples as training, and outputs the calibrated functional profiles for the much larger number of 16S-amplicon samples.}, } @article {pmid33407079, year = {2021}, author = {Smith, NW and Shorten, PR and Altermann, E and Roy, NC and McNabb, WC}, title = {Examination of hydrogen cross-feeders using a colonic microbiota model.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {3}, pmid = {33407079}, issn = {1471-2105}, mesh = {Bacteria/*metabolism ; *Colon/metabolism/microbiology ; *Gastrointestinal Microbiome ; Humans ; Hydrogen/*metabolism ; Models, Biological ; Sulfides/metabolism ; }, abstract = {BACKGROUND: Hydrogen cross-feeding microbes form a functionally important subset of the human colonic microbiota. The three major hydrogenotrophic functional groups of the colon: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens, have been linked to wide ranging impacts on host physiology, health and wellbeing.

RESULTS: An existing mathematical model for microbial community growth and metabolism was combined with models for each of the three hydrogenotrophic functional groups. The model was further developed for application to the colonic environment via inclusion of responsive pH, host metabolite absorption and the inclusion of host mucins. Predictions of the model, using two existing metabolic parameter sets, were compared to experimental faecal culture datasets. Model accuracy varied between experiments and measured variables and was most successful in predicting the growth of high relative abundance functional groups, such as the Bacteroides, and short chain fatty acid (SCFA) production. Two versions of the colonic model were developed: one representing the colon with sequential compartments and one utilising a continuous spatial representation. When applied to the colonic environment, the model predicted pH dynamics within the ranges measured in vivo and SCFA ratios comparable to those in the literature. The continuous version of the model simulated relative abundances of microbial functional groups comparable to measured values, but predictions were sensitive to the metabolic parameter values used for each functional group. Sulphate availability was found to strongly influence hydrogenotroph activity in the continuous version of the model, correlating positively with SRB and sulphide concentration and negatively with methanogen concentration, but had no effect in the compartmentalised model version.

CONCLUSIONS: Although the model predictions compared well to only some experimental measurements, the important features of the colon environment included make it a novel and useful contribution to modelling the colonic microbiota.}, } @article {pmid33406976, year = {2021}, author = {Egan, M and Dempsey, E and Ryan, CA and Ross, RP and Stanton, C}, title = {The Sporobiota of the Human Gut.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-17}, doi = {10.1080/19490976.2020.1863134}, pmid = {33406976}, issn = {1949-0984}, abstract = {The human gut microbiome is a diverse and complex ecosystem that plays a critical role in health and disease. The composition of the gut microbiome has been well studied across all stages of life. In recent years, studies have investigated the production of endospores by specific members of the gut microbiome. An endospore is a tough, dormant structure formed by members of the Firmicutes phylum, which allows for greater resistance to otherwise inhospitable conditions. This innate resistance has consequences for human health and disease, as well as in biotechnology. In particular, the formation of endospores is strongly linked to antibiotic resistance and the spread of antibiotic resistance genes, also known as the resistome. The term sporobiota has been used to define the spore-forming cohort of a microbial community. In this review, we present an overview of the current knowledge of the sporobiota in the human gut. We discuss the development of the sporobiota in the infant gut and the perinatal factors that may have an effect on vertical transmission from mother to infant. Finally, we examine the sporobiota of critically important food sources for the developing infant, breast milk and powdered infant formula.}, } @article {pmid33406974, year = {2021}, author = {Clements, TW and Tolonen, M and Ball, CG and Kirkpatrick, AW}, title = {Secondary Peritonitis and Intra-Abdominal Sepsis: An Increasingly Global Disease in Search of Better Systemic Therapies.}, journal = {Scandinavian journal of surgery : SJS : official organ for the Finnish Surgical Society and the Scandinavian Surgical Society}, volume = {}, number = {}, pages = {1457496920984078}, doi = {10.1177/1457496920984078}, pmid = {33406974}, issn = {1799-7267}, abstract = {Secondary peritonitis and intra-abdominal sepsis are a global health problem. The life-threatening systemic insult that results from intra-abdominal sepsis has been extensively studied and remains somewhat poorly understood. While local surgical therapy for perforation of the abdominal viscera is an age-old therapy, systemic therapies to control the subsequent systemic inflammatory response are scarce. Advancements in critical care have led to improved outcomes in secondary peritonitis. The understanding of the effect of secondary peritonitis on the human microbiome is an evolving field and has yielded potential therapeutic targets. This review of secondary peritonitis discusses the history, classification, pathophysiology, diagnosis, treatment, and future directions of the management of secondary peritonitis. Ongoing clinical studies in the treatment of secondary peritonitis and the open abdomen are discussed.}, } @article {pmid33406628, year = {2021}, author = {Li, P and Killinger, BA and Ensink, E and Beddows, I and Yilmaz, A and Lubben, N and Lamp, J and Schilthuis, M and Vega, IE and Woltjer, R and Pospisilik, JA and Brundin, P and Brundin, L and Graham, SF and Labrie, V}, title = {Gut Microbiota Dysbiosis Is Associated with Elevated Bile Acids in Parkinson's Disease.}, journal = {Metabolites}, volume = {11}, number = {1}, pages = {}, doi = {10.3390/metabo11010029}, pmid = {33406628}, issn = {2218-1989}, support = {0//Farmer Family Foundation/ ; W81XWH1810512//Department of Defense/ ; 1R21NS112614-01/NS/NINDS NIH HHS/United States ; 1R01NS113894-01A1/NS/NINDS NIH HHS/United States ; 1R01NS114409-01A1/NS/NINDS NIH HHS/United States ; 0//Gibby & Friends vs. Parky Award/ ; 1R01NS110838-01A1/NS/NINDS NIH HHS/United States ; 1R21AG067083-01//National Institutes on Aging/ ; AARG-17-530020//Alzheimer's Association/United States ; MJFF16201//Michael J. Fox Foundation/ ; }, abstract = {The gut microbiome can impact brain health and is altered in Parkinson's disease (PD). The vermiform appendix is a lymphoid tissue in the cecum implicated in the storage and regulation of the gut microbiota. We sought to determine whether the appendix microbiome is altered in PD and to analyze the biological consequences of the microbial alterations. We investigated the changes in the functional microbiota in the appendix of PD patients relative to controls (n = 12 PD, 16 C) by metatranscriptomic analysis. We found microbial dysbiosis affecting lipid metabolism, including an upregulation of bacteria responsible for secondary bile acid synthesis. We then quantitatively measure changes in bile acid abundance in PD relative to the controls in the appendix (n = 15 PD, 12 C) and ileum (n = 20 PD, 20 C). Bile acid analysis in the PD appendix reveals an increase in hydrophobic and secondary bile acids, deoxycholic acid (DCA) and lithocholic acid (LCA). Further proteomic and transcriptomic analysis in the appendix and ileum corroborated these findings, highlighting changes in the PD gut that are consistent with a disruption in bile acid control, including alterations in mediators of cholesterol homeostasis and lipid metabolism. Microbially derived toxic bile acids are heightened in PD, which suggests biliary abnormalities may play a role in PD pathogenesis.}, } @article {pmid33406416, year = {2021}, author = {Gnainsky, Y and Zfanya, N and Elgart, M and Omri, E and Brandis, A and Mehlman, T and Itkin, M and Malitsky, S and Adamski, J and Soen, Y}, title = {Systemic Regulation of Host Energy and Oogenesis by Microbiome-Derived Mitochondrial Coenzymes.}, journal = {Cell reports}, volume = {34}, number = {1}, pages = {108583}, doi = {10.1016/j.celrep.2020.108583}, pmid = {33406416}, issn = {2211-1247}, abstract = {Gut microbiota have been shown to promote oogenesis and fecundity, but the mechanistic basis of remote influence on oogenesis remained unknown. Here, we report a systemic mechanism of influence mediated by bacterial-derived supply of mitochondrial coenzymes. Removal of microbiota decreased mitochondrial activity and ATP levels in the whole-body and ovary, resulting in repressed oogenesis. Similar repression was caused by RNA-based knockdown of mitochondrial function in ovarian follicle cells. Reduced mitochondrial function in germ-free (GF) females was reversed by bacterial recolonization or supplementation of riboflavin, a precursor of FAD and FMN. Metabolomics analysis of GF females revealed a decrease in oxidative phosphorylation and FAD levels and an increase in metabolites that are degraded by FAD-dependent enzymes (e.g., amino and fatty acids). Riboflavin supplementation opposed this effect, elevating mitochondrial function, ATP, and oogenesis. These findings uncover a bacterial-mitochondrial axis of influence, linking gut bacteria with systemic regulation of host energy and reproduction.}, } @article {pmid33406219, year = {2021}, author = {Saccon, TD and Nagpal, R and Yadav, H and Cavalcante, MB and Nunes, ADC and Schneider, A and Gesing, A and Hughes, B and Yousefzadeh, M and Tchkonia, T and Kirkland, JL and Niedernhofer, LJ and Robbins, PD and Masternak, MM}, title = {Senolytic combination of Dasatinib and Quercetin alleviates intestinal senescence and inflammation and modulates the gut microbiome in aged mice.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {}, number = {}, pages = {}, doi = {10.1093/gerona/glab002}, pmid = {33406219}, issn = {1758-535X}, abstract = {Cellular senescence contributes to age-related disorders including physical dysfunction, disabilities and mortality caused by tissue inflammation and damage. Senescent cells accumulate in multiple tissues with aging and at etiological sites of multiple chronic disorders. The senolytic drug combination, Dasatinib plus Quercetin (D+Q), is known to reduce senescent cell abundance in aged mice. However, the effects of long-term D+Q treatment on intestinal senescent cell and inflammatory burden and microbiome composition in aged mice remain unknown. Here, we examine the effect of D+Q on senescence (p16 Ink4a and p21 Cip1) and inflammation (Cxcl1, Il1β, Il6, Mcp1, and Tnfα) markers in small (ileum) and large (caecum and colon) intestine in aged mice (n=10) compared to age-matched placebo-treated mice (n=10). Additionally, we examine microbial composition along the intestinal tract in these mice. D+Q-treated mice show significantly lower senescent cell (p16 and p21 expression) and inflammatory (Cxcl1, Il1β, Il6, Mcp1 and Tnfα expression) burden in small and large intestine compared with control mice. Further, we find specific microbial signatures in ileal, cecal, colonic and fecal regions that are distinctly modulated by D+Q, with modulation being most prominent in small intestine. Further analyses reveal specific correlation of senescence and inflammation markers with specific microbial signatures. Together, these data demonstrate that the senolytic treatment reduces intestinal senescence and inflammation while altering specific microbiota signatures and suggest that the optimized senolytic regimens might improve health via reducing intestinal senescence, inflammation and microbial dysbiosis in older subjects.}, } @article {pmid33406089, year = {2021}, author = {Patumcharoenpol, P and Nakphaichit, M and Panagiotou, G and Senavonge, A and Suratannon, N and Vongsangnak, W}, title = {MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome.}, journal = {PLoS computational biology}, volume = {17}, number = {1}, pages = {e1008487}, pmid = {33406089}, issn = {1553-7358}, abstract = {Investigating metabolic functional capability of a human gut microbiome enables the quantification of microbiome changes, which can cause a phenotypic change of host physiology and disease. One possible way to estimate the functional capability of a microbial community is through inferring metagenomic content from 16S rRNA gene sequences. Genome-scale models (GEMs) can be used as scaffold for functional estimation analysis at a systematic level, however up to date, there is no integrative toolbox based on GEMs for uncovering metabolic functions. Here, we developed the MetGEMs (metagenome-scale models) toolbox, an open-source application for inferring metabolic functions from 16S rRNA gene sequences to facilitate the study of the human gut microbiome by the wider scientific community. The developed toolbox was validated using shotgun metagenomic data and shown to be superior in predicting functional composition in human clinical samples compared to existing state-of-the-art tools. Therefore, the MetGEMs toolbox was subsequently applied for annotating putative enzyme functions and metabolic routes related in human disease using atopic dermatitis as a case study.}, } @article {pmid33406075, year = {2021}, author = {Abundo, MEC and Ngunjiri, JM and Taylor, KJM and Ji, H and Ghorbani, A and K C, M and Weber, BP and Johnson, TJ and Lee, CW}, title = {Assessment of two DNA extraction kits for profiling poultry respiratory microbiota from multiple sample types.}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0241732}, pmid = {33406075}, issn = {1932-6203}, abstract = {Characterization of poultry microbiota is becoming increasingly important due to the growing need for microbiome-based interventions to improve poultry health and production performance. However, the lack of standardized protocols for sampling, sample processing, DNA extraction, sequencing, and bioinformatic analysis can hinder data comparison between studies. Here, we investigated how the DNA extraction process affects microbial community compositions and diversity metrics in different chicken respiratory sample types including choanal and tracheal swabs, nasal cavity and tracheal washes, and lower respiratory lavage. We did a side-by-side comparison of the performances of Qiagen DNeasy blood and tissue (BT) and ZymoBIOMICS DNA Miniprep (ZB) kits. In general, samples extracted with the BT kit yielded higher concentrations of total DNA while those extracted with the ZB kit contained higher numbers of bacterial 16S rRNA gene copies per unit volume. Therefore, the samples were normalized to equal amounts of 16S rRNA gene copies prior to sequencing. For each sample type, all predominant bacterial taxa detected in samples extracted with one kit were present in replicate samples extracted with the other kit and did not show significant differences at the class level. However, a few differentially abundant shared taxa were observed at family and genus levels. Furthermore, between-kit differences in alpha and beta diversity metrics at the amplicon sequence variant level were statistically indistinguishable. Therefore, both kits perform similarly in terms of 16S rRNA gene-based poultry microbiome analysis for the sample types analyzed in this study.}, } @article {pmid33405413, year = {2021}, author = {Miniet, AA and Grunwell, JR and Coopersmith, CM}, title = {The microbiome and the immune system in critical illness.}, journal = {Current opinion in critical care}, volume = {Publish Ahead of Print}, number = {}, pages = {}, doi = {10.1097/MCC.0000000000000800}, pmid = {33405413}, issn = {1531-7072}, abstract = {PURPOSE OF REVIEW: Although the gut microbiome plays a crucial role in the maintenance of health, it is hypothesized to drive morbidity and mortality in critically ill patients. This review describes the relationship between the gut microbiome and the immune system in critical illness.

RECENT FINDINGS: The gut microbiome is converted to a pathobiome in the ICU, characterized by decreased microbial diversity and pathogen predominance. These changes are induced by a pathologic microenvironment and are further exacerbated by common medical treatments initiated in the ICU. The conversion of the microbiome to a pathobiome has direct consequences on the regulation of inflammation and immunity by loss of beneficial host responses and initiation of maladaptive changes that can further propagate critical illness.

SUMMARY: The gut microbiome is dramatically altered in the ICU. In light of constant crosstalk between the microbiome and the host immune system, the pathobiome may play a key mechanistic role in driving a maladaptive response in critically ill patients. The pathobiome represents a potential therapeutic target in the management of critical illness whereby restoration of a healthier microbiome may directly alter the host inflammatory response, which could lead to improved patient outcomes.}, } @article {pmid33405294, year = {2020}, author = {Donovan, C and Liu, G and Shen, S and Marshall, JE and Kim, RY and Alemao, CA and Budden, KF and Choi, JP and Kohonen-Corish, M and El-Omar, EM and Yang, IA and Hansbro, PM}, title = {The role of the microbiome and the NLRP3 inflammasome in the gut and lung.}, journal = {Journal of leukocyte biology}, volume = {108}, number = {3}, pages = {925-935}, doi = {10.1002/JLB.3MR0720-472RR}, pmid = {33405294}, issn = {1938-3673}, support = {1120152//National Health and Medical Research Council/ ; 1138402//National Health and Medical Research Council/ ; }, abstract = {The nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) family, pyrin domain-containing protein 3 (NLRP3) inflammasome, is one of the most well-characterized inflammasomes, activated by pathogen-associated molecular patterns and damage-associated molecular patterns, including from commensal or pathogenic bacterial and viral infections. The NLRP3 inflammasome promotes inflammatory cell recruitment and regulates immune responses in tissues such as the gastrointestinal tract and the lung, and is involved in many diseases that affect the gut and lung. Recently, the microbiome in the gut and the lung, and the crosstalk between these organs (gut-lung axis), has been identified as a potential mechanism that may influence disease in a bidirectional manner. In this review, we focus on themes presented in this area at the 2019 World Congress on Inflammation. We discuss recent evidence on how the microbiome can affect NLRP3 inflammasome responses in the gut and lung, the role of this inflammasome in regulating gut and lung inflammation in disease, and its potential role in the gut-lung axis. We highlight the exponential increase in our understanding of the NLRP3 inflammasome due to the synthesis of the NLRP3 inflammasome inhibitor, MCC950, and propose future studies that may further elucidate the roles of the NLRP3 inflammasome in gut and lung diseases.}, } @article {pmid33405258, year = {2021}, author = {Hoang, DM and Levy, EI and Vandenplas, Y}, title = {The impact of Caesarean section on the infant gut microbiome.}, journal = {Acta paediatrica (Oslo, Norway : 1992)}, volume = {110}, number = {1}, pages = {60-67}, doi = {10.1111/apa.15501}, pmid = {33405258}, issn = {1651-2227}, abstract = {AIM: Description of the impact of caesarean section on the infant gut microbiome, infant health and solutions to restore the dysbiosis.

METHODS: We searched PubMed and Google Scholar for relevant articles. Only articles published in English were selected. Separate searches were performed for each topic. We selected 60 articles published between 1999 and 2019 by extracting subject headings and key words of interest for this topic.

RESULTS: Caesarean section is an obstetrical procedure that is increasing in prevalence worldwide. On top of the maternal and neonatal risks that this procedure carries, it also induces a dysbiosis of the infant intestinal microbiome possibly challenging the health outcome for the infant. Antibiotics administered during Caesarean deliveries contribute to the development of the gut microbiome. Nonetheless, breastfeeding and several interventions such as vaginal seeding and supplementation with probiotics, prebiotics and synbiotics may contribute to the restoration of the dysbiosis.

CONCLUSION: Caesarean section is associated with the development of an imbalance of the infant gut microbiome. Long-term consequences of this imbalance are debated. Besides breastfeeding, other strategies to restore this dysbiosis need further studies before they can be recommended.}, } @article {pmid33404835, year = {2021}, author = {Cheng, R and Cheng, L and Zhao, Y and Wang, L and Wang, S and Zhang, J}, title = {Biosynthesis and prebiotic activity of a linear levan from a new Paenibacillus isolate.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {2}, pages = {769-787}, pmid = {33404835}, issn = {1432-0614}, support = {31600043//National Natural Science Foundation of China/ ; 2015M581803//Postdoctoral Research Foundation of China/ ; }, abstract = {Levan, a type of β (2→6)-linked fructan, is a promising biopolymer with distinct properties and extensive applications in the fields of food, pharmaceutical, cosmetics, etc. However, the commercial availability of levan is still limited due to the relatively high production costs. Here, a new Paenibacillus sp. strain FP01 was isolated and identified as an efficient fructan producer with high yield (around 89.5 g/L fructan was obtained under 180 g/L sucrose) and conversation rate (49.7%). The fructan named Plev was structurally characterized as a linear levan-type fructan with a molecular mass of 3.11 × 106 Da. Aqueous solutions of Plev exhibited a non-Newtonian behavior at concentrations 3-5%. Heating and chilling had no obvious effects on apparent viscosities of Plev solutions. Plev also had good rheological stabilities toward pH (3-11) and metal salts (Na+, K+, Ca2+, Mg2+). Microbiome and metabolome analysis showed that Plev intervention increased the abundance of beneficial bacteria and elevated the levels of short-chain fatty acids (SCFAs) in feces of mice. Taken together, Plev could be considered a potential thickener and prebiotic supplement in food industry.Key points• Paenibacillus sp. strain FP01 was identified as a high-efficient levan producer.• The levan Plev from FP01 exhibited good rheological properties and stabilities.• The in vivo prebiotic activities of linear levan were revealed.}, } @article {pmid33404833, year = {2021}, author = {Zhang, Y and Shen, J and Shi, X and Du, Y and Niu, Y and Jin, G and Wang, Z and Lyu, J}, title = {Gut microbiome analysis as a predictive marker for the gastric cancer patients.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {2}, pages = {803-814}, pmid = {33404833}, issn = {1432-0614}, support = {2019RC012//Medicine and Health Research Foundation of Zhejiang Province in China/ ; 2019KY017//Medicine and Health Research Foundation of Zhejiang Province in China/ ; WKJ-ZJ-2019//Key projects jointly constructed by the Ministry and the province of Zhejiang Medical and Health Science and Technology Project in China/ ; 2019ZZ001//Key and Major Projects of Traditional Chinese Medicine Scientific Research Foundation of Zhejiang Province in China/ ; 2017KY216//Medicine and Health Research Foundation of Zhejiang Province in China/ ; 2017KY486//Medicine and Health Research Foundation of Zhejiang Province in China/ ; }, abstract = {Gut microbiota have been implicated in the development of cancer. Colorectal and gastric cancers, the major gastrointestinal tract cancers, are closely connected with the gut microbiome. Nevertheless, the characteristics of gut microbiota composition that correlate with gastric cancer are unclear. In this study, we investigated gut microbiota alterations during the progression of gastric cancer to identify the most relevant taxa associated with gastric cancer and evaluated the potential of the microbiome as an indicator for the diagnosis of gastric cancer. Compared with the healthy group, gut microbiota composition and diversity shifted in patients with gastric cancer. Different bacteria were used to design a random forest model, which provided an area under the curve value of 0.91. Verification samples achieved a true positive rate of 0.83 in gastric cancer. Principal component analysis showed that gastritis shares some microbiome characteristics of gastric cancer. Chemotherapy reduced the elevated bacteria levels in gastric cancer by more than half. More importantly, we found that the genera Lactobacillus and Megasphaera were associated with gastric cancer.Key Points• Gut microbiota has high sensitivity and specificity in distinguishing patients with gastric cancer from healthy individuals, indicating that gut microbiota is a potential noninvasive tool for the diagnosis of gastric cancer.• Gastritis shares some microbiota features with gastric cancer, and chemotherapy reduces the microbial abundance and diversity in gastric cancer patients.• Two bacterial taxa, namely, Lactobacillus and Megasphaera, are predictive markers for gastric cancer.}, } @article {pmid33404820, year = {2021}, author = {Leiva, D and Fernández-Mendoza, F and Acevedo, J and Carú, M and Grube, M and Orlando, J}, title = {The Bacterial Community of the Foliose Macro-lichen Peltigera frigida Is More than a Mere Extension of the Microbiota of the Subjacent Substrate.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33404820}, issn = {1432-184X}, support = {1181510//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; }, abstract = {Lichens host highly diverse microbial communities, with bacteria being one of the most explored groups in terms of their diversity and functioning. These bacteria could partly originate from symbiotic propagules developed by many lichens and, perhaps more commonly and depending on environmental conditions, from different sources of the surroundings. Using the narrowly distributed species Peltigera frigida as an object of study, we propose that bacterial communities in these lichens are different from those in their subjacent substrates, even if some taxa might be shared. Ten terricolous P. frigida lichens and their substrates were sampled from forested sites in the Coyhaique National Reserve, located in an understudied region in Chile. The mycobiont identity was confirmed using partial 28S and ITS sequences. Besides, 16S fragments revealed that mycobionts were associated with the same cyanobacterial haplotype. From both lichens and substrates, Illumina 16S amplicon sequencing was performed using primers that exclude cyanobacteria. In lichens, Proteobacteria was the most abundant phylum (37%), whereas soil substrates were dominated by Acidobacteriota (39%). At lower taxonomic levels, several bacterial groups differed in relative abundance among P. frigida lichens and their substrates, some of them being highly abundant in lichens but almost absent in substrates, like Sphingomonas (8% vs 0.2%), and others enriched in lichens, as an unassigned genus of Chitinophagaceae (10% vs 2%). These results reinforce the idea that lichens would carry some components of their microbiome when propagating, but they also could acquire part of their bacterial community from the substrates.}, } @article {pmid33402693, year = {2021}, author = {Cleary, DW and Morris, DE and Anderson, RA and Jones, J and Alattraqchi, AG and A Rahman, NI and Ismail, S and Razali, MS and Mohd Amin, R and Abd Aziz, A and Esa, NK and Amiruddin, S and Chew, CH and Simin, H and Abdullah, R and Yeo, CC and Clarke, SC}, title = {The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {1}, pmid = {33402693}, issn = {2055-5008}, support = {NA//Higher Education Funding Council for England (HEFCE)/ ; NA//Higher Education Funding Council for England (HEFCE)/ ; NA//Higher Education Funding Council for England (HEFCE)/ ; NA//Higher Education Funding Council for England (HEFCE)/ ; }, abstract = {Much microbiome research has focused on populations that are predominantly of European descent, and from narrow demographics that do not capture the socio-economic and lifestyle differences which impact human health. Here we examined the airway microbiomes of the Orang Asli, the indigenous peoples of Malaysia. A total of 130 participants were recruited from two sites in the north-eastern state of Terengganu in Peninsular Malaysia. Using 16S rRNA sequencing, the nasal microbiome was significantly more diverse in those aged 5-17 years compared to 50+ years (p = 0.023) and clustered by age (PERMANOVA analysis of the Bray-Curtis distance, p = 0.001). Hierarchical clustering of Bray-Curtis dissimilarity scores revealed six microbiome clusters. The largest cluster (n = 28; 35.4%) had a marked abundance of Corynebacterium. In the oral microbiomes Streptococcus, Neisseria and Haemophilus were dominant. Using conventional microbiology, high levels of Staphylococcus aureus carriage were observed, particularly in the 18-65 age group (n = 17/36; 47.2% 95% CI: 30.9-63.5). The highest carriage of pneumococci was in the <5 and 5 to 17 year olds, with 57.1% (4/7) and 49.2% (30/61), respectively. Sixteen pneumococcal serotypes were identified, the most common being the nonvaccine-type 23A (14.6%) and the vaccine-type 6B (9.8%). The prevalence of pneumococcal serotypes covered by pneumococcal conjugate vaccines support introduction into a Malaysian national immunisation schedule. In addition, the dominance of Corynebacterium in the airway microbiomes is intriguing given their role as a potentially protective commensal with respect to acute infection and respiratory health.}, } @article {pmid33402350, year = {2021}, author = {Ding, J and Zhou, H and Luo, L and Xiao, L and Yang, K and Yang, L and Zheng, Y and Xu, K and He, C and Han, C and Luo, H and Qin, C and Akinyemi, FT and Gu, C and Zhou, Z and Huang, Q and Meng, H}, title = {Heritable Gut Microbiome Associated with Salmonella enterica Serovar Pullorum Infection in Chickens.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33402350}, issn = {2379-5077}, abstract = {Pullorum disease is one of the most common diarrhea-related diseases caused by Salmonella enterica subspecies enterica serovar Gallinarum biovar Pullorum (S Pullorum); it negatively affects the poultry industry. However, limited studies have explored the association between the gut microbiota and S Pullorum infection in chickens. In the present study, we performed a microbiome comparison and a microbiome genome-wide association study (mGWAS) to investigate the association among the host genetics, the gut microbiota, and pullorum disease in chickens. We found that S Pullorum infection in chickens could alter the abundance of 39 bacterial genera (P < 0.05). The altered structure and composition of the gut microbiota were also detected in the offspring. mGWAS results revealed host genetic variants to be prominently associated with gut microbial diversity and individual microbes. The pathogens Pelomonas and Brevundimonas, which had a high abundance in positive parent chickens and their offspring, were significantly associated with several genetic mutations in immunity-related genes, such as TGIF1, TTLL12, and CCR7 This finding explained why Pelomonas and Brevundimonas were heritable in S Pullorum-infected chickens. The heritable gut microbes and identified genetic variants could provide references for the selection of resistant chickens and the elimination of pullorum disease.IMPORTANCE The present study investigated the association among the host genome, the gut microbiome, and S Pullorum infection in chickens. The results suggested that the gut microbial structure is altered in S Pullorum-infected chickens. The diversity and abundance of the gut microbiota remarkably differed between the offspring coming from S Pullorum-positive and S Pullorum-negative chickens. Heritable gut microbiota were detected in the offspring. Moreover, host genetic variants were associated with microbial diversity and individual gut microbes. The pathogens Pelomonas and Brevundimonas, which exhibited a high heritability in S Pullorum-positive parents and their offspring, were associated with several genetic mutations in immunity-related genes.}, } @article {pmid33402349, year = {2021}, author = {Odriozola, I and Abrego, N and Tláskal, V and Zrůstová, P and Morais, D and Větrovský, T and Ovaskainen, O and Baldrian, P}, title = {Fungal Communities Are Important Determinants of Bacterial Community Composition in Deadwood.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33402349}, issn = {2379-5077}, abstract = {Fungal-bacterial interactions play a key role in the functioning of many ecosystems. Thus, understanding their interactive dynamics is of central importance for gaining predictive knowledge on ecosystem functioning. However, it is challenging to disentangle the mechanisms behind species associations from observed co-occurrence patterns, and little is known about the directionality of such interactions. Here, we applied joint species distribution modeling to high-throughput sequencing data on co-occurring fungal and bacterial communities in deadwood to ask whether fungal and bacterial co-occurrences result from shared habitat use (i.e., deadwood's properties) or whether there are fungal-bacterial interactive associations after habitat characteristics are taken into account. Moreover, we tested the hypothesis that the interactions are mainly modulated through fungal communities influencing bacterial communities. For that, we quantified how much the predictive power of the joint species distribution models for bacterial and fungal community improved when accounting for the other community. Our results show that fungi and bacteria form tight association networks (i.e., some species pairs co-occur more frequently and other species pairs co-occur less frequently than expected by chance) in deadwood that include common (or opposite) responses to the environment as well as (potentially) biotic interactions. Additionally, we show that information about the fungal occurrences and abundances increased the power to predict the bacterial abundances substantially, whereas information about the bacterial occurrences and abundances increased the power to predict the fungal abundances much less. Our results suggest that fungal communities may mainly affect bacteria in deadwood.IMPORTANCE Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Applying joint species distribution modeling to high-throughput sequencing data on co-occurring fungal-bacterial communities in deadwood, we found evidence that nonrandom fungal-bacterial associations derive from shared habitat use as well as (potentially) biotic interactions. Importantly, the combination of cross-validations and conditional cross-validations helped us to answer the question about the directionality of the biotic interactions, providing evidence that suggests that fungal communities may mainly affect bacteria in deadwood. Our modeling approach may help gain insight into the directionality of interactions between different components of the microbiome in other environments.}, } @article {pmid33401951, year = {2021}, author = {}, title = {Corrigendum to Associations Between Dysmenorrhea Symptom-Based Phenotypes and Vaginal Microbiome: A Pilot Study.}, journal = {Biological research for nursing}, volume = {}, number = {}, pages = {1099800420988144}, doi = {10.1177/1099800420988144}, pmid = {33401951}, issn = {1552-4175}, } @article {pmid33401586, year = {2021}, author = {Choudhry, H}, title = {The Microbiome and Its Implications in Cancer Immunotherapy.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {1}, pages = {}, pmid = {33401586}, issn = {1420-3049}, abstract = {Cancer is responsible for ~18 million deaths globally each year, representing a major cause of death. Several types of therapy strategies such as radiotherapy, chemotherapy and more recently immunotherapy, have been implemented in treating various types of cancer. Microbes have recently been found to be both directly and indirectly involved in cancer progression and regulation, and studies have provided novel and clear insights into the microbiome-mediated emergence of cancers. Scientists around the globe are striving hard to identify and characterize these microbes and the underlying mechanisms by which they promote or suppress various kinds of cancer. Microbes may influence immunotherapy by blocking various cell cycle checkpoints and the production of certain metabolites. Hence, there is an urgent need to better understand the role of these microbes in the promotion and suppression of cancer. The identification of microbes may help in the development of future diagnostic tools to cure cancers possibly associated with the microbiome. This review mainly focuses on various microbes and their association with different types of cancer, responses to immunotherapeutic modulation, physiological responses, and prebiotic and postbiotic effects.}, } @article {pmid33401401, year = {2021}, author = {Eshghjoo, S and Jayaraman, A and Sun, Y and Alaniz, RC}, title = {Microbiota-Mediated Immune Regulation in Atherosclerosis.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {1}, pages = {}, pmid = {33401401}, issn = {1420-3049}, support = {DK118334/NH/NIH HHS/United States ; R01AI110642/NH/NIH HHS/United States ; }, abstract = {There is a high level of interest in identifying metabolites of endogenously produced or dietary compounds generated by the gastrointestinal (GI) tract microbiota, and determining the functions of these metabolites in health and disease. There is a wealth of compelling evidence that the microbiota is linked with many complex chronic inflammatory diseases, including atherosclerosis. Macrophages are key target immune cells in atherosclerosis. A hallmark of atherosclerosis is the accumulation of pro-inflammatory macrophages in coronary arteries that respond to pro-atherogenic stimuli and failure of digesting lipids that contribute to foam cell formation in atherosclerotic plaques. This review illustrates the role of tryptophan-derived microbiota metabolites as an aryl hydrocarbon receptor (AhR) ligand that has immunomodulatory properties. Also, microbiota-dependent trimethylamine-N-oxide (TMAO) metabolite production is associated with a deleterious effect that promotes atherosclerosis, and metabolite indoxyl sulfate has been shown to exacerbate atherosclerosis. Our objective in this review is to discuss the role of microbiota-derived metabolites in atherosclerosis, specifically the consequences of microbiota-induced effects of innate immunity in response to atherogenic stimuli, and how specific beneficial/detrimental metabolites impact the development of atherosclerosis by regulating chronic endotoxemic and lipotoxic inflammation.}, } @article {pmid33401080, year = {2021}, author = {Naqvi, S and Asar, TO and Kumar, V and Al-Abbasi, FA and Alhayyani, S and Kamal, MA and Anwar, F}, title = {A cross-talk between gut microbiome, salt and hypertension.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {134}, number = {}, pages = {111156}, doi = {10.1016/j.biopha.2020.111156}, pmid = {33401080}, issn = {1950-6007}, abstract = {Cardiac disorders contribute to one of the major causes of fatality across the world. Hypertensive patients, even well maintained on drugs, possess a high risk to cardiovascular diseases. It is, therefore, highly important to identify different factors and pathways that lead to risk and progression of cardiovascular disorders. Several animals and human studies suggest that taxonomical alterations in the gut are involved in the cardiovascular physiology. In this article, with the help of various experimental evidences, we suggest that the host gut-microbiota plays an important in this pathway. Short chain fatty acids (SCFAs) and Trimethyl Amine -n-Oxide (TMAO) are the two major products of gut microbiome. SCFAs present a crucial role in regulating the blood pressure, while TMAO is involved in pathogenesis of atherosclerosis and other coronary artery diseases, including hypertension. We prove that there exists a triangular bridge connecting the gap between dietary salt, hypertension and gut microbiome. We also present some of the dietary interventions which can regulate and control microbiota that can prevent cardiovascular complications.We strongly believe that this article would improve the understanding the role of gut microbiota in hypertension, and will be helpful in the development of novel therapeutic strategies for prevention of hypertension through restoring gut microbiome homeostasis in the near future.}, } @article {pmid33400410, year = {2021}, author = {Sun, MD and Rieder, EA}, title = {Psychosocial Stress and Mechanisms of Skin Health: A Comprehensive Update.}, journal = {Journal of drugs in dermatology : JDD}, volume = {20}, number = {1}, pages = {62-69}, doi = {10.36849/JDD.2021.5608}, pmid = {33400410}, issn = {1545-9616}, abstract = {Although the relationship between psychosocial stress and skin health is commonly invoked in both the scientific and popular literature, its underlying mechanisms are still not well understood. In this review, we provide a comprehensive update on the pathophysiology of stress and its clinical impact on skin homeostasis. The recent characterization of a bidirectional HPA stress axis in the skin has illuminated peripheral stress pathways, with effects spanning inflammation, atopy, barrier function, dermal thinning, wound healing, and melanogenesis. Additionally, new research into the cutaneous microbiome suggests the development of stress-induced dysbiosis through the &ldquo;gut-brain-skin&rdquo; axis. These new findings help contextualize how lifestyle factors such as diet, personal care practices, and sleep patterns may mediate and sometimes amplify the cutaneous impacts of psychological stress. We aim to clarify these clinically important relationships and highlight areas of future study that have widespread academic, clinical, and commercial implications. J Drugs Dermatol. 2021;20(1):62-29. doi:10.36849/JDD.2021.5608.}, } @article {pmid33400366, year = {2021}, author = {Sun, A and Jiao, XY and Chen, Q and Trivedi, P and Li, Z and Li, F and Zheng, Y and Lin, Y and Hu, HW and He, JZ}, title = {Fertilization alters protistan consumers and parasites in crop-associated microbiomes.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15385}, pmid = {33400366}, issn = {1462-2920}, support = {CARS-06-13.5-A20//China Agriculture Research System/ ; DP210100332//Australian Research Council/ ; 31901291//Natural National Science Foundation of China/ ; }, abstract = {Crop plants carry an enormous diversity of microbiota that provide massive benefits to hosts. Protists, as the main microbial consumers and a pivotal driver of biogeochemical cycling processes, remain largely understudied in the plant microbiome. Here, we characterized the diversity and composition of protists in sorghum leaf phyllosphere, and rhizosphere and bulk soils, collected from an 8-year field experiment with multiple fertilization regimes. Phyllosphere was an important habitat for protists, dominated by Rhizaria, Alveolata and Amoebozoa. Rhizosphere and bulk soils had a significantly higher diversity of protists than the phyllosphere, and the protistan community structure significantly differed among the three plant-soil compartments. Fertilization significantly altered specific functional groups of protistan consumers and parasites. Variation partitioning models revealed that soil properties, bacteria and fungi predicted a significant proportion of the variation in the protistan communities. Changes in protists may in turn significantly alter the compositions of bacterial and fungal communities from the top-down control in food webs. Altogether, we provide novel evidence that fertilization significantly affects the functional groups of protistan consumers and parasites in crop-associated microbiomes, which have implications for the potential changes in their ecological functions under intensive agricultural managements.}, } @article {pmid33400239, year = {2021}, author = {Shah, S and Hindley, L and Hill, A}, title = {Are New Antiretroviral Treatments Increasing the Risk of Weight Gain?.}, journal = {Drugs}, volume = {}, number = {}, pages = {}, pmid = {33400239}, issn = {1179-1950}, abstract = {There is a growing body of evidence from both observational and randomised trials implicating integrase inhibitors, particularly dolutegravir and bictegravir, with the development of weight gain and obesity in people living with HIV. Evidence with cabotegravir, the newest integrase inhibitor, is limited. Reasons for weight gain are currently unknown. Proposed mechanisms include improved tolerability, direct impact on adipogenesis, and gut microbiome disturbance. Clinical trials have found that weight gain with integrase inhibitors is greatest for women and people of Black ethnicity. Evidence suggests that the nucleoside reverse transcriptase backbone has additional effects on weight gain, with tenofovir alafenamide potentially enhancing the weight gain effect. Weight gain and obesity have long-term consequences, including metabolic syndrome, development of type 2 diabetes mellitus, cardiovascular disease and adverse birth outcomes. However, the current evidence for the medium and long-term effects of weight gain associated with integrase inhibitors is limited. There is an urgent need for clinical trials with longer follow-up periods and standardised endpoints to evaluate these effects. New thresholds for weight gain should be established as guidance for clinicians to stop treatment where weight gain is excessive. Novel treatments such as doravirine could offer a suitable therapy alternative, with current evidence showing efficacy with limited effect on weight gain.}, } @article {pmid33400081, year = {2021}, author = {Janeiro, MH and Ramírez, MJ and Solas, M}, title = {Dysbiosis and Alzheimer's Disease: Cause or Treatment Opportunity?.}, journal = {Cellular and molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {33400081}, issn = {1573-6830}, abstract = {Recent investigations have increased the interest on the connection between the microorganisms inhabiting the gut (gut microbiota) and human health. An imbalance of the intestinal bacteria representation (dysbiosis) could lead to different diseases, ranging from obesity and diabetes, to neurological disorders including Alzheimer's disease (AD). The term "gut-brain axis" refers to a crosstalk between the brain and the gut involving multiple overlapping pathways, including the autonomic, neuroendocrine, and immune systems as well as bacterial metabolites and neuromodulatory molecules. Through this pathway, microbiota can influence the onset and progression of neuropathologies such as AD. This review discusses the possible interaction between the gut microbiome and AD, focusing on the role of gut microbiota in neuroinflammation, cerebrovascular degeneration and Aβ clearance.}, } @article {pmid33399932, year = {2021}, author = {Aguero, CM and Eyer, PA and Crippen, TL and Vargo, EL}, title = {Reduced Environmental Microbial Diversity on the Cuticle and in the Galleries of a Subterranean Termite Compared to Surrounding Soil.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {33399932}, issn = {1432-184X}, abstract = {Termites are intimately tied to the microbial world, as they utilize their gut microbiome for the conversion of plant cellulose into necessary nutrients. Subterranean termites must also protect themselves from the vast diversity of harmful microbes found in soil. However, not all soil microbes are harmful, such as Streptomyces and methanotrophic bacteria that some species of termites harbor in complex nest structures made of fecal material. The eastern subterranean termite, Reticulitermes flavipes, has a simple nest structure consisting of fecal lined galleries. We tested the hypothesis that R. flavipes maintains a select microbial community in its nests to limit the penetration of harmful soilborne pathogens and favor the growth of beneficial microbes. Using Illumina sequencing, we characterized the bacterial and fungal communities in the surrounding soil, in the nest galleries, and on the cuticle of workers. We found that the galleries provide a more beneficial microbial community than the surrounding soil. Bacterial and fungal diversity was highest in the soil, lower in the galleries, and least on the cuticle. Bacterial communities clustered together according to the substrate from which they were sampled, but this clustering was less clear in fungal communities. Most of the identified bacterial and fungal taxa were unique to one substrate, but the soil and gallery communities had very similar phylum-level taxonomic profiles. Notably, the galleries of R. flavipes also harbored both the potentially beneficial Streptomyces and the methanotrophic Methylacidiphilales, indicating that these microbial associations in fecal material pre-date the emergence of complex fecal nest structures. Surprisingly, several pathogenic groups were relatively abundant in the galleries and on the cuticle, suggesting that pathogens may accumulate within termite nests over time while putatively remaining at enzootic level during the lifetime of the colony.}, } @article {pmid33399261, year = {2021}, author = {da Silva Vale, A and de Melo Pereira, GV and de Carvalho Neto, DP and Sorto, RD and Goés-Neto, A and Kato, R and Soccol, CR}, title = {Facility-specific 'house' microbiome ensures the maintenance of functional microbial communities into coffee beans fermentation: implications for source tracking.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.12921}, pmid = {33399261}, issn = {1758-2229}, support = {151885/2019-2//CNPq/ ; 303254/2017-3//CNPq/ ; }, abstract = {This work aimed at studying the unconfirmed hypothesis predicting the existence of a connection between coffee farm microbiome and the resulting spontaneous fermentation process. Using Illumina-based amplicon sequencing, 360 prokaryotes and 397 eukaryotes were identified from coffee fruits and leaves, over-ripe fruits, water used for coffee de-pulping, depulped coffee beans, soil, and temporal fermentation samples at an experimental farm in Honduras. Coffee fruits and leaves were mainly associated with high incidence of Enterobacteriaceae, Pseudomonas, Colletotrichum, and Cladosporium. The proportion of Enterobacteriaceae was increased when leaves and fruits were collected on the ground compared to those from the coffee tree. Coffee farm soil showed the richest microbial diversity with marked presence of Bacillus. Following the fermentation process, microorganisms present in depulped coffee beans (Leuconostoc, Gluconobater, Pichia, Hanseniaspora, and Candida) represented more than 90% of the total microbial community, which produced lactic acid, ethanol, and several volatile compounds. The community ecology connections described in this study showed that coffee fruit provides beneficial microorganisms for the fermentation process. Enterobacteria, Colletotrichum, and other microbial groups present in leaves, fruit surface, over-ripe fruits, and soil may transfer unwanted aromas to coffee beans, so they should be avoided from having access to the fermentation tank.}, } @article {pmid33399257, year = {2021}, author = {Puigdemont, A and D'Andreano, S and Ramió-Lluch, L and Cuscó, A and Francino, O and Brazis, P}, title = {Effect of an anti-inflammatory pomegranate otic treatment on the clinical evolution and microbiota profile of dogs with otitis externa.}, journal = {Veterinary dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/vde.12930}, pmid = {33399257}, issn = {1365-3164}, support = {//LETI Laboratorios/ ; }, abstract = {BACKGROUND: Canine otitis externa (OE) is a common disease characterised by inflammation of the epithelial tissue of the external ear canal. Secondary infections are frequent, and Malassezia pachydermatis and Staphylococcus pseudintermedius are routinely isolated and treated with antifungal and antibiotic compounds.

HYPOTHESIS/OBJECTIVES: To analyse the otitis ear microbiome before and after a treatment with prednisolone plus pomegranate or antimicrobial drugs ANIMALS: 15 dogs with nonpurulent OE.

METHODS AND MATERIALS: A 30 day, double-blinded, multicentre, randomized and controlled parallel-group (1:1) trial was conducted in 15 dogs with nonpurulent OE, following two different topical treatments (prednisolone plus pomegranate versus prednisolone plus antibiotic and antifungal drugs). On days (D)0, D15 and D30, serum and skin otic samples were collected, and clinical examination and microbiome analysis (bacteria and fungi) were performed. Results were compared with validated otitis clinical scores to assess the effectiveness of both treatments.

RESULTS: Nine bacterial and four fungal families were detected during the three time-points tested. An increase in fungal diversity (Shannon index) and composition was the most significant change observed after both treatments. At treatment D15 and D30, the reduction in clinical signs was statistically significant in both treatment groups (P ≤ 0.05). Prednisolone plus pomegranate cleanser treatment was able to control the clinical signs of otitis as well as the bacterial and fungal overgrowth.

Mild otitis cases associated with microbial overgrowth may be managed with topical antiseptic and anti-inflammatory agents without the need for antibiotic and/or antifungal compounds.}, } @article {pmid33398958, year = {2020}, author = {Tan, Y and Hu, H and Li, C and Luo, X and Tan, Y and Dai, L}, title = {[Research progress and applications of strain analysis based on metagenomic data].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {36}, number = {12}, pages = {2610-2621}, doi = {10.13345/j.cjb.200380}, pmid = {33398958}, issn = {1872-2075}, mesh = {Algorithms ; Computational Biology ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; }, abstract = {Strain is the fundamental unit in microbial taxonomy. The functional diversity among strains has great influence on host phenotypes. With the development of microbiome research, knowing the composition and functional capacities of complex microbial communities at the strain level has become increasingly valuable in scientific research and clinical applications. This review introduces the principles of bioinformatics algorithms for strain analysis based on metagenomic data, the applications in microbiome research and directions of future development.}, } @article {pmid33398955, year = {2020}, author = {Zhang, Y and Cao, J and Zhao, N and Wang, J}, title = {[Virome: the next hotspot in microbiome research].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {36}, number = {12}, pages = {2566-2581}, doi = {10.13345/j.cjb.200372}, pmid = {33398955}, issn = {1872-2075}, mesh = {Animals ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Virome ; *Viruses/genetics ; }, abstract = {Virome is the collective term for the viral collection or viral metagenomes that are distributed in various environments. Viruses can be found in bodies of water, glaciers, plants, animals, and even some viruses, which are classified as eukaryotes, prokaryotes and subviruses. Viruses play very important role in maintaining environmental homeostasis and ecosystem balance, and are especially closely related to human health. In recent years, with the advancement of sequencing technology and data analysis, we are able to gain more insights into the virome and explore its potential role in the ecological niche by metagenomic sequencing. A large amount of viral data have been obtained from glaciers, oceans, and various plants and animals, and numerous unknown viruses have been discovered. Virome has been studied mainly through metagenomic data mining, as well as virus-like particles separation and enrichment. To date, several different methods for viral isolation and enrichment exist, and numerous bioinformatic analyses of the virome have been performed. However, there is a lack of specific and complete reviews on the enrichment and data analysis methods for the virome. Thus, our review will summarize viral isolation and enrichment methods and data analysis, and present some of the landmark research conducted by the enrichment method, to provide a reference for researchers of interest and further advance the field of virome research.}, } @article {pmid33398952, year = {2020}, author = {Chen, T and Zhang, T and Yang, Y and Zhao, B and Wu, C}, title = {[Quantification of microbial DNA in laboratory environment during DNA extraction].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {36}, number = {12}, pages = {2541-2547}, doi = {10.13345/j.cjb.200526}, pmid = {33398952}, issn = {1872-2075}, mesh = {DNA ; DNA, Bacterial/genetics ; *Laboratories ; *Metagenomics ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {Metagenomic sequencing provides a powerful tool for microbial research. However, traditional experimental DNA extraction process will inevitably mix with environmental microorganisms which float in the air. It is still unclear whether the mixed environmental microbial DNA will heavily affect the metagenomic results of samples with extremely low microbial content. In this study, we first collected environmental bacteria in the laboratory and quantified the mixed environmental microbial DNA content during DNA extraction based on a qPCR-based quantification assay. We then extracted DNA from pure water in order to determine the mixed microbial taxons during extraction under open environment. At last, we extracted total DNA from a skin sample in a Biosafety cabinet or under open laboratory environment, to assess the impact of the mixed environmental microorganisms on the metagenomic results. Our results showed that DNA extraction under open laboratory environment in Beijing region resulted in 28.9 pg contaminant, which may accout for 30% of total DNA amount from skin samples. Metagenomic analysis revealed that the main incorporated environmental taxons were Cutibacterium acnes and Escherichia coli. Tens of environmental bacteria were foisted in the skin DNA samples, which largely decreased the relative abundance of dominant species and thus deteriorated the result accuracy. Therefore, analyzing microbial composition of samples with extremely low DNA content should better performed under aseptic environment.}, } @article {pmid33398951, year = {2020}, author = {Duan, Y and Lü, N and Cai, F and Zhu, B}, title = {[Variations of gut microbiome composition under different preservation solutions and periods].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {36}, number = {12}, pages = {2525-2540}, doi = {10.13345/j.cjb.200475}, pmid = {33398951}, issn = {1872-2075}, mesh = {Bacteria/genetics ; Feces ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; Specimen Handling ; }, abstract = {Gut microbiota is closely related to human health, and its composition can give us health information. The large-scale population sampling is required on gut microbiome research; however, fresh feces samples are not easy to obtain, and rapid low-temperature freezing is difficult to achieve. With the development of technology, preservation solutions are widely used for sample collection, storage, and transport under normal temperature conditions. Preservation solutions can be used in large scale sample collection, wide geographical distribution, diverse on-site sampling conditions, heavy workload, and poor transportation conditions. In this study, five healthy volunteers were recruited. After collecting their fresh stool samples, effect of 5 different commercial preservation solutions was evaluated at room temperature. Samples in different preservation solutions after placing fresh stool samples at the 0, 1, 3, 7, 15, and 30 days were collected. All samples were tested by 16S rRNA V3-V4 high-throughput sequencing to analyze the influence of microbiome composition in different preservation solutions. The results show that different preservation solutions had distinct effects on the gut microbiome composition. Compared with the control, different preservation solutions had little effect on the amount of OUTs; preservation solutions A, B and C were closer to the control in the composition of the gut microbiota, but preservation solution D significantly changed the composition by increasing Actinobacteria and Firmicutes abundance. With the time, all solutions tended to reduce the diversity of the microbiota. Preservation solution E significantly reduced the diversity of the flora; on the 30th day, all five solutions changed the composition; the individual differences in the composition of the gut microbiome were the main factors affecting the similarity of each sample, and were derived from different stools donors. The same samples, no matter which storage solution and storage time, were directly closer to each other. Different storage solutions had different effects on the content of Gram-positive bacilli, Gram-positive cocci and Gram-negative bacteria. Storage solutions C and E reduced the abundance of Bifidobacterium, whereas storage solution D increased; except that preservation solution E relatively reduced the abundance of Lactobacillus, but the preservation solution A, B, C, and D were all closer to the control. Except for the greater difference in preservation solution D, preservation solution C was the closest to the control group on Streptococcus; preservation solution D reduced Ruminococcaceae UCG 003 than the control group. However, other preservation solutions were not much different from the control group; different preservation solutions increased the abundance of Escherichia-Shigella than the control group, and preservation solutions A and B increased the abundance of Klebsiella, but preservation solution C, D, and E were closer to the control group. Overall, preservation solution C performed better in stabilizing the composition of the gut microbiota. This study provides reference for standardized microbiome projects. Subsequent research can choose a targeted preservation solution and preservation time based on this study.}, } @article {pmid33398950, year = {2020}, author = {Duan, Y and Wang, S and Chen, Y and Yang, R and Li, H and Zhu, H and Tong, Y and Wu, W and Fu, Y and Hu, S and Wang, J and Xin, Y and Zhao, F and Bao, Y and Zhang, W and Li, J and Zeng, M and Niu, H and Zhou, X and Li, Y and Cui, S and Yuan, J and Li, J and Wang, J and Liu, D and Ni, M and Sun, Q and Deng, Y and Zhu, B}, title = {[Expert consensus on microbiome sequencing and analysis].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {36}, number = {12}, pages = {2516-2524}, doi = {10.13345/j.cjb.200386}, pmid = {33398950}, issn = {1872-2075}, mesh = {China ; Consensus ; Humans ; Industry ; *Microbiota ; }, abstract = {In the past ten years, the research and application of microbiome has continued to increase. The microbiome has gradually become the research focus in the fields of life science, environmental science, and medicine. Meanwhile, many countries and organizations around the world are launching their own microbiome projects and conducting a multi-faceted layout, striving to gain a strategic position in this promising field. In addition, whether it is scientific research or industrial applications, there has been a climax of research and a wave of investment and financing, accordingly, products and services related to the microbiome are constantly emerging. However, due to the rapid development of microbiome sequencing and analysis related technologies and methods, the research and application from various countries have not yet unified on the standards of technology, programs, and data. Domestic industry participants also have insufficient understanding of the microbiome. New methods, technologies, and theories have not yet been fully accepted and used. In addition, some of the existing standards and guidelines are too general with poor practicality. This not only causes obstacles in the integration of scientific research data and waste of resources, but also gives related companies unfair competition opportunity. More importantly, China still lacks national standards related to the microbiome, and the national microbiome project is still in the process of preparation. In this context, the experts and practitioners of the microbiome worked together and developed the consensus of experts. It can not only guide domestic scientific research and industrial institutions to regulate the production, learning and research of the microbiome, the application can also provide reference technical basis for the relevant national functional departments, protect the scale and standardized corporate company's interests, strengthen industry self-discipline, avoid unregulated enterprises from disrupting the market, and ultimately promote the benign development of microbiome-related industries.}, } @article {pmid33398949, year = {2020}, author = {Duan, Y and Zhu, B}, title = {[Preface for microbiome sequencing and analysis].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {36}, number = {12}, pages = {2511-2515}, doi = {10.13345/j.cjb.200800}, pmid = {33398949}, issn = {1872-2075}, mesh = {Animals ; Bacteria/genetics ; China ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Microbiota/genetics ; RNA, Ribosomal, 16S ; }, abstract = {Microbes are the most important commensal organisms in humans, animals and plants, and are the major habitants in soil, sediment, water, air and other habitats. The analysis of microbiome in these habitats has become a basic research technique. As a fast developing technology in recent years, microbiome sequencing and analysis have been widely used in human health, environmental pollution control, food industry, agriculture and animal husbandry and other fields. In order to sort out and summarize the current status, development and application prospects of microbiome sequencing and analysis technologies, this special issue has prepared a collection of 16 papers in this field, that comprise sample preservation and processing, single microbe genome sequencing and analysis, and microbiome feature analysis in special habitats, microbiome related databases and algorithms, and microbiome sequencing and analysis expert consensus. It also introduced in detail the development trend of the microbiome sequencing and analysis, in order to promote the rapid development of the microbiome sequencing and analysis industry and scientific research in China, and provide necessary reference for the healthy development of related industries.}, } @article {pmid33398182, year = {2021}, author = {Ozen, A and Kasap, N and Vujkovic-Cvijin, I and Apps, R and Cheung, F and Karakoc-Aydiner, E and Akkelle, B and Sari, S and Tutar, E and Ozcay, F and Uygun, DK and Islek, A and Akgun, G and Selcuk, M and Sezer, OB and Zhang, Y and Kutluk, G and Topal, E and Sayar, E and Celikel, C and Houwen, RHJ and Bingol, A and Ogulur, I and Eltan, SB and Snow, AL and Lake, C and Fantoni, G and Alba, C and Sellers, B and Chauvin, SD and Dalgard, CL and Harari, O and Ni, YG and Wang, MD and Devalaraja-Narashimha, K and Subramanian, P and Ergelen, R and Artan, R and Guner, SN and Dalgic, B and Tsang, J and Belkaid, Y and Ertem, D and Baris, S and Lenardo, MJ}, title = {Broadly effective metabolic and immune recovery with C5 inhibition in CHAPLE disease.}, journal = {Nature immunology}, volume = {}, number = {}, pages = {}, pmid = {33398182}, issn = {1529-2916}, support = {HHSN316201300006W/HHSN27200002//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; SAG-C-TUP-230119-0018//Marmara Üniversitesi (Marmara University)/ ; }, abstract = {Complement hyperactivation, angiopathic thrombosis and protein-losing enteropathy (CHAPLE disease) is a lethal disease caused by genetic loss of the complement regulatory protein CD55, leading to overactivation of complement and innate immunity together with immunodeficiency due to immunoglobulin wasting in the intestine. We report in vivo human data accumulated using the complement C5 inhibitor eculizumab for the medical treatment of patients with CHAPLE disease. We observed cessation of gastrointestinal pathology together with restoration of normal immunity and metabolism. We found that patients rapidly renormalized immunoglobulin concentrations and other serum proteins as revealed by aptamer profiling, re-established a healthy gut microbiome, discontinued immunoglobulin replacement and other treatments and exhibited catch-up growth. Thus, we show that blockade of C5 by eculizumab effectively re-establishes regulation of the innate immune complement system to substantially reduce the pathophysiological manifestations of CD55 deficiency in humans.}, } @article {pmid33398153, year = {2021}, author = {Nissen, JN and Johansen, J and Allesøe, RL and Sønderby, CK and Armenteros, JJA and Grønbech, CH and Jensen, LJ and Nielsen, HB and Petersen, TN and Winther, O and Rasmussen, S}, title = {Improved metagenome binning and assembly using deep variational autoencoders.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {33398153}, issn = {1546-1696}, support = {NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; }, abstract = {Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop variational autoencoders for metagenomic binning (VAMB), a program that uses deep variational autoencoders to encode sequence coabundance and k-mer distribution information before clustering. We show that a variational autoencoder is able to integrate these two distinct data types without any previous knowledge of the datasets. VAMB outperforms existing state-of-the-art binners, reconstructing 29-98% and 45% more near-complete (NC) genomes on simulated and real data, respectively. Furthermore, VAMB is able to separate closely related strains up to 99.5% average nucleotide identity (ANI), and reconstructed 255 and 91 NC Bacteroides vulgatus and Bacteroides dorei sample-specific genomes as two distinct clusters from a dataset of 1,000 human gut microbiome samples. We use 2,606 NC bins from this dataset to show that species of the human gut microbiome have different geographical distribution patterns. VAMB can be run on standard hardware and is freely available at https://github.com/RasmussenLab/vamb .}, } @article {pmid33398106, year = {2021}, author = {Machado, D and Maistrenko, OM and Andrejev, S and Kim, Y and Bork, P and Patil, KR and Patil, KR}, title = {Polarization of microbial communities between competitive and cooperative metabolism.}, journal = {Nature ecology & evolution}, volume = {}, number = {}, pages = {}, pmid = {33398106}, issn = {2397-334X}, support = {686070//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 686070//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 686070//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; SCB//European Molecular Biology Laboratory (EMBL Heidelberg)/ ; SCB//European Molecular Biology Laboratory (EMBL Heidelberg)/ ; SCB//European Molecular Biology Laboratory (EMBL Heidelberg)/ ; SCB//European Molecular Biology Laboratory (EMBL Heidelberg)/ ; MRC Toxicology Unit//RCUK | Medical Research Council (MRC)/ ; }, abstract = {Resource competition and metabolic cross-feeding are among the main drivers of microbial community assembly. Yet the degree to which these two conflicting forces are reflected in the composition of natural communities has not been systematically investigated. Here, we use genome-scale metabolic modelling to assess the potential for resource competition and metabolic cooperation in large co-occurring groups (up to 40 members) across thousands of habitats. Our analysis reveals two distinct community types, which are clustered at opposite ends of a spectrum in a trade-off between competition and cooperation. At one end are highly cooperative communities, characterized by smaller genomes and multiple auxotrophies. At the other end are highly competitive communities, which feature larger genomes and overlapping nutritional requirements, and harbour more genes related to antimicrobial activity. The latter are mainly present in soils, whereas the former are found in both free-living and host-associated habitats. Community-scale flux simulations show that, whereas competitive communities can better resist species invasion but not nutrient shift, cooperative communities are susceptible to species invasion but resilient to nutrient change. We also show, by analysing an additional data set, that colonization by probiotic species is positively associated with the presence of cooperative species in the recipient microbiome. Together, our results highlight the bifurcation between competitive and cooperative metabolism in the assembly of natural communities and its implications for community modulation.}, } @article {pmid33398069, year = {2021}, author = {Ebmeyer, S and Kristiansson, E and Larsson, DGJ}, title = {A framework for identifying the recent origins of mobile antibiotic resistance genes.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {8}, pmid = {33398069}, issn = {2399-3642}, support = {2018-02835//Vetenskapsrådet (Swedish Research Council)/ ; 2018-05771//Vetenskapsrådet (Swedish Research Council)/ ; 2018-00787//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; }, abstract = {Since the introduction of antibiotics as therapeutic agents, many bacterial pathogens have developed resistance to antibiotics. Mobile resistance genes, acquired through horizontal gene transfer, play an important role in this process. Understanding from which bacterial taxa these genes were mobilized, and whether their origin taxa share common traits, is critical for predicting which environments and conditions contribute to the emergence of novel resistance genes. This knowledge may prove valuable for limiting or delaying future transfer of novel resistance genes into pathogens. The literature on the origins of mobile resistance genes is scattered and based on evidence of variable quality. Here, we summarize, amend and scrutinize the evidence for 37 proposed origins of mobile resistance genes. Using state-of-the-art genomic analyses, we supplement and evaluate the evidence based on well-defined criteria. Nineteen percent of reported origins did not fulfill the criteria to confidently assign the respective origin. Of the curated origin taxa, >90% have been associated with infection in humans or domestic animals, some taxa being the origin of several different resistance genes. The clinical emergence of these resistance genes appears to be a consequence of antibiotic selection pressure on taxa that are permanently or transiently associated with the human/domestic animal microbiome.}, } @article {pmid33397942, year = {2021}, author = {Rodrigues, RR and Gurung, M and Li, Z and García-Jaramillo, M and Greer, R and Gaulke, C and Bauchinger, F and You, H and Pederson, JW and Vasquez-Perez, S and White, KD and Frink, B and Philmus, B and Jump, DB and Trinchieri, G and Berry, D and Sharpton, TJ and Dzutsev, A and Morgun, A and Shulzhenko, N}, title = {Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet-induced diabetes.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {101}, pmid = {33397942}, issn = {2041-1723}, support = {R01 DK103761/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bilirubin/blood ; Diabetes Mellitus, Type 2/*etiology/genetics/*microbiology ; *Diet, Western ; Gastrointestinal Microbiome ; Gene Expression Regulation ; Glucose/metabolism ; Glutathione/blood/metabolism ; Humans ; Lactobacillus/*metabolism ; Lipid Metabolism ; Male ; Metabolomics ; Mice, Inbred C57BL ; Mitochondria, Liver/*metabolism/ultrastructure ; Reproducibility of Results ; Transcriptome/genetics ; }, abstract = {Western diet (WD) is one of the major culprits of metabolic disease including type 2 diabetes (T2D) with gut microbiota playing an important role in modulating effects of the diet. Herein, we use a data-driven approach (Transkingdom Network analysis) to model host-microbiome interactions under WD to infer which members of microbiota contribute to the altered host metabolism. Interrogation of this network pointed to taxa with potential beneficial or harmful effects on host's metabolism. We then validate the functional role of the predicted bacteria in regulating metabolism and show that they act via different host pathways. Our gene expression and electron microscopy studies show that two species from Lactobacillus genus act upon mitochondria in the liver leading to the improvement of lipid metabolism. Metabolomics analyses revealed that reduced glutathione may mediate these effects. Our study identifies potential probiotic strains for T2D and provides important insights into mechanisms of their action.}, } @article {pmid33397897, year = {2021}, author = {Zhang, F and Zuo, T and Yeoh, YK and Cheng, FWT and Liu, Q and Tang, W and Cheung, KCY and Yang, K and Cheung, CP and Mo, CC and Hui, M and Chan, FKL and Li, CK and Chan, PKS and Ng, SC}, title = {Longitudinal dynamics of gut bacteriome, mycobiome and virome after fecal microbiota transplantation in graft-versus-host disease.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {65}, pmid = {33397897}, issn = {2041-1723}, mesh = {Adolescent ; Biodiversity ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Graft vs Host Disease/*microbiology/*virology ; Humans ; Male ; Microbiota ; *Mycobiome ; *Virome ; }, abstract = {Fecal microbiota transplant (FMT) has emerged as a potential treatment for severe colitis associated with graft-versus-host disease (GvHD) following hematopoietic stem cell transplant. Bacterial engraftment from FMT donor to recipient has been reported, however the fate of fungi and viruses after FMT remains unclear. Here we report longitudinal dynamics of the gut bacteriome, mycobiome and virome in a teenager with GvHD after receiving four doses of FMT at weekly interval. After serial FMTs, the gut bacteriome, mycobiome and virome of the patient differ from compositions before FMT with variable temporal dynamics. Diversity of the gut bacterial community increases after each FMT. Gut fungal community initially shows expansion of several species followed by a decrease in diversity after multiple FMTs. In contrast, gut virome community varies substantially over time with a stable rise in diversity. The bacterium, Corynebacterium jeikeium, and Torque teno viruses, decrease after FMTs in parallel with an increase in the relative abundance of Caudovirales bacteriophages. Collectively, FMT may simultaneously impact on the various components of the gut microbiome with distinct effects.}, } @article {pmid33397732, year = {2021}, author = {Moentadj, R and Wang, Y and Bowerman, K and Rehaume, L and Nel, H and O Cuiv, P and Stephens, J and Baharom, A and Maradana, M and Lakis, V and Morrison, M and Wells, T and Hugenholtz, P and Benham, H and Le Cao, KA and Thomas, R}, title = {Streptococcus species enriched in the oral cavity of patients with RA are a source of peptidoglycan-polysaccharide polymers that can induce arthritis in mice.}, journal = {Annals of the rheumatic diseases}, volume = {}, number = {}, pages = {}, doi = {10.1136/annrheumdis-2020-219009}, pmid = {33397732}, issn = {1468-2060}, abstract = {OBJECTIVES: Analysis of oral dysbiosis in individuals sharing genetic and environmental risk factors with rheumatoid arthritis (RA) patients may illuminate how microbiota contribute to disease susceptibility. We studied the oral microbiota in a prospective cohort of patients with RA, first-degree relatives (FDR) and healthy controls (HC), then genomically and functionally characterised streptococcal species from each group to understand their potential contribution to RA development.

METHODS: After DNA extraction from tongue swabs, targeted 16S rRNA gene sequencing and statistical analysis, we defined a microbial dysbiosis score based on an operational taxonomic unit signature of disease. After selective culture from swabs, we identified streptococci by sequencing. We examined the ability of streptococcal cell walls (SCW) from isolates to induce cytokines from splenocytes and arthritis in ZAP-70-mutant SKG mice.

RESULTS: RA and FDR were more likely to have periodontitis symptoms. An oral microbial dysbiosis score discriminated RA and HC subjects and predicted similarity of FDR to RA. Streptococcaceae were major contributors to the score. We identified 10 out of 15 streptococcal isolates as S. parasalivarius sp. nov., a distinct sister species to S. salivarius. Tumour necrosis factor and interleukin 6 production in vitro differed in response to individual S. parasalivarius isolates, suggesting strain specific effects on innate immunity. Cytokine secretion was associated with the presence of proteins potentially involved in S. parasalivarius SCW synthesis. Systemic administration of SCW from RA and HC-associated S. parasalivarius strains induced similar chronic arthritis.

CONCLUSIONS: Dysbiosis-associated periodontal inflammation and barrier dysfunction may permit arthritogenic insoluble pro-inflammatory pathogen-associated molecules, like SCW, to reach synovial tissue.}, } @article {pmid33397505, year = {2021}, author = {Roy, PH and Partridge, SR and Hall, RM}, title = {Comment on "Conserved phylogenetic distribution and limited antibiotic resistance of class 1 integrons revealed by assessing the bacterial genome and plasmid collection" by A.N. Zhang et al.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {3}, pmid = {33397505}, issn = {2049-2618}, abstract = {An article published in Microbiome in July 2018 uses incorrect definitions of integron integrase IntI1 and of class 1 integrons that affect the interpretation of the data.}, } @article {pmid33397500, year = {2021}, author = {LaPelusa, M and Donoviel, D and Branzini, SE and Carlson, PE and Culler, S and Cheema, AK and Kaddurah-Daouk, R and Kelly, D and de Cremoux, I and Knight, R and Krajmalnik-Brown, R and Mayo, SL and Mazmanian, SK and Mayer, EA and Petrosino, JF and Garrison, K}, title = {Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {2}, pmid = {33397500}, issn = {2049-2618}, support = {NNX16AO69A//Translational Research Institute for Space Health (TRISH)/ ; }, abstract = {The inaugural "Microbiome for Mars" virtual workshop took place on July 13, 2020. This event assembled leaders in microbiome research and development to discuss their work and how it may relate to long-duration human space travel. The conference focused on surveying current microbiome research, future endeavors, and how this growing field could broadly impact human health and space exploration. This report summarizes each speaker's presentation in the order presented at the workshop.}, } @article {pmid33397406, year = {2021}, author = {Zhang, R and Walker, AR and Datta, S}, title = {Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge.}, journal = {Biology direct}, volume = {16}, number = {1}, pages = {1}, pmid = {33397406}, issn = {1745-6150}, support = {1UL1TR000064/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: Composition of microbial communities can be location-specific, and the different abundance of taxon within location could help us to unravel city-specific signature and predict the sample origin locations accurately. In this study, the whole genome shotgun (WGS) metagenomics data from samples across 16 cities around the world and samples from another 8 cities were provided as the main and mystery datasets respectively as the part of the CAMDA 2019 MetaSUB "Forensic Challenge". The feature selecting, normalization, three methods of machine learning, PCoA (Principal Coordinates Analysis) and ANCOM (Analysis of composition of microbiomes) were conducted for both the main and mystery datasets.

RESULTS: Features selecting, combined with the machines learning methods, revealed that the combination of the common features was effective for predicting the origin of the samples. The average error rates of 11.93 and 30.37% of three machine learning methods were obtained for main and mystery datasets respectively. Using the samples from main dataset to predict the labels of samples from mystery dataset, nearly 89.98% of the test samples could be correctly labeled as "mystery" samples. PCoA showed that nearly 60% of the total variability of the data could be explained by the first two PCoA axes. Although many cities overlapped, the separation of some cities was found in PCoA. The results of ANCOM, combined with importance score from the Random Forest, indicated that the common "family", "order" of the main-dataset and the common "order" of the mystery dataset provided the most efficient information for prediction respectively.

CONCLUSIONS: The results of the classification suggested that the composition of the microbiomes was distinctive across the cities, which could be used to identify the sample origins. This was also supported by the results from ANCOM and importance score from the RF. In addition, the accuracy of the prediction could be improved by more samples and better sequencing depth.}, } @article {pmid33397404, year = {2021}, author = {Ragonnaud, E and Biragyn, A}, title = {Gut microbiota as the key controllers of "healthy" aging of elderly people.}, journal = {Immunity & ageing : I & A}, volume = {18}, number = {1}, pages = {2}, pmid = {33397404}, issn = {1742-4933}, support = {IRP/AG/NIA NIH HHS/United States ; }, abstract = {Extrinsic factors, such as lifestyle and diet, are shown to be essential in the control of human healthy aging, and thus, longevity. They do so by targeting at least in part the gut microbiome, a collection of commensal microorganisms (microbiota), which colonize the intestinal tract starting after birth, and is established by the age of three. The composition and abundance of individual microbiota appears to continue to change until adulthood, presumably reflecting lifestyle and geographic, racial, and individual differences. Although most of these changes appear to be harmless, a major shift in their composition in the gut (dysbiosis) can trigger harmful local and systemic inflammation. Recent reports indicate that dysbiosis is increased in aging and that the gut microbiota of elderly people is enriched in pro-inflammatory commensals at the expense of beneficial microbes. The clinical consequence of this change remains confusing due to contradictory reports and a high degree of variability of human microbiota and methodologies used. Here, we present the authors' thoughts that underscore dysbiosis as a primary cause of aging-associated morbidities, and thus, premature death of elderly people. We provide evidence that the dysbiosis triggers a chain of pathological and inflammatory events. Examples include alteration of levels of microbiota-affected metabolites, impaired function and integrity of the gastrointestinal tract, and increased gut leakiness. All of these enhance systemic inflammation, which when associated with aging is termed inflammaging, and result in consequent aging-associated pathologies.}, } @article {pmid33397283, year = {2021}, author = {Drengenes, C and Eagan, TML and Haaland, I and Wiker, HG and Nielsen, R}, title = {Exploring protocol bias in airway microbiome studies: one versus two PCR steps and 16S rRNA gene region V3 V4 versus V4.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {3}, pmid = {33397283}, issn = {1471-2164}, abstract = {BACKGROUND: Studies on the airway microbiome have been performed using a wide range of laboratory protocols for high-throughput sequencing of the bacterial 16S ribosomal RNA (16S rRNA) gene. We sought to determine the impact of number of polymerase chain reaction (PCR) steps (1- or 2- steps) and choice of target marker gene region (V3 V4 and V4) on the presentation of the upper and lower airway microbiome. Our analyses included lllumina MiSeq sequencing following three setups: Setup 1 (2-step PCR; V3 V4 region), Setup 2 (2-step PCR; V4 region), Setup 3 (1-step PCR; V4 region). Samples included oral wash, protected specimen brushes and protected bronchoalveolar lavage (healthy and obstructive lung disease), and negative controls.

RESULTS: The number of sequences and amplicon sequence variants (ASV) decreased in order setup1 > setup2 > setup3. This trend appeared to be associated with an increased taxonomic resolution when sequencing the V3 V4 region (setup 1) and an increased number of small ASVs in setups 1 and 2. The latter was considered a result of contamination in the two-step PCR protocols as well as sequencing across multiple runs (setup 1). Although genera Streptococcus, Prevotella, Veillonella and Rothia dominated, differences in relative abundance were observed across all setups. Analyses of beta-diversity revealed that while oral wash samples (high biomass) clustered together regardless of number of PCR steps, samples from the lungs (low biomass) separated. The removal of contaminants identified using the Decontam package in R, did not resolve differences in results between sequencing setups.

CONCLUSIONS: Differences in number of PCR steps will have an impact of final bacterial community descriptions, and more so for samples of low bacterial load. Our findings could not be explained by differences in contamination levels alone, and more research is needed to understand how variations in PCR-setups and reagents may be contributing to the observed protocol bias.}, } @article {pmid33397232, year = {2021}, author = {Hajiagha, MN and Taghizadeh, S and Asgharzadeh, M and Dao, S and Ganbarov, K and Köse, Ş and Kafil, HS}, title = {Gut microbiota And Human Body Interactions; Its Impact on Health: a review.}, journal = {Current pharmaceutical biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.2174/1389201022666210104115836}, pmid = {33397232}, issn = {1873-4316}, abstract = {Gut microbiota (GM) as an organ of the human body has a particular and autonomous function that related to it. This review aimed to investigate human intestinal and gut microbiota interaction and its impact on health. As a creation referable database about this dynamic and complex organ, several comprehensive projects are implemented by using culture-dependent (culturomics), culture independent methods (e.g metagenomics, mathematics model), and Gnotobiological together. This study was done by searching PubMed, Scopus and Google scholar database in the gut, health microbiota and interaction keywords. The first acquired microbiota during pregnancy or childbirth is colonized in the gut by using specific and non-specific mechanisms. That`s structure and shape reach relative stability with selection pressure along with host development until adulthood and keep its resilience against external or internal variables depending on the host genetics and negative feedback. Due to several research individuals have 2 functional group microbiota including the core (common between vast majorities human) and flexible (transient population) microbiome. The most important role of the GM in the human body can be summarized in three basic landscapes: metabolic, immune system, and gut-brain axis interaction. So that loss of microbial population balance will lead to disorder and disease.}, } @article {pmid33397034, year = {2020}, author = {Dao, T and Green, AE and Kim, YA and Bae, SJ and Ha, KT and Gariani, K and Lee, MR and Menzies, KJ and Ryu, D}, title = {Sarcopenia and Muscle Aging: A Brief Overview.}, journal = {Endocrinology and metabolism (Seoul, Korea)}, volume = {35}, number = {4}, pages = {716-732}, doi = {10.3803/EnM.2020.405}, pmid = {33397034}, issn = {2093-5978}, support = {2020R1A2C2010964//National Research Foundation of Korea/ ; //Ministry of Science and ICT/ ; MOP 159455/CAPMC/CIHR/Canada ; RGPIN 2018-06838//Natural Sciences and Engineering Research Council of Canada/ ; DGECR 2018-00012//Natural Sciences and Engineering Research Council of Canada/ ; //University of Ottawa Brain and Mind Research Institute/ ; }, abstract = {The world is facing the new challenges of an aging population, and understanding the process of aging has therefore become one of the most important global concerns. Sarcopenia is a condition which is defined by the gradual loss of skeletal muscle mass and function with age. In research and clinical practice, sarcopenia is recognized as a component of geriatric disease and is a current target for drug development. In this review we define this condition and provide an overview of current therapeutic approaches. We further highlight recent findings that describe key pathophysiological phenotypes of this condition, including alterations in muscle fiber types, mitochondrial function, nicotinamide adenine dinucleotide (NAD+) metabolism, myokines, and gut microbiota, in aged muscle compared to young muscle or healthy aged muscle. The last part of this review examines new therapeutic avenues for promising treatment targets. There is still no accepted therapy for sarcopenia in humans. Here we provide a brief review of the current state of research derived from various mouse models or human samples that provide novel routes for the development of effective therapeutics to maintain muscle health during aging.}, } @article {pmid33396811, year = {2020}, author = {Baslam, M and Mitsui, T and Sueyoshi, K and Ohyama, T}, title = {Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants.}, journal = {International journal of molecular sciences}, volume = {22}, number = {1}, pages = {}, pmid = {33396811}, issn = {1422-0067}, abstract = {C and N are the most important essential elements constituting organic compounds in plants. The shoots and roots depend on each other by exchanging C and N through the xylem and phloem transport systems. Complex mechanisms regulate C and N metabolism to optimize plant growth, agricultural crop production, and maintenance of the agroecosystem. In this paper, we cover the recent advances in understanding C and N metabolism, regulation, and transport in plants, as well as their underlying molecular mechanisms. Special emphasis is given to the mechanisms of starch metabolism in plastids and the changes in responses to environmental stress that were previously overlooked, since these changes provide an essential store of C that fuels plant metabolism and growth. We present general insights into the system biology approaches that have expanded our understanding of core biological questions related to C and N metabolism. Finally, this review synthesizes recent advances in our understanding of the trade-off concept that links C and N status to the plant's response to microorganisms.}, } @article {pmid33396683, year = {2020}, author = {Kuramae, EE and Dimitrov, MR and da Silva, GHR and Lucheta, AR and Mendes, LW and Luz, RL and Vet, LEM and Fernandes, TV}, title = {On-Site Blackwater Treatment Fosters Microbial Groups and Functions to Efficiently and Robustly Recover Carbon and Nutrients.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/microorganisms9010075}, pmid = {33396683}, issn = {2076-2607}, support = {729.004.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 2013/50351-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 206884/2014-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 99999.008090/2015-07;0622/2014//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {Wastewater is considered a renewable resource water and energy. An advantage of decentralized sanitation systems is the separation of the blackwater (BW) stream, contaminated with human pathogens, from the remaining household water. However, the composition and functions of the microbial community in BW are not known. In this study, we used shotgun metagenomics to assess the dynamics of microbial community structure and function throughout a new BW anaerobic digestion system installed at The Netherlands Institute of Ecology. Samples from the influent (BW), primary effluent (anaerobic digested BW), sludge and final effluent of the pilot upflow anaerobic sludge blanket (UASB) reactor and microalgae pilot tubular photobioreactor (PBR) were analyzed. Our results showed a decrease in microbial richness and diversity followed by a decrease in functional complexity and co-occurrence along the different modules of the bioreactor. The microbial diversity and function decrease were reflected both changes in substrate composition and wash conditions. Our wastewater treatment system also decreased microbial functions related to pathogenesis. In summary, the new sanitation system studied here fosters microbial groups and functions that allow the system to efficiently and robustly recover carbon and nutrients while reducing pathogenic groups, ultimately generating a final effluent safe for discharge and reuse.}, } @article {pmid33396537, year = {2020}, author = {Wark, G and Samocha-Bonet, D and Ghaly, S and Danta, M}, title = {The Role of Diet in the Pathogenesis and Management of Inflammatory Bowel Disease: A Review.}, journal = {Nutrients}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/nu13010135}, pmid = {33396537}, issn = {2072-6643}, abstract = {Inflammatory bowel diseases, which include ulcerative colitis and Crohn's disease, are chronic relapsing and remitting inflammatory diseases of the gastrointestinal tract that are increasing in prevalence and incidence globally. They are associated with significant morbidity, reduced quality of life to individual sufferers and are an increasing burden on society through direct and indirect costs. Current treatment strategies rely on immunosuppression, which, while effective, is associated with adverse events. Epidemiological evidence suggests that diet impacts the risk of developing IBD and modulates disease activity. Using diet as a therapeutic option is attractive to patients and clinicians alike due to its availability, low cost and few side effects. Diet may influence IBD risk and disease behaviour through several mechanisms. Firstly, some components of the diet influence microbiota structure and function with downstream effects on immune activity. Secondly, dietary components act to alter the structure and permeability of the mucosal barrier, and lastly dietary elements may have direct interactions with components of the immune response. This review will summarise the mechanisms of diet-microbial-immune system interaction, outline key studies examining associations between diet and IBD and evidence demonstrating the impact of diet on disease control. Finally, this review will outline current prescribed dietary therapies for active CD.}, } @article {pmid33396441, year = {2020}, author = {Li, Y and Lv, M and Wang, J and Tian, Z and Yu, B and Wang, B and Liu, J and Liu, H}, title = {Dandelion (Taraxacum mongolicum Hand.-Mazz.) Supplementation-Enhanced Rumen Fermentation through the Interaction between Ruminal Microbiome and Metabolome.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/microorganisms9010083}, pmid = {33396441}, issn = {2076-2607}, support = {2018YFD0501604//National Key Research and Development Program of China/ ; 2020FZZX001-07//Fundamental Research Funds for the Central Universities/ ; }, abstract = {This study investigated the effects of dandelion on the ruminal metabolome and microbiome in lactating dairy cows. A total of 12 mid-lactation dairy cows were selected and randomly classified into two groups, supplementing dandelion with 0 (CON) and 200 g/d per cow (DAN) above basal diet, respectively. Rumen fluid samples were collected in the last week of the trial for microbiome and metabolome analysis. The results showed that supplementation of DAN increased the concentrations of ammonia nitrogen, acetate, and butyrate significantly. The rumen bacterial community was significantly changed in the DAN group, with Bacterioidetes, Firmicutes, and Proteobacteria being the main ruminal bacterial phyla. The abundance of Ruminococcaceae_NK4A214_group, UCG_005, and Christensenellaceae_R_7_group were relatively higher, whereas that of Erysipelotrichaceae_UCG_002 and Dialister were lower in the DAN than those in the CON. Metabolomics analysis showed that the content of d-glucose, serotonin, ribulose-5-phosphate, and d-glycerate were higher in the DAN group. These metabolites were enriched in the starch and sucrose metabolism, pentose phosphate pathway, tryptophan metabolism, and glycerolipid metabolism. The ribulose-5-phosphate and d-glycerate were correlated with Ruminococcaceae_NK4A214_group, UCG_005, and Christensenellaceae_R-7_group positively. This study demonstrated that the supplementation of dandelion impacts the ruminal microorganisms and metabolites in a way that rumen fermentation was enhanced in lactating dairy cows.}, } @article {pmid33396397, year = {2020}, author = {Voidarou, C and Antoniadou, Μ and Rozos, G and Tzora, A and Skoufos, I and Varzakas, T and Lagiou, A and Bezirtzoglou, E}, title = {Fermentative Foods: Microbiology, Biochemistry, Potential Human Health Benefits and Public Health Issues.}, journal = {Foods (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, doi = {10.3390/foods10010069}, pmid = {33396397}, issn = {2304-8158}, abstract = {Fermented foods identify cultures and civilizations. History, climate and the particulars of local production of raw materials have urged humanity to exploit various pathways of fermentation to produce a wide variety of traditional edible products which represent adaptations to specific conditions. Nowadays, industrial-scale production has flooded the markets with ferments. According to recent estimates, the current size of the global market of fermented foods is in the vicinity of USD 30 billion, with increasing trends. Modern challenges include tailor-made fermented foods for people with special dietary needs, such as patients suffering from Crohn's disease or other ailments. Another major challenge concerns the safety of artisan fermented products, an issue that could be tackled with the aid of molecular biology and concerns not only the presence of pathogens but also the foodborne microbial resistance. The basis of all these is, of course, the microbiome, an aggregation of different species of bacteria and yeasts that thrives on the carbohydrates of the raw materials. In this review, the microbiology of fermented foods is discussed with a special reference to groups of products and to specific products indicative of the diversity that a fermentation process can take. Their impact is also discussed with emphasis on health and oral health status. From Hippocrates until modern approaches to disease therapy, diet was thought to be of the most important factors for health stability of the human natural microbiome. After all, to quote Pasteur, "Gentlemen, the microbes will have the last word for human health." In that sense, it is the microbiomes of fermented foods that will acquire a leading role in future nutrition and therapeutics.}, } @article {pmid33396382, year = {2020}, author = {Battistini, C and Ballan, R and Herkenhoff, ME and Saad, SMI and Sun, J}, title = {Vitamin D Modulates Intestinal Microbiota in Inflammatory Bowel Diseases.}, journal = {International journal of molecular sciences}, volume = {22}, number = {1}, pages = {}, pmid = {33396382}, issn = {1422-0067}, support = {DK105118/NH/NIH HHS/United States ; R01DK114126/NH/NIH HHS/United States ; CDMRP BC191198//U.S. Department of Defense/ ; 2018/21584-4 and #2019/02583-0)//Funda&#x00E7;&#x00E3;o de Amparo &#x00E0; Pesquisa do Estado de S&#x00E3;o Paulo/ ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic inflammation of the gastrointestinal tract (GIT), including Crohn's disease (CD) and ulcerative colitis (UC), which differ in the location and lesion extensions. Both diseases are associated with microbiota dysbiosis, with a reduced population of butyrate-producing species, abnormal inflammatory response, and micronutrient deficiency (e.g., vitamin D hypovitaminosis). Vitamin D (VitD) is involved in immune cell differentiation, gut microbiota modulation, gene transcription, and barrier integrity. Vitamin D receptor (VDR) regulates the biological actions of the active VitD (1α,25-dihydroxyvitamin D3), and is involved in the genetic, environmental, immune, and microbial aspects of IBD. VitD deficiency is correlated with disease activity and its administration targeting a concentration of 30 ng/mL may have the potential to reduce disease activity. Moreover, VDR regulates functions of T cells and Paneth cells and modulates release of antimicrobial peptides in gut microbiota-host interactions. Meanwhile, beneficial microbial metabolites, e.g., butyrate, upregulate the VDR signaling. In this review, we summarize the clinical progress and mechanism studies on VitD/VDR related to gut microbiota modulation in IBD. We also discuss epigenetics in IBD and the probiotic regulation of VDR. Furthermore, we discuss the existing challenges and future directions. There is a lack of well-designed clinical trials exploring the appropriate dose and the influence of gender, age, ethnicity, genetics, microbiome, and metabolic disorders in IBD subtypes. To move forward, we need well-designed therapeutic studies to examine whether enhanced vitamin D will restore functions of VDR and microbiome in inhibiting chronic inflammation.}, } @article {pmid33395654, year = {2020}, author = {Kakabadze, E and Grdzelishvili, N and Sanikidze, L and Makalatia, K and Chanishvili, N}, title = {REVIVAL OF MICROBIAL THERAPEUTICS, WITH EMPHASIS ON PROBIOTIC LACTOBACILLUS (REVIEW).}, journal = {Georgian medical news}, volume = {}, number = {308}, pages = {129-134}, pmid = {33395654}, issn = {1512-0112}, mesh = {Dysbiosis/therapy ; Humans ; Lactobacillus ; *Microbiota ; *Probiotics/therapeutic use ; }, abstract = {The idea to use living microorganisms for disease prevention and treatment was introduced a century ago, but yet the full potential and benefits of microbial therapeutics has not been entirely understood. In the light of developments of human microbiome studies, probiotics are gaining new momentum, where health benefit conferring by Lactobacillus are emerging as one of the novel approaches in the treatment and prophylactics of dysbiosis. The present review focuses on the origin and development of the probiotic's concept, mechanisms of action and anticipated use of probiotic Lactobacillus as well as of microbial therapeutics. The required regulatory frameworks associated with probiotic use and marketing are discussed.}, } @article {pmid33395479, year = {2021}, author = {Habiba, M and Heyn, R and Bianchi, P and Brosens, I and Benagiano, G}, title = {The development of the human uterus: morphogenesis to menarche.}, journal = {Human reproduction update}, volume = {27}, number = {1}, pages = {1-26}, doi = {10.1093/humupd/dmaa036}, pmid = {33395479}, issn = {1460-2369}, abstract = {There is emerging evidence that early uterine development in humans is an important determinant of conditions such as ontogenetic progesterone resistance, menstrual preconditioning, defective deep placentation and pre-eclampsia in young adolescents. A key observation is the relative infrequency of neonatal uterine bleeding and hormone withdrawal at birth. The origin of the uterus from the fusion of the two paramesonephric, or Müllerian, ducts was described almost 200 years ago. The uterus forms around the 10th week of foetal life. The uterine corpus and the cervix react differently to the circulating steroid hormones during pregnancy. Adult uterine proportions are not attained until after puberty. It is unclear if the endometrial microbiome and immune response-which are areas of growing interest in the adult-play a role in the early stages of uterine development. The aim is to review the phases of uterine development up until the onset of puberty in order to trace the origin of abnormal development and to assess current knowledge for features that may be linked to conditions encountered later in life. The narrative review incorporates literature searches of Medline, PubMed and Scopus using the broad terms individually and then in combination: uterus, development, anatomy, microscopy, embryology, foetus, (pre)-puberty, menarche, microbiome and immune cells. Identified articles were assessed manually for relevance, any linked articles and historical textbooks. We included some animal studies of molecular mechanisms. There are competing theories about the contributions of the Müllerian and Wolffian ducts to the developing uterus. Endometrium features are suggestive of an oestrogen effect at 16-20 weeks gestation. The discrepancy in the reported expression of oestrogen receptor is likely to be related to the higher sensitivity of more recent techniques. Primitive endometrial glands appear around 20 weeks. Features of progestogen action are expressed late in the third trimester. Interestingly, progesterone receptor expression is higher at mid-gestation than at birth when features of endometrial maturation are rare. Neonatal uterine bleeding occurs in around 5% of neonates. Myometrial differentiation progresses from the mesenchyme surrounding the endometrium at the level of the cervix. During infancy, the uterus and endometrium remain inactive. The beginning of uterine growth precedes the onset of puberty and continues for several years after menarche. Uterine anomalies may result from fusion defects or atresia of one or both Müllerian ducts. Organogenetic differentiation of Müllerian epithelium to form the endometrial and endocervical epithelium may be independent of circulating steroids. A number of genes have been identified that are involved in endometrial and myometrial differentiation although gene mutations have not been demonstrated to be common in cases of uterine malformation. The role, if any, of the microbiome in relation to uterine development remains speculative. Modern molecular techniques applied to rodent models have enhanced our understanding of uterine molecular mechanisms and their interactions. However, little is known about functional correlates or features with relevance to adult onset of uterine disease in humans. Prepubertal growth and development lends itself to non-invasive diagnostics such as ultrasound and MRI. Increased awareness of the occurrence of neonatal uterine bleeding and of the potential impact on adult onset disease may stimulate renewed research in this area.}, } @article {pmid33395434, year = {2021}, author = {Carter, JK and Bhattacharya, D and Borgerding, JN and Fiel, MI and Faith, JJ and Friedman, SL}, title = {Modeling dysbiosis of human NASH in mice: Loss of gut microbiome diversity and overgrowth of Erysipelotrichales.}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0244763}, pmid = {33395434}, issn = {1932-6203}, support = {R01 DK056621/DK/NIDDK NIH HHS/United States ; T32 GM062754/GM/NIGMS NIH HHS/United States ; R01 DK112978/DK/NIDDK NIH HHS/United States ; R01 DK124133/DK/NIDDK NIH HHS/United States ; P30 CA196521/CA/NCI NIH HHS/United States ; T32 GM007280/GM/NIGMS NIH HHS/United States ; R56 DK056621/DK/NIDDK NIH HHS/United States ; }, abstract = {BACKGROUND & AIM: Non-alcoholic steatohepatitis (NASH) is a severe form of non-alcoholic fatty liver disease (NAFLD) that is responsible for a growing fraction of cirrhosis and liver cancer cases worldwide. Changes in the gut microbiome have been implicated in NASH pathogenesis, but the lack of suitable murine models has been a barrier to progress. We have therefore characterized the microbiome in a well-validated murine NASH model to establish its value in modeling human disease.

METHODS: The composition of intestinal microbiota was monitored in mice on a 12- or 24-week NASH protocol consisting of high fat, high sugar Western Diet (WD) plus once weekly i.p injection of low-dose CCl4. Additional mice were subjected to WD-only or CCl4-only conditions to assess the independent effect of these variables on the microbiome.

RESULTS: There was substantial remodeling of the intestinal microbiome in NASH mice, characterized by declines in both species diversity and bacterial abundance. Based on changes to beta diversity, microbiota from NASH mice clustered separately from controls in principal coordinate analyses. A comparison between WD-only and CCl4-only controls with the NASH model identified WD as the primary driver of early changes to the microbiome, resulting in loss of diversity within the 1st week. A NASH signature emerged progressively at weeks 6 and 12, including, most notably, a reproducible bloom of the Firmicute order Erysipelotrichales.

CONCLUSIONS: We have established a valuable model to study the role of gut microbes in NASH, enabling us to identify a new NASH gut microbiome signature.}, } @article {pmid33394885, year = {2020}, author = {Ho, T and Sarkar, A and Szalacha, L and Groer, MW}, title = {Intestinal Microbiome in Preterm Infants Influenced by Enteral Iron Dosing.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {Publish Ahead of Print}, number = {}, pages = {}, doi = {10.1097/MPG.0000000000003033}, pmid = {33394885}, issn = {1536-4801}, abstract = {OBJECTIVES: To compare the intestinal microbiome in very low birth weight (VLBW) infants who received different enteral iron supplementation (EIS) doses.

STUDY DESIGN: Longitudinal stool collection in 80 VLBW infants were conducted up to 2 months postnatally in a prospective study. The 16S rRNA regions V4 was used to calculate microbiome compositions and the Piphillin software was use for bacterial functional prediction. Linear mixed effect models and Wilcoxon rank-sum tests were performed to examine the relationships between initial EIS dosage and stool microbiome and bacterial functional potential.

RESULTS: There were 105 samples collected before and 237 collected after EIS started from infants with birth gestational age and weight of 28.1 ± 2.4 weeks and 1103 ± 210 grams, respectively. The average postnatal age at start of EIS was 17.9 ± 6.9 days and the average initial EIS dose was 4.8 ± 1.1 mg/kg/day. Infants who were started on ≥6 mg/kg/day had higher abundances of Proteus and Bifidobacterium and a lower alpha diversity than those started on lower doses (p < 0.05). Infants given higher EIS doses had higher bacterial predicted functional potentials for ferroptosis and epithelial invasion after 2 weeks post EIS.

CONCLUSIONS: Higher EIS dosage is linked to higher abundances of Proteus and Bifidobacterium, and a less diverse microbiome and higher predicted potential of bacterial epithelial invasion. These observational findings should be further studied in a randomized study to elucidate the optimal dosage of EIS in VLBW infants.

An infographic is available for this article at:http://links.lww.com/MPG/C149.}, } @article {pmid33394582, year = {2020}, author = {Khalaf, RT and Furuta, GT and Wagner, BD and Robertson, CE and Andrews, R and Stevens, MJ and Fillon, SA and Zemanick, ET and Harris, JK}, title = {Influence of Acid Blockade on the Aerodigestive Tract Microbiome in Children With Cystic Fibrosis.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1097/MPG.0000000000003010}, pmid = {33394582}, issn = {1536-4801}, abstract = {BACKGROUND: Acid blockade is commonly prescribed in patients with cystic fibrosis (CF). Growing concerns, however, exist about its possible role in the pathophysiology of pulmonary infections. We aimed to investigate if acid blockade alters esophageal and respiratory microbiota leading to dysbiosis and inflammation.

METHODS: We performed a cross sectional study of children with CF who were either prescribed acid blockade or not. Samples from the gastrointestinal and respiratory tracts were obtained and microbiome analyzed. Mixed effect models were used to compare outcomes between cohorts and across sampling sites. A random subject intercept was included to account for the multiple sampling sites per individual.

RESULTS: A cohort of 25 individuals, 44% girls with median age of 13.8 years [IQR 11.2--14.8] were enrolled. Alpha diversity, total bacterial load, and beta diversity were similar across anatomic compartments, across the upper gastrointestinal tract, and in respiratory samples. Similar alpha diversity, total bacterial load, and beta diversity results were also observed when comparing individuals on versus those off acid blockade. IL-8 was elevated in the distal versus proximal esophagus in the whole cohort (P < 0.01). IL-8 concentrations were similar in the distal esophagus in patients on and off acid blockade, but significantly greater in the proximal esophagus of subjects on treatment (P < 0.01).

CONCLUSIONS: On the basis of these data, acid blockade use does not appear to influence the microbiome of the aerodigestive tract in children with cystic fibrosis suggesting a complex interplay between these medications and the bacterial composition of the esophagus and lung.}, } @article {pmid33394421, year = {2021}, author = {Maurya, AP and Rajkumari, J and Pandey, P}, title = {Enrichment of antibiotic resistance genes (ARGs) in polyaromatic hydrocarbon-contaminated soils: a major challenge for environmental health.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {33394421}, issn = {1614-7499}, abstract = {Polyaromatic hydrocarbons (PAHs) are widely spread ecological contaminants. Antibiotic resistance genes (ARGs) are present with mobile genetic elements (MGE) in the bacteria. There are molecular evidences that PAHs may induce the development of ARGs in contaminated soils. Also, the abundance of ARGs related to tetracycline, sulfonamides, aminoglycosides, ampicillin, and fluoroquinolones is high in PAH-contaminated environments. Genes encoding the efflux pump are located in the MGE and, along with class 1 integrons, have a significant role as a connecting link between PAH contamination and enrichment of ARGs. The horizontal gene transfer mechanisms further make this interaction more dynamic. Therefore, necessary steps to control ARGs into the environment and risk management plan of PAHs should be enforced. In this review, influence of PAH on evolution of ARGs in the contaminated soil, and its spread in the environment, has been described. The co-occurrence of antibiotic resistance and PAH degradation abilities in bacterial isolates has raised the concerns. Also, presence of ARGs in the microbiome of PAH-contaminated soil has been discussed as environmental hotspots for ARG spread. In addition to this, the possible links of molecular interactions between ARGs and PAHs, and their effect on environmental health has been explored.}, } @article {pmid33394400, year = {2021}, author = {Zhou, W and Dong, J and Ding, D and Long, L and Suo, A and Lin, X and Yang, Q and Lin, L and Zhang, Y and Ling, J}, title = {Rhizosphere microbiome dynamics in tropical seagrass under short-term inorganic nitrogen fertilization.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {33394400}, issn = {1614-7499}, support = {XDA13020300//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 41676163, 41406191, 41676107 and 41976147//National Natural Science Foundation of China/ ; 201806010017//Pearl River S&T Nova Program of Guangzhou/ ; GML2019ZD0402//Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 2018YFC1406505, 2017YFC0506301 and 2018FY100105//National Key Research and Development Program of China/ ; ISEE2018ZD02//Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences/ ; 2015A020216016//the Guangdong Province Public Welfare Research and Capacity Building Project/ ; 2017B030314052//the Science and Technology Planning Project of Guangdong Province, China/ ; }, abstract = {Rhizosphere microbes are crucial to seagrass meadows because they promote plant growth and heath. However, information concerning the response of rhizosphere microorganisms in seagrass sediment in the presence of different nitrogen sources is lacking. Here, by means of high-throughput sequencing, we investigated how addition of inorganic nitrogen affects the rhizosphere microbiome of the tropical seagrass Thalassia hemperichii. A seagrass culture system was set up to conduct a nitrogen addition (ammonium and nitrate) simulation experiment. We found that the relative abundance of Proteobacteria and Bacteroidetes was increased in inorganic nitrogen-enriched samples, whereas that of Acidobacteria decreased under ammonium enrichment, especially after 35 days. High levels of inorganic nitrogen addition caused a significant decrease in the relative abundance of Desulfobacteraceae, Sulfurovaceae, and Spirochaetes, which are primarily involved in sulfur cycling. Additionally, the abundance of microbes in the seagrass rhizosphere reached the highest after the ammonium-enrichment treatment. Among the analyzed seagrass photosynthetic characteristics, seagrass leaves presented the highest light utility in treatments receiving nitrate, followed by the control groups and ammonium-enrichment groups. Moreover, 16S rRNA gene-predicted functional analysis suggested that some functions related to metabolism of amino acids and signal transduction were enriched in samples receiving high ammonium, whereas nitrate addition enriched predicted functions related to diseases. These findings provide new insights into the response of microbial communities to different types of nitrogen additions in seagrass ecosystems.}, } @article {pmid33394167, year = {2021}, author = {Perler, BK and Reinhart, EM and Montgomery, M and Maynard, M and Shapiro, JM and Belenky, P and Chan, PA}, title = {Evaluation of the Microbiome in Men Taking Pre-exposure Prophylaxis for HIV Prevention.}, journal = {AIDS and behavior}, volume = {}, number = {}, pages = {}, pmid = {33394167}, issn = {1573-3254}, support = {W81XWH-18-1-0198//U.S. Department of Defense/ ; R21AT010366/AT/NCCIH NIH HHS/United States ; P20GM121344//Brown University/ ; }, abstract = {Tenofovir-based regimens as pre-exposure prophylaxis (PrEP) are highly effective at preventing HIV infection. The most common side-effect is gastrointestinal (GI) distress which may be associated with changes in the microbiome. Dysbiosis of the microbiome can have numerous health-related consequences. To understand the effect of PrEP on dysbiosis, we evaluated 27 individuals; 14 were taking PrEP for an average of 171 weeks. Sequencing of 16S rRNA was performed using self-collected rectal swabs. Mixed beta diversity testing demonstrated significant differences between PrEP and non-PrEP users with Bray-Curtis and unweighted UniFrac analyses (p = 0.05 and 0.049, respectively). At the genus level, there was a significant reduction in Finegoldia, along with a significant increase in Catenibacterium and Prevotella in PrEP users. Prevotella has been associated with inflammatory pathways, insulin resistance and cardiovascular disease, while Catenibacterium has been associated with morbid obesity and metabolic syndrome. Overall, these results suggest that PrEP may be associated with some degree of microbiome dysbiosis, which may contribute to GI symptoms. Long-term impact of these changes is unknown.}, } @article {pmid33394136, year = {2021}, author = {Wenzel, UO and Ehmke, H and Bode, M}, title = {Immune mechanisms in arterial hypertension. Recent advances.}, journal = {Cell and tissue research}, volume = {}, number = {}, pages = {}, pmid = {33394136}, issn = {1432-0878}, abstract = {Increasing evidence indicates that hypertension and hypertensive end-organ damage are not only mediated by hemodynamic injury. Inflammation also plays an important role in the pathophysiology and contributes to the deleterious consequences of this disease. Cells of the innate immune system including monocyte/macrophages and dendritic cells can promote blood pressure elevation via effects mostly on kidney and vascular function. Moreover, convincing evidence shows that T and B cells from the adaptive immune system are involved in hypertension and hypertensive end-organ damage. Skin monocyte/macrophages, regulatory T cells, natural killer T cells, and myeloid-derived suppressor cells have been shown to exert blood pressure controlling effects. Sodium intake is undoubtedly indispensable for normal body function but can be detrimental when taken in excess of dietary requirements. Sodium levels also modulate the function of monocyte/macrophages, dendritic cells, and different T cell subsets. Some of these effects are mediated by changes in the microbiome and metabolome that can be found after high salt intake. Modulation of the immune response can reduce severity of blood pressure elevation and hypertensive end-organ damage in several animal models. The purpose of this review is to briefly summarize recent advances in immunity and hypertension as well as hypertensive end-organ damage.}, } @article {pmid33393445, year = {2021}, author = {Sakai, Y and Hamano, H and Ochi, H and Abe, F and Masuda, K and Iino, H}, title = {Lactulose ingestion causes an increase in the abundance of gut-resident bifidobacteria in Japanese women: a randomised, double-blind, placebo-controlled crossover trial.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-12}, doi = {10.3920/BM2020.0100}, pmid = {33393445}, issn = {1876-2891}, abstract = {The genus Bifidobacterium comprises various bacterial species, and the complement of species within the human intestinal tract differs from individual to individual. The balance of these bifidobacterial species remains poorly understood, although it is known that the abundance of bifidobacteria increases following the ingestion of prebiotics. We previously conducted a randomised, placebo-controlled, double-blind, crossover study of 2 g/day lactulose ingestion for 2 weeks in 60 Japanese women. To study the effect of lactulose ingestion on each bifidobacterial species, here, we measured the abundance of each of the principal bifidobacterial species. After lactulose ingestion, the log cell counts of the Bifidobacterium adolescentis group (8.97±0.08 vs 9.39±0.08, P=0.0019), Bifidobacterium catenulatum group (9.45±0.10 vs 9.65±0.10, P=0.0032) and Bifidobacterium longum group (9.01±0.07 vs 9.29±0.07, P=0.0012) were significantly higher than in the placebo ingestion control group. However, the log cell counts were similar for Bifidobacterium breve (8.12±0.12 vs 8.33±0.12, P=0.20), Bifidobacterium bifidum (9.08±0.12 vs 9.42±0.14, P=0.095) and Bifidobacterium animalis subspecies lactis (8.65±0.53 vs 8.46±0.46, P=0.77). Cluster analysis of the log cell count data at the bifidobacterial species level revealed three distinct clusters, but the combinations and ratios of the constituent bifidobacteria were not affected by lactulose ingestion. Furthermore, principal coordinate analysis of the intestinal microbiota in the lactulose and placebo ingestion groups using Illumina MiSeq showed no significant differences in the intestinal microbiota as a whole. These results suggest that 2 g/day lactulose ingestion for 2 weeks significantly increases the abundance of intestinal bifidobacteria, but does not affect the intestinal microbiota as a whole.}, } @article {pmid33393360, year = {2021}, author = {Fajardo Rebollar, E and Estrada, K and Grande, R and Ek Ramos, MJ and Ruiz Vargas, G and Villegas-Torres, OG and Juárez, A and Sánchez-Flores, A and Camino, CD}, title = {Bacterial and fungal microbiome profiling in chilhuacle negro chili (Capsicum annuum L.) associated with fruit rot disease.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-09-20-2098-RE}, pmid = {33393360}, issn = {0191-2917}, abstract = {Chilhuacle negro chili (Capsicum annuum L.) is an ancient Mexican landrace that is deeply linked to the culinary heritage of the country. Due to the high profitability and uniqueness of this crop, the "Universidad Autónoma del Estado de Morelos", is one of the Mexican institutions exploring its production in controlled environments. In the summer of 2018, the production of chilhuacle negro plants was seriously affected by an unidentified pathogen causing fruit rot, which reduced its quality, yield and market value. Therefore, the main objective of this work was to study and characterize the fruit microbiota, which could help reveal the causal agent of this disease. Using DNA metabarcoding coupled with Illumina and nanopore sequencing technologies, both healthy and infected chili fruit, along with greenhouse bioaerosols, were collected and analyzed. We also explored the bacterial and fungal microbiota using microbiological techniques to isolate some of the culturable bacterial and fungal species. Our results suggest that the seedborne fungus Alternaria alternata is activated during the maturation stage of chilhuacle negro fruit, triggering a microbiome imbalance which may in turn enable the establishment of other opportunistic pathogenic fungi during fruit decay, such as Mucor sp. To our knowledge, this is the first study of the chilhuacle negro chili microbiome, which can shed some light on our understanding of one of the main diseases that affect this valuable crop.}, } @article {pmid33393203, year = {2021}, author = {Adamczyk, M and Rüthi, J and Frey, B}, title = {Root exudates increase soil respiration and alter microbial community structure in alpine permafrost and active layer soils.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15383}, pmid = {33393203}, issn = {1462-2920}, support = {SNSF 31BD30_172464/CLIMARCTIC-CH//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; //Swiss Polar Institute and Dr. Frederik Paulsen/ ; }, abstract = {Due to climate warming, alpine ecosystems are changing rapidly. Ongoing upward migrations of plants and thus an increase of easily decomposable substrates will strongly affect the soil microbiome. To understand how belowground communities will respond to such changes, we set up an incubation experiment with permafrost and active soil layers from northern (NW) and southern (SE) slopes of a mountain ridge on Muot da Barba Peider in the Swiss Alps and incubated them with or without artificial root exudates (AREs) at two temperatures, 4°C or 15°C. The addition of AREs resulted in elevated respiration across all soil types. Bacterial and fungal alpha diversity decreased significantly, coinciding with strong shifts in microbial community structure in ARE-treated soils. These shifts in bacterial community structure were driven by an increased abundance of fast-growing copiotrophic taxa. Fungal communities were predominantly affected by AREs in SE active layer soils and shifted towards fast-growing opportunistic yeast. In contrast, in the colder NW facing active layer and permafrost soils fungal communities were more influenced by temperature changes. These findings demonstrate the sensitivity of soil microbial communities in high alpine ecosystems to climate change and how shifts in these communities may lead to functional changes impacting biogeochemical processes.}, } @article {pmid33392741, year = {2021}, author = {Taulé, C and Vaz-Jauri, P and Battistoni, F}, title = {Insights into the early stages of plant-endophytic bacteria interaction.}, journal = {World journal of microbiology & biotechnology}, volume = {37}, number = {1}, pages = {13}, pmid = {33392741}, issn = {1573-0972}, abstract = {The plant holobiont is a complex entity composed of the plant and the organisms that live in and on it including its microbiota. The plant microbiota includes, among other microorganisms, bacterial endophytes, which are bacteria that can invade living plant tissues without causing symptoms of disease. The interaction between the endophytic bacterial microbiota and their plant host has profound influences on their fitness and depends on biotic and abiotic factors. For these interactions to be established, the bacteria have to be present at the right time, in the right place either colonizing the soil or the seed. In this review we summarize the current knowledge regarding the sources of the bacterial endophytic microbiome and the processes involved in the assemblage of the resulting community during the initial stages of plant development. The adaptations that allow the spatial approximation of soil- and seed-borne bacteria towards infection and colonization of the internal tissues of plants will be addressed in this review.}, } @article {pmid33392671, year = {2021}, author = {Yan, D and Liu, Y and Che, X and Mi, S and Jiao, Y and Guo, L and Li, S}, title = {Changes in the Microbiome of the Inner Surface of Clear Aligners After Different Usage Periods.}, journal = {Current microbiology}, volume = {}, number = {}, pages = {}, pmid = {33392671}, issn = {1432-0991}, support = {81570998//National Natural Science Foundation of China/ ; 81600891//National Natural Science Foundation of China/ ; 81974149//National Natural Science Foundation of China/ ; 81991504//National Natural Science Foundation of China/ ; QML20181501//Beijing Hospitals Authority Youth Programme/ ; Z161100000516203//Beijing Municipal Science & Technology Commission/ ; 2016-2-2141//The Capital Health Research and Development of Special/ ; 2017A17//Beijing Baiqianwan Talents Project/ ; DFL20181501//Beijing Municipal Administration of Hospitals' Ascent Plan/ ; }, abstract = {Clear aligners are removable orthodontic appliances that cover the tooth surface. The microbial composition and pH of the inner surface of aligners directly affect the enamel health. In this study, eight subjects who used the same type of clear aligners were instructed to brush their teeth normally and to not clean their aligners until sampling. Saliva and the contents of the inner surface of the aligners (liquid and plaque) were collected at 0 h (T0), 4 h (T4), 8 h (T8), 12 h (T12), and 24 h (T24) after usage, and pH values and microbial compositions were measured. The microbial composition was analyzed with 16S rRNA gene sequencing, and changes were assessed based on operational taxonomic unit abundance. The pH, alpha diversity values, and abundance of specific microbes on the inner surface of the aligners gradually decreased from T0 to T24 (P < 0.05). An insignificant increase in microbial community beta diversity was observed from T0 to T24. Principal component analysis revealed that the microbial composition at T0 was different from at T12 and T24. The relative abundances of phylum Firmicutes (P < 0.01), orders Lactobacillales and Bacteroidales (P < 0.05), and genus Streptococcus and species Streptococcus infantis increased significantly, while those of genera Actinomyces and Rothia and species Rothia aeria decreased significantly at T24 (P < 0.05). These findings reveal that uncleaned aligners might lead to enamel damage, especially after continuous usage for 12 h. Thus, clear aligners should be cleaned after 12 h of usage or at least within 24 h of usage.}, } @article {pmid33392303, year = {2020}, author = {Huang, QY and Yao, F and Zhou, CR and Huang, XY and Wang, Q and Long, H and Wu, QM}, title = {Role of gut microbiome in regulating the effectiveness of metformin in reducing colorectal cancer in type 2 diabetes.}, journal = {World journal of clinical cases}, volume = {8}, number = {24}, pages = {6213-6228}, pmid = {33392303}, issn = {2307-8960}, abstract = {The prevalence of colorectal cancer (CRC) and type 2 diabetes mellitus (T2DM) is increasing globally. It is rarely noticed that the incidence of CRC is higher in patients with T2DM. What needs to be mentioned is that metformin, a commonly used clinical drug for T2DM, attracts scholars' attention because of its benefits in lowering the risk of developing CRC. Hence, we try to find the common grounds of initiation of T2DM and CRC and the reason why metformin reduces the risk of CRC in patients with T2DM. We noticed consistent changes of gut microbiota, such as elevated Bacteroides, Prevotella and Bifidobacterium and depressed Firmicutes and Lactobacillus. Furthermore, many studies in recent years have proved that the efficacy of metformin, such as improving blood glucose, depends on the gut microbiota. Coincidentally, the progression of CRC is inseparable from the contributions of gut microbiota. Therefore, we first proposed the concept of the metformin-gut microbiota-CRC (in T2DM) axis to explain the effect of metformin in reducing CRC in patients with T2DM. In this review, we elaborated the new concept and its potential clinical application value.}, } @article {pmid33392266, year = {2020}, author = {Song, K and Wright, FA and Zhou, YH}, title = {Systematic Comparisons for Composition Profiles, Taxonomic Levels, and Machine Learning Methods for Microbiome-Based Disease Prediction.}, journal = {Frontiers in molecular biosciences}, volume = {7}, number = {}, pages = {610845}, pmid = {33392266}, issn = {2296-889X}, abstract = {Microbiome composition profiles generated from 16S rRNA sequencing have been extensively studied for their usefulness in phenotype trait prediction, including for complex diseases such as diabetes and obesity. These microbiome compositions have typically been quantified in the form of Operational Taxonomic Unit (OTU) count matrices. However, alternate approaches such as Amplicon Sequence Variants (ASV) have been used, as well as the direct use of k-mer sequence counts. The overall effect of these different types of predictors when used in concert with various machine learning methods has been difficult to assess, due to varied combinations described in the literature. Here we provide an in-depth investigation of more than 1,000 combinations of these three clustering/counting methods, in combination with varied choices for normalization and filtering, grouping at various taxonomic levels, and the use of more than ten commonly used machine learning methods for phenotype prediction. The use of short k-mers, which have computational advantages and conceptual simplicity, is shown to be effective as a source for microbiome-based prediction. Among machine-learning approaches, tree-based methods show consistent, though modest, advantages in prediction accuracy. We describe the various advantages and disadvantages of combinations in analysis approaches, and provide general observations to serve as a useful guide for future trait-prediction explorations using microbiome data.}, } @article {pmid33392192, year = {2020}, author = {Chen, S and Wu, X and Wang, X and Shao, Y and Tu, Q and Yang, H and Yin, J and Yin, Y}, title = {Responses of Intestinal Microbiota and Immunity to Increasing Dietary Levels of Iron Using a Piglet Model.}, journal = {Frontiers in cell and developmental biology}, volume = {8}, number = {}, pages = {603392}, pmid = {33392192}, issn = {2296-634X}, abstract = {Iron is an essential metal for both animals and microbiota. In general, neonates and infants of humans and animals are at the risk of iron insufficiency. However, excess dietary iron usually causes negative impacts on the host and microbiota. This study aimed to investigate overloaded dietary iron supplementation on growth performance, the distribution pattern of iron in the gut lumen and the host, intestinal microbiota, and intestine transcript profile of piglets. Sixty healthy weaning piglets were randomly assigned to six groups: fed on diets supplemented with ferrous sulfate monohydrate at the dose of 50 ppm (Fe50 group), 100 ppm (Fe100 group), 200 ppm (Fe200 group), 500 ppm (Fe500 group), and 800 ppm (Fe800), separately, for 3 weeks. The results indicated that increasing iron had no significant effects on growth performance, but increased diarrheal risk and iron deposition in intestinal digesta, tissues of intestine and liver, and serum. High iron also reduced serum iron-binding capacity, apolipoprotein, and immunoglobin A. The RNA-sequencing analysis revealed that iron changed colonic transcript profile, such as interferon gamma-signal transducer and activator of transcription two-based anti-infection gene network. Increasing iron also shifted colonic and cecal microbiota, such as reducing alpha diversity and the relative abundance of Clostridiales and Lactobacillus reuteri and increasing the relative abundance of Lactobacillus and Lactobacillus amylovorus. Collectively, this study demonstrated that high dietary iron increased diarrheal incidence, changed intestinal immune response-associated gene expression, and shifted gut microbiota. The results would enhance our knowledge of iron effects on the gut and microbiome in piglets and further contribute to understanding these aspects in humans.}, } @article {pmid33391862, year = {2020}, author = {Huang, G and Zhang, Y and Xu, Q and Zheng, N and Zhao, S and Liu, K and Qu, X and Yu, J and Wang, J}, title = {DHA content in milk and biohydrogenation pathway in rumen: a review.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e10230}, pmid = {33391862}, issn = {2167-8359}, abstract = {Docosahexaenoic acid (DHA) is an essential human nutrient that may promote neural health and development. DHA occurs naturally in milk in concentrations that are influenced by many factors, including the dietary intake of the cow and the rumen microbiome. We reviewed the literature of milk DHA content and the biohydrogenation pathway in rumen of dairy cows aim to enhance the DHA content. DHA in milk is mainly derived from two sources: α-linolenic acid (ALA) occurring in the liver and consumed as part of the diet, and overall dietary intake. Rumen biohydrogenation, the lymphatic system, and blood circulation influence the movement of dietary intake of DHA into the milk supply. Rumen biohydrogenation reduces DHA in ruminal environmental and limits DHA incorporation into milk. The fat-1 gene may increase DHA uptake into the body but this lacks experimental confirmation. Additional studies are needed to define the mechanisms by which different dietary sources of DHA are associated with variations of DHA in milk, the pathway of DHA biohydrogenation in the rumen, and the function of the fat-1 gene on DHA supply in dairy cows.}, } @article {pmid33391689, year = {2020}, author = {Whitaker, BK and Christian, N and Chai, Q and Clay, K}, title = {Foliar fungal endophyte community structure is independent of phylogenetic relatedness in an Asteraceae common garden.}, journal = {Ecology and evolution}, volume = {10}, number = {24}, pages = {13895-13912}, pmid = {33391689}, issn = {2045-7758}, abstract = {Phylogenetic distance among host species represents a proxy for host traits that act as biotic filters to shape host-associated microbiome community structure. However, teasing apart potential biotic assembly mechanisms, such as host specificity or local species interactions, from abiotic factors, such as environmental specificity or dispersal barriers, in hyperdiverse, horizontally transmitted microbiomes remains a challenge. In this study, we tested whether host phylogenetic relatedness among 18 native Asteraceae plant species and spatial distance between replicated plots in a common garden affects foliar fungal endophyte (FFE) community structure. We found that FFE community structure varied significantly among host species, as well as host tribes, but not among host subfamilies. However, FFE community dissimilarity between host individuals was not significantly correlated with phylogenetic distance between host species. There was a significant effect of spatial distance among host individuals on FFE community dissimilarity within the common garden. The significant differences in FFE community structure among host species, but lack of a significant host phylogenetic effect, suggest functional differences among host species not accounted for by host phylogenetic distance, such as metabolic traits or phenology, may drive FFE community dissimilarity. Overall, our results indicate that host species identity and the spatial distance between plants can determine the similarity of their microbiomes, even across a single experimental field, but that host phylogeny is not closely tied to FFE community divergence in native Asteraceae.}, } @article {pmid33391669, year = {2020}, author = {Parker, ES and Moczek, AP}, title = {Don't stand so close to me: Microbiota-facilitated enemy release dynamics in introduced Onthophagus taurus dung beetles.}, journal = {Ecology and evolution}, volume = {10}, number = {24}, pages = {13640-13648}, pmid = {33391669}, issn = {2045-7758}, abstract = {Microbial symbionts can influence their hosts in stunningly diverse ways. Emerging research suggests that an underappreciated facet of these relationships is the influence microbes can have on their host's responses to novel, or stressful, environmental conditions. We sought to address these and related questions in populations resulting from the recent introduction and subsequent rapid range expansion of Onthophagus taurus dung beetles. Specifically, we manipulated both microbial communities and rearing temperature to detect signatures of developmental and life history differentiation in response to the local thermal conditions in two populations derived from the southern most (Florida) and northern most (Michigan) extremes of the exotic Eastern U.S. range of O. taurus. We then sought to determine the contributions, if any, of host-associated microbiota to this differentiation. We found that when reared under common garden conditions individuals from Florida and Michigan populations differed significantly in developmental performance measures and life history traits, consistent with population divergence. At the same time, and contrary to our predictions, we failed to find support for the hypothesis that animals perform better if reared at temperatures that match their location of origin and that performance differences may be mediated by host-associated microbiota. Instead, we found that microbiome swapping across host populations improved developmental performance in both populations, consistent with enemy release dynamics. We discuss the implications of our results for our understanding of the rapid spread of exotic O. taurus through the Eastern United States and the significance of symbiosis in host responses to novel environmental conditions more broadly.}, } @article {pmid33391629, year = {2020}, author = {Gopinath, D and Kunnath Menon, R and Chun Wie, C and Banerjee, M and Panda, S and Mandal, D and Behera, PK and Roychoudhury, S and Kheur, S and George Botelho, M and Johnson, NW}, title = {Salivary bacterial shifts in oral leukoplakia resemble the dysbiotic oral cancer bacteriome.}, journal = {Journal of oral microbiology}, volume = {13}, number = {1}, pages = {1857998}, pmid = {33391629}, issn = {2000-2297}, abstract = {Objective: While some oral carcinomas appear to arise de novo, others develop within long-standing conditions of the oral cavity that have malignant potential, now known as oral potentially malignant disorders (OPMDs). The oral bacteriome associated with OPMD has been studied to a lesser extent than that associated with oral cancer. To characterize the association in detail we compared the bacteriome in whole mouth fluid (WMF) in patients with oral leukoplakia, oral cancer and healthy controls. Methods: WMF bacteriome from 20 leukoplakia patients, 31 patients with oral cancer and 23 healthy controls were profiled using the Illumina MiSeq platform. Sequencing reads were processed using DADA2, and taxonomical classification was performed using the phylogenetic placement method. Sparse Partial Least Squares Regression Discriminant Analysis model was used to identify bacterial taxa that best discriminate the studied groups. Results: We found considerable overlap between the WMF bacteriome of leukoplakia and oral cancer while a clearer separation between healthy controls and the former two disorders was observed. Specifically, the separation was attributed to 14 taxa belonging to the genera Megaspheara, unclassified enterobacteria, Prevotella, Porphyromonas, Rothia and Salmonella, Streptococcus, and Fusobacterium. The most discriminative bacterial genera between leukoplakia and oral cancer were Megasphaera, unclassified Enterobacteriae, Salmonella and Prevotella.Conclusion: Oral bacteria may play a role in the early stages of oral carcinogenesis as a dysbiotic bacteriome is associated with oral leukoplakia and this resembles that of oral cancer more than healthy controls. Our findings may have implications for developing oral cancer prevention strategies targeting early microbial drivers of oral carcinogenesis.}, } @article {pmid33391351, year = {2020}, author = {Sterzenbach, T and Pioch, A and Dannemann, M and Hannig, C and Weber, MT}, title = {Quantification of Bacterial Colonization in Dental Hard Tissues Using Optimized Molecular Biological Methods.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {599137}, pmid = {33391351}, issn = {1664-8021}, abstract = {Bacterial infections of root canals and the surrounding dental hard tissue are still a challenge due to biofilm formation as well as the complex root canal anatomy. However, current methods for analyzing biofilm formation, bacterial colonization of root canals and dental hard tissue [e.g., scanning electron microscopy, confocal laser scanning microscopy (CLSM) or determination of colony forming units (CFU)] are time-consuming and only offer a selective qualitative or semi-quantitative analysis. The aim of the present study is the establishment of optimized molecular biological methods for DNA-isolation and quantification of bacterial colonization via quantitative PCR (qPCR) from dental hard tissue. Root canals of human premolars were colonized with Enterococcus faecalis. For isolation of DNA, teeth were then grinded with a cryo mill. Since the hard tissues dentin and especially enamel belong to the hardest materials in the human organism, the isolation of bacterial DNA from root dentin is very challenging. Therefore, treatment steps for the isolation of DNA from grinded teeth were systematically analyzed to allow improved recovery of bacterial DNA from dental hard tissues. Starting with the disintegration of the peptidoglycan-layer of bacterial cells, different lysozyme solutions were tested for efficacy. Furthermore, incubation times and concentrations of chelating agents such as EDTA were optimized. These solutions are crucial for the disintegration of teeth and hence improve the accessibility of bacterial DNA. The final step was the determination of prior bacterial colonization of each root canal as determined by qPCR and comparing the results to alternative methods such as CFU. As a result of this study, optimized procedures for bacterial DNA-isolation from teeth were established, which result in an increased recovery rate of bacterial DNA. This method allows a non-selective and straightforward procedure to quantify bacterial colonization from dental hard tissue. It can be easily adapted for other study types such as microbiome studies and for comparable tissues like bones.}, } @article {pmid33391330, year = {2020}, author = {Sevanto, S and Grossiord, C and Klein, T and Reed, S}, title = {Editorial: Plant-Soil Interactions Under Changing Climate.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {621235}, pmid = {33391330}, issn = {1664-462X}, } @article {pmid33391292, year = {2020}, author = {Lavelle, EC and Carsetti, R and Pickl, WF and Wiedermann, U}, title = {Editorial: Challenges in Vaccinology.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {632537}, doi = {10.3389/fimmu.2020.632537}, pmid = {33391292}, issn = {1664-3224}, } @article {pmid33391206, year = {2020}, author = {Stiemsma, LT and Davis, SD and Brewster, JL}, title = {Analysis of Microbial Water Contamination, Soil Microbial Community Structure, and Soil Respiration in a Collaborative First-Year Students as Scholars Program (SAS).}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {590035}, pmid = {33391206}, issn = {1664-302X}, abstract = {The persistence of college students in STEM majors after their first-year of college is approximately 50%, with underrepresented populations displaying even higher rates of departure. For many undergraduates, their first-year in college is defined by large class sizes, poor access to research faculty, and minimal standing in communities of scholars. Pepperdine University and Whittier College, funded by a National Science Foundation award to Improve Undergraduate Stem Education (NSF IUSE), partnered in the development of first-year classes specifically geared to improve student persistence in STEM and academic success. This Students as Scholars Program (SAS) engaged first-year undergraduates in scholarly efforts during their first semester in college with a careful approach to original research design and mentoring by both faculty and upperclassmen experienced in research. Courses began by introducing hypothesis formulation and experimental design partnered with the scientific focus of each course (ecological, biochemical, microbiological). Students split into research teams, explored the primary literature, designed research projects, and executed experiments over a 6-7 week period, collecting, analyzing, and interpreting data. Microbiology-specific projects included partnerships with local park managers to assess water quality and microbial coliform contamination at specified locations in a coastal watershed. In addition, students explored the impact of soil salinity on microbial community structure. Analysis of these samples included next-generation sequencing and microbiome compositional analysis via collaboration with students from an upper division microbiology course. This cross-course collaboration facilitated additional student mentoring opportunities between upperclassmen and first-year students. This approach provided first-year students an introduction to the analysis of complex data sets using bioinformatics and statistically reliable gas-exchange replicates. Assessment of the impact of this program revealed students to view the research as challenging, but confidence building as they take their first steps as biology majors. In addition, the direct mentorship of first-year students by upperclassmen and faculty was viewed positively by students. Ongoing assessments have revealed SAS participants to display a 15% increased persistence rate in STEM fields when compared to non-SAS biology majors.}, } @article {pmid33391192, year = {2020}, author = {Klarenberg, IJ and Keuschnig, C and Warshan, D and Jónsdóttir, IS and Vilhelmsson, O}, title = {The Total and Active Bacterial Community of the Chlorolichen Cetraria islandica and Its Response to Long-Term Warming in Sub-Arctic Tundra.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {540404}, pmid = {33391192}, issn = {1664-302X}, abstract = {Lichens are traditionally defined as a symbiosis between a fungus and a green alga and or a cyanobacterium. This idea has been challenged by the discovery of bacterial communities inhabiting the lichen thalli. These bacteria are thought to contribute to the survival of lichens under extreme and changing environmental conditions. How these changing environmental conditions affect the lichen-associated bacterial community composition remains unclear. We describe the total (rDNA-based) and potentially metabolically active (rRNA-based) bacterial community of the lichen Cetaria islandica and its response to long-term warming using a 20-year warming experiment in an Icelandic sub-Arctic tundra. 16S rRNA and rDNA amplicon sequencing showed that the orders Acetobacterales (of the class Alphaproteobacteria) and Acidobacteriales (of the phylum Acidobacteria) dominated the bacterial community. Numerous amplicon sequence variants (ASVs) could only be detected in the potentially active community but not in the total community. Long-term warming led to increases in relative abundance of bacterial taxa on class, order and ASV level. Warming altered the relative abundance of ASVs of the most common bacterial genera, such as Granulicella and Endobacter. The potentially metabolically active bacterial community was also more responsive to warming than the total community. Our results suggest that the bacterial community of the lichen C. islandica is dominated by acidophilic taxa and harbors disproportionally active rare taxa. We also show for the first time that climate warming can lead to shifts in lichen-associated bacterial community composition.}, } @article {pmid33390939, year = {2020}, author = {Bao, T and He, F and Zhang, X and Zhu, L and Wang, Z and Lu, H and Wang, T and Li, Y and Yang, S and Wang, H}, title = {Inulin Exerts Beneficial Effects on Non-Alcoholic Fatty Liver Disease via Modulating gut Microbiome and Suppressing the Lipopolysaccharide-Toll-Like Receptor 4-Mψ-Nuclear Factor-κB-Nod-Like Receptor Protein 3 Pathway via gut-Liver Axis in Mice.}, journal = {Frontiers in pharmacology}, volume = {11}, number = {}, pages = {558525}, pmid = {33390939}, issn = {1663-9812}, abstract = {Background: Non-alcoholic fatty liver disease (NAFLD) is a common metabolic disease worldwide with chronic low-grade inflammation and alteration of gut microbiota. Inulin (INU) has been confirmed to exhibit benefit for metabolic diseases. The aim of this study was to clarify the effects and mechanism of INU on NAFLD inflammation via gut-liver axis. Methods: C57BL/6 mice were randomly divided into four groups: normal diet group (ND); high-fat diet group (HFD); ND with INU group (ND-INU); HFD with INU group (HFD-INU). After 14 weeks of feeding, mice were sacrificed and associated indications were investigated. Results: Significant increases of body weight, liver weight, liver biochemical aspartate aminotransferase, alanine aminotransferase, triglyceride, total cholesterol and pro-inflammatory indicators (Lipopolysaccharide, interleukin (IL)-18, IL-1β, TNF-α and IL-6), as well as a reduction of plasma IL-10 were observed in HFD group, while INU treatment restored these abnormal indicators. The ratio of hepatic macrophages (Mψs) and Toll-like receptor 4+ Mψs were both reduced with INU intervention. Nuclear factor-κB, nod-like receptor protein 3, apoptosis-associated speck-like protein and caspase-1 were decreased in HFD-INU group. Additionally, the results of 16S rRNA sequencing and analysis showed that INU administration modulated the composition of gut microbial community in NAFLD mice by up-regulating the abundances of Akkermansia and Bifidobacterium as well as down-regulating the abundances of Blautia and the ratio of Firmicutes/Bacteroidetes. Short-chain fatty acids including acetic acid, propionic acid and butyric acid, were increased with INU treatment. Correlation analysis revealed close relationships among inflammatory indicators, metabolic indicators as well as gut microbiota/its metabolite short-chain fatty acids. Conclusion: INU prevents NAFLD via modulating gut microbiota and suppressing Lipopolysaccharide-Toll-like receptor 4-Mψ-Nuclear factor-κB-nod-like receptor protein 3 inflammatory pathway via the gut-liver axis.}, } @article {pmid33390852, year = {2021}, author = {Bruellman, R and Llorente, C}, title = {A Perspective Of Intestinal Immune-Microbiome Interactions In Alcohol-Associated Liver Disease.}, journal = {International journal of biological sciences}, volume = {17}, number = {1}, pages = {307-327}, pmid = {33390852}, issn = {1449-2288}, support = {P30 DK120515/DK/NIDDK NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; }, abstract = {Uncovering the intricacies of the gut microbiome and how it interacts with the host immune system has opened up pathways in the search for the treatment of disease conditions. Alcohol-associated liver disease is a major cause of death worldwide. Research has shed light on the breakdown of the protective gut barriers, translocation of gut microbes to the liver and inflammatory immune response to microbes all contributing to alcohol-associated liver disease. This knowledge has opened up avenues for alternative therapies to alleviate alcohol-associated liver disease based on the interaction of the commensal gut microbiome as a key player in the regulation of the immune response. This review describes the relevance of the intestinal immune system, the gut microbiota, and specialized and non-specialized intestinal cells in the regulation of intestinal homeostasis. It also reflects how these components are altered during alcohol-associated liver disease and discusses new approaches for potential future therapies in alcohol-associated liver disease.}, } @article {pmid33390317, year = {2020}, author = {Pope, CE and Vo, AT and Hayden, HS and Weiss, EJ and Durfey, S and McNamara, S and Ratjen, A and Grogan, B and Carter, S and Nay, L and Parsek, MR and Singh, PK and McKone, EF and Aitken, ML and Rosenfeld, MR and Hoffman, LR}, title = {Changes in fecal microbiota with CFTR modulator therapy: A pilot study.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2020.12.002}, pmid = {33390317}, issn = {1873-5010}, support = {K24 HL141669/HL/NHLBI NIH HHS/United States ; }, abstract = {Studies have demonstrated that people with CF with pancreatic insufficiency (PI) have fecal dysbioses. Evidence suggests the causes of these dysbioses are multifactorial, and that important drivers include antibiotic exposure, dietary intake, and CF gastrointestinal tract dysfunction, including nutrient malabsorption. In this pilot study, we tested whether initiation of the CFTR modulator treatments ivacaftor (in a cohort of pancreatic sufficient (PS) people with CF and an R117H CFTR variant) or lumacaftor/ivacaftor (in a cohort of PI people with CF and an F508del variant) changed fecal measures of malabsorption or fecal microbiomes. While we identified no statistically significant fecal changes with either treatment, we detected trends in the PI cohort when initiating lumacaftor/ivacaftor towards decreased fecal fat content and towards fecal microbiomes that more closely resembled the fecal microbiota of people without PI. While these findings support a model in which nutrient malabsorption resulting from CF-induced PI drives fecal dysbiosis, they must be validated in future, larger studies of fecal microbiome and malabsorption outcomes with highly effective CFTR modulator therapies.}, } @article {pmid33389908, year = {2020}, author = {Wang, J and Yang, Z and Li, W}, title = {Deciphering the Role of Human Gastrointestinal Microbiota in the Pathogenesis of Vaginal Infection and Cervical Cancer.}, journal = {Journal of environmental pathology, toxicology and oncology : official organ of the International Society for Environmental Toxicology and Cancer}, volume = {39}, number = {4}, pages = {365-373}, doi = {10.1615/JEnvironPatholToxicolOncol.2020035637}, pmid = {33389908}, issn = {2162-6537}, abstract = {The human microbiota typically contains symbionts and supports the host, although it can be commensal or reciprocal and pathogenic in its host function, immunity, and diet. Modern studies indicate that perturbations in the microbiome may be present in quite a few diseases, including inflammation and cancer. To be more specific, changes in the microbiomes of the gut and vagina may be related to various gynecologic cancers (cervical, uterine, and ovarian). Furthermore, the gastrointestinal microbiota can be altered by environmental factors and pre-existing morbidities and may cause nausea, vomiting, diarrhea, constipation, bloating, and abdominal pain. A healthy female gut microbiome is dominated by Bifidobacterium, Lactobacillus, Bacteroides, Clostridium, Escherichia, Streptococcus, and Ruminococcus; the vaginal microbiome includes Firmicutes, specifically Lactobacilli spp. However, the gram-variable coccobacillus Gardnerella vaginalis (previously known as Haemophilus vaginalis) dominates the microbiota of biological vaginosis (BV) and includes several anaerobic organisms. Vaginal microbiota perturbations can cause vaginal pain, sexual dysfunction, and urinary symptoms. In the current review paper, we explore recent research along with existing gaps in knowledge related to the association of changes in microbiota diversity and the pathogenesis of vaginal infection-associated cervical cancer.}, } @article {pmid33389862, year = {2020}, author = {Malla, RR}, title = {Microbiome Conundrum in Colon Cancer: Development, Progression, and Therapeutics.}, journal = {Critical reviews in oncogenesis}, volume = {25}, number = {2}, pages = {129-139}, doi = {10.1615/CritRevOncog.2020035135}, pmid = {33389862}, issn = {0893-9675}, abstract = {Colon cancer (CC) is a major global health challenge. Diet, microbiome, obesity, and family history are some of the etiological factors that contribute to the occurrence of CC. Recent investigations have established a strong correlation between colonic microbiota composition and CC. The microbiota protects or damages colonic cells, depending on the type of metabolites and their mechanism of action. Microbiota dysbiosis enhances CC-cell proliferation and promotes metastasis. The microbiota modulates CC progression by epigenetic modifications mediated through either microbial metabolites or structural component interactions with host colon epithelial cells. In addition, gut homeostasis correlates with modulation of host inflammatory and immune responses. This review highlights the microbiome conundrum in tumor growth and metastasis, epigenetic regulation, tumor microenvironment maintenance, microbiome-derived reactive oxygen species in tumor progression, and microbiome-derived metabolites in CC prevention. Understanding the microbiome conundrum in CC development and progression will aid in developing a diet-based therapeutic strategy for colon tumorigenesis management.}, } @article {pmid33389354, year = {2021}, author = {Rimoldi, S and Antonini, M and Gasco, L and Moroni, F and Terova, G}, title = {Intestinal microbial communities of rainbow trout (Oncorhynchus mykiss) may be improved by feeding a Hermetia illucens meal/low-fishmeal diet.}, journal = {Fish physiology and biochemistry}, volume = {}, number = {}, pages = {}, pmid = {33389354}, issn = {1573-5168}, support = {2016-01-01//This research was partially funded by AGER, Network Foundation, Project Fine Feed for Fish (4F)./ ; 818367.//This work was also co-funded by the EU Horizon 2020 AquaIMPACT (Genomic and nutritional Innovations for genetically superior farmed fish to improve efficiency in European aquaculture)/ ; }, abstract = {With demands and reliance on aquaculture still growing, there are various challenges to allow sustainable growth and the shift from fishmeal (FM) to other protein sources in aquafeed formulations is one of the most important. In this regard, interest in the use of insect meal (IM) in aquafeeds has grown rapidly. Accordingly, the aim of the present study was to assess the effects of dietary IM from Hermetia illucens (Hi) larvae included in a low-FM diet on gut microbial communities of rainbow trout (Oncorhynchus mykiss), in terms of both composition and function of microbiome. A feeding trial was conducted using 192 trout of about 100-g mean initial weight. Fish were fed in quadruplicate (4 tanks/diet) for 131 days with two diets: the control (Ctrl) contained 20% of FM as well as other protein sources, whereas the Hi diet contained 15% of Hi larvae meal to replace 50% of the FM contained in the Ctrl diet. High-throughput sequencing of 16S rRNA gene was used to identify the major feed and gut bacterial taxa, whereas Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis was performed on gut bacterial genomes to identify the major active biological pathways. The inclusion of IM led to an increase in Firmicutes, mainly represented by Bacilli class and to a drastic reduction of Proteobacteria. Beneficial genera, such as Lactobacillus and Bacillus, were enriched in the gut of fish fed with the Hi diet, whereas the number of bacteria assigned to the pathogenic Aeromonas genus was drastically reduced in the same fish group. The metagenome functional data provided evidence that dietary IM inclusion can shape the metabolic activity of trout gut microbiota. In particular, intestinal microbiome of fish fed with IM may have the capacity to improve dietary carbohydrate utilization. Therefore, H. illucens meal is a promising protein source for trout nutrition, able to modulate gut microbial community by increasing the abundance of some bacteria taxa that are likely to play a key role in fish health.}, } @article {pmid33387530, year = {2020}, author = {Kummen, M and Thingholm, LB and Rühlemann, MC and Holm, K and Hansen, SH and Moitinho-Silva, L and Liwinski, T and Zenouzi, R and Storm-Larsen, C and Midttun, Ø and McCann, A and Ueland, PM and Høivik, ML and Vesterhus, M and Trøseid, M and Laudes, M and Lieb, W and Karlsen, TH and Bang, C and Schramm, C and Franke, A and Hov, JR}, title = {Altered gut microbial metabolism of essential nutrients in primary sclerosing cholangitis.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2020.12.058}, pmid = {33387530}, issn = {1528-0012}, abstract = {BACKGROUND AND AIMS: To influence host and disease phenotype, compositional microbiome changes, which have been demonstrated in patients with primary sclerosing cholangitis (PSC), must be accompanied by functional changes. We therefore aimed to characterize the genetic potential of the gut microbiome in PSC compared to healthy controls (HCs) and inflammatory bowel disease (IBD).

METHODS: Fecal DNA from two cohorts (one Norwegian and one German), in total comprising 136 patients with PSC (58% with IBD), 158 HCs and 93 IBD patients without PSC were subjected to metagenomic shotgun sequencing, generating 17 billion paired end sequences, which were processed using HUMAnN2 and MetaPhlAn2, and analyzed using generalized linear models and random effects meta-analyses.

RESULTS: PSC patients had fewer microbial genes compared to HC (P<.0001). Compared to HC, PSC patients showed enrichment and increased prevalence of Clostridium species, and a depletion of e.g., Eubacterium spp. and Ruminococcus obeum. Patients with PSC showed marked differences in the abundance of genes related to vitamin B6 synthesis and branched chain amino acid (BCAA) synthesis (Qfdr<.05). Targeted metabolomics of plasma from an independent set of PSC patients and controls found reduced concentrations of vitamin B6 and BCAAs in PSC (P<.0001), which strongly associated with reduced liver transplantation-free survival (log-rank P<.001). No taxonomic or functional differences were detected between PSC patients with and without IBD.

CONCLUSION: The gut microbiome of PSC patients exhibits large functional differences compared to HC, including microbial metabolism of essential nutrients. Alterations in related circulating metabolites associated with disease course, suggesting that microbial functions may be relevant for the disease process in PSC.}, } @article {pmid33387437, year = {2020}, author = {Zdziarski, P}, title = {[Veillonella atypica in tumor as a tripartite interaction: commensal - tumor - patient].}, journal = {Polski merkuriusz lekarski : organ Polskiego Towarzystwa Lekarskiego}, volume = {48}, number = {288}, pages = {452-456}, pmid = {33387437}, issn = {1426-9686}, mesh = {*Carcinoma, Non-Small-Cell Lung ; Female ; Humans ; *Lung Neoplasms/drug therapy ; Mouth ; Tumor Microenvironment ; Veillonella ; }, abstract = {Veillonella spp is part of the normal flora of the mouth, bowels and vagina, but in most of the studies the immunomodulatory properties of intestinal microbiota was described. Despite of numerous studies on immunomodulatory activity of the microbiome's, most of them are focused on the intestinal microbiome. On the contrary, last finding of lung cancer patients shows higher level of Capnocytophaga and Veillonella, which may serve as potential biomarkers. Unfortunately, in local tumor microenvironment the competition for access to oxygen and nutrients within the microbiological context are not strictly described. In the case report such unique interaction with importance in clinical course of non small cell lung cancer (NSCLC) was described.

A CASE REPORT: Patient with NSCLC was admitted to surgical procedure. Unluckily, patients before therapy suffered brain trauma (metastases and meningitis were excluded). The oncologic intervention delayed: patients has not receive neoadjuvant chemotherapy. Within near 2 months the infectious process dominated with high acute phase reaction. It predominated over the process of cancer with significant decrease of initial tumor size. After surgical procedure histological examination showed 60% of the tumor was necrotic. Microbiological analysis of tumor specimen reveal Veillonella spp., identified as Veillonella atypica with high abundance. Because the serious complication patients do not receive adjuvant chemotherapy: the surgical resection was complicated by severe systemic inflammatory response syndrome (SIRS) but with low level lactate.

CONCLUSIONS: Our observation indicate significant role of commensal anaerobic bacteria in clinical history of cancer patient, opportunistic type of infectious process as well as therapeuthic prospect: proliferative potential and anaerobic glycolysis of commensal Veillonella reduce access of cancer cells to nutrition's. It shed light on crucial role of innate immune response, acute phase reaction and neutrophils in immunotherapy outcome. Contrary to previous studies with statistical coexistence of several bacteria and cancer our observation was evidence-based: tumor specimen was microbiologically analysed.}, } @article {pmid33386895, year = {2021}, author = {Liao, H and Fan, H and Li, Y and Yao, H}, title = {Influence of reductive soil disinfestation or biochar amendment on bacterial communities and their utilization of plant-derived carbon in the rhizosphere of tomato.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {2}, pages = {815-825}, pmid = {33386895}, issn = {1432-0614}, support = {41525002, 41471206, 41601249//National Natural Science Foundation of China/ ; }, abstract = {Root-associated microorganisms play an important role in plant nutrition and productivity. However, our understanding of how a plant-microbiome system responds to pre-planting soil management remains limited. Here, continuous labeling with 13CO2 gas combined with stable isotope probing (SIP) was applied to explore bacterial utilization of plant-derived carbon (C) in the tomato rhizosphere as affected by biochar amendment or reductive soil disinfestation (RSD). Our results showed that RSD treatment strongly shaped the soil bacterial community composition, while biochar soil amendment had little impact on the community in the rhizosphere of tomato. We observed that the bacterial community in the RSD treatment, which actively utilized plant-derived C, belonged to various phyla (i.e., Proteobacteria, Cyanobacteria, Verrucomicrobia, and Acidobacteria), while the genus Streptomyces (phylum Actinobacteria) was the main bacterial taxa that actively utilized plant-derived C in the biochar and control treatments. This study provides evidence that biochar application or RSD pre-planting soil management practices induced distinct bacterial utilization of plant-derived C, which may in turn regulate plant productivity in agricultural systems. KEY POINTS: • Genus Streptomyces was the main bacterial group utilizing plant-derived carbon in both control and biochar treatments. • Reductive soil disinfestation altered bacterial utilization of plant-derived carbon. • Biochar did not alter the composition of the bacterial communities but had more labeled bacterial taxa utilizing plant-derived carbon.}, } @article {pmid33386869, year = {2021}, author = {López, SMY and Pastorino, GN and Balatti, PA}, title = {Volatile organic compounds profile synthesized and released by endophytes of tomato (Solanum lycopersici L.) and their antagonistic role.}, journal = {Archives of microbiology}, volume = {}, number = {}, pages = {}, pmid = {33386869}, issn = {1432-072X}, support = {PICT-2016-0794//Agencia Nacional de Promoción Científica y Tecnológica/ ; Subsidio 2017//Comisión de Investigaciones Científicas/ ; }, abstract = {The endophytic microbiome uses mechanisms such as the secretion of diffusible antibiotic molecules, synthesis and release of volatile organic compounds, and/or toxins to protect plants. The aim of this research was to study the volatile organic compounds (VOCs) profile as well as the diffusible secondary metabolites produced and released by endophytic bacteria isolated from tomato plants that in in-vitro assays prevented growth of pathogenic fungi. Bacteria belonging to seven genera (Acinetobacter, Arthrobacter, Bacillus, Microbacterium, Pantoea, Pseudomonas, and Stenotrophomonas) were isolated from different tissues of tomato plants with and without symptoms of Gray leaf spot, a disease provoked by Stemphylium lycopersici. In vitro, antagonistic assays were performed and the effect of volatile and soluble compounds released by endophytic bacteria on the growth of pathogenic fungi was determined. The VOCs synthesized by the endophytes were extracted, identified and quantified. These isolates representatives of seven bacterial genera inhibited the growth of three fungal pathogens of tomato S. lycopersici, Alternaria alternata and Corynespora cassiicola, which was related to the synthesis of soluble compounds as well as VOCs. Endophytes synthesize and release different VOCs, probably due to the different type of interaction that each bacterium establishes with the fungus, presenting a range of fungal growth inhibition.}, } @article {pmid33386517, year = {2021}, author = {Ray, P and Pandey, U and Das, D and Aich, P}, title = {Vancomycin-Induced Changes in Host Immunity and Behavior: Comparative Genomic and Metagenomic Analysis in C57BL/6 and BALB/c Mice.}, journal = {Digestive diseases and sciences}, volume = {}, number = {}, pages = {}, pmid = {33386517}, issn = {1573-2568}, abstract = {BACKGROUND: The consequence of treatment with antibiotics on the gut microbiota can be destructive. The antibiotics, however, can be utilized to understand the role of gut microbiota on the host physiology.

AIM: Earlier, we reported the efficacy of vancomycin in gut microbiota perturbation. We continued to understand the effect of restoration kinetics of perturbed gut microbiota on the immunity and behavior of Th1 (C57BL/6)- and Th2 (BALB/c)-biased mice.

METHODS: We studied restoration kinetics of the gut microbiota for two months following the withdrawal of vancomycin treatment in both mice strains. We analyzed cecal microbiome composition, different behavioral assays, and expression of select genes associated with stress and barrier function in gut and brain.

RESULTS: Metagenomic analysis of gut microbiota revealed that the treatment with vancomycin caused a significant decrease in the relative abundance of Firmicutes and Bacteroidetes phyla with a time-dependent increase in Proteobacteria and Verrucomicrobia phyla. Maximum restoration (> 70%) of gut microbiota happened by the 15th day of withdrawal of vancomycin. BALB/c mice showed a more efficient restoration of gut microbiota compared to C57BL/6 mice. We established the correlation patterns of gut microbiota alteration and its effect on (a) the behavior of mice, (b) expression of key brain molecules, and (c) immunity-related genes.

CONCLUSIONS: The results revealed that the gut microbiome profiling, behavior, and immune responses varied significantly between Th1- and Th2-biased mice. By withdrawing the treatment with vancomycin of major gut microbes, important physiological and behavioral changes of both mice strains returned to the normal (untreated control) level.}, } @article {pmid33386052, year = {2020}, author = {Lissoni, A and Agliardi, E and Peri, A and Marchioni, R and Abati, S}, title = {Oral microbiome and mucosal trauma as risk factors for oral cancer: beyond alcohol and tobacco. A literature review.}, journal = {Journal of biological regulators and homeostatic agents}, volume = {34}, number = {6 Suppl. 3}, pages = {11-18}, pmid = {33386052}, issn = {0393-974X}, abstract = {Oral and oropharyngeal cancer represents the sixth more common type of cancer affecting the worldwide population. It has been estimated the number of 650,000 new cases per year globally and a greater prevalence has been registered among men. The main risk factors for oral cancer such as tobacco smoking and alcohol are uncontroversial and have been deeply investigated and evidenced in the scientific literature. Recently, viral infections related to Human Papilloma Virus (HPV), with the genotype 16 and 32, have shown a correlation mainly with oropharyngeal cancer (OPC) especially in the non-smoking and non-drinkers young adults. Its transmission is mainly related to sexually transmitted diseases (STDs) although its involvement in oral squamous cell carcinoma (OSCC) is still unclear. This review aims to explore the hypotheses of the OSCC etiology and other possible risk factors, such as chronic traumatisms, chronic periodontitis, and poor oral hygiene that affect directly the oral mucosa and might trigger the carcinogenesis process that should not be underestimated. Furthermore, in the last 10 years, the role of oral microbiome gained attention as a predicting biomarker, for a possible bacterial, viral, and fungal involvement in tumorigenesis.}, } @article {pmid33385493, year = {2020}, author = {Fan, HN and Zhu, P and Zhang, J and Zhu, JS}, title = {Mucosal microbiome dysbiosis associated with duodenum bulb inflammation.}, journal = {Microbial pathogenesis}, volume = {150}, number = {}, pages = {104711}, doi = {10.1016/j.micpath.2020.104711}, pmid = {33385493}, issn = {1096-1208}, abstract = {BACKGROUND: There is high morbidity in clinical patients with duodenum bulb inflammation. Mucosa-associated microbiota, which are closely related to inflammatory processes, may have a pathogenic role, but the duodenum bulb microbial signature is poorly studied.

OBJECTIVE: This study aimed to characterize microbial changes associated with duodenum bulb inflammation.

METHODS: Mucosal biopsy is commonly used to assess microbial communities associated with the intestinal mucosa. Sixteen patients (8 with duodenum bulb inflammation and 8 controls) underwent gastroscopy, and duodenal bulb biopsies were obtained. Diagnoses were based on both endoscopic and histological findings. To determine microbiota composition and diversity, 454 pyrosequencing of bacterial 16S rRNA and multiple bioinformatics analyses were performed. OTU-level alpha diversity indices, such as the Chao1 richness estimator, abundance-based coverage estimator (ACE) metric, Shannon diversity index, and Simpson index, were calculated using the OTU table in QIIME.

RESULTS: More OTUs were identified in the normal samples (781) than in the inflammatory samples (553). Metastats analysis identified 19 phyla and 97 genera that were significantly different between the two groups, and the beta diversity was significantly different between the two groups (unweighted UniFrac: P = 0.001; weighted UniFrac: P = 0.001). For all individuals, composition analyses showed that the most abundant phyla in the duodenal bulb samples were Fusobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. The phylogenetic diversity of the microbiota in the duodenal bulbs of healthy volunteers was higher than that in volunteers with inflammation. Dominant microbes differed between the DN samples and DI samples. The most frequently represented genera in the DN samples were Cetobacterium, Aeromonadaceae, and Clostridium (accounting for 58.4%, 8.5%, and 4.8% of the total, respectively), and the dominant genera in the DI samples were Cetobacterium, Cupriavidus, and Helicobacter (accounting for 43.6%, 13.1%, 4.5% of the total, respectively). Significant differences in the microbiota were observed between those exhibiting an inflammatory state and the controls.

CONCLUSIONS: These results confirm that the dominant species in duodenum bulbs differ between healthy subjects and patients with inflammation and that mucosal microbiome dysbiosis is involved in the development of duodenum bulb inflammation.}, } @article {pmid33385335, year = {2021}, author = {Shapiro, JM and de Zoete, MR and Palm, NW and Laenen, Y and Bright, R and Mallette, M and Bu, K and Bielecka, AA and Xu, F and Hurtado-Lorenzo, A and Shah, SA and Cho, JH and LeLeiko, NS and Sands, BE and Flavell, RA and Clemente, JC}, title = {Immunoglobulin A Targets a Unique Subset of the Microbiota in Inflammatory Bowel Disease.}, journal = {Cell host & microbe}, volume = {29}, number = {1}, pages = {83-93.e3}, doi = {10.1016/j.chom.2020.12.003}, pmid = {33385335}, issn = {1934-6069}, abstract = {The immunopathogenesis of inflammatory bowel disease (IBD) has been attributed to a combination of host genetics and intestinal dysbiosis. Previous work in a small cohort of IBD patients suggested that pro-inflammatory bacterial taxa are highly coated with secretory immunoglobulin IgA. Using bacterial fluorescence-activated cell sorting coupled with 16S rRNA gene sequencing (IgA-SEQ), we profiled IgA coating of intestinal microbiota in a large cohort of IBD patients and identified bacteria associated with disease and treatment. Forty-three bacterial taxa displayed significantly higher IgA coating in IBD compared with controls, including 8 taxa exhibiting differential IgA coating but similar relative abundance. Patients treated with anti-TNF-α therapies exhibited dramatically altered microbiota-specific IgA responses compared with controls. Furthermore, increased IgA coating of Oscillospira was associated with a delay in time to surgery. These results demonstrate that investigating IgA responses to microbiota can uncover potential disease-modifying taxa and reveal improved biomarkers of clinical course in IBD.}, } @article {pmid33385118, year = {2021}, author = {Jaiswal, SK and Agarwal, SM and Thodum, P and Sharma, VK}, title = {SkinBug: an artificial intelligence approach to predict human skin microbiome-mediated metabolism of biotics and xenobiotics.}, journal = {iScience}, volume = {24}, number = {1}, pages = {101925}, pmid = {33385118}, issn = {2589-0042}, abstract = {In addition to being pivotal for the host health, the skin microbiome possesses a large reservoir of metabolic enzymes, which can metabolize molecules (cosmetics, medicines, pollutants, etc.) that form a major part of the skin exposome. Therefore, to predict the complete metabolism of any molecule by skin microbiome, a curated database of metabolic enzymes (1,094,153), reactions, and substrates from ∼900 bacterial species from 19 different skin sites were used to develop "SkinBug." It integrates machine learning, neural networks, and chemoinformatics methods, and displays a multiclass multilabel accuracy of up to 82.4% and binary accuracy of up to 90.0%. SkinBug predicts all possible metabolic reactions and associated enzymes, reaction centers, skin microbiome species harboring the enzyme, and the respective skin sites. Thus, SkinBug will be an indispensable tool to predict xenobiotic/biotic metabolism by skin microbiome and will find applications in exposome and microbiome studies, dermatology, and skin cancer research.}, } @article {pmid33384986, year = {2020}, author = {Arora, K and Green, M and Prakash, S}, title = {The Microbiome and Alzheimer's Disease: Potential and Limitations of Prebiotic, Synbiotic, and Probiotic Formulations.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {8}, number = {}, pages = {537847}, pmid = {33384986}, issn = {2296-4185}, abstract = {The Microbiome has generated significant attention for its impacts not only on gastrointestinal health, but also on signaling pathways of the enteric and central nervous system via the microbiome gut-brain axis. In light of this, microbiome modulation may be an effective therapeutic strategy for treating or mitigating many somatic and neural pathologies, including neurodegenerative disorders. Alzheimer's disease (AD) is a chronic neurodegenerative disease that interferes with cerebral function by progressively impairing memory, thinking and learning through the continuous depletion of neurons. Although its etiopathogenesis remains uncertain, recent literature endorses the hypothesis that probiotic, prebiotic and synbiotic supplementation alters AD-like symptoms and improves many of its associated disease biomarkers. Alternatively, a dysfunctional microbiota impairs the gut epithelial barrier by inducing chronic gastric inflammation, culminating in neuroinflammation and accelerating AD progression. The findings in this review suggest that probiotics, prebiotics or synbiotics have potential as novel biological prophylactics in treatment of AD, due to their anti-inflammatory and antioxidant properties, their ability to improve cognition and metabolic activity, as well as their capacity of producing essential metabolites for gut and brain barrier permeability.}, } @article {pmid33384969, year = {2020}, author = {Kang, X and Wang, Y and Li, S and Sun, X and Lu, X and Rajaofera, MJN and Lu, Y and Kang, L and Zheng, A and Zou, Z and Xia, Q}, title = {Comparative Analysis of the Gut Microbiota of Adult Mosquitoes From Eight Locations in Hainan, China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {596750}, pmid = {33384969}, issn = {2235-2988}, abstract = {The midgut microbial community composition, structure, and function of field-collected mosquitoes may provide a way to exploit microbial function for mosquito-borne disease control. However, it is unclear how adult mosquitoes acquire their microbiome, how the microbiome affects life history traits and how the microbiome influences community structure. We analyzed the composition of 501 midgut bacterial communities from field-collected adult female mosquitoes, including Aedes albopictus, Aedes galloisi, Culex pallidothorax, Culex pipiens, Culex gelidus, and Armigeres subalbatus, across eight habitats using the HiSeq 4000 system and the V3-V4 hyper-variable region of 16S rRNA gene. After quality filtering and rarefaction, a total of 1421 operational taxonomic units, belonging to 29 phyla, 44 families, and 43 genera were identified. Proteobacteria (75.67%) were the most common phylum, followed by Firmicutes (10.38%), Bacteroidetes (6.87%), Thermi (4.60%), and Actinobacteria (1.58%). The genera Rickettsiaceae (33.00%), Enterobacteriaceae (20.27%), Enterococcaceae (7.49%), Aeromonadaceae (7.00%), Thermaceae (4.52%), and Moraxellaceae (4.31%) were dominant in the samples analyzed and accounted for 76.59% of the total genera. We characterized the midgut bacterial communities of six mosquito species in Hainan province, China. The gut bacterial communities were different in composition and abundance, among locations, for all mosquito species. There were significant differences in the gut microbial composition between some species and substantial variation in the gut microbiota between individuals of the same mosquito species. There was a marked variation in different mosquito gut microbiota within the same location. These results might be useful in the identification of microbial communities that could be exploited for disease control.}, } @article {pmid33384968, year = {2020}, author = {Stamps, BW and Lyon, WJ and Irvin, AP and Kelley-Loughnane, N and Goodson, MS}, title = {A Pilot Study of the Effect of Deployment on the Gut Microbiome and Traveler's Diarrhea Susceptibility.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {589297}, pmid = {33384968}, issn = {2235-2988}, abstract = {Traveler's diarrhea (TD) is a recurrent and significant issue for many travelers including the military. While many known enteric pathogens exist that are causative agents of diarrhea, our gut microbiome may also play a role in TD susceptibility. To this end, we conducted a pilot study of the microbiome of warfighters prior to- and after deployment overseas to identify marker taxa relevant to TD. This initial study utilized full-length 16S rRNA gene sequencing to provide additional taxonomic resolution toward identifying predictive taxa.16S rRNA analyses of pre- and post-deployment fecal samples identified multiple marker taxa as significantly differentially abundant in subjects that reported diarrhea, including Weissella, Butyrivibrio, Corynebacterium, uncultivated Erysipelotrichaceae, Jeotgallibaca, unclassified Ktedonobacteriaceae, Leptolinea, and uncultivated Ruminiococcaceae. The ability to identify TD risk prior to travel will inform prevention and mitigation strategies to influence diarrhea susceptibility while traveling.}, } @article {pmid33384966, year = {2020}, author = {Zeng, J and Zhang, G and Chen, C and Li, K and Wen, Y and Zhao, J and Wu, P}, title = {Alterations in Urobiome in Patients With Bladder Cancer and Implications for Clinical Outcome: A Single-Institution Study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {555508}, pmid = {33384966}, issn = {2235-2988}, abstract = {Numerous studies indicate that resident microbiome exists in urine of healthy individuals and dysbiosis of the urobiome (urinary microbiome) may be associated with pathological conditions. This study was performed to characterize the alterations in urobiome and explore its implications of clinical outcome in male patients with bladder cancer. 62 male patients with bladder cancer and 19 non-neoplastic controls were recruited. The follow-up study cohort included 40 patients who were diagnosed with non-muscle invasive bladder cancer (NMIBC) and underwent transurethral resection of bladder tumor (TURBT). Mid-stream urine samples were collected from all the participants the day before cystoscopy. DNA was extracted from urine pellet samples and processed for high throughput 16S rRNA amplicon sequencing of the V4 region using Illumina MiSeq. Sequencing reads were filtered using QIIME and clustered using UPARSE. We found bacterial richness indices (Observed Species index, Chao1 index, Ace index; all P < 0.01) increased in cancer group when compared with non-neoplastic group, while there were no differences in Shannon and Simpson index between two groups. During a median follow-up time of 12 (5.25-25) months, 5/40 (12.5%)of the patients developed recurrence and no patient suffered from progression to muscle-invasive disease. Species diversity of the microbiome was significantly higher in the recurrence group compared with non-recurrence group in patients with NMIBC after TURBT. The LEfSe analysis demonstrated that 9 genera were increased (e.g., Micrococcus and Brachybacterium) in recurrence group. To our knowledge we report the relative comprehensive study to date of the male bladder cancer urinary microbiome and its relationship to pathogenesis and clinical outcomes. Given our preliminary data, additional studies evaluating the urine microbiome in relation to clinical outcomes are warranted to improve our understanding of tumor recurrence after TURBT.}, } @article {pmid33384902, year = {2020}, author = {Santos-Júnior, CD and Pan, S and Zhao, XM and Coelho, LP}, title = {Macrel: antimicrobial peptide screening in genomes and metagenomes.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e10555}, pmid = {33384902}, issn = {2167-8359}, abstract = {Motivation: Antimicrobial peptides (AMPs) have the potential to tackle multidrug-resistant pathogens in both clinical and non-clinical contexts. The recent growth in the availability of genomes and metagenomes provides an opportunity for in silico prediction of novel AMP molecules. However, due to the small size of these peptides, standard gene prospection methods cannot be applied in this domain and alternative approaches are necessary. In particular, standard gene prediction methods have low precision for short peptides, and functional classification by homology results in low recall.

Results: Here, we present Macrel (for metagenomic AMP classification and retrieval), which is an end-to-end pipeline for the prospection of high-quality AMP candidates from (meta)genomes. For this, we introduce a novel set of 22 peptide features. These were used to build classifiers which perform similarly to the state-of-the-art in the prediction of both antimicrobial and hemolytic activity of peptides, but with enhanced precision (using standard benchmarks as well as a stricter testing regime). We demonstrate that Macrel recovers high-quality AMP candidates using realistic simulations and real data.

Availability: Macrel is implemented in Python 3. It is available as open source at https://github.com/BigDataBiology/macrel and through bioconda. Classification of peptides or prediction of AMPs in contigs can also be performed on the webserver: https://big-data-biology.org/software/macrel.}, } @article {pmid33384896, year = {2020}, author = {Gallo, BD and Farrell, JM and Leydet, B}, title = {Use of next generation sequencing to compare simple habitat and species level differences in the gut microbiota of an invasive and native freshwater fish species.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e10237}, pmid = {33384896}, issn = {2167-8359}, abstract = {Research on the gut microbiome of host organisms has rapidly advanced with next generation sequencing (NGS) and high-performance computing capabilities. Nonetheless, gut microbiome research has focused on mammalian organisms in laboratory settings, and investigations pertaining to wild fish gut microbiota remain in their infancy. We applied a procedure (available at https://github.com/bngallo1994) for sampling of the fish gut for use in NGS to describe microbial community structure. Our approach allowed for high bacterial OTU diversity coverage (>99.7%, Good's Coverage) that led to detection of differences in gut microbiota of an invasive (Round Goby) and native (Yellow Bullhead) fish species and collected from the upper St. Lawrence River, an environment where the gut microbiota of fish had not previously been tested. Additionally, results revealed habitat level differences in gut microbiota using two distance metrics (Unifrac, Bray-Curtis) between nearshore littoral and offshore profundal collections of Round Goby. Species and habitat level differences in intestinal microbiota may be of importance in understanding individual and species variation and its importance in regulating fish health and physiology.}, } @article {pmid33384680, year = {2020}, author = {Amacker, N and Gao, Z and Agaras, BC and Latz, E and Kowalchuk, GA and Valverde, CF and Jousset, A and Weidner, S}, title = {Biocontrol Traits Correlate With Resistance to Predation by Protists in Soil Pseudomonads.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {614194}, pmid = {33384680}, issn = {1664-302X}, abstract = {Root-colonizing bacteria can support plant growth and help fend off pathogens. It is clear that such bacteria benefit from plant-derived carbon, but it remains ambiguous why they invest in plant-beneficial traits. We suggest that selection via protist predation contributes to recruitment of plant-beneficial traits in rhizosphere bacteria. To this end, we examined the extent to which bacterial traits associated with pathogen inhibition coincide with resistance to protist predation. We investigated the resistance to predation of a collection of Pseudomonas spp. against a range of representative soil protists covering three eukaryotic supergroups. We then examined whether patterns of resistance to predation could be explained by functional traits related to plant growth promotion, disease suppression and root colonization success. We observed a strong correlation between resistance to predation and phytopathogen inhibition. In addition, our analysis highlighted an important contribution of lytic enzymes and motility traits to resist predation by protists. We conclude that the widespread occurrence of plant-protective traits in the rhizosphere microbiome may be driven by the evolutionary pressure for resistance against predation by protists. Protists may therefore act as microbiome regulators promoting native bacteria involved in plant protection against diseases.}, } @article {pmid33384671, year = {2020}, author = {Han, F and Wu, G and Zhang, Y and Zheng, H and Han, S and Li, X and Cai, W and Liu, J and Zhang, W and Zhang, X and Hu, D}, title = {Streptococcus thermophilus Attenuates Inflammation in Septic Mice Mediated by Gut Microbiota.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {598010}, pmid = {33384671}, issn = {1664-302X}, abstract = {Sepsis is a life-threatening organ dysfunction condition caused by a dysregulated host response to infection and lack of effective treatment method. Supplementation of probiotics has emerged as a potential biotherapy for inflammatory diseases in recent years, but its role in protecting viscera against the damage caused by sepsis and the underlying mechanism is poorly understood. Streptococcus thermophilus 19 is one of the most well-studied probiotics, which is selected in this study among seven strains isolated from homemade yogurt due to its optimal ability of suppressing the inflammation response in vitro. It showed significant decrease in the expression of TNF-α, IL-1β, and IL-6 in the co-culture of S. thermophilus 19 and LPS-treated mouse macrophage. The effect of S. thermophilus 19 in mice and the response of mice gut microbiota were subsequently investigated. In LPS-induced septic mouse model, S. thermophilus 19 was highly resistant to LPS and exhibited significantly decreased expressions of inflammatory factors compared to LPS-treated mice. A MiSeq-based 16S rDNA sequence analysis revealed that the decrease of gut microbial diversity in mice intraperitoneally injected with 1 mg/ml LPS were mitigated by the administration of S. thermophilus 19. Fusobacterium significantly decreased during the development of sepsis and rose again after supplement strain 19, while Flavonifractor showed the opposite trend, which demonstrated these two genera were the key bacteria that may function in the mice gut microbiota for alleviation of LPS-induced inflammation reaction. To conclude, S. thermophilus 19 may be a potential candidate for novel biotherapeutic interventions against inflammation caused by sepsis.}, } @article {pmid33384669, year = {2020}, author = {Chen, L and Li, J and Zhu, W and Kuang, Y and Liu, T and Zhang, W and Chen, X and Peng, C}, title = {Skin and Gut Microbiome in Psoriasis: Gaining Insight Into the Pathophysiology of It and Finding Novel Therapeutic Strategies.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {589726}, pmid = {33384669}, issn = {1664-302X}, abstract = {Psoriasis affects the health of myriad populations around the world. The pathogenesis is multifactorial, and the exact driving factor remains unclear. This condition arises from the interaction between hyperproliferative keratinocytes and infiltrating immune cells, with poor prognosis and high recurrence. Better clinical treatments remain to be explored. There is much evidence that alterations in the skin and intestinal microbiome play an important role in the pathogenesis of psoriasis, and restoration of the microbiome is a promising preventive and therapeutic strategy for psoriasis. Herein, we have reviewed recent studies on the psoriasis-related microbiome in an attempt to confidently identify the "core" microbiome of psoriasis patients, understand the role of microbiome in the pathogenesis of psoriasis, and explore new therapeutic strategies for psoriasis through microbial intervention.}, } @article {pmid33383810, year = {2020}, author = {Lecamwasam, A and Nelson, TM and Rivera, L and Ekinci, EI and Saffery, R and Dwyer, KM}, title = {Gut Microbiome Composition Remains Stable in Individuals with Diabetes-Related Early to Late Stage Chronic Kidney Disease.}, journal = {Biomedicines}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/biomedicines9010019}, pmid = {33383810}, issn = {2227-9059}, abstract = {(1) Background: Individuals with diabetes and chronic kidney disease display gut dysbiosis when compared to healthy controls. However, it is unknown whether there is a change in dysbiosis across the stages of diabetic chronic kidney disease. We investigated a cross-sectional study of patients with early and late diabetes associated chronic kidney disease to identify possible microbial differences between these two groups and across each of the stages of diabetic chronic kidney disease. (2) Methods: This cross-sectional study recruited 95 adults. DNA extracted from collected stool samples were used for 16S rRNA sequencing to identify the bacterial community in the gut. (3) Results: The phylum Firmicutes was the most abundant and its mean relative abundance was similar in the early and late chronic kidney disease group, 45.99 ± 0.58% and 49.39 ± 0.55%, respectively. The mean relative abundance for family Bacteroidaceae, was also similar in the early and late group, 29.15 ± 2.02% and 29.16 ± 1.70%, respectively. The lower abundance of Prevotellaceae remained similar across both the early 3.87 ± 1.66% and late 3.36 ± 0.98% diabetic chronic kidney disease groups. (4) Conclusions: The data arising from our cohort of individuals with diabetes associated chronic kidney disease show a predominance of phyla Firmicutes and Bacteroidetes. The families Ruminococcaceae and Bacteroidaceae represent the highest abundance, while the beneficial Prevotellaceae family were reduced in abundance. The most interesting observation is that the relative abundance of these gut microbes does not change across the early and late stages of diabetic chronic kidney disease, suggesting that this is an early event in the development of diabetes associated chronic kidney disease. We hypothesise that the dysbiotic microbiome acquired during the early stages of diabetic chronic kidney disease remains relatively stable and is only one of many risk factors that influence progressive kidney dysfunction.}, } @article {pmid33383647, year = {2020}, author = {Weinstein, N and Garten, B and Vainer, J and Minaya, D and Czaja, K}, title = {Managing the Microbiome: How the Gut Influences Development and Disease.}, journal = {Nutrients}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/nu13010074}, pmid = {33383647}, issn = {2072-6643}, support = {1R01DC013904//The National Institutes of Health/ ; }, abstract = {The microbiome lies at the forefront of scientific research, as researchers work to uncover its mysterious influence on human development and disease. This paper reviews how the microbiome is studied, how researchers can improve its study, and what clinical applications microbiome research might yield. For this review, we analyzed studies concerning the role of the microbiome in disease and early development, the common methodologies by which the microbiome is researched in the lab, and modern clinical treatments for dysbiosis and their possible future applications. We found that the gut microbiome is essential for proper development of various physiological systems and that gut dysbiosis is a clear factor in the etiology of various diseases. Furthermore, we found that germ-free animal models and microbiome manipulation techniques are inadequate, reducing the efficacy of microbiome research. Nonetheless, research continues to show the significance of microbiome manipulation in the clinical treatment of disease, having shown great promise in the prevention and treatment of dysbiosis. Though the clinical applications of microbiome manipulation are currently limited, the significance of dysbiosis in the etiology of a wide array of diseases indicates the significance of this research and highlights the need for more effective research methods concerning the microbiome.}, } @article {pmid33383497, year = {2020}, author = {Auer, F and Jarvas, G and Guttman, A}, title = {Recent advances in the analysis of human milk oligosaccharides by liquid phase separation methods.}, journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences}, volume = {1162}, number = {}, pages = {122497}, doi = {10.1016/j.jchromb.2020.122497}, pmid = {33383497}, issn = {1873-376X}, abstract = {Human milk is a complex, dynamically changing biological fluid, which contains a large amount of non-conjugated carbohydrates, referred to as human milk oligosaccharides (HMOs). These HMOs are very important for the infants as they play important roles in the formation of the gut microbiome, the immune system and support brain development. HMOs show highly complex structural diversity due to numerous linkage possibilities of the building monosaccharides. In order to elucidate their structure-function relationship and to develop more effective infant formulas, cutting-edge analytical technologies are in great demand. In this paper, we review the current strategies for HMO analysis based on liquid phase separation methods. High performance liquid chromatography, capillary electrophoresis and their hyphenation with mass spectrometry are critically reviewed, emphasizing their advantages and disadvantages from practical point of views. Recent advances of the methods are categorized according to their application fields.}, } @article {pmid33383302, year = {2020}, author = {Alberoni, D and Favaro, R and Baffoni, L and Angeli, S and Di Gioia, D}, title = {Neonicotinoids in the agroecosystem: In-field long-term assessment on honeybee colony strength and microbiome.}, journal = {The Science of the total environment}, volume = {762}, number = {}, pages = {144116}, doi = {10.1016/j.scitotenv.2020.144116}, pmid = {33383302}, issn = {1879-1026}, abstract = {Bees can be severely affected by various plant protection products (PPP). Among these, neonicotinoid insecticides are of concern as they have been shown to be responsible for extensive honeybee colonies death when released into the environment. Also, sublethal neonicotinoid doses contaminating single honeybees and their colonies (e.g. through contaminated pollen) are responsible for honeybees physiological alterations with probable implication also on microbiome functionality. Honeybees show symbiotic interactions with specific gut bacteria that can enhance the adult host performances. Among the known mechanisms, the modulation of the immune system, the degradation of recalcitrant secondary plant metabolites, pollen digestion, and hormonal signaling, are the most important functional benefits for the host honeybee. To date, few research efforts have aimed at revealing the impact of PPP on the gut microbial community of managed and wild honeybees. The majority of the existing literature relays on cage or semifield tests of short duration for research investigating neonicotinoids-gut microbiome interactions. This research wanted to unravel the impact of two neonicotinoids (i.e. imidacloprid and thiacloprid) in natural field conditions up to 5 weeks of exposure. A long-term impact of neonicotinoids on gut microbial community of honeybees was observed. The alterations affected several microbial genera and species such as Frischella spp., lactobacilli and bifidobacteria, whose shifting is implicated in intestinal dysbiosis. Long-term impact leading to dysbiosis was detected in case of exposure to imidacloprid, whereas thiacloprid exposure stimulated temporary dysbiosis. Moreover, the microbial diversity was significantly reduced in neonicotinoid-treated groups. Overall, the reported results support a compromised functionality of the gut microbial community, that might reflect a lower efficiency in the ecosystemic functionality of honeybees.}, } @article {pmid33383254, year = {2020}, author = {Zhou, R and Yu, Q and Li, T and Long, M and Wang, Y and Feng, T and Su, W and Yang, J and Li, H}, title = {Carcass decomposition influences the metabolic profiles and enriches noxious metabolites in different water types by widely targeted metabolomics.}, journal = {Chemosphere}, volume = {269}, number = {}, pages = {129400}, doi = {10.1016/j.chemosphere.2020.129400}, pmid = {33383254}, issn = {1879-1298}, abstract = {Carcass decomposition could be considered as a common phenomenon in nature. However, during degradation processes, animal carcasses produce many toxic and harmful metabolites, posing potential ecological risks to water safety, thereby threatening human health. However, the metabolites produced by decomposition of animal corpses are not well understood. In this study, building on our previous baseline study of microbial community between the experimental groups (with animal carcasses) and control groups (without carcasses), the samples at the ultimate stage (19th day) of carcass decomposition were chosen to investigate the metabolic profiles and uncover the relationships between water quality, microbes and noxious metabolites in two types of water (Yellow River water and tap water) using fish as animal model by widely targeted metabolomics. Our results showed amino acid metabolomics, indole and its derivatives, and pyridine and pyridine derivatives mainly occurred in the corpse groups, suggesting that these metabolites are markers of carcass decomposition. And some noxious metabolites (e.g., polyamine, amines, and benzene and substituted derivatives) highly associated with carcass decomposition, which revealed new insights into how to investigate the hazard materials in water. And these noxious metabolites in the corpse groups were even increased 214543-fold in average compared with the control groups. Meanwhile, treatment was the most important factor affecting the water metabolites while microbiome contributed a small proportion to the metabolic profiles. Several opportunistic pathogenic genera Comamonas, Bacteriodes and Alcaligenes co-occurred most frequently with several kinds of polyamines and amines while some dominant genera Rhodoferax, Delftia and Brevundimonas had significant positive relationships with specific benzene and substituted derivatives. This work demonstrates that carcass decomposition causes water quality deterioration by producing various toxic metabolites, thus providing new insights into noxious metabolites when exposed to animal carcasses in aquatic environment.}, } @article {pmid33383197, year = {2020}, author = {Gomes Carvalho Alves, KL and Granja-Salcedo, YT and Messana, JD and Carneiro de Souza, V and Generoso Ganga, MJ and Detogni Colovate, PH and Kishi, LT and Berchielli, TT}, title = {Rumen bacterial diversity in relation to nitrogen retention in beef cattle.}, journal = {Anaerobe}, volume = {}, number = {}, pages = {102316}, doi = {10.1016/j.anaerobe.2020.102316}, pmid = {33383197}, issn = {1095-8274}, abstract = {This study aimed to characterize the rumen bacterial diversity of beef steers differing in the efficiency of nitrogen retention (ENR). Eight castrated steers and fitted with ruminal silicone - and duodenal T-type cannulas were used in a cross-over design with three consecutive periods and three diets. During each experimental period, nitrogen balance was measured, and based on the efficiency of N utilization data, steers were split into three ENR groups: high (HNR, 56.6% ± 3.3%, n = 10), medium (MNR, 45.8% ± 2.2%, n = 6), and low (LNR, 37.7% ±1.9%, n = 8) using the NbClust package version 2.0.4 in R. Prevotellaceae, Lactobacillaceae, Leuconostocaceae, Clostridiales_Incertae_Sedis_XIII, Lachnospiraceae, and Peptostreptococcaceae were more abundant in LNR (P < 0.05) compared to HNR or MNR. Negative correlations were found between N retention and Mogibacterium, Anaerofustis, Butyrivibrio, Coprococcus, Hespellia, Lactonifactor and Lachnospiraceae (r ≤ -0.61; P≤ 0.05). Prevotella, Hespellia, Lactonifactor, Lachnospiraceae_other, and Anaerobiospirillum were positively correlated between urinary N excretion (r > 0.55; P < 0.01), and negative correlations were found with Elusimicrobia, Victivallis and Treponema (r < -0.41; P < 0.05). The adjustment of the rumen bacterial community differed significantly between the N use retention groups. The high N retention in beef cattle was associated with less abundant bacteria in the rumen; however, N fixation capacity and uncharacterized rumen microorganisms need to be elucidated in future studies. In contrast, lower N utilization was associated with high abundance of bacteria that promote greater urinary N excretion through ruminal protein degradation.}, } @article {pmid33382981, year = {2020}, author = {McCormick, BA and Chang, EB}, title = {The Gut Microbiome: Reaching the Promise Through Discovery- Advancing Knowledge and Discovery of the Gut Microbiome in the Age of Precision Medicine.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2020.12.035}, pmid = {33382981}, issn = {1528-0012}, } @article {pmid33382980, year = {2020}, author = {Dohlman, AB and Arguijo Mendoza, D and Ding, S and Gao, M and Dressman, H and Iliev, ID and Lipkin, SM and Shen, X}, title = {The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2020.12.001}, pmid = {33382980}, issn = {1934-6069}, abstract = {Studying the microbial composition of internal organs and their associations with disease remains challenging due to the difficulty of acquiring clinical biopsies. We designed a statistical model to analyze the prevalence of species across sample types from The Cancer Genome Atlas (TCGA), revealing that species equiprevalent across sample types are predominantly contaminants, bearing unique signatures from each TCGA-designated sequencing center. Removing such species mitigated batch effects and isolated the tissue-resident microbiome, which was validated by original matched TCGA samples. Gene copies and nucleotide variants can further distinguish mixed-evidence species. We, thus, present The Cancer Microbiome Atlas (TCMA), a collection of curated, decontaminated microbial compositions of oropharyngeal, esophageal, gastrointestinal, and colorectal tissues. This led to the discovery of prognostic species and blood signatures of mucosal barrier injuries and enabled systematic matched microbe-host multi-omic analyses, which will help guide future studies of the microbiome's role in human health and disease.}, } @article {pmid33382954, year = {2021}, author = {Laforest-Lapointe, I and Becker, AB and Mandhane, PJ and Turvey, SE and Moraes, TJ and Sears, MR and Subbarao, P and Sycuro, LK and Azad, MB and Arrieta, MC}, title = {Maternal consumption of artificially sweetened beverages during pregnancy is associated with infant gut microbiota and metabolic modifications and increased infant body mass index.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-15}, pmid = {33382954}, issn = {1949-0984}, abstract = {Artificial sweetener consumption by pregnant women has been associated with an increased risk of infant obesity, but the underlying mechanisms are unknown. We aimed to determine if maternal consumption of artificially sweetened beverages (ASB) during pregnancy is associated with modifications of infant gut bacterial community composition and function during the first year of life, and whether these alterations are linked with infant body mass index (BMI) at one year of age. We studied 100 infants from the prospective Canadian CHILD Cohort Study, selected based on maternal ASB consumption during pregnancy (50 non-consumers and 50 daily consumers). BMI was higher among ASB-exposed infants. Infant stool (16S rRNA gene sequencing) and urine (untargeted metabolomics) were acquired in early (3-4 months) and late (12 months) infancy. We identified four microbiome clusters, of which two recapitulated the maturation trajectory of the infant gut bacterial communities from immature (Cluster 1) to mature (Cluster 4) and two deviated from this trajectory (Clusters 2 and 3). Maternal ASB consumption did not differ between clusters, but was associated with community-level shifts in infant gut bacterial taxonomy structure and depletion of several Bacteroides sp. in Cluster 2. In the complete dataset, urine succinate and spermidine levels at 3 months were higher in ASB-exposed infants, and urine succinate was positively associated with BMI at one-year-old. Overall, gestational exposure to ASB was associated with gut microbiota structure in infants from Cluster 2, and gut microbiota structure was associated with infant BMI. Gestational exposure to ASB was positively associated with infant urine succinate and spermidine. Succinate was found to mediate 29% of the effect of ASB exposure on BMI at one-year-old, revealing a potential role of this metabolite in increased infant weight linked to gestational ASB consumption. As we face an unprecedented rise in childhood obesity, future studies should evaluate the causal relationships between maternal ASB consumption (a modifiable exposure), gut microbiota and metabolites, infant metabolism, and body composition.}, } @article {pmid33382948, year = {2021}, author = {Liu, W and Sun, Z and Ma, C and Zhang, J and Ma, C and Zhao, Y and Wei, H and Huang, S and Zhang, H}, title = {Exposure to soil environments during earlier life stages is distinguishable in the gut microbiome of adult mice.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-13}, pmid = {33382948}, issn = {1949-0984}, abstract = {Environmental exposure during earlier life stages can govern the assembly and development of gut microbiota, yet it is insufficiently understood. In this study, ex-germ-free mice were cohoused with distinct soil-microbiota (from desert, steppe, and forest) beddings within 60 days after birth and subsequently transferred to new soil beddings from 60 to 90th day. Using metagenomic shotgun sequencing, firstly, we found soil microbes from natural environments (birthplace) greatly influenced the gut community assembly in the housing experiment. About 27% microbial species and 12% functional components that associated with birthplaces at Day 60 were still discriminatory of birthplaces after transferring mice to new environments. Moreover, prior soil-exposure types are associated with the magnitude of temporal microbiome change due to environmental shifts. The appropriate soil-exposure (e.g., steppe) might help mice gut microbiome adapt to changing environments or host development. Our study demonstrated the continuous soil-exposure history earlier is associated with the gut microbiome individuality and development later.}, } @article {pmid33382917, year = {2020}, author = {Scott, EM and Lewin, AC and Leis, ML}, title = {Current ocular microbiome investigations limit reproducibility and reliability: Critical review and opportunities.}, journal = {Veterinary ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1111/vop.12854}, pmid = {33382917}, issn = {1463-5224}, abstract = {Enthusiasm for research describing microbial communities using next-generation sequencing (NGS) has outpaced efforts to standardize methodology. Without consistency in the way research is carried out in this field, the comparison of data between studies is near impossible and the utility of results remains limited. This holds true for bacterial microbiome research of the ocular surface, and other sites, in both humans and animals. In addition, the ocular surface remains under-explored when compared to other mucosal sites. Low bacterial biomass samples from the ocular surface lead to further technical challenges. Taken together, two major problems were identified: (1) Normalization of the workflow in studies utilizing NGS to investigate the ocular surface bacteriome is necessary in order to propel the field forward and improve research impact through cross-study comparisons. (2) Current microbiome profiling technology was developed for high bacterial biomass samples (such as feces or soil), posing a challenge for analyses of samples with low bacterial load such as the ocular surface. This article reviews the challenges and limitations currently facing ocular microbiome research and provides recommendations for minimum reporting standards for veterinary ophthalmologists and clinician scientists to limit inter-study variation, improve reproducibility, and ultimately render results from these studies more impactful. The move toward normalization of methodology will expedite and maximize the potential for microbiome research to translate into meaningful discovery and tangible clinical applications.}, } @article {pmid33382741, year = {2020}, author = {Peter, C and Thoms, S and Koch, F and Sartoris, FJ and Bickmeyer, U}, title = {Effects of sponge-derived Ageladine A on the photosynthesis of different microalgal species and strains.}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0244095}, pmid = {33382741}, issn = {1932-6203}, abstract = {Fluorescent natural compounds have been identified in several marine hosts of microalgae. Their prevalence, and the energy the host is expending on their synthesis, suggests an important, yet poorly understood ecological role. It has been suggested that some of these natural products may enhance the photosynthesis of microbial symbionts. In this study, the effect of Ageladine A (Ag A), a pH-dependent fluorophore found in sponges of the genus Agelas, on the photosynthesis of nine microalgal species and strains was examined. The data showed that the variety of effects of Ag A additions differed between species, and even strains within a species. While in one strain of Synechococcus sp., the presence of Ag A increased gross photosynthesis under UV light exposure, it decreased in another. And while in the chlorophyte T. chuii overall metabolic activity was greatly reduced under all forms of lighting, photosynthesis in T. lutea was positively affected by the addition of Ag A. The variety of effects of Ag A on photosynthesis observed in this study indicate a complex interaction of Ag A with microalgal cells and suggests that a host may be able to shape its own symbiotic microbiome with self-produced natural products.}, } @article {pmid33382620, year = {2021}, author = {Mei, F and Meng, K and Gu, Z and Yun, Y and Zhang, W and Zhang, C and Zhong, Q and Pan, F and Shen, X and Xia, G and Chen, H}, title = {Arecanut (Areca catechu L.) Seed Polyphenol-Ameliorated Osteoporosis by Altering Gut Microbiome via LYZ and the Immune System in Estrogen-Deficient Rats.}, journal = {Journal of agricultural and food chemistry}, volume = {69}, number = {1}, pages = {246-258}, doi = {10.1021/acs.jafc.0c06671}, pmid = {33382620}, issn = {1520-5118}, abstract = {Polyphenol can improve osteoporosis and is closely associated with gut microbiota, while the mechanism and the relationship among polyphenol, osteoporosis, and gut microbiota colonization remain unclear. Here, an osteoporosis rat model established by ovariectomy was employed to investigate the improving mechanism of arecanut (Areca catechu L.) seed polyphenol (ACP) on osteoporosis by regulating gut microbiota. We analyzed the bone microstructure, Paneth cells, regulating microbial protein (lysozyme (LYZ)), proinflammatory cytokines, macrophage infiltration levels, and gut microbial communities in a rat. ACP improved the trabecular microstructure compared to OVX, including the increased trabecular number (Tb.N) (P < 0.01) and trabecular thickness (Tb.Th) (P < 0.001) and decreased trabecular separation (Tb.Sp) (P < 0.01). At the phylum level, Bacteroidetes was increased after ovariectomy (P < 0.001) and Firmicutes and Proteobacteria were increased in ACP (P < 0.001). Antiosteoporosis groups with lower LYZ and Paneth cells (P < 0.001) showed that the microbiota Alistipes, which have a negative effect on bone metabolism were decreased in ACP (P < 0.001). Altogether, these studies showed that the estrogen deficiency could induce the shedding of Paneth cells, which leads to the decrease of LYZ, while ACP could increase the LYZ expression by maintaining the population of Paneth cells in an estrogen-deficient host, which were implicated in gut microbiota regulation and improved osteoporosis by controlling the inflammatory reaction.}, } @article {pmid33382431, year = {2020}, author = {Abernathy, BE and Schoenfuss, TC and Bailey, AS and Gallaher, DD}, title = {Polylactose Exhibits Prebiotic Activity and Reduces Adiposity and Nonalcoholic Fatty Liver Disease in Rats Fed a High-Fat Diet.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1093/jn/nxaa376}, pmid = {33382431}, issn = {1541-6100}, support = {T32 DK083250/DK/NIDDK NIH HHS/United States ; }, abstract = {BACKGROUND: Prebiotic dietary fibers change the intestinal microbiome favorably and provide a health benefit to the host.

OBJECTIVES: Polylactose is a novel fiber, synthesized by extrusion of lactose. We evaluated its prebiotic activity by determining its fermentability, effect on the microbiota, and effects on adiposity and liver lipids in a diet-induced obesity animal model.

METHODS: Male Wistar rats (4-5 wk old) were fed normal-fat (NF, 25% fat energy) or high-fat (HF, 51% fat energy) diets containing different fibers (6% fiber of interest and 3% cellulose, by weight), including cellulose (NFC and HFC, negative and positive controls, respectively), polylactose (HFPL), lactose matched to residual lactose in the HFPL diet, and 2 established prebiotic fibers: polydextrose (HFPD) and fructooligosaccharide (HFFOS). After 10 wk of feeding, organs were harvested and cecal contents collected.

RESULTS: HFPL animals had greater cecum weight (3 times greater than HFC) and lower cecal pH (∼1 pH unit lower than HFC) than all other groups, suggesting that polylactose is more fermentable than other prebiotic fibers (HFPD, HFFOS; P < 0.05). HFPL animals also had increased taxonomic abundance of the probiotic species Bifidobacterium in the cecum relative to all other groups (P < 0.05). Epididymal fat pad weight was significantly decreased in the HFPL group (29% decrease compared with HFC) compared with all other HF groups (P < 0.05) and did not differ from the NFC group. Liver lipids and cholesterol were reduced in HFPL animals when compared with HFC animals (P < 0.05).

CONCLUSIONS: Polylactose is a fermentable fiber that elicits a beneficial change in the gut microbiota as well as reducing adiposity in rats fed HF diets. These effects of polylactose were greater than those of 2 established prebiotics, fructooligosaccharide and polydextrose, suggesting that polylactose is a potent prebiotic.}, } @article {pmid33382352, year = {2021}, author = {Vijay, A and Astbury, S and Le Roy, C and Spector, TD and Valdes, AM}, title = {The prebiotic effects of omega-3 fatty acid supplementation: A six-week randomised intervention trial.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-11}, pmid = {33382352}, issn = {1949-0984}, abstract = {Prebiotics are compounds in food that benefit health via affecting the gut microbiome. Omega-3 fatty acids have been associated with differences in gut microbiome composition and are widely accepted to have health benefits, although recent large trials have been inconclusive. We carried out a 6-week dietary intervention comparing the effects of daily supplementation with 500 mg of omega-3 versus 20 g of a well-characterized prebiotic, inulin. Inulin supplementation resulted in large increases in Bifidobacterium and Lachnospiraceae. In contrast, omega-3 supplementation resulted in significant increases in Coprococcus spp. and Bacteroides spp, and significant decreases in the fatty-liver associated Collinsella spp. On the other hand, similar to the results with inulin supplementation which resulted in significant increases in butyrate, iso-valerate, and iso-butyrate (p < .004), omega-3 supplementation resulted in significant increases in iso-butyrate and isovalerate (p < .002) and nearly significant increases in butyrate (p < .053). Coprococcus, which was significantly increased post-supplementation with omega-3, was found to be positively associated with iso-butyric acid (Beta (SE) = 0.69 (0.02), P = 1.4 x 10-3) and negatively associated with triglyceride-rich lipoproteins such as VLDL (Beta (SE) = -0.381 (0.01), P = .001) and VLDL-TG (Beta (SE) = -0.372 (0.04), P = .001) after adjusting for confounders. Dietary omega-3 alters gut microbiome composition and some of its cardiovascular effects appear to be potentially mediated by its effect on gut microbial fermentation products indicating that it may be a prebiotic nutrient.}, } @article {pmid33382003, year = {2021}, author = {Papadakis, G and Kandaraki, EA and Garidou, A and Koutsaki, M and Papalou, O and Diamanti-Kandarakis, E and Peppa, M}, title = {Tailoring treatment for PCOS phenotypes.}, journal = {Expert review of endocrinology & metabolism}, volume = {16}, number = {1}, pages = {9-18}, doi = {10.1080/17446651.2021.1865152}, pmid = {33382003}, issn = {1744-8417}, abstract = {Introduction: Polycystic ovary syndrome (PCOS) is one of the most common endocrinopathies in reproductive-aged women. Hyperandrogenism, polycystic ovaries, chronic anovulation, and metabolic aberrations are its common features. The treatment approach focuses on the main aberrations, which characterize the different phenotypes. Areas covered: Management strategies targeting the metabolic phenotype include lifestyle modifications for weight loss and improvement of dietary habits, as well as medication, such as insulin-sensitizers. The treatment of hyperandrogenic phenotype includes cosmetic procedures and the combined oral contraceptives with or without antiandrogens. The therapeutic approach to reproductive phenotype includes diet and lifestyle modifications, clomiphene citrate, and aromatase inhibitors. Alternative treatments include dietary supplements, herbs, resveratrol, myo-inositol, and acupuncture. Expert opinion: New studies have shown that higher anti-Müllerian hormone levels, gut microbiome composition, and plasma metabolomics are new parameters that are related to the most severe phenotypes. The clinical phenotypes can change over the lifespan with weight gain and can coexist in the same individual. Individualized treatment remains the main approach but grouping the phenotypes and following therapeutic recommendations may prove to be also clinically appropriate.}, } @article {pmid33381966, year = {2020}, author = {Yu, Z and Schwarz, C and Zhu, L and Chen, L and Shen, Y and Yu, P}, title = {Hitchhiking Behavior in Bacteriophages Facilitates Phage Infection and Enhances Carrier Bacteria Colonization.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.0c06969}, pmid = {33381966}, issn = {1520-5851}, abstract = {Interactions between bacteriophages (phages) and biofilms remain poorly understood despite the broad implications for microbial ecology, water quality, and microbiome engineering. Here, we demonstrate that lytic coliphage PHH01 can hitchhike on carrier bacteria Bacillus cereus to facilitate its infection of host bacteria, Escherichia coli, in biofilms. Specifically, PHH01 could adsorb onto the flagella of B. cereus, and thus phage motility was increased, resulting in 4.36-fold more effective infection of E. coli in biofilm relative to free PHH01 alone. Moreover, phage infection mitigated interspecies competition and enhanced B. cereus colonization; the fraction of B. cereus in the final biofilm increased from 9% without phages to 43% with phages. The mutualistic relationship between the coliphage and carrier bacteria was substantiated by migration tests on an E. coli lawn: the conjugation of PHH01 and B. cereus enhanced B. cereus colonization by 6.54-fold compared to B. cereus alone (6.15 vs 0.94 cm2 in 24 h) and PHH01 migration by 5.15-fold compared to PHH01 alone (10.3 vs 2.0 mm in 24 h). Metagenomic and electron microscopic analysis revealed that the phages of diverse taxonomies and different morphologies could be adsorbed by the flagella of B. cereus, suggesting hitchhiking on flagellated bacteria might be a widespread strategy in aquatic phage populations. Overall, our study highlights that hitchhiking behavior in phages can facilitate phage infection of biofilm bacteria, promote carrier bacteria colonization, and thus significantly influence biofilm composition, which holds promise for mediating biofilm functions and moderating associated risks.}, } @article {pmid33381745, year = {2020}, author = {Woodruff, KL and Hummel, GL and Austin, KJ and Smith, TL and Cunningham-Hollinger, HC}, title = {Influence of the maternal rumen microbiome on development of the calf meconium and rumen microbiome.}, journal = {Translational animal science}, volume = {4}, number = {Suppl 1}, pages = {S169-S173}, pmid = {33381745}, issn = {2573-2102}, } @article {pmid33381671, year = {2021}, author = {Rizk, MG and Thackray, VG}, title = {Intersection of Polycystic Ovary Syndrome and the Gut Microbiome.}, journal = {Journal of the Endocrine Society}, volume = {5}, number = {2}, pages = {bvaa177}, pmid = {33381671}, issn = {2472-1972}, support = {P50 HD012303/HD/NICHD NIH HHS/United States ; R01 HD095412/HD/NICHD NIH HHS/United States ; T32 HD007203/HD/NICHD NIH HHS/United States ; }, abstract = {The etiology of polycystic ovary syndrome (PCOS) remains unclear, although studies indicate that both genetic and environmental factors contribute to the syndrome. In 2012, Tremellen and Pearce proposed the idea that dysbiosis of the intestinal (gut) microbiome is a causative factor of metabolic and reproductive manifestations of PCOS. In the past 5 years, studies in both humans and rodent models have demonstrated that changes in the taxonomic composition of gut bacteria are associated with PCOS. Studies have also clearly shown that these changes in gut microbiota are associated with PCOS as opposed to obesity, since these changes are observed in women with PCOS that are both of a normal weight or obese, as well as in adolescent girls with PCOS and obesity compared with body mass index- and age-matched females without the disorder. Additionally, studies in both women with PCOS and rodent models of PCOS demonstrated that hyperandrogenism is associated with gut microbial dysbiosis, indicating that androgens may modulate the gut microbial community in females. One study reported that the fecal microbiome transplantation of stool from women with PCOS or exposure to certain bacteria resulted in a PCOS-like phenotype in mice, while other studies showed that exposure to a healthy gut microbiome, pre/probiotics, or specific gut metabolites resulted in protection from developing PCOS-like traits in mice. Altogether, these results suggest that dysbiosis of the gut microbiome may be sufficient to develop PCOS-like symptoms and that modulation of the gut microbiome may be a potential therapeutic target for PCOS.}, } @article {pmid33381452, year = {2020}, author = {Ekine-Afolabi, BA and Njan, AA and Rotimi, SO and R I, A and Elbehi, AM and Cash, E and Adeyeye, A}, title = {The Impact of Diet on the Involvement of Non-Coding RNAs, Extracellular Vesicles, and Gut Microbiome-Virome in Colorectal Cancer Initiation and Progression.}, journal = {Frontiers in oncology}, volume = {10}, number = {}, pages = {583372}, pmid = {33381452}, issn = {2234-943X}, abstract = {Cancer is the major cause of morbidity and mortality in the world today. The third most common cancer and which is most diet related is colorectal cancer (CRC). Although there is complexity and limited understanding in the link between diet and CRC, the advancement in research methods have demonstrated the involvement of non-coding RNAs (ncRNAs) as key regulators of gene expression. MicroRNAs (miRNAs) which are a class of ncRNAs are key players in cancer related pathways in the context of dietary modulation. The involvement of ncRNA in cancer progression has recently been clarified throughout the last decade. ncRNAs are involved in biological processes relating to tumor onset and progression. The advances in research have given insights into cell to cell communication, by highlighting the pivotal involvement of extracellular vesicle (EV) associated-ncRNAs in tumorigenesis. The abundance and stability of EV associated ncRNAs act as a new diagnostic and therapeutic target for cancer. The understanding of the deranging of these molecules in cancer can give access to modulating the expression of the ncRNAs, thereby influencing the cancer phenotype. Food derived exosomes/vesicles (FDE) are gaining interest in the implication of exosomes in cell-cell communication with little or no understanding to date on the role FDE plays. There are resident microbiota in the colon; to which the imbalance in the normal intestinal occurrence leads to chronic inflammation and the production of carcinogenic metabolites that lead to neoplasm. Limited studies have shown the implication of various types of microbiome in CRC incidence, without particular emphasis on fungi and protozoa. This review discusses important dietary factors in relation to the expression of EV-associated ncRNAs in CRC, the impact of diet on the colon ecosystem with particular emphasis on molecular mechanisms of interactions in the ecosystem, the influence of homeostasis regulators such as glutathione, and its conjugating enzyme-glutathione S-transferase (GST) polymorphism on intestinal ecosystem, oxidative stress response, and its relationship to DNA adduct fighting enzyme-0-6-methylguanine-DNA methyltransferase. The understanding of the molecular mechanisms and interaction in the intestinal ecosystem will inform on the diagnostic, preventive and prognosis as well as treatment of CRC.}, } @article {pmid33381303, year = {2020}, author = {Lukiw, WJ}, title = {Human gastrointestinal (GI) tract microbiome-derived pro-inflammatory neurotoxins from Bacteroides fragilis: Effects of low fiber diets and environmental and lifestyle factors.}, journal = {Integrative food, nutrition and metabolism}, volume = {7}, number = {1}, pages = {}, pmid = {33381303}, issn = {2056-8339}, support = {R01 AG018031/AG/NIA NIH HHS/United States ; R01 AG038834/AG/NIA NIH HHS/United States ; R01 EY006311/EY/NEI NIH HHS/United States ; }, } @article {pmid33381248, year = {2020}, author = {Zhang, J and Su, L and Wang, Y and Deng, S}, title = {Improved High-Throughput Sequencing of the Human Oral Microbiome: From Illumina to PacBio.}, journal = {The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2020}, number = {}, pages = {6678872}, pmid = {33381248}, issn = {1712-9532}, abstract = {Background: A comprehensive understanding of the commensal microflora and its relation to health is essential for preventing and combating diseases. The aim of this study was to examine the structure of the oral microbiome by using different sequencing technologies. Material and Methods. Five preschool children with no symptoms of oral and systemic diseases were recruited. Samples of saliva were collected. A 468 bp insert size library was constructed on the MiSeq platform and then subjected to 300 bp paired-end sequencing. Libraries with longer insert sizes, including a full-length 16S rDNA gene, were sequenced on the PacBio RS II platform.

Results: A total of 122.6 Mb of raw data, including 244,967 high-quality sequences, were generated by the MiSeq platform, while 134.6 Mb of raw data, including 70,030 high-quality reads, were generated by the PacBio RS II platform. Clustering of the unique sequences into OTUs at 3% dissimilarity resulted in an average of 225 OTUs on the MiSeq platform; however, the number of OTUs generated on the PacBio RS II platform was 449, far greater than the number of OTUs generated on the MiSeq platform. A total of 437 species belonging to 10 phyla and 60 genera were detected by the PacBio RS II platform, while 163 species belonging to 12 phyla and 72 genera were detected by the MiSeq platform.

Conclusions: The oral microflora of healthy Chinese children were analyzed. Compared with traditional 16S rRNA sequencing technology, the PacBio system, despite providing a lower amount of clean data, surpassed the resolution of the MiSeq platform by improving the read length and annotating the nucleotide sequences at the species or strain level. This trial is registered with NCT02341352.}, } @article {pmid33381156, year = {2020}, author = {Xu, X and Xie, Z and Yang, Z and Li, D and Xu, X}, title = {A t-SNE Based Classification Approach to Compositional Microbiome Data.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {620143}, pmid = {33381156}, issn = {1664-8021}, abstract = {As a data-driven dimensionality reduction and visualization tool, t-distributed stochastic neighborhood embedding (t-SNE) has been successfully applied to a variety of fields. In recent years, it has also received increasing attention for classification and regression analysis. This study presented a t-SNE based classification approach for compositional microbiome data, which enabled us to build classifiers and classify new samples in the reduced dimensional space produced by t-SNE. The Aitchison distance was employed to modify the conditional probabilities in t-SNE to account for the compositionality of microbiome data. To classify a new sample, its low-dimensional features were obtained as the weighted mean vector of its nearest neighbors in the training set. Using the low-dimensional features as input, three commonly used machine learning algorithms, logistic regression (LR), support vector machine (SVM), and decision tree (DT) were considered for classification tasks in this study. The proposed approach was applied to two disease-associated microbiome datasets, achieving better classification performance compared with the classifiers built in the original high-dimensional space. The analytic results also showed that t-SNE with Aitchison distance led to improvement of classification accuracy in both datasets. In conclusion, we have developed a t-SNE based classification approach that is suitable for compositional microbiome data and may also serve as a baseline for more complex classification models.}, } @article {pmid33381121, year = {2020}, author = {Fidelle, M and Yonekura, S and Picard, M and Cogdill, A and Hollebecque, A and Roberti, MP and Zitvogel, L}, title = {Resolving the Paradox of Colon Cancer Through the Integration of Genetics, Immunology, and the Microbiota.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {600886}, pmid = {33381121}, issn = {1664-3224}, abstract = {While colorectal cancers (CRC) are paradigmatic tumors invaded by effector memory lymphocytes, the mechanisms accounting for the relative resistance of MSI negative CRC to immunogenic cell death mediated by oxaliplatin and immune checkpoint inhibitors has remained an open conundrum. Here, we propose the viewpoint where its microenvironmental contexture could be explained -at least in part- by macroenvironmental cues constituted by the complex interplay between the epithelial barrier, its microbial ecosystem, and the local immune system. Taken together this dynamic ménage-à-trois offers novel coordinated actors of the humoral and cellular immune responses actionable to restore sensitivity to immune checkpoint inhibition. Solving this paradox involves breaking tolerance to crypt stem cells by inducing the immunogenic apoptosis of ileal cells in the context of an ileal microbiome shifted towards immunogenic bacteria using cytotoxicants. This manoeuver results in the elicitation of a productive Tfh and B cell dialogue in mesenteric lymph nodes culminating in tumor-specific memory CD8+ T cell responses sparing the normal epithelium.}, } @article {pmid33381096, year = {2020}, author = {Napieralski, SA and Roden, EE}, title = {The Weathering Microbiome of an Outcropping Granodiorite.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {601907}, pmid = {33381096}, issn = {1664-302X}, abstract = {Microorganisms have long been recognized for their capacity to catalyze the weathering of silicate minerals. While the vast majority of studies on microbially mediated silicate weathering focus on organotrophic metabolism linked to nutrient acquisition, it has been recently demonstrated that chemolithotrophic ferrous iron [Fe(II)] oxidizing bacteria (FeOB) are capable of coupling the oxidation of silicate mineral Fe(II) to metabolic energy generation and cellular growth. In natural systems, complex microbial consortia with diverse metabolic capabilities can exist and interact to influence the biogeochemical cycling of essential elements, including iron. Here we combine microbiological and metagenomic analyses to investigate the potential interactions among metabolically diverse microorganisms in the near surface weathering of an outcrop of the Rio Blanco Quartz Diorite (DIO) in the Luquillo Mountains of Puerto Rico. Laboratory based incubations utilizing ground DIO as metabolic energy source for chemolithotrophic FeOB confirmed the ability of FeOB to grow via the oxidation of silicate-bound Fe(II). Dramatically accelerated rates of Fe(II)-oxidation were associated with an enrichment in microorganisms with the genetic capacity for iron oxidizing extracellular electron transfer (EET) pathways. Microbially oxidized DIO displayed an enhanced susceptibility to the weathering activity of organotrophic microorganisms compared to unoxidized mineral suspensions. Our results suggest that chemolithotrophic and organotrophic microorganisms are likely to coexist and contribute synergistically to the overall weathering of the in situ bedrock outcrop.}, } @article {pmid33381090, year = {2020}, author = {Ni, Q and Ye, Z and Wang, Y and Chen, J and Zhang, W and Ma, C and Li, K and Liu, Y and Liu, L and Han, Z and Gao, T and Jian, Z and Li, S and Li, C}, title = {Gut Microbial Dysbiosis and Plasma Metabolic Profile in Individuals With Vitiligo.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {592248}, pmid = {33381090}, issn = {1664-302X}, abstract = {Autoimmune diseases are increasingly linked to aberrant gut microbiome and relevant metabolites. However, the association between vitiligo and the gut microbiome remains to be elucidated. Thus, we conducted a case-control study through 16S rRNA sequencing and serum untargeted-metabolomic profiling based on 30 vitiligo patients and 30 matched healthy controls. In vitiligo patients, the microbial composition was distinct from that of healthy controls according to the analysis on α- and β-diversity (P < 0.05), with a characteristic decreased Bacteroidetes: Firmicutes ratio. Meanwhile, the levels of 23 serum metabolites (including taurochenodeoxycholate and L-NG-monomethyl-arginine) in the vitiligo patients were different from those in the healthy individuals and showed significant correlations with some microbial markers. We found that Corynebacterium 1, Ruminococcus 2, Jeotgalibaca and Psychrobacter were correlated significantly with disease duration and serum IL-1β level in vitiligo patients. And Psychrobacter was identified as the most predictive features for vitiligo by machine learning analysis ("importance" = 0.0236). Finally, combining multi-omics data and joint prediction models with accuracies up to 0.929 were established with dominant contribution of Corynebacterium 1 and Psychrobacter. Our findings replenished the previously unknown relationship between gut dysbiosis and vitiligo circulating metabolome and enrolled the gut-skin axis into the understanding of vitiligo pathogenesis.}, } @article {pmid33380931, year = {2020}, author = {Royal, C and Gray, C}, title = {Allergy Prevention: An Overview of Current Evidence.}, journal = {The Yale journal of biology and medicine}, volume = {93}, number = {5}, pages = {689-698}, pmid = {33380931}, issn = {1551-4056}, abstract = {Background: There has been a rapid rise in allergic disorders across the globe. This has increased research into the determinants of allergy development, to identify factors that may be manipulated to mitigate risk. An opportune window in immunological development appears to exist in early life whereby certain exposures may promote or prevent the development of an allergic disposition. Furthermore, factors that affect the composition and diversity of the microbiome in early life have been explored. In this review, we discuss current literature and recommendations relating to exposures that may prevent allergy development or promote tolerance. Risk factors and recommendations: Delivery by caesarean section, omission of breastfeeding, vitamin D insufficiency, and environmental exposures, such as cigarette smoke exposure, all increase the risk of an allergic predisposition. Dietary diversity during pregnancy, lactation, and in infancy is protective. Breastfeeding for at least 4 months reduces the risk of eczema. Recommendations for food-allergen exposure has shifted from delayed introduction to early introduction as a tolerance-inducing strategy. Supplements such as probiotics and vitamins during pregnancy and infancy have yet to produce conclusive results for allergy prevention. Emollient use in infancy has not been shown to be protective against eczema or food allergy.}, } @article {pmid33380819, year = {2020}, author = {Khmaladze, I and Leonardi, M and Fabre, S and Messaraa, C and Mavon, A}, title = {The Skin Interactome: A Holistic "Genome-Microbiome-Exposome" Approach to Understand and Modulate Skin Health and Aging.}, journal = {Clinical, cosmetic and investigational dermatology}, volume = {13}, number = {}, pages = {1021-1040}, pmid = {33380819}, issn = {1178-7015}, abstract = {Higher demands on skin care cosmetic products for strong performance drive intense research to understand the mechanisms of skin aging and design strategies to improve overall skin health. Today we know that our needs and influencers of skin health and skin aging change throughout our life journey due to both extrinsic factors, such as environmental factors and lifestyle factors, as well as our intrinsic factors. Furthermore, we need to consider our microflora, a collection of micro-organisms such as bacteria, viruses, and fungi, which is a living ecosystem in our gut and on our skin, that can have a major impact on our health. Here, we are viewing a holistic approach to understand the collective effect of the key influencers of skin health and skin aging both reviewing how each of them impact the skin, but more importantly to identify molecular conjunction pathways of these different factors in order to get a better understanding of the integrated "genome-microbiome-exposome" effect. For this purpose and in order to translate molecularly the impact of the key influencers of skin health and skin aging, we built a digital model based on system biology using different bioinformatics tools. This model is considering both the positive and negative impact of our genome (genes, age/gender), exposome: external (sun, pollution, climate) and lifestyle factors (sleep, stress, exercise, nutrition, skin care routine), as well as the role of our skin microbiome, and allowed us in a first application to evaluate the effect of the genome in the synthesis of collagen in the skin and the determination of a suitable target for boosting pro-collagen synthesis. In conclusion, we have, through our digital holistic approach, defined the skin interactome concept, as an advanced tool to better understand the molecular genesis of skin aging and further develop a strategy to balance the influence of the exposome and microbiome to protect, prevent, and delay the appearance of skin aging signs and preserve good skin health condition. In addition, this model will aid in identifying and optimizing skin treatment options based on external triggers, as well as helping to design optimal treatments modulating the intrinsic pathways.}, } @article {pmid33380398, year = {2020}, author = {Zhai, Q and Ren, T and Fu, Y and Zhang, Z and Li, L and Li, Y and Meng, Y}, title = {[Characteristics of cervical microecology in late reproductive-age women with different grades of cervical lesions].}, journal = {Nan fang yi ke da xue xue bao = Journal of Southern Medical University}, volume = {40}, number = {12}, pages = {1768-1775}, doi = {10.12122/j.issn.1673-4254.2020.12.11}, pmid = {33380398}, issn = {1673-4254}, abstract = {OBJECTIVE: To analyze the characteristics of cervical microecology in late reproductive-age women with cervical lesions and explore new methods for preventing cervical lesions.

METHODS: Cervical smears were obtained from a total of 147 women of late reproductive age, including 24 with high-risk HPV infection (HR-HPV), 27 with low-grade squamous intra-epithelial lesions (LSIL), 36 with high-grade squamous intra-epithelial lesions (HSIL), 35 with cervical cancer (CC) and 25 healthy women. llumina MiSeq sequencing of V3-V4 region of the 16S rRNA gene amplicons was used to characterize the vaginal microbiota of the women. OTUs analysis of the valid data was performed, and the α-diversity (Chao1, Simpson's Index and Shannon Index) and β-diversity (T-test, weighted UniFrac β diversity, and MetaStat analysis) were evaluated.

RESULTS: Dilution curve and species accumulation boxplot validated the quality of the samples. OTUs analysis of the 5 groups demonstrated that cervical bacterial genus consisted primarily of Lactobacillus, Garrotella and Prussiella. With the aggravation of the lesions, the expression abundance of Lactobacillus was decreased, and Gardnerella and Prussiella were increased. The Chao1, Simpson and Shannon indexex showed no significant difference. T test indicated that 9 to 15 genera from 4 groups showed significant difference from the healthy control group. In all but the LSIL group, Lactobacillus (P1-2=0.025, P1-3=0.025, P1-4 < 0.001), Gardiner (P1-2=0.01, P1-3=0.001, P1-4 < 0.001), and Pruella (P1-2=0.047, P1-3=0.023, P1-4=0.048) showed the highest abundance in the cervical smears. The abundance of Gardiner (P1-3=0.021), Ignatius (P1-3=0.015) and Streptococcus (P1-3=0.041) was the highest in women with LSIL as compared with healthy women. In all the 5 groups, MetaStat analysis showed that lactobacillus (P1-4=0.025), gardnella (P1-2=0.004, P1-4=0.002, P1-5=0.001) and proctella (P3-5=0.005) had the highest abundance in the cervical flora.

CONCLUSIONS: The abundance of Lactobacillus, Gardnella and Proctella is the highest in cervical bacteria at the genus level and may vary with disease progression. The α-diversity does not differ significantly, suggesting that apart from pathological factors, physiological factors also contribute to the difference in α-diversity. Women with LSIL have the most similar cervical flora to healthy women, which is consistent with the prognosis of the disease and confirms that the expression of cervical microecology is related to disease prognosis and may serve as a biological indicator for favoralble prognosis.}, } @article {pmid33380389, year = {2020}, author = {Liu, Y and Huang, Y and Cai, W and Li, D and Zheng, W and Xiao, Y and Liu, Y and Zhao, H and Pan, S}, title = {[Effect of oral Lactobacillusrhamnosus GR-1 and Lactobacillusreuteri RC-14 on vaginal Group B Streptococcus colonization and vaginal microbiome in late pregnancy].}, journal = {Nan fang yi ke da xue xue bao = Journal of Southern Medical University}, volume = {40}, number = {12}, pages = {1753-1759}, doi = {10.12122/j.issn.1673-4254.2020.12.09}, pmid = {33380389}, issn = {1673-4254}, abstract = {OBJECTIVE: To explore the effects of intervention with oral probiotic Lactobacillus rhamnosus GR-1 and Lactobacillusreuteri RC-14 on vaginal Group B Streptococcus (GBS) colonization, pregnancy outcome and vaginal microbiome in GBS-positive women in the third trimester of pregnancy.

METHODS: This study were conducted among 155 women in the third trimester of pregnancy with positive results of GBS culture in the Outpatient Department of Zhujiang Hospital from March to November, 2019. After excluding 32 patients who received lactobacillus intervention for less than 2 weeks or underwent postpartum GBS retesting, the women were divided into oral probiotics intervention group (60 cases) and non-intervention group (63 cases). According to the results of GBS retesting, the 60 women in the intervention group were divided into GBS-negative group (18 cases) and persistent GBS-positive group (42 cases). At the end of the intervention, the rates of negative GBS culture result were calculated and the pregnancy outcomes were compared. From 5 women randomly selected from the intervention group, samples of vaginal secretions were collected before and after the intervention for amplicon sequencing and bioinformatics analysis.

RESULTS: At the end of the intervention, the GBS-negative rate in the intervention group was 30% (18/60), as compared with 23% (3/13) in the non-intervention group. Probiotic intervention significantly reduced the incidence of premature rupture of membranes (P < 0.05) and reduced the use of antibiotics during pregnancy (P < 0.05). OTU analysis of the vaginal secretions suggested probiotic intervention decreased the total sequence number and GBS sequence number, increased the species composition, and significantly decreased GBS abundance (P < 0.05). Probiotics intervention also significantly decreased the species abundance of Enterococcus, Staphylococcus and Streptococcus in the vaginal flora (P < 0.05).

CONCLUSIONS: Intervention with oral probiotics can reduce vaginal GBS colonization in late pregnancy and improve the pregnancy outcome. Lactobacillus is capable of reducing the abundance of GBS and other pathogenic bacteria to improve the microbiome of vaginal flora.}, } @article {pmid33380119, year = {2020}, author = {Šiarnik, P and Klobučníková, K and Mucska, I and Hlucháňová, A and Hanus, O and Turčáni, P and Kollár, B}, title = {Obstructive sleep apnea and hypertension: the role of gut microbiome.}, journal = {Vnitrni lekarstvi}, volume = {66}, number = {7}, pages = {415-419}, pmid = {33380119}, issn = {0042-773X}, mesh = {Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Hypertension/complications/epidemiology ; *Sleep Apnea Syndromes ; *Sleep Apnea, Obstructive/complications ; }, abstract = {Obstructive sleep apnea is common disorder affecting approximately one quarter of the common population. Prevalence is even higher in a population with increased vascular risk. Obstructive sleep apnea is a significant risk factor for hypertension, with approximately 50% of obstructive sleep apnea patients suffering hypertension. While the relationship between sleep apnea and hypertension has been firmly established, mechanisms linking these disorders are still poorly understood. Importance of sympathetic nervous system and renin-angiotensin-aldosterone system hyperactivity as well as endothelial dysfunction is suspected. There is increasing evidence supporting gut dysbiosis as one of the underlying mechanisms. Current article describes possible mechanisms linking obstructive sleep apnea with the development of hypertension. The role of gut microbiota in this process is discussed more closely.}, } @article {pmid33379176, year = {2020}, author = {Crivelli, JJ and Mitchell, T and Knight, J and Wood, KD and Assimos, DG and Holmes, RP and Fargue, S}, title = {Contribution of Dietary Oxalate and Oxalate Precursors to Urinary Oxalate Excretion.}, journal = {Nutrients}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/nu13010062}, pmid = {33379176}, issn = {2072-6643}, support = {665510//American Urological Association Foundation/ ; 5K01DK106284-04/DK/NIDDK NIH HHS/United States ; 1R03DK123542-01/DK/NIDDK NIH HHS/United States ; 5R01DK087967-08/DK/NIDDK NIH HHS/United States ; 1R01DK126774-01/DK/NIDDK NIH HHS/United States ; 5K08DK115833-02/DK/NIDDK NIH HHS/United States ; 5P20DK119788-02/DK/NIDDK NIH HHS/United States ; 5K01DK114332-03/DK/NIDDK NIH HHS/United States ; }, abstract = {Kidney stone disease is increasing in prevalence, and the most common stone composition is calcium oxalate. Dietary oxalate intake and endogenous production of oxalate are important in the pathophysiology of calcium oxalate stone disease. The impact of dietary oxalate intake on urinary oxalate excretion and kidney stone disease risk has been assessed through large cohort studies as well as smaller studies with dietary control. Net gastrointestinal oxalate absorption influences urinary oxalate excretion. Oxalate-degrading bacteria in the gut microbiome, especially Oxalobacter formigenes, may mitigate stone risk through reducing net oxalate absorption. Ascorbic acid (vitamin C) is the main dietary precursor for endogenous production of oxalate with several other compounds playing a lesser role. Renal handling of oxalate and, potentially, renal synthesis of oxalate may contribute to stone formation. In this review, we discuss dietary oxalate and precursors of oxalate, their pertinent physiology in humans, and what is known about their role in kidney stone disease.}, } @article {pmid33379148, year = {2020}, author = {Lee, NY and Suk, KT}, title = {The Role of the Gut Microbiome in Liver Cirrhosis Treatment.}, journal = {International journal of molecular sciences}, volume = {22}, number = {1}, pages = {}, pmid = {33379148}, issn = {1422-0067}, support = {HURF-2018-67//Hallym University/ ; NRF-2020R1A6A1A03043026//Korea National Research/ ; }, abstract = {Liver cirrhosis is one of the most prevalent chronic liver diseases worldwide. In addition to viral hepatitis, diseases such as steatohepatitis, autoimmune hepatitis, sclerosing cholangitis and Wilson's disease can also lead to cirrhosis. Moreover, alcohol can cause cirrhosis on its own and exacerbate chronic liver disease of other causes. The treatment of cirrhosis can be divided into addressing the cause of cirrhosis and reversing liver fibrosis. To this date, there is still no clear consensus on the treatment of cirrhosis. Recently, there has been a lot of interest in potential treatments that modulate the gut microbiota and gut-liver axis for the treatment of cirrhosis. According to recent studies, modulation of the gut microbiome by probiotics ameliorates the progression of liver disease. The precise mechanism for relieving cirrhosis via gut microbial modulation has not been identified. This paper summarizes the role and effects of the gut microbiome in cirrhosis based on experimental and clinical studies on absorbable antibiotics, probiotics, prebiotics, and synbiotics. Moreover, it provides evidence of a relationship between the gut microbiome and liver fibrosis.}, } @article {pmid33378964, year = {2021}, author = {Wei, H and Wang, L and An, Z and Xie, H and Liu, W and Du, Q and Guo, Y and Wu, X and Li, S and Shi, Y and Zhang, X and Liu, H}, title = {QiDiTangShen granules modulated the gut microbiome composition and improved bile acid profiles in a mouse model of diabetic nephropathy.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {133}, number = {}, pages = {111061}, doi = {10.1016/j.biopha.2020.111061}, pmid = {33378964}, issn = {1950-6007}, abstract = {QiDiTangShen granules (QDTS), a traditional Chinese herbal medicine, have been used in clinical practice for treating diabetic kidney disease for several years. In our previous study, we have demonstrated that QDTS displayed good efficacy on reducing proteinuria in mice with diabetic nephropathy (DN). However, the exact mechanism by which QDTS exerts its reno-protection remains largely unknown. To ascertain whether QDTS could target the gut microbiota-bile acid axis, the db/db mice were adopted as a mouse model of DN. After a 12-week of treatment, we found that QDTS significantly reduced urinary albumin excretion (UAE), and attenuated the pathological injuries of kidney in the db/db mice, while the body weight and blood glucose levels of those mice were not affected. In addition, we found that QDTS significantly altered the gut microbiota composition, and decreased serum levels of total bile acid (TBA) and BA profiles such as β-muricholic acid (β-MCA), taurocholic acid (TCA), tauro β-muricholic acid (Tβ-MCA) and deoxycholic acid (DCA). These BAs are associated with the activation of farnesoid X receptor (FXR), which is highly expressed in kidney. However, there was no significant difference between QDTS-treated and -untreated db/db mice regarding the renal expression of FXR, indicating that other mechanisms may be involved. Conclusively, our study revealed that QDTS significantly alleviated renal injuries in mice with DN. The gut microbiota-bile acid axis may be an important target for the reno-protection of QDTS in DN, but the specific mechanism merits further study.}, } @article {pmid33378947, year = {2021}, author = {Wu, L and Feng, J and Li, J and Yu, Q and Ji, J and Wu, J and Dai, W and Guo, C}, title = {The gut microbiome-bile acid axis in hepatocarcinogenesis.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {133}, number = {}, pages = {111036}, doi = {10.1016/j.biopha.2020.111036}, pmid = {33378947}, issn = {1950-6007}, abstract = {Hepatocellular carcinoma (HCC) is the most common primary liver malignancy and is a leading cause of cancer-related deaths globally, with few effective therapeutic options. Bile acids (BAs) are synthesized from cholesterol in the liver and can be modulated by farnesoid X receptor (FXR) and G-protein coupled BA receptor 1 (GPBAR1/TGR5). Alterations in BAs can affect hepatic metabolic homeostasis and contribute to the pathogenesis of liver cancer. Increasing evidence points to the key role of bacterial microbiota in the promotion and development of liver cancer. They are also involved in the regulation of BA synthesis and metabolism. The purpose of this review is to integrate related articles involving gut microbiota, BAs and HCC, and review how the gut microbiota-BA signaling axis can possibly influence the development of HCC.}, } @article {pmid33378710, year = {2020}, author = {Deng, Y and Tang, D and Hou, P and Shen, W and Li, H and Wang, T and Liu, R}, title = {Dysbiosis of gut microbiota in patients with esophageal cancer.}, journal = {Microbial pathogenesis}, volume = {150}, number = {}, pages = {104709}, doi = {10.1016/j.micpath.2020.104709}, pmid = {33378710}, issn = {1096-1208}, abstract = {A number of studies have identified that gut microbiota influences the development of cancer. However, there is little known about gut microbiota and esophageal cancer (EC). The aim of this study was to investigate the gut microbiota profile associated with EC. In this study, 23 patients with EC and 23 sex- and age-matched healthy controls (NC) were recruited between July 2019 and August 2019 at Huai'an First People's Hospital (Huai'an, China) and the gut microbiota was analyzed by 16S rRNA gene sequencing of fresh stool samples. We found that the microbial richness of intestinal flora in patients with EC were higher than NC, whereas evenness did not change obviously. Principal coordinate analysis (PCoA) and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) analysis both revealed that a distinct separation in bacterial community composition between the EC and NC. At the phylum level, the EC group showed significantly higher abundances of Firmicutes and Actinobacteria, but a lower Bacteroidetes than NC. At the genus level, a significantly increased abundance of Streptococcus, Bifidobacterium, Subdoligranulum, Blautia, Romboutsia, Collinsella, Paeniclostridium, Dorea, and Atopobium were observed in EC patients, while Lachnospira, Bacteroides, Agathobacter, Lachnoclostridium, Parabacteroides, Paraprevotella, Butyricicoccus, Tyzzerella, Fusicatenibacter, and Sutterella were reduced. Receiver operating characteristic (ROC) analysis revealed that Lachnospira, Bacteroides, Streptococcus, and Bifidobacterium both achieved a high accuracy in EC diagnosis (area under the curve was more than 0.85), and the Lachnospira was found to be the best classifier. This study firstly characterized the gut microbiota composition of EC patients and screened out the optimal potential microbiota biomarkers for EC diagnosis. It may provide a fundamental reference for further studies on the gut microbiome for the diagnosis and treatment of EC.}, } @article {pmid33378384, year = {2020}, author = {Martin, MJ and Zain, NMM and Hearson, G and Rivett, DW and Koller, G and Wooldridge, DJ and Rose, G and Gharbia, SE and Forbes, B and Bruce, KD and Harrison, TW}, title = {The airways microbiome of individuals with asthma treated with high and low doses of inhaled corticosteroids.}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0244681}, pmid = {33378384}, issn = {1932-6203}, abstract = {BACKGROUND: Inhaled corticosteroids (ICS) are the mainstay of asthma treatment, but evidence suggests a link between ICS usage and increased rates of respiratory infections. We assessed the composition of the asthmatic airways microbiome in asthma patients taking low and high dose ICS and the stability of the microbiome over a 2 week period.

METHODS: We prospectively recruited 55 individuals with asthma. Of these, 22 were on low-dose ICS and 33 on high-dose ICS (16 on budesonide, 17 on fluticasone propionate). Sputum from each subject underwent DNA extraction, amplification and 16S rRNA gene sequencing of the bacterial component of the microbiome. 19 subjects returned for further sputum induction after 24 h and 2 weeks.

RESULTS: A total of 5,615,037 sequencing reads revealed 167 bacterial taxa in the asthmatic airway samples, with the most abundant being Streptococcus spp. No significant differences in sputum bacterial load or overall community composition were seen between the low- and high-dose ICS groups. However, Streptococcus spp. showed significantly higher relative abundance in subjects taking low-dose ICS (p = 0.002). Haemophilus parainfluenzae was significantly more abundant in subjects on high-dose fluticasone propionate than those on high-dose budesonide (p = 0.047). There were no statistically significant changes in microbiota composition over a 2-week period.

DISCUSSION: Whilst no significant differences were observed between the low- and high-dose ICS groups, increased abundance of the potential pathogen H. parainfluenzae was observed in patients taking high-dose fluticasone propionate compared to those taking high-dose budesonide. The microbiota were stable over fourteen days, providing novel evidence of the established community of bacteria in the asthmatic airways.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov NCT02671773.}, } @article {pmid33378284, year = {2020}, author = {Afolayan, AO and Ayeni, FA}, title = {Metagenomic Analysis of Bacterial Communities in Water and Soil of the Fulani and non-Fulani in Nigeria.}, journal = {Journal of infection in developing countries}, volume = {14}, number = {12}, pages = {}, doi = {10.3855/jidc.12975}, pmid = {33378284}, issn = {1972-2680}, abstract = {INTRODUCTION: Interactions between environmental factors (water and soil) and humans are inevitable, particularly in rural and semi-urbanized regions. As such, knowledge on the microbial constituents of these environmental factors is key to understanding potential risk to public health. However, the microbial profile of soil and water present in vulnerable human communities in Nigeria is currently unknown. This study sought to investigate the composition of soil and water microbiota in the environment inhabited by recently studied human communities (the Fulani nomadic group and the urbanized Jarawa ethnic group) and estimate the contribution of these environmental factors to the microbiome of the aforementioned human communities.

METHODOLOGY: Soil and water samples were collected from the Fulani and non-Fulani community in Jengre (Plateau State, Nigeria) and Jos (Plateau State, Nigeria), respectively. Genomic DNA was extracted from these environmental samples, followed by Illumina sequencing of the V4 region of the 16S rRNA gene and bioinformatics analysis via Quantitative Insights into Microbial Ecology QIIME.

RESULTS: There is abundance of Proteobacteria (43%) signature members in soil samples obtained from both human communities. Analysis of the water samples revealed the abundance of Proteobacteria, particularly in water sourced from the borehole (Fulani). Pseudomonas (30%) had higher relative abundance in the drinking water of the Fulani.

CONCLUSIONS: The drinking water of the Fulani could be a potential health risk to the studied Fulani community. Factors that increase the abundance of public health threats and health risk, such as hygiene practices, soil and water quality need to be studied further for the improvement of health in vulnerable populations.}, } @article {pmid33378160, year = {2020}, author = {Vargason, AM and Anselmo, AC}, title = {Evaluation of Surface Modified Live Biotherapeutic Products for Oral Delivery.}, journal = {ACS biomaterials science & engineering}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsbiomaterials.0c01405}, pmid = {33378160}, issn = {2373-9878}, abstract = {Live biotherapeutic products (LBPs), including symbiotic and genetically engineered bacteria, are a promising class of emerging therapeutics that are widely investigated both preclinically and clinically for their oral delivery to the gastrointestinal (GI) tract. One emergent delivery strategy involves the direct functionalization of LBP surfaces through noncovalent or covalent modifications to control LBP interactions with the GI microenvironment, thereby improving their viability, attachment, or therapeutic effect. However, unlike other therapeutic modalities, LBPs are living organisms which present two unique challenges for surface modifications: (1) this approach can directly interfere with key LBP biological processes (e.g., colonization, metabolite secretion) and (2) modification can be variable due to the dynamic nature of LBP surfaces. Collectively, these factors remain uncharacterized as they relate to the oral delivery of LBPs. Herein, we leverage our previously reported surface modification platform, which enables LBP surface-presentation of targeting ligands, to broadly evaluate and characterize surface modifications on LBPs. Specifically, we evaluate how LBP growth affects the dilution of surface-presented targeting ligands and the subsequent loss of specific target attachment over time. Next, we describe key surface modification parameters (e.g., concentration, residence time) that can be optimized to facilitate LBP target attachment. We then characterize how bioconjugation influences the suitability of LBPs for oral delivery by evaluating their growth, viability, storage, toxicity against mammalian cells, and in vivo colonization. Broadly, we describe key parameters that influence the performance of surface modified LBPs and subsequently outline an experimental pipeline for characterizing and evaluating their suitability for oral delivery.}, } @article {pmid33378051, year = {2020}, author = {Casciaro, M and Di Salvo, E and Pioggia, G and Gangemi, S}, title = {Microbiota and microRNAs in lung diseases: mutual influence and role insights.}, journal = {European review for medical and pharmacological sciences}, volume = {24}, number = {24}, pages = {13000-13008}, doi = {10.26355/eurrev_202012_24205}, pmid = {33378051}, issn = {2284-0729}, abstract = {Trillions of microbial cells colonize human body both internally and externally. The prevalent amount of these reside in the gastrointestinal tract (gut microbiome). Gut microflora support the transformation of food nutrients. The products of this modification processes both modulate gastro-intestinal immunity, and influence other organs such as lung and brain. Recently, it was reported the role of micro-RNAs (miRNAs) as regulators in different pathways of the innate and/or adaptive immune responses. Latest studies discussed the aptitude of probiotics strains to balance the host immune response at a post-transcriptional level by controlling miRNAs expression. We speculated a model of lung immune regulation driven by the axis microbiota-microRNAs, involving asthma, acute injury, cancer and COPD. Based on this axis, we propose a novel approach based on the modification of microRNAs expression centered not exclusively on antagomiRs but also on microbiota modification in order to further potentiate their therapeutic effects.}, } @article {pmid33378048, year = {2020}, author = {Czajkowska, A and Kaźmierczak-Siedlecka, K and Jamioł-Milc, D and Gutowska, I and Skonieczna-Żydecka, K}, title = {Gut microbiota and its metabolic potential.}, journal = {European review for medical and pharmacological sciences}, volume = {24}, number = {24}, pages = {12971-12977}, doi = {10.26355/eurrev_202012_24201}, pmid = {33378048}, issn = {2284-0729}, abstract = {OBJECTIVE: The incidence of obesity and other metabolic-related diseases has been gradually increasing. Multiple genetic as well as environmental factors play a significant role in the pathogenesis of these entities. Currently, the involvement of gut microbiota in metabolic processes has been acknowledged. This paper focuses on obesity, type 2 diabetes, and nonalcoholic fatty liver disease regarding their link with microbiome structure and its function.

MATERIALS AND METHODS: We analyzed literature available in PubMed, Embase, and Google Scholar databases regarding a linkage of metabolic-associated diseases and gut microbiota RESULTS: Gut microbiota plays a significant role in host metabolism. Depending on its composition; however, it may contribute to the development of metabolic-associated diseases. In this context, not only composition of gut microbiota is important, but also its activity. Short-chain fatty acids or lipopolysaccharides are crucial metabolites involved in maintaining metabolic balance.

CONCLUSIONS: Gut microbiota malfunctions might potentially induce obesity, type 2 diabetes, and nonalcoholic fatty liver disease.}, } @article {pmid33377531, year = {2020}, author = {Fang, C and Wu, L and Zhu, C and Xie, WZ and Hu, H and Zeng, XT}, title = {A potential therapeutic strategy for prostatic disease by targeting the oral microbiome.}, journal = {Medicinal research reviews}, volume = {}, number = {}, pages = {}, doi = {10.1002/med.21778}, pmid = {33377531}, issn = {1098-1128}, support = {2019FFB03902//Nature Science Foundation of Hubei Province/ ; WJ2019H035//Health Commission of Hubei Province Scientific Research Project/ ; 2042020kf1081//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Nowadays, human microbiome research is rapidly growing and emerging evidence has witnessed the critical role that oral microbiome plays in the process of human health and disease. Oral microbial dysbiosis has been confirmed as a contributory cause for diseases in multiple body systems, ranging from the oral cavity to the gastrointestinal, endocrine, immune, cardiovascular, and even nervous system. As research progressing, oral microbiome-based diagnosis and therapy are proposed and applied, which may represent potential drug targets in systemic diseases. Recent studies have uncovered the possible association between periodontal disease and prostatic disease, suggesting new prevention and therapeutic treatment for the disease by targeting periodontal pathogens. Thus, we performed this review to first explore the association between the oral microbiome and prostatic disease, according to current knowledge based on published articles, and then mainly focus on the underlying molecular and cellular mechanisms and the potential prevention and treatment derived from these mechanistic studies.}, } @article {pmid33377127, year = {2020}, author = {Mitchell, CM and Mazzoni, C and Hogstrom, L and Bryant, A and Bergerat, A and Cher, A and Pochan, S and Herman, P and Carrigan, M and Sharp, K and Huttenhower, C and Lander, ES and Vlamakis, H and Xavier, RJ and Yassour, M}, title = {Delivery Mode Affects Stability of Early Infant Gut Microbiota.}, journal = {Cell reports. Medicine}, volume = {1}, number = {9}, pages = {100156}, pmid = {33377127}, issn = {2666-3791}, support = {K99 DK113224/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 DK092405/DK/NIDDK NIH HHS/United States ; U54 HG003067/HG/NHGRI NIH HHS/United States ; }, abstract = {Mode of delivery strongly influences the early infant gut microbiome. Children born by cesarean section (C-section) lack Bacteroides species until 6-18 months of age. One hypothesis is that these differences stem from lack of exposure to the maternal vaginal microbiome. Here, we re-evaluate this hypothesis by comparing the microbial profiles of 75 infants born vaginally or by planned versus emergent C-section. Multiple children born by C-section have a high abundance of Bacteroides in their first few days of life, but at 2 weeks, both C-section groups lack Bacteroides (primarily according to 16S sequencing), despite their difference in exposure to the birth canal. Finally, a comparison of microbial strain profiles between infants and maternal vaginal or rectal samples finds evidence for mother-to-child transmission of rectal rather than vaginal strains. These results suggest differences in colonization stability as an important factor in infant gut microbiome composition rather than birth canal exposure.}, } @article {pmid33377094, year = {2020}, author = {Alavi, S and Hsiao, A}, title = {Protocol for Microbiome Transplantation in Suckling Mice during Vibrio cholerae Infection to Study Commensal-Pathogen Interactions.}, journal = {STAR protocols}, volume = {1}, number = {3}, pages = {100200}, pmid = {33377094}, issn = {2666-1667}, support = {R35 GM124724/GM/NIGMS NIH HHS/United States ; }, abstract = {The gut microbiome plays an important role in the exclusion of pathogens and, thus, infection outcomes. Microbiome-pathogen interaction studies are complicated by a lack of tractable animal models and differences in animal model versus human microbiomes. We have adapted the suckling mouse model of infection of the human pathogen Vibrio cholerae to clear murine microbes and establish human-associated gut microbes during infection. Our method allows for the easy examination of the contribution of different human microbial communities to enteropathogenesis. For complete details on the use and execution of this protocol, please refer to Alavi et al. (2020).}, } @article {pmid33377042, year = {2020}, author = {Reitmeier, S and Kiessling, S and Neuhaus, K and Haller, D}, title = {Comparing Circadian Rhythmicity in the Human Gut Microbiome.}, journal = {STAR protocols}, volume = {1}, number = {3}, pages = {100148}, pmid = {33377042}, issn = {2666-1667}, abstract = {Targeted sequencing of 16S rRNA genes enables the analysis of microbiomes. Here, we describe a protocol for the collection, storage, and preparation of fecal samples. We describe how we cluster similar sequences and assign bacterial taxonomies. Using diversity analysis and machine learning, we can extract disease-associated features. We also describe a circadian analysis to identify the presence or absence of rhythms in taxonomies. Differences in rhythmicity between cohorts can contribute to determining disease-associated bacterial signatures. For complete details on the use and execution of this protocol, please refer to Reitmeier et al. (2020).}, } @article {pmid33376926, year = {2020}, author = {Buchalter, DB and Teo, GM and Kirby, DJ and Aggarwal, VK and Long, WJ}, title = {Surgical Approach to Total Hip Arthroplasty Affects the Organism Profile of Early Periprosthetic Joint Infections.}, journal = {JB & JS open access}, volume = {5}, number = {4}, pages = {}, pmid = {33376926}, issn = {2472-7245}, abstract = {The optimal approach for total hip arthroplasty (THA) remains hotly debated. While wound complications following the direct anterior approach are higher than with other approaches, the organism profile of periprosthetic joint infections (PJIs) by approach remains unknown. Our goal was to compare the organism profiles of PJIs following direct anterior and non-anterior THA.

Methods: We retrospectively reviewed 12,549 primary THAs (4,515 direct anterior and 8,034 non-anterior) that had been performed between January 2012 and September 2019 at a university-affiliated single-specialty orthopaedic hospital to identify patients with an early postoperative PJI. Criteria used for the diagnosis of a PJI were the National Healthcare Safety Network, which screens for PJI that occurs within 90 days of index arthroplasty, and the Musculoskeletal Infection Society guidelines. Patient demographic information and organism characteristics were recorded for analysis.

Results: We identified 84 patients (38 who underwent the direct anterior approach and 46 who underwent the non-anterior approach) with an early postoperative PJI following primary THA (0.67% total THA PJI rate, 0.84% direct anterior THA PJI rate, and 0.57% non-anterior THA PJI rate). The direct anterior THA cohort had a significantly lower body mass index and American Society of Anesthesiologists score than the non-anterior THA cohort (29.5 versus 35.2 kg/m2, p < 0.0001; 2.29 versus 2.63, p = 0.016, respectively). Regarding organism profile, patients in the direct anterior THA cohort had significantly more monomicrobial gram-negative infections than the non-anterior THA cohort (4 versus 0, p = 0.038). We did not identify any demographic risk factors other than approach for gram-negative PJI. There were no significant differences in methicillin-resistant Staphylococcus aureus, methicillin-sensitive Staphylococcus aureus, coagulase-negative Staphylococcus, obligate anaerobes, polymicrobial, or PJIs due to other organisms by approach.

Conclusions: Direct anterior THA approaches have a greater risk of monomicrobial gram-negative PJI, likely due to the unique microbiome of the inguinal region. While targeted infection prophylaxis may reduce these infections, it is not entirely effective on its own. Future studies with larger sample sizes are required to help us develop more targeted perioperative infection prophylaxis.

Level of Evidence: Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.}, } @article {pmid33376575, year = {2021}, author = {Bergmann, KC and Krause, L and Hiller, J and Becker, S and Kugler, S and Tapparo, M and Pfaar, O and Zuberbier, T and Kramer, MF and Guethoff, S and Graessel, A}, title = {First evaluation of a symbiotic food supplement in an allergen exposure chamber in birch pollen allergic patients.}, journal = {The World Allergy Organization journal}, volume = {14}, number = {1}, pages = {100494}, pmid = {33376575}, issn = {1939-4551}, abstract = {Background: Allergic rhinitis/rhinoconjunctivitis is the most common immune disease worldwide, but still largely underestimated, underdiagnosed, and undertreated. Dysbiosis and reduced microbial diversity is linked to the development of allergies, and the immunomodulatory effects of pro- and prebiotics might be used to counteract microbiome dysbiosis in allergy. Adequate symbiotic (multi-strain pro-, plus prebiotic) supplementation can be suggested as a complementary approach in the management of allergic rhinitis.

Objective: The effects of the daily intake of a symbiotic food supplement (combination of Lactobacillus acidophilus NCFM and Bifidobacterium lactis BL-04 with Fructo-Oligosaccharides) for 4 months in birch pollen allergic rhinoconjunctivitis patients were investigated for the first time in an allergen exposure chamber (AEC) allowing standardised, reproducible pollen exposure before and after intake.

Methods: Eligible patients were exposed to birch pollen (8000 pollen/m³ for 120 min) at the GA2LEN AEC, at baseline (V1) and final visit (V3) outside the season. The Total Symptom Score (TSS) and the scores for nose, eye, bronchial system, and others were evaluated every 10 min during exposure. Other secondary endpoints were the changes in well-being, Peak Nasal Inspiratory Flow (PNIF), lung function parameters, and safety. Co-primary endpoints were differences in Total Nasal Symptom Score (TNSS) and TSS after 120 min of exposure between both visits. Temporal evolution of symptom scores were analysed in an exploratory way using linear mixed effects models.

Results: 27 patients (mean age 45 years, 15% male) completed the study. Both co-primary endpoints showed significant improvement after intake of the symbiotic. Median TNSS and TSS were decreased 50% and 80% at 120 min (adjusted p-value = 0.025 and p < 0.01 respectively).All four symptom scores and the personal well-being, improved to a clinically relevant extent over time, visible by a weaker increase in symptoms during 120 min of the final birch pollen exposure. No relevant differences were observed for PNIF, PEF, and spirometry. There were no airway obstructions or lung restrictions before and after both exposures. Late phase reactions after exposure were reduced after V3, documenting a better birch pollen tolerability of the pati