Category Archives: General Microbiome

October 9, 2021

Posted on by

Highlights!

Commensal microbiota divergently affect myeloid subsets in the mammalian central nervous system during homeostasis and disease – Roman Sankowski – The EMBO Journal → This study shows how perturbations in the microbiota drive changes in gene expression profiles in the CNS-associated macrophages, with concomitant effects on the  CNS myeloid cells, including Alzheimer-associated repercussions in a specialized murine model.

Coordination of root auxin with the fungus Piriformospora indica and bacterium Bacillus cereus enhances rice rhizosheath formation under soil drying – Feiyun Xu – The ISME Journal → In this study, authors report a cooperative effect of an endophytic fungus and a plant growth-promoting bacterium in rhizosheath formation when moderate soil drying, an agricultural technique used to improve water utilization, is performed.

Human and General Microbiome

Review: The role of Akkermansia muciniphila in obesity, diabetes and atherosclerosis – Alka Hasani – Journal of Medical Microbiology

Review: How can probiotic improve irritable bowel syndrome symptoms? – Indira Benjak Horvat – World Journal of Gastrointestinal Surgery

Meta-Analysis of the Composition of Human Intestinal Gases – Andre Modesto – Digestive Diseases and Sciences

Effectiveness of Probiotics and Prebiotics Against Acute Liver Injury: A Meta-Analysis – Sheng Xu – Frontiers in Medicine

The bacterial gut microbiome of probiotic-treated very-preterm infants: changes from admission to discharge – Jacob A F Westaway – Pediatric Research

Discovery of β-N-acetylglucosaminidases from screening metagenomic libraries and their use as thioglycoligase mutants – Gregor Tegl – Organic & Biomolecular Chemistry

Animal Microbiome

Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents – Jason L Anders – Scientific Reports

Changes in rumen microbial community composition in yak in response to seasonal variations – Xiaodan Huang – Journal of Applied Microbiology

Faecalicatena faecalis sp. nov., a moderately alkaliphilic bacterial strain isolated from swine faeces – Byeong Seob Oh – Antonie van Leeuwenhoek

Plant Microbiome

Capacity of soil bacteria to reach the phyllosphere and convergence of floral communities despite soil microbiota variation – Julien Massoni –  PNAS

Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds – Flavia Tarquinio – Frontiers in Microbiology

Fungi Microbiome

Widespread bacterial diversity within the bacteriome of fungi – Aaron J Robinson – Communications Biology

Environmental Microbiome

Preprint: Genomic and metabolic adaptations of biofilms to ecological windows of opportunities in glacier-fed streams – Susheel Bhanu Busi – Biorxiv

October 8, 2021

Posted on by

Today’s digest features a metagenomic meta-study on faecal microbiota transplantation, RibDif for count and compare 16S rRNA genes within a genus, and more. Also, there is a new FEMS Microbiology Letters collection of articles highlighting the evolution of education during the COVID-19 pandemic.

There is still time to join in the second 🌎 Microbiome Virtual International Forum 🌏. Recordings from previous MVIF can be found here.

And, the #Microber2021 just started! Check out this microbe edition of #Inktober drawing challenge – during October, every day a new scientific art on microbiology topic.

Global microbiome

Cultivating Healthy Connections: Exploring and Engineering the Microbial Flow That Shapes Microbiomes – Travis J. Wiles – mSystems

Neonatal microbiome

Presence of distinctive microbiome in the first-pass meconium of newborn infants – Jenni Turunen – Scientific Reports

Respiratory microbiome

Divergence of bacterial communities in the lower airways of CF patients in early childhood – John B. O’Connor – PlosOne

Gut microbiome

Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation – Thomas Schmidt – bioRxiv

Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth–gut axis – Vishnu Prasoodanan P. K. – npj Biofilms and Microbiomes

Animal microbiome

Phylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate vast taxonomic diversity, open genomes and an abundance of carbohydrate-active enzyme family isoforms – Sara E. Pidcock – Microbial Genomics

Animal experiment

Metabolic modulation of tumours with engineered bacteria for immunotherapy – Fernando P. Canale – Nature

Citrobacter amalonaticus Inhibits the Growth of Citrobacter rodentium in the Gut Lumen – Caroline Mullineaux-Sanders – mBio

Regulation of blood–brain barrier integrity by microbiome-associated methylamines and cognition by trimethylamine N-oxide – Lesley Hoyles – bioRxiv

Effects of prebiotic oligofructose-enriched inulin on gut-derived uremic toxins and disease progression in rats with adenine-induced chronic kidney disease – Ebru Melekoglu – PlosOne

Plant microbiome

Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria – Claudia Sanchis-López – mSystems

Food

Bacteriocinogenic lactic acid bacteria in the traditional cereal-based beverage Boza: a genomic and functional approach – Luciano Lopes Queiroz – bioRxiv

Bioinformatics

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes – Francisco Zorrilla – Nucleic Acids Research

RibDif: can individual species be differentiated by 16S sequencing? – Mikael Lenz Strube – Bioinformatics Advances

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale – Carlos P Cantalapiedra – Molecular Biology and Evolution

Sequencing DNA with nanopores: Troubles and biases – Clara Delahaye and Jacques Nicolas – PlosOne

Webinars &c

Conference: Microbiome Virtual International Conference #MVIF – October 14 (Pacific Live)/15 (Atlantic Reply)

Webinar: EMBARK Fall Webinars – a webinar series focused on AMR research

Microscopy Live! – Geology – an hour of live electron microscopy, guided by the audience – Plymouth Electron Microscopy Centre (October 29)

For more, check out a collection of microbiome events HERE!

Happy #Microber2021, sci-art October!

October 06, 2021

Posted on by

General microbiome

The intestinal 3M (microbiota, metabolism, metabolome) Zeitgeist – from fundamentals to future challenges – Dey et al. – Free Radical Biology and Medicine

Pregnancy and early life

Gut microbiota changes in preeclampsia, abnormal placental growth and healthy pregnant women – Huang et al. – BMC Microbiology

Human respiratory microbiome

Refinement of microbiota analysis of specimens from patients with respiratory infections using next-generation sequencing – Ikegami et al. – Scientific Reports

Human skin microbiome

Experimental Dermatology Special Issue with Focus on ‘Skin microbiome and antimicrobial peptides’

Human gut microbiome

[REVIEW]Gut microbiome in pediatric acute leukemia: from predisposition to cure – Masetti et al. – Blood Advances

Animal microbiome

Effects of moderate exercise on hepatic amino acid and fatty acid composition, liver transcriptome, and intestinal microbiota in channel catfish (Ictalurus punctatus) – Zhang et al. – Comparative Biochemistry and Physiology Part D: Genomics and Proteomics

Metagenomic Sequencing Reveals that High-Grain Feeding Alters the Composition and Metabolism of Cecal Microbiota and Induces Cecal Mucosal Injury in Sheep – Xie, Wang & Mao – mSystems

Plant, root, and soil microbiome

Biodegradable and conventional microplastics exhibit distinct microbiome, functionality, and metabolome changes in soil – Sun et al. – Journal of Hazardous Materials

Soil microbiota and microarthropod communities in oil contaminated sites in the European Subarctic – Melekhina et al. – Scientific Reports

Fast and persistent responses of alpine permafrost microbial communities to in situ warming – Perez-Mon et al. – Science of The Total Environment

Built environment (subways, indoor surfaces)

Environmental dynamics of hospital microbiome upon transfer from a major hospital to a new facility – Ashokan et al. – Journal of Infection

Bioinformatics

[Commentary]Predicting Microbiome Metabolism and Interactions through Integrating Multidisciplinary Principles – Schmidt, Ghadermazi & Chan – mSystems

Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data – Armstrong et al. – mSystems

October 5, 2021

Posted on by

Today’s digest includes a description of how probiotics modulate B cells in Peyer’s patches published in Microbiome, a review in ISME on microbial storage in soil and multiple recent Cell Host & Microbe articles covering the plant immune system and colonisation resistance to Salmonella and Klebsiella.

General microbiome

Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria – Pérez-Carrascal et al. Microbiome

Molecular basis of a bacterial-amphibian symbiosis revealed by comparative genomics, modeling, and functional testing – Brunetti et al. ISME

Human gut microbiome

Gut microbiota involved in leptospiral infections – Xie et al. ISME

Identification of Faecalibacterium prausnitzii strains for gut microbiome-based intervention in Alzheimer’s-type dementia – Ueda et al. Cell Reports Medicine

Fecal microbial transplantation and fiber supplementation in patients with severe obesity and metabolic syndrome: a randomized double-blind, placebo-controlled phase 2 trial – Mocanu et al. Nature Medicine

Gut bacteria identified in colorectal cancer patients promote tumourigenesis via butyrate secretion – Okumura et al. Nature Communications

E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source – Eberl et al. Cell Host & Microbe

Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition – Osbelt et al. Cell Host & Microbe

Human Oral Microbiome

Distinct B cell subsets in Peyer’s patches convey probiotic effects by Limosilactobacillus reuteri – Liu et al. Microbiome

Human Oral Microbiome

Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter – Granehäll et al. Microbiome

Soil & Plant microbiomes

[REVIEW] Microbial storage and its implications for soil ecology – Mason-Jones et al. ISME

Gammaproteobacteria, a core taxon in the guts of soil fauna, are potential responders to environmental concentrations of soil pollutants – Zhang et al. Microbiome

Plant immune system activation is necessary for efficient root colonization by auxin-secreting beneficial bacteria – Tzipilevich et al. Cell Host & Microbe

October 1, 2021

Posted on by

Multi-site human microbiome

Diagnostic and prognostic potential of the oral and gut microbiome for lung adenocarcinoma – Lim et al. – Clinical and Translational Medicine

Human oral microbiome

Individuals with substance use disorders have a distinct oral microbiome pattern – Kosciolek et al. – Brain, Behavior, & Immunity – Health

Human skin microbiome

[REVIEW]The Dynamics of Skin Microbiota in Shoulder Surgery Infections – Fatima, Bjarnsholt & Bay – Journal of Pathology, Microbiology and Immunology

Human gut microbiome

[REVIEW]Mucins, gut microbiota, and postbiotics role in colorectal cancer – Pothuraju et al. – Gut Microbes

Age and the aging process significantly alter the small bowel microbiome – Leite et al. – Cell Reports

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Guidelines for reporting on animal fecal transplantation (GRAFT) studies: recommendations from a systematic review of murine transplantation protocols – Secombe et al. – Gut Microbes

Alpha-synuclein alters the faecal viromes of rats in a gut-initiated model of Parkinson’s disease – Stockdale et al. – Communications Biology

[PREPRINT]First trimester gut microbiome induces Inflammation-dependent gestational diabetes phenotype in mice – Pinto et al. – medRxiv

[PREPRINT]High-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice provides novel insight on the impact of host genetics – Doms et al. – bioRxiv

Plant, root, and soil microbiome

Effects of microplastics on soil microbiome: The impacts of polymer type, shape, and concentration – Sun et al. – Science of the total Environment

Bioinformatics

Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA preprocessing chimeric reads – Kiguchi et al. – DNA Research

BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes – Andreu et al. – mSystems

Increasing the power of interpretation for soil metaproteomics data – Jouffret – Microbiome

September 30, 2021

Posted on by

Today’s digest includes a quantification of bacterial strains after fecal microbiota transplantation, a network analysis of the strawberry greenhouse soil microbiome after soil amendments, and an article about enhanced copper-resistance genes in Alteromonas macleodii. Also included are multiple preprints on topics such as denitrification pathways present in tunda soil metagenomes as well as the response of Endozoicomonas, a core coral bacterial group, to heat stress and host lysates.

General microbiome

Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature – Achtman et al. – PLOS Genetics

Preprint: Role of the mobilome in the global dissemination of the carbapenem resistance gene blaNDM – Acman et al. – bioRxiv

Preprint: Existence of log-phase Escherichia coli persisters and lasting memory of a starvation pulse – Svenningsen et al. – bioRxiv

Human gut microbiome

Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes – Aggarwala et al. – Nature Microbiology

Animal microbiome

A role for arthropods as vectors of multidrug-resistant Enterobacterales in surgical site infections from South Asia – Hassan et al. – Nature Microbiology

Plant, root, and soil microbiome

Response of soil microbiome structure and its network profiles to four soil amendments in monocropping strawberry greenhouse – Liu et al. – PLOS One

Preprint: Truncated denitrifiers dominate the denitrification pathway in tundra soil metagenomes – Pessi et al. – bioRxiv

Water and extremophile microbiome

Preprint: Response of Endozoicomonas montiporae to heat stress and coral host lysates – Chan et al. – bioRxiv

Enhanced copper-resistance gene repertoire in Alteromonas macleodii strains isolated from copper-treated marine coatings – Cusick et al. – PLOS One

Bacterial community structure of early-stage biofilms is dictated by temporal succession rather than substrate types in the southern coastal seawater of India – Sushmitha et al. – PLOS One

Preprint: Ecological stochasticity and phage induction diversify bacterioplankton communities at the microscale – Szabo et al. – bioRxiv

September 28, 2021

Posted on by

Retraction Note

Retraction Note: IspH inhibitors kill Gram-negative bacteria and mobilize immune clearance – Singh et al. – Nature

Human oral microbiome

Oral Microbiota Profile of Individuals Who Abuse Methamphetamine – Yang et al. – Frontiers in Cellular and Infection Microbiology

The baseline oral microbiota predicts the response of locally advanced oral squamous cell carcinoma patients to induction chemotherapy: A prospective longitudinal study – Rui et al. – Radiotherapy and Oncology

Human gut microbiome

Gut microbiome in people living with HIV is associated with impaired thiamine and folate syntheses – Park et al. – Microbial Pathogenesis

[REVIEW]The impact of pelvic radiotherapy on the gut microbiome and its role in radiation-induced diarrhoea: a systematic review – Wang et al. – BMC Radiation Oncology

[REVIEW]Gut Microbiota-Mediated Modulation of Cancer Progression and Therapy Efficacy – Cheng et al. – Frontiers in Cell and Developmental Biology

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Xylanase impact beyond performance: A microbiome approach in laying hens – van Hoeck et al. – PLOS One

Dysbiosis of the gut microbiome impairs mouse skeletal muscle adaptation to exercise – Valentino et al. – The Journal of Physiology

Lactic Acid Bacteria Strains Differently Modulate Gut Microbiota and Metabolic and Immunological Parameters in High-Fat Diet-Fed Mice – Fabersani et al. – Frontiers in Nutrition

Animal microbiome (for animals in the wild)

Alteration of Gut Microbiota of a Food-Storing Hibernator, Siberian Chipmunk Tamias sibiricus – Zhou, Wang & Yi – Microbial Ecology

[PREPRINT]Bacterial community dynamics during embryonic development of the little skate (Leucoraja erinacea) – Mika et al. – bioRxiv

Multi-omics reveals the positive leverage of plant secondary metabolites on the gut microbiota in a non-model mammal – Wang et al. – Microbiome

Plant, root, and soil microbiome

Trophic level drives the host microbiome of soil invertebrates at a continental scale – Zhu et al. – Microbiome

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Genomic signatures of Lake Erie bacteria suggest interaction in the Microcystis phycosphere – Hoke et al. – PLOS One

Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling – Tee et al. – Microbiome

Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants – Nikolova et al. – Microbiome

Built environment (subways, indoor surfaces)

The short-term effect of residential home energy retrofits on indoor air quality and microbial exposure: A case-control study – Nguyen, Holmes & Angenent – PLOS One

September 25, 2021

Posted on by

Highlights!

Review: Bacterial Translocation as Inflammatory Driver in Crohn’s Disease – Raquel Linares – Frontiers in Cell and Developmental Biology

Review:  The Gut Microbiome and Inflammatory Bowel Diseases – Yue Shan – Annual Review of Medicine

Vegan vs. omnivore diets paradox: A whole-metagenomic approach for defining metabolic networks during the race in ultra-marathoners- a before and after study  design – Aslı Devrim-Lanpir – PloS ONE

The Prebiotic Potential of Inulin-type Fructans: A Systematic Review – Riley L Hughes – Advances in Nutrition

Next-generation prebiotic promotes selective growth of bifidobacteria, suppressing Clostridioides difficile – Rika Hirano – Gut Microbes

timeOmics: an R package for longitudinal multi-omics data integration – Antoine Bodein – Bioinformatics 

Automation of QIIME2 Metagenomic Analysis Platform – Calvin Fung – Current Protocols

Human and General Microbiome

Persistence of functional microbiota composition across generations – Christian Ramos – Scientific Reports

Gastric microbiota in patients with Helicobacter pylori-negative gastric MALT lymphoma. – Takahide Tanaka – Medicine

Lachnospira is a signature of antihistamine efficacy in chronic spontaneous urticarial – Runqiu Liu – Experimental Dermatology

Association of Female Genital Schistosomiasis With the Cervicovaginal Microbiota and Sexually Transmitted Infections in Zambian Women – Amy S Sturt – Open Forum Infectious Diseases

Gut Lactobacillus Level Is a Predictive Marker for Coronary Atherosclerotic Lesions Progress and Prognosis in Patients With Acute Coronary Syndrome – Jing Gao – Frontiers in Cellular and Infection Microbiology

Causal Effects of Gut Microbiome on Systemic Lupus Erythematosus: A Two-Sample Mendelian Randomization Study – Kun Xiang – Frontiers in Immunology

Vaginal microbiome as a tool for prediction of chorioamnionitis in preterm labor: a pilot study – Daichi Urushiyama – Scientific Reports

Genital mycoplasma infection and spontaneous preterm birth outcome: a prospective cohort study. – Giulia Karnauchovas Porto Cunha – BJOG

Endometrial microbiota is more diverse in people with endometriosis than symptomatic controls – Jocelyn M Wessels – Scientific Reports

Periodontitis associates with species-specific gene expression of the oral microbiota – Daniel Belstrøm – NPJ biofilms and microbiomes

Review: Interplay and cooperation of Helicobacter pylori and gut microbiota in gastric carcinogenesis – Seyedeh Zahra Bakhti – BMC Microbiology

Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species – Hassan Zafar – Microbial Physiology

Review: Mass spectrometry-based metabolomics in microbiome investigations – Anelize Bauermeister – Nature Reviews Microbiology

Gut microbiota depletion exacerbates cholestatic liver injury via loss of FXR signalling – Kai Markus Schneider – Nature Metabolism

Review: Chains of evidence from correlations to causal molecules in microbiome-linked diseases. – Snehal N Chaudhari – Nature Chemical Biology

Review: Host and microbiota metabolic signals in aging and longevity – Yue Zhou – Nature Chemical Biology

Fecal filtrate transplantation protects against necrotizing enterocolitis – Anders Brunse – The ISME Journal

High-fat diet increases the severity of Giardia infection in association with low-grade inflammation and gut microbiota dysbiosis – Thibault Allain – Scientific Reports

Beneficial Microbes and Compounds

Effects of konjac glucomannan with different molecular weights on gut microflora with antibiotic perturbance in in-vitro fecal fermentation – Yu-Heng Mao – Carbohydrate Polymers

Review: Interactions between dietary polyphenols and aging gut microbiota: A review – Sergio Davinelli – BioFactors

Safety and efficacy of using heat-killed Lactobacillus plantarum L-137: High-dose and long-term use effects on immune-related safety and intestinal bacterial flora – Hiroko Nakai – Journal of Immunotoxicology

Faecalibacterium prausnitzii Attenuates DSS-Induced Colitis by Inhibiting the Colonization and Pathogenicity of Candida albicans – Xiaqiong Mao – Molecular Nutrition & Food Research

Minireview: Probiotics, Prebiotics, and Synbiotics for the Prevention of Necrotizing Enterocolitis. – Kiera Murphy – Frontiers in Nutrition

Review: Main drivers of (poly)phenol effects on human health: metabolite production and/or gut microbiota-associated metabotypes? – Carlos E Iglesias-Aguirre – Food & Function

Inhibitory effects of Lactobacillus casei Shirota against both Candida auris and Candida spp. isolates that cause vulvovaginal candidiasis and are resistant to antifungals – Aline Lorenzoni Paniágua – BMC Complementary Medicine and Therapies

Fructooligosaccharides: From Breast Milk Components to Potential Supplements. A Systematic Review– Valentina De Cosmi – Advances in Nutrition

Effects of Microbiota-Driven Therapy on Circulating Trimethylamine-N-Oxide Metabolism: A Systematic Review and Meta-Analysis – Lina Miao – Frontiers in Cardiovascular Medicine

Animal Microbiome

The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya. – Rehema Liyai – PeerJ

Marked Seasonal Variation in Structure and Function of Gut Microbiota in Forest and Alpine Musk Deer – Feng Jiang – Frontiers in Microbiology

Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes – Amanda C Perofsky – Molecular Ecology

Association of female reproductive tract microbiota with egg production in layer chickens – Yuan Su – GigaScience

Plant Microbiome

Bacillus subtilis Colonization of Arabidopsis thaliana Roots Induces Multiple Biosynthetic Clusters for Antibiotic Production – Harsh Maan – Frontiers in Cellular and Infection Microbiology

Environmental Microbiome

Review: Prospects for multi-omics in the microbial ecology of water engineering – Elizabeth A McDaniel – Water Research

Bioinformatics

QSDB-a graphical Quorum Sensing Database – Karsten Klein – Database

Testing microbiome association using integrated quantile regression models – Tianying Wang – Bioinformatics 

timeOmics: an R package for longitudinal multi-omics data integration – Antoine Bodein – Bioinformatics 

Automation of QIIME2 Metagenomic Analysis Platform – Calvin Fung – Current Protocols

September 14, 2021

Posted on by

General microbiome

[REVIEW]Host specificity of the gut microbiome – Mallott & Amato – Nature Reviews Microbiology

[COMMENT]Harnessing the power of host–microbe symbioses to address grand challenges – Hentschel – Nature Reviews Microbiology

The intratumoral microbiome: Characterization methods and functional impact – Heymann et al. – Cancer Letters

Human oral microbiome

Oral hygiene and oral microbiota in children and young people with neurological impairment and oropharyngeal dysphagia – Fregatto et al. – Scientific Reports

Human skin microbiome/virome

[PREPRINT]The Application of The Skin Virome for Human Identification – Graham et al. – bioRxiv

Human vaginal microbiome

Vaginal microbiome topic modeling of laboring Ugandan women with and without fever – Movassagh et al. – NPJ Biofilms and Microbes

Human nearly-sterile sites (blood, organs, brain)

Plasma metagenomic sequencing to detect and quantify bacterial DNA in ICU patients suspected of sepsis – Kisat et al. – The Journal of Trauma and Acute Care Surgery

Human gut microbiome

The gut microbiome in konzo – Bramble et al. – Nature Communications

High-salt diet mediates interplay between NK cells and gut microbiota to induce potent tumor immunity – Rizvi et al. – Science Advances

The Firmicutes/Bacteroidetes ratio of the human gut microbiota is associated with prostate enlargement – Takezawa et al. – The Prostate

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Gut microbiota from green tea polyphenol-dosed mice improves intestinal epithelial homeostasis and ameliorates experimental colitis – Wu et a. – Microbiome

Differential perturbations of gut microbial profiles and co-occurrence networks among phases of methamphetamine-induced conditioned place preference – Wang et al. – Journal of Neuroscience Research

Gut microbiota regulation of P-glycoprotein in the intestinal epithelium in maintenance of homeostasis – Foley et al. – Microbiome

Vitamin A supplementation ameliorates ulcerative colitis in gut microbiota–dependent manner – Pang et al. – Food Research International

Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period – Suriyaphol et al. – Scientific Reports

Bioinformatics

A statistical model for describing and simulating microbial community profiles – Ma et al. – PLOS Computational Biology

September 11, 2021

Posted on by

Highlights!

Bioaccumulation of therapeutic drugs by human gut bacteria – Martina Klünemann – Nature → In this article, the authors showed new bacteria-drug interactions and observed that some microbe communities bioaccumulate drugs.

Eight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian Permafrost – Katie Sipes – Applied and Environmental Microbiology → Interesting features from a set of eight ≥80% complete MAGs from Siberian permafrost soil. 

Review: Analysis the Link between Periodontal Diseases and Alzheimer’s Disease: A Systematic Review – Leslie Borsa – International Journal of Environmental Research and Public Health → This systematic review found that “an association between periodontal disease and Alzheimer’s disease”, suggesting that “the treatment of periodontal disease could be a way to explore Alzheimer’s disease prevention”.

Transplantation of gut microbiota derived from Alzheimer’s disease mouse model impairs memory function and neurogenesis in C57BL/6 mice – Namkwon Kim – Brain, Behavior, and Immunity → Microbiota transplantation from an Alzheimer mouse model into a healthy model, showing effects in neurological parameters.

General Microbiome 

Controllers of cutaneous regulatory T cells: ultraviolet radiation and the skin microbiome. – Thomas Schwarz – Biological Chemistry

The effects of cigarette smoking on the salivary and tongue microbiome – Nao Suzuki – Clinical and Experimental Dental Research

Review: Oral Microbiota Variation: A Risk Factor for Development and Poor Prognosis of Esophageal Cancer. – Xiaobo Song – Digestive Diseases and Sciences

The gastric microbiota in patients with Crohn’s disease; a preliminary study – Jerzy Ostrowski – Scientific Reports

Saliva-derived microcosm biofilms grown on different oral surfaces in vitro – Xiaolan Li – NPJ biofilms and microbiomes

Plasma Metabolomic and Intestinal Microbial Analyses of Patients With Severe Aplastic Anemia – Yuanyuan Shao – Frontiers in Cell and Developmental Biology

Review: Gastrointestinal mucosal immunity and COVID-19 – Tsvetelina Velikova – World Journal of Gastroenterology

Review: Exploring the global vaginal microbiome and its impact on human health – Linda Abou Chacra – Microbial Pathogenesis

Review: Gut microbiome in acute pancreatitis: A review based on current literature – Bharati Kadamb Patel – World Journal of Gastroenterology

Review: Parkinson’s Disease and Gut Microbiota – Masaaki Hirayama – Annals of Nutrition & Metabolism

Beneficial Microbes, Compounds and Interventions

Dietary Pterostilbene and Resveratrol Modulate the Gut Microbiota Influenced by Circadian Rhythm Dysregulation – Yen-Chun Koh – Molecular Nutrition & Food Research

Lactobacillus rhamnosus Affects Rat Peritoneal Cavity Cell Response to Stimulation with Gut Microbiota: Focus on the Host Innate Immunity – Stanislava Stanojević – Inflammation

Fisetin Improves Hyperuricemia-Induced Chronic Kidney Disease via Regulating Gut Microbiota-Mediated Tryptophan Metabolism and Aryl Hydrocarbon Receptor Activation. – Qian Ren – Journal of Agricultural and Food Chemistry

Comparative effects of alive and pasteurized Akkermansia muciniphila on normal diet-fed mice – Fatemeh Ashrafian – Scientific Reports

Review: Fruits and their impact on the gut microbiota, gut motility and constipation – Zoi Katsirma – Food & Function

Review: Rare sugars: Metabolic Impacts and Mechanisms of Action – a Scoping Review – Alison Smith – The British Journal of Nutrition

Plant Microbiome

Invasive Grass Dominance over Native Forbs Is Linked to Shifts in the Bacterial Rhizosphere Microbiome. – Marina L LaForgia – Microbial ecology

Coupling the endophytic microbiome with the host transcriptome in olive roots – Antonio J Fernández-González – Computational and Structural Biotechnology Journal

Fungi Microbiome

Succession and potential role of bacterial communities during Pleurotus ostreatus production – Renáta Bánfi – FEMS Microbiology Ecology

Wastewater Microbiome

Metagenomic Analysis of Antibiotic Resistance Genes in Untreated Wastewater From Three Different Hospitals – Xiurong Guo – Frontiers in Microbiology

Bioinformatics

Learning Sparse Log-Ratios for High-Throughput Sequencing Data – Elliott Gordon-Rodriguez – Bioinformatics

gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites – Liang Cheng – Nucleic Acids Research

Experimental Techniques

Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits – Kathrin Janssen – Applications in Plant Sciences

Other

Metagenome-Assembled Genome Sequences Obtained from a Reactivated Kombucha Microbial Community Exposed to a Mars-Like Environment outside the International Space Station – Imchang Lee – Microbiology Resource Announcements

Mon-microbiome picks

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa – Eduan Wilkinson – Science