Category Archives: Human gut

October 5, 2021

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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

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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

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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

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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 22, 2021

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Grant application (US specific grant)
Call for application for Biocodex Microbiota Foundation’s 2021 research grant ($50,000 US) which can be applied to new or existing research aimed at helping understand gut microbiota and its impact beyond the human digestive system.
Deadline: October 15th, 2021
Link: https://www.biocodexmicrobiotafoundation.com/national-call-projects/usa

Human skin microbiome

[Commentary]Food for thought: does host diet affect skin microbes? – Schneider & Nelson – British Journal of Dermatology

Host traits, lifestyle and environment are associated with human skin bacteria – Moitinho-Silva et al – British Journal of Dermatology

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

Deciphering the low abundance microbiota of presumed aseptic hip and knee implants – Carr et al. – PLOS One

Human gut microbiome

[REVIEW]Next Generation Microbiome Research: Identification of Keystone Species in the Metabolic Regulation of Host-Gut Microbiota Interplay – Tudela, Claus & Saleh – Front. Cell Dev. Biol.

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

Commensal microbe-derived acetate suppresses NAFLD/NASH development via hepatic FFAR2 signalling in mice – Aoki et al. – Microbiome

Animal microbiome (for animals in the wild)

16 S rRNA gene diversity and gut microbial composition of the Indian white shrimp (Penaeus indicus) – Patil et al. – Antonie van Leeuwenhoek

Plant, root, and soil microbiome

Disease-induced changes in plant microbiome assembly and functional adaptation – Gao et al. – Microbiome

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

Diversity and distribution of viruses inhabiting the deepest ocean on Earth – Jian et al. – The ISME Journal

Deep-sea shipwrecks represent island-like ecosystems for marine microbiomes – Hamdan et al – The ISME Journal

The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole – Martin et al. – Nature Comminications

Phages and viruses

A 2021 taxonomy update for the family Smacoviridae – Krupovic & Varsani – Archives of Virology

Bioinformatics

[PREPRINT]MIMOSA2: A metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data – Noecker, Eng & Borenstein – bioRxiv

Identifying indicator species in ecological habitats using Deep Optimal Feature Learning – Tsai, Baldwin & Gopaluni – PLOS One

September 14, 2021

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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 10, 2021

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In today’s digest read about a discovery of new Bordetella bronchiseptica-specific temperate and highly abundant siphoviruses that lead to the creation of a new genus Vojvodinavirus, biases in public human microbiome data, infant gut strain persistence, and more. Also, check out a list of upcoming microbiome events. Happy Friday!

Global microbiome

*Public human microbiome data dominated by highly developed countries – Richard J. Abdill – bioRxiv

Gut microbiome

Chinese gut microbiota and its associations with staple food type, ethnicity, and urbanization – Jing Lu – npj Biofilms and Microbiomes

Gut microbiota alterations in response to sleep length among African-origin adults – Na Fei – PlosOne

Bioaccumulation of therapeutic drugs by human gut bacteria – Martina Klünemann – Nature

*Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition – Yue Clare Lou – Cell Reports Medicine

Skin microbiome

Cotton and Surgical Face Masks in Community Settings: Bacterial Contamination and Face Mask Hygiene – Lize Delanghe – Frontiers in Medicine

Animal microbiome

The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps? – Chiara Crestani – Microbial Genomics

Viruses and phages

*Are Bordetella bronchiseptica Siphoviruses (Genus Vojvodinavirus) Appropriate for Phage Therapy—Bacterial Allies or Foes? – Aleksandra Petrovic Fabijan – Viruses

Water microbiome

Functional Redundancy in Ocean Microbiomes Controls Trait Stability – Taylor M. Royalty and Andrew D. Steen – bioRxiv

Bioinformatics

SHOOT: phylogenetic gene search and ortholog inference – David Emms and Steven Kelly – bioRxiv

Ultra-resolution Metagenomics: When Enough Is Not Enough – Falk Hildebrand – mSystems

Computational challenges and opportunities in spatially resolved transcriptomic data analysis – Lyla Atta & Jean Fan – Nature Communications

*BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data – Chenhao Li – Plos Computational Biology

Webinars &c

Conference: Microbiome Virtual International Conference #MVIF – September 14/16 (Atlantic/Pacific)

Course + Symposium: 2021 ISB Virtual Microbiome Series – October 13-15

Webinar: EMBARK Fall Webinars – a webinar series where invited speakers will be presenting their AMR research and be contrasted to EMBARK members presenting the work performed in the project.

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

September 7, 2021

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Today’s digest features some excellent human and mouse microbiome research, a highly detailed study of human associated Bifidobacterium longum, as well as a non microbiome picks on the history of rhinoceros in Cell and how to write a lab protocol in Nature.

General microbiome

Exploring Microbiome Functional Dynamics through Space and Time with Trait-Based Theory – Bittleston et al. mSystems

Human gut microbiome

Effects of antibiotic duration on the intestinal microbiota and resistome: The PIRATE RESISTANCE project, a cohort study nested within a randomized trial – Leo et al. EBioMedicine

Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals  – Tarallo et al. Gut

Associations between the gut microbiome and metabolome in early life – Nguyen et al. BMC Microbiology

Animal Experiments

The composition of the gut microbiota following early-life antibiotic exposure affects host health and longevity in later life – Lynn et al. Cell Reports

Human gut-derived B. longum subsp. longum strains protect against aging in a D-galactose-induced aging mouse model – Xiao et al. Microbiome

Water Microbiome

Arms race in a cell: genomic, transcriptomic, and proteomic insights into intracellular phage–bacteria interplay in deep-sea snail holobionts – Zhou et al. Microbiome

Soil microbiome

Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil – Starr et al. mSphere

Bioinformatics

Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ) – Ling et al. Microbiome

Non-microbiome picks

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family – Lie et al. Cell

Five keys to writing a reproducible lab protocol – Nature

September 06, 2021

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General microbiome

[PREPRINT]Host-microbiome protein-protein interactions capture mechanisms in human disease – Zhou, Beltran & Brito – bioRxiv

Prognostic correlations with the microbiome of breast cancer subtypes – Banerjee et al. – Cell Death & Disease

Pregnancy and early life

[REVIEW]Composition of the vaginal microbiota during pregnancy in women living in sub-Saharan Africa: a PRISMA-compliant review – Juliana et al. – BMC Pregnancy and Childbirth

Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage – Seki et al. – Cell Host & Microbe

Multi-site human microbiome

[PREPRINT]Comparing Fecal, Saliva, and Chicha Microbiomes Between Mothers and Children in an Indigenous Ecuadorian Cohort – Adams et al. – bioRxiv

Human respiratory microbiome

Alterations of gut microbiota in patients with active pulmonary tuberculosis in China: A pilot study – Shi et al. – International Journal of Infectious Diseases

Human oral microbiome

The effects of periodontitis associated microbiota on the development of oral squamous cell carcinoma – Hu, Shen & Tian – Biochemical and Biophysical Research Communications

Human gut microbiome

Parasites and diet as main drivers of the Malagasy gut microbiome richness and function – Mondot et al. – Scientific Reports

[REVIEW]The second brain: The connection between gut microbiota composition and multiple sclerosis = Farshbafnadi, Agah & Rezaei – Journal of Neuroimmunology

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

Thymic development of gut-microbiota-specific T cells – Zegarra-Ruiz et al – Nature

High-fat diet alters stress behavior, inflammatory parameters and gut microbiota in Tg APP mice in a sex-specific manner – Yanguas-Casas – Neurobiology of Diesease

Sex-dependent effects on the gut microbiota and host metabolome in type 1 diabetic mice – Zhang et al. – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

Bioinformatics

Efficient computation of Faith’s phylogenetic diversity with applications in characterizing microbiomes – Armstrong et al. – Genome Research

September 01, 2021

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General microbiome

Circulating microbiome DNA: An emerging paradigm for cancer liquid biopsy – Chen et al. – Cancer letters

Human-associated microbiota suppress invading bacteria even under disruption by antibiotics – Letten et al. – The ISME Journal

[PERSPECTIVE]Crosstalk between γδ T cells and the microbiota – Papotto, Yilmaz & Silva-Santos – Nature Microbiology

Pregnancy and early life

Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life – Tsukuda et al. – The ISME Journal

Deterministic transition of enterotypes shapes the infant gut microbiome at an early age – Xiao et al. – Genome Biology

Human oral microbiome

[REVIEW]Association between metabolic syndrome and periodontitis: The role of lipids, inflammatory cytokines, altered host response, and the microbiome – Pirih et al. – Periodontology 2000

[REVIEW]Fungal diseases: Oral dysbiosis in susceptible hosts – Villar & Dongari-Bagtzoglou – Periodontology 2000

[REVIEW]The oral microbiome: Role of key organisms and complex networks in oral health and disease – Sedghi et al. – Periodontology 2000

Human gut microbiome

Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes – Kim et al. – Genome Medicine

[REVIEW]The promise of the gut microbiome as part of individualized treatment strategies – Schupack et al. – Nature Reviews Gastroenterology & Hepatology

[REVIEW]The gut microbiome and efficacy of cancer immunotherapy – Robiello et al. – Pharmacology & Therapeutics

Integrated analysis of the faecal metagenome and serum metabolome reveals the role of gut microbiome-associated metabolites in the detection of colorectal cancer and adenoma – Chen et al. – Gut

Animal/Insect microbiome

Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes – Gupta et al. – Microbiome

Social networks strongly predict the gut microbiota of wild mice – Raulo et al. – The ISME Journal

Genetic identity and genotype × genotype interactions between symbionts outweigh species level effects in an insect microbiome – Smee, Raines & Ferrari – The ISME Journal

[REVIEW]The effects of raw-meat diets on the gastrointestinal microbiota of the cat and dog: a review – Butowski et al. – New Zealand Veterinary Journal

Plant, root, and soil microbiome

Predicting spatial patterns of soil bacteria under current and future environmental conditions – Mod et al. – The ISME Journal

Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype – Stopnisek & Shade – The ISME Journal

Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota – Wippel et al. – Nature Microbiology

Bioinformatics/Techniques

Functional meta-omics provide critical insights into long- and short-read assemblies – Galata et al. – Briefings in Bioinformatics

[PREPRINT]BiomeHorizon: visualizing microbiome time series data in R – Fink et al. – bioRxiv

Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota – Shibata et al. – PLOS ONE

MicFunPred: A conserved approach to predict functional profiles from 16S rRNA gene sequence data – Mongad et al. – Genomics