October 20, 2021

General microbiome

[REVIEW]Controlled Complexity: Optimized Systems to Study the Role of the Gut Microbiome in Host Physiology – Glowacki, Engelhart & Ahern – Frontiers in Microbiology

[REVIEW]Microbiota-brain interactions: Moving toward mechanisms in model organisms – Nagpal & Cryan – Neuron

Functional attractors in microbial community assembly – Estrela et al. – Cell Systems

Bloodstream infections’ origins following fecal microbiota transplantation: a strain- level analysis – Eshel et al. – Blood Advances

Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota – Ma et al. – Communications Biology

Multi-site human microbiome

[PREPRINT]Obesity influences composition of salivary and fecal microbiota and impacts the interactions between bacterial taxa – Bombin et al. – bioRxiv

Human vaginal microbiome

Does probiotics work for bacterial vaginosis and vulvovaginal candidiasis – Han & Ren – Current Opinion in Pharmacology

Human gut microbiome

A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations – Muller, Algavi & Borenstein – Microbiome

Specific gut microbiome signatures and the associated pro-inflamatory functions are linked to pediatric allergy and acquisition of immune tolerance – de Filippis et al. – Nature Communications

Drinking Water Source and Intake Are Associated with Distinct Gut Microbiota Signatures in US and UK Populations – Vanhaecke et al. – The Journal of Nutrition

The Gut Microbiota during a Behavioral Weight Loss Intervention – Stanislawski et al. – Nutrients

Effect of chewing betel nut on the gut microbiota of Hainanese – Ying et al. – PLOS One

[PREPRINT]Codiversification of gut microbiota with humans – Suzuki et al. – bioRxiv

Response to PD-1-Based Immunotherapy for Non-Small Cell Lung Cancer Altered by Gut Microbiota – He et al. – Oncology and Therapy

Human metabolome

Changes in serum and urinary metabolomic profile after a dietary intervention in patients with irritable bowel syndrome – Nybacka et al. – PLOS One

The influence of the gut microbiome on BCG-induced trained immunity – Strazar et al. – Genome Biology

Animal microbiome

Weaning age and its effect on the development of the swine gut microbiome and resistome – Holman et at. – bioRxiv

Sandalwood seed oil improves insulin sensitivity in high-fat/high-sucrose diet-fed rats associated with altered intestinal microbiota and its metabolites – Gao et al. – Food & Function

Plant, root, and soil microbiome

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil – Trubl et al. – Microbiome

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

PREPRINT[]Bacterial, phytoplankton, and viral dynamics of meromictic Lake Cadagno offer insights into the Proterozoic ocean microbial loop – Saini et al. – bioRxiv

Metagenomic analysis provides functional insights into seasonal change of a non-cyanobacterial prokaryotic community in temperate coastal waters – Matsumoto et al. – PLOS One

[PREPRINT]Survival of hatchery grown native oysters is associated with specific gut-associated bacteria at various locations within the Puget Sound – Kunselmann et al. – bioRxiv

Built environment (subways, indoor surfaces)

Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity – Cobo-Diaz et al. – Microbiome

Food microbiology

Effects of ultrasound treatments on wine microorganisms – Munoz et al. – Ultrasonics Sonochemistry

Effect of roasting conditions on cocoa bioactivity and gut microbiota modulation – Maldonado-Mateus et al. – Food & Function

Bioinformatics

[PREPRINT]Development of a metatranscriptomic analysis method for multiple intestinal sites and its application to the common marmoset intestine – Uehara et al. – bioRxiv

Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics – Arikawa et al. – Microbiome

[PREPRINT]Metagenome assembly of high-fidelity long reads with hifiasm-meta – Feng et al. – arXiv.org

Fast and Accurate Distance-based Phylogenetic Placement using Divide and Conquer – Balaban et al. – Molecular Ecology Resources

Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)

Should You Get a Microbiome Test? – Anahad O’Connor – New York Times

October 5, 2021

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

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 28, 2021

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 14, 2021

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

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 01, 2021

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

August 18, 2021

Call for Papers

Cells is calling for papers for a special issue on “Interplay of Gene Expression Regulation and Microbiome”. Deadline for paper submission: 30th of November 2021

General microbiome

[REVIEW]The Cancer Microbiome: Recent Highlights and Knowledge Gaps – Knippel, Drewes & Sears – Cancer Discoveries

[REVIEW]Healthy Patients Are Not the Best Controls for Microbiome-Based Clinical Studies: Example of Sjögren’s Syndrome in a Systematic Review – Doare et al. – Frontiers in Immunology

[REVIEW]The varying effects of antibiotics on gut microbiota – Yang et al. – AMB Express

[REVIEW]Prevotella diversity, niches and interactions with the human host – Tett et al. – Nature Reviews Microbiology

Bacterial colonization dynamics and antibiotic resistance gene dissemination in the hospital environment after first patient occupancy: a longitudinal metagenetic study – Klassert et al. – Microbiome

Long-term biodiversity intervention shapes health-associated commensal microbiota among urban day-care children – Roslund et al. – Environment International

Multi-site human microbiome

Different responses of the oral, nasal and lung microbiomes to cigarette smoke – Pfeiffer et al. – Thorax

Human skin microbiome

[REVIEW]The power and potential of BIOMAP to elucidate host-microbiome interplay in skin inflammatory diseases – Alenius et al. – Experimental Dermatology

[PREPRINT]Bacterial DNA on the skin surface overrepresents the viable skin microbiome – Acosta et al. – bioRxiv

Human oral microbiome

[REVIEW]The role of oral bacteria in inflammatory bowel disease – Read, Curtis & Neves

Inflammation-type dysbiosis of the oral microbiome associates with the duration of COVID-19 symptoms and long-COVID – Haran et al. – JCI insight

Human gut microbiome

[REVIEW]Phage Diversity in the Human Gut Microbiome: a Taxonomist’s Perspective – Adriaenssens – mSystems

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

IL-10 Deficiency Accelerates Type 1 Diabetes Development via Modulation of Innate and Adaptive Immune Cells and Gut Microbiota in BDC2.5 NOD Mice – Huang et al. – Frontiers in Immunology

Genetically determined hypertensive phenotype affects gut microbiota composition, but not vice versa – Konopelski et al. – Journal of Hypertension

Plant, root, and soil microbiome

Plant developmental stage drives the differentiation in ecological role of the maize microbiome – Xiong et al. – Microbiome

Bioinformatics

ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach – Dovrolis et al. – PLOS Computational Biology

[PREPRINT]SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs) – Pan et al. – bioRxiv

[PREPRINT]Network analysis of ten thousand genomes shed light on Pseudomonas diversity and classification – Passarelli-Araujo, Franco & Venancio – bioRxiv

Techniques

[PREPRINT]The clinical utility of two high-throughput 16S rRNA gene sequencing workflows for taxonomic assignment of unidentifiable bacterial pathogens in MALDI-TOF MS – Lao et al. – bioRxiv

July 16, 2021

Today’s digest features studies on environmental contamination of carbapenem-resistant Klebsiella pneumoniae in China (spoiler: extensive contamination, but has negligible impact on patient colonisation), the dynamic change and correlation of microbiome from different body sites to the treatment response as well as immune-related adverse events of immunotherapy in lung cancer patients, and more.

Also, check out a regularly-updated collection of FREE, ONLINE microbiome events. Happy Friday!

Human microbiome

*Prospective correlation between the patient microbiome with response to and development of immune-mediated adverse effects to immunotherapy in lung cancer – Justin Chau – BMC Cancer

Gut microbiome

Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner – Emmanuel Montassier – Nature Microbiology

Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects – Sandeep Verma – PlosOne

Differences in the individual curative effect of acupuncture for obese women with polycystic ovary syndrome based on metagenomic analysis: study protocol for a randomized controlled trial – Huaying Fan – Trials

Comparative Analysis of 16S rRNA Gene and Metagenome Sequencing in Pediatric Gut Microbiomes – Danielle Peterson – Frontiers in Microbiology

Resistome

*Spread of Carbapenem-Resistant Klebsiella pneumoniae in an Intensive Care Unit: A Whole-Genome Sequence-Based Prospective Observational Study – Li Wei – Microbiology Spectrum

*Linezolid- and multidrug-resistant enterococci in raw commercial dog food, Europe, 2019–2020 – Ana R. Freitas – Emerging Infectious Diseases

Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study – Huan Chen – PeerJ

Predicting antibiotic resistance gene abundance in activated sludge using shotgun metagenomics and machine learning – Yuepeng Sun – Water Research

Animal microbiome

Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers – Déborah Romaskevis Gomes Lopes – Journal of Animal Science and Biotechnology

Animal experiment

An osmotic laxative renders mice susceptible to prolonged Clostridioides difficile colonization and hinders clearance – Sarah Tomkovich – bioRxiv

Bioinformatics

Critical Assessment of Metagenome Interpretation – the second round of challenges – F. Meyer – bioRxiv

Disentangling environmental effects in microbial association networks – Maria Deutschmann – bioRxiv

Webinars &c

Microbiome Virtual International Conference #MVIF – September 14

June 25, 2021

This week, the microbial sciences community worldwide (virtually) united at the World Microbe Forum – meeting highlights you can find here #WorldMicrobeForum.

Today’s digest features studies on group B Streptococcus pathogenesis, dental microbiota and aGVHD Risk, a book about writing and publishing papers, and more. Also, check out a collection of FREE, ONLINE microbiome events. Happy Friday!


Read about the experiences of 338 early career researchers from 36 countries with their mentors in Mentorship in life sciences: voices of mentees by A. Murat Eren (Meren)!


General microbiome

Behind the paper: Describing and naming bacteria in the 21st century – Thomas Hitch – Nature blog

Hierarchical control of microbial community assembly – Sammy Pontrelli – bioRxiv

Resistome

*L-form switching confers antibiotic, phage and stress tolerance in pathogenic Escherichia coli – Aleksandra Petrovic Fabijan – bioRxiv

Gut microbiome

A newly identified protein from Akkermansia muciniphila stimulates GLP-1 secretion – Patrice D. Cani and Claude Knauf – Cell Metabolism

Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics – Anna Pryszlak – arXiv

Dispersal strategies shape persistence and evolution of human gut bacteria – Falk Hildebrand – Cell Host & Microbe

Urinary microbiome

Review: Urinary Microbiome: Yin and Yang of the Urinary Tract – Virginia Perez-Carrasco – Frontiers in Cellular and Infection Microbiology

Vaginal microbiome

Cysteine dependence in Lactobacillus iners constitutes a novel therapeutic target to modify the vaginal microbiota – Seth M. Bloom – bioRxiv

*A type VII secretion system in Group B Streptococcus mediates cytotoxicity and virulence – Brady L Spencer – bioRxiv

Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omics – Zhuye Jie – Genomics, Proteomics & Bioinformatics

Predictive functional analysis reveals inferred features unique to cervicovaginal microbiota of African women with bacterial vaginosis and high-risk human papillomavirus infection – Harris Onywera – PlosOne

Effect of metronidazole on vaginal microbiota associated with asymptomatic bacterial vaginosis – Daniel Ruiz-Perez – Access Microbiology

Oral microbiome

*Dental Biofilm Microbiota Dysbiosis Is Associated With the Risk of Acute Graft-Versus-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation – Vitor Heidrich – Frontiers in Immunology

Fusobacterium nucleatum metabolically integrates commensals and pathogens in oral biofilms – Akito Sakanaka – bioRxiv

Animal microbiome

*Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches – Sharon A. Huws – Microbiome

Animal experiments

A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes – Marion Darnaud – bioRxiv

Bioinformatics

GUNC: detection of chimerism and contamination in prokaryotic genomes – Askarbek Orakov – BMC Genome Biology

metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies – Senying Lai – bioRxiv

Open challenges for microbial network construction and analysis – Karoline Faust – The ISME Journal 2021

STRipy: a graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data – Andreas Halman – bioRxiv

Adapting macroecology to microbiology: using occupancy modelling to assess functional profiles across metagenomes – Angus S Hilts – bioRxiv


Webinars &c

Microbiome Virtual International Conference #MVIF – September 14

The International Conference on Group B Strep (ICGBS) – July 20-22

World Enterococcus Day – July 15 – Registration here

BiATA2021 Bioinformatics: from Algorithms to Applications – July 12–15 


LSfM Lecture Series & Workshops : “The Dark Side of Science: Misconduct in Biomedical Research” Dr. Elisabeth Bik – more info here – June 30

EMBARK Webinars – Kimberly Kline “Pathogenesis and persistence during Enterococcus faecalis biofilm-associated infection” and Sofia Forslund “High-throughput measurement of host and microbiota” – EMBARK project – June 30


Writing

Writing and Publishing Scientific Papers: A Primer for the Non-English Speaker – Gábor Lövei – OpenBook Publishers


Art

From Scientist to SciArtist – Eliza Wolfson