Tag Archives: metagenomics

November 14, 2025

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Gut Microbiome & Host Health

Sleep deprivation disrupts diurnal rhythmicity of gut microbiota and blood inflammatory cytokines in mice — Weiran Shan et al. (PLOS ONE)

Chemical modulation of gut bacterial metabolism induces colanic acid and extends the lifespan of nematode and mammalian hosts — Guo Hu et al. (PLOS Biology)

The role of hypothyroidism in cirrhosis pathogenesis: A retrospective cohort study and multi-omics integration analysis — Ziyang Yang et al. (PLOS Genetics)

Multi-omics analysis reveals metabolic regulation of phosphatidylcholine, triglycerides, phosphatidylethanolamine, and cardiolipin metabolism in mouse liver with MASLD — Hong Liang & Kang Song (PLOS ONE)

Metabolomics and glucose tolerance in pregnancy and postpartum: The PONCH study — Ulrika Andersson-Hall et al. (PLOS ONE)

Microbial Pathogens, Immunity & Infection

Exploring the gut microbiota of Pacific white shrimp suffering pale shrimp disease — Lalitphan Kitsanayanyong et al. (PLOS ONE)

Dominance of Zygosaccharomyces and shifts in bacterial pathways under antimicrobial pressure — Maria Cecilia Rasuk et al. (PLOS ONE)

How transcriptional networks control Verticillium plant infection — Ying-Yu Chen et al. (PLOS Pathogens)

Integrative machine learning and multi-omics framework identifies shared biomarkers for rheumatoid arthritis and ulcerative colitis — Meili Liu et al. (PLOS ONE)

The cervicovaginal microbiome associates with spatially restricted host transcriptional signatures throughout the ectocervical epithelium — Vilde Kaldhusdal et al. (PLOS Pathogens)

Characterization of ORF19.7608 (PPP1), a biofilm-induced gene of Candida albicans — Nmerichukwu C. Iwuchukwu et al. (PLOS ONE)

Differential regulation of the eicosanoid biosynthesis pathway during Enterocytozoon hepatopenaei infection in shrimp — Wananit Wimuttisuk et al. (PLOS ONE)

Animal, Environmental & Soil Microbiomes

Cuts or carcasses? Diet form affects fecal microbial and fiber fractions in Asiatic lions — Mengmeng Sun et al. (PLOS ONE)

From pre-oral secretions to gut digestion: How Lucilia sericata larvae handle Leishmania major — Azam Malekian et al. (PLOS ONE)

Targeted pathogen profiling of ancient feces reveals common enteric infections (725–920 CE) — Drew Capone et al. (PLOS ONE)

Starve or share? Phosphate availability shapes plant–microbe interactions — Maja Schmidt et al. (PLOS Pathogens)

Pathogenicity and transmission of Morganella morganii in honey bees — Yijun Chen & Qiang Huang (PLOS Pathogens)

Mitogenomics of the tropical bont tick reveals vertical and horizontal transmission of Rickettsia africae — Elisha Chatanga et al. (PLOS NTDs)

Differentiation of bacterial communities in the coral Orbicella faveolata across life-cycle stages — Amanda Pérez-Trejo et al. (PLOS ONE)

Insect-derived polymer hydrogel based on fibroin matrix from whole silkworm larvae — Maki Yamazaki et al. (PLOS ONE)

Thermophilic microbiome acclimation improves anaerobic digestion of food waste — Hengxuan Shao et al. (PLOS ONE)

Epidemiology, Public Health & Clinical Microbiology

Assessing piperacillin/tazobactam vs. ceftriaxone + metronidazole for children with perforated appendicitis — Daniel Briatico et al. (PLOS ONE)

Prevalence and antimicrobial resistance of multidrug-resistant Staphylococcus epidermidis in raw milk — Inamullah et al. (PLOS ONE)

Hematological ratios, immune-related adverse events, and mortality in patients receiving immune checkpoint inhibitors — Sophie Lekkerkerker et al. (PLOS ONE)

Geographical and climatic risk factors for COVID-19 in southwest Iran — Koorosh Nikaein et al. (PLOS ONE)

Anthropometric and neurocognitive consequences of Campylobacter, ETEC, and norovirus infections: A systematic review — Patricia B. Pavlinac et al. (PLOS NTDs)

Neuroscience, Immunology & Molecular Networks

Skin melanin is associated with body temperature regulation in humans and mice — Kale S. Bongers et al. (PLOS ONE)

Oxytocin neurons drive melanocortin circuit maturation via vesicle release — Pierre-Yves Barelle et al. (PLOS Biology)

Elucidation and application of the neuroimmune axis between depression and autoimmune diseases — Fu Sun et al. (PLOS ONE)

Quantifying microbial interactions using an iterative generalized Lotka–Volterra approach — Yue Huang et al. (PLOS Computational Biology)

September 4, 2024

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Good morning (or afternoon, or evening, wherever you are in the world reading this,) Microbiome Digesters! Today’s post features a piece from Nature highlighting the ethical dilemmas and evolving approaches in Indigenous microbiome research. Indigenous peoples have historically faced exploitation through extraction of their lands, biological samples, and genetic data without proper consent. Researchers are re-evaluating their methods, shifting towards more respectful and collaborative practices that involve Indigenous communities in designing studies and ensuring they benefit from the findings. Check out the piece by Sam Jones for Nature to learn more.

An ethical way forward for Indigenous microbiome research – Sam Jones – Nature Outlook: The human microbiome

Human gut microbiome

Interplay between particle size and microbial ecology in the gut microbiome – Jeffrey Letourneau et al – ISME Journal

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome – Niccolò Carlino – Cell

A streamlined culturomics case study for the human gut microbiota research – Hyunjoon Park et al – Scientific Reports

Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia – Getnet Tesfaw et al – Nature Communications

Association of maternal gut microbial metabolites with gestational diabetes mellitus: evidence from an original case-control study, meta-analysis, and Mendelian randomization – Mengxin Yao et al – European Journal of Clinical Nutrition

The Microleaks study: 16S community profile and metagenomic shotgun sequencing signatures associated with anastomotic leak – Emily C. Hoedt et al – NPJ Gut & Liver

Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome – Stefanie Duller et al – Nature Communications

Characterization of gut microbiota in the Uyghur osteopenia population – Kunchen Teng et al – Scientific Reports

Spaceflight alters host-gut microbiota interactions – E. Gonzalez et al – NPJ Biofilms & Microbiomes

Other human microbiome

Bacterial association with metals enables in vivo monitoring of urogenital microbiota using magnetic resonance imaging – Sarah C. Donnelly et al – Communications Biology

Urine metabolomic profiles of autism and autistic traits – A twin study – Abishek Arora et al – PLOS One

Animal microbiome

Massive expansion of the pig gut virome based on global metagenomic mining – Jiandui Mi et al – NPJ Biofilms & Microbiomes

Marine sponge microbe provides insights into evolution and virulence of the tubercle bacillus – Sacha J. Pidot et al – PLOS Pathogens

Exploring the interactions between Nosema ceranae infection and the honey bee gut microbiome – Edmund Lau et al – Scientific Reports

Metagenomic characterisation of canine skin reveals a core healthy skin microbiome – Michaella J. Whittle et al – Scientific Reports

CHIKV infection drives shifts in the gastrointestinal microbiome and metabolites in rhesus monkeys – Hongyu Chen et al – BMC Microbiome

Effects of dietary restriction and one-carbon metabolite supplementation during the first 63 days of gestation on the maternal gut, vaginal, and blood microbiota in cattle – Sarah M. Luecke et al – BMC Animal Microbiome

Aloe arborescens supplementation in drying-off dairy cows: influence on rumen, rectum and milk microbiomes – Paola Cremonesi et al – BMC Animal Microbiome

Comparative genomics identifies key adaptive traits of sponge-associated microbial symbionts – Paul A. O’Brien et al – Environmental Microbiology

Plant, root & soil microbiome

Deciphering the role of rhizosphere microbiota in modulating disease resistance in cabbage varieties – Xingxing Ping et al – BMC Microbiome

Oak seedling microbiome assembly under climate warming and drought – Daniel Hoefle et al – BMC Environmental Microbiome

The ancestral environment of teosinte populations shapes their root microbiome – Christopher J. Barnes et al – BMC Environmental Microbiome

Water & marine microbiome

Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans – Funing Tian et al – BMC Microbiome

Global distribution, diversity, and ecological niche of Picozoa, a widespread and enigmatic marine protist lineage – BMC Microbiome

Microbial core communities in activated sludge plants are strongly affected by immigration and geography – Sofie Zacho Vertergaard et al – BMC Environmental Microbiome

The eukaryome of modern microbialites reveals distinct colonization across aquatic ecosystems – Anthony M. Bonacolta et al – NPJ Biofilms & Microbiomes

Methods & techniques

[PREPRINT] Domestic freezer storage: a solution for preserving stool microbiota integrity for at-home collection – Paula Momo Cabrera et al – bioRxiv

COVID-19 prevention behaviors and dietary habits among undergraduate students: A health belief model approach – Doreen Liou – PLOS One

A catalog of small proteins from the global microbiome – Yiqian Duan et al – Nature Communications

June 26, 2024

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Human gut microbiome

Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut – Nick Quinn-Bohmann et al – Nature Microbiology

Island biogeography theory provides a plausible explanation for why larger vertebrates and taller humans have more diverse gut microbiomes – Katherine Ramos Sarmiento et al – ISME Journal

Dietary fibre directs microbial tryptophan metabolism via metabolic interactions in the gut microbiota – Anurag K. Sinha – Nature Microbiology

Animal models

The zebrafish gut microbiome influences benzo[a]pyrene developmental neurobehavioral toxicity – Keaton Stagaman et al – Nature Scientific Reports

Modulation of gut microbiota composition due to early weaning stress induces depressive behavior during the juvenile period in mice – Itsuka Kamimura et al – BMC Animal Microbiome

Antibiotics affect the pharmacokinetics of n-butylphthalide in vivo by altering the intestinal microbiota – Xiangchen Li et al – PLOS One

Trilobatin ameliorates dextran sulfate sodium-induced ulcerative colitis in mice via the NF-κB pathway and alterations in gut microbiota – Nanbo Wang et al – PLOS One

Animal microbiome

Gut microbiota and immune profiling of microbiota-humanised versus wildtype mouse models of hepatointestinal schistosomiasis – K.A. Stark et al – BMC Animal Microbiome

Analysis of differences in the rumen microbiome and metabolic function in prepartum dairy cows with different body condition scores – Dewei Du et al – BMC Animal Microbiome

Improvement of insulin sensitivity by dietary fiber consumption during late pregnant sows is associated with gut microbiota regulation of tryptophan metabolism – Yang Li – BMC Animal Microbiome

Gut microbiota diversity in a dung beetle (Catharsius molossus) across geographical variations and brood ball-mediated microbial transmission – Hao-Yu Chen et al – PLOS One

Water & extremophile microbiomes

Metagenomic insights into Heimdallarchaeia clades from the deep-sea cold seep and hydrothermal vent – Rui Liu – BMC Environmental Microbiome

Metagenomic insights into microbial adaptation to the salinity gradient of a typical short residence-time estuary – Ziheng Wu et al – BMC Microbiome

Plant, root, & soil microbiome

Microbial consortium assembly and functional analysis via isotope labelling and single-cell manipulation of polycyclic aromatic hydrocarbon degraders – Jibing Li – ISME Journal

Chemolithoautotrophic diazotrophs dominate dark nitrogen fixation in mangrove sediments – Shasha Wang et al – ISME Journal

Other microbes

Cellular interactions and evolutionary origins of endosymbiotic relationships with ciliates – Qi Song et al – ISME Journal

Bioinformatics & tools

Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling – Worakorn Phumiphanjarphak & Pakorn Aiewsakun – BMC Bioinformatics

Methods

Soft autonomous ingestible device for sampling the small-intestinal microbiome – Ruben Del-Rio-Ruiz et al – Cell Device

May 15, 2024

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Human gut microbiome

A shared group of bacterial taxa in the duodenal microbiota of undernourished Pakistani children with environmental enteric dysfunction – Najeeha T Iqbal – mSphere

Gut microbiota, blood metabolites, and left ventricular diastolic dysfunction in US Hispanics/Latinos – Kai Luo – BMC Microbiome

Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition – Xuanji Li – BMC Microbiome

Impact of the gut microbiome composition on social decision-making – Marie Falkenstein – PNAS Nexus

Veillonella and Bacteroides are associated with gestational diabetes mellitus exposure and gut microbiota immaturity – Fernanda Valdez-Palomares – PLOS One

[REVIEW] The neonatal gut microbiome and global health – Pinaki Panigrahi – Gut Microbes

Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation – Shusan Sargisan – BMC Microbiome

Vaginal microbiome

16S rRNA female reproductive microbiome investigation reveals Dalfopristin, Clorgyline, and Hydrazine as potential therapeutics for the treatment of bacterial vaginosis – Sudeepti Kulshrestha – Diagnostic Microbiology and Infectious Disease

Fecal transplant from vaginally seeded infants decreases intraabdominal adiposity in mice – Sivaranjani Namasivayam – Gut Microbes

Animal microbiome

Viruses contribute to microbial diversification in the rumen ecosystem and are associated with certain animal production traits – Ming Yan & Zhongtang Yu – BMC Microbiome

Quantitative microbiome profiling of honey bee (Apis mellifera) guts is predictive of winter colony loss in northern Virginia (USA) – David B. Carlini – Nature Scientific Reports

How do phytophagous insects affect phyllosphere fungi? Tracking fungi from milkweed to monarch caterpillar frass reveals communities dominated by fungal yeast – Ryoko Oono – Environmental Microbiology

Beneficial microbes & compounds

The gut lactic acid bacteria metabolite, 10-oxo- cis-6, trans-11-octadecadienoic acid, suppresses inflammatory bowel disease in mice by modulating the NRF2 pathway and GPCR-signaling – Miki Ando – Frotiers in Immunology

Effect of weight loss program using prebiotics and probiotics on body composition, physique, and metabolic products: longitudinal intervention study – Nayera E Hassan – Nature Scientific Reports

Origin of the neonatal gut microbiota and probiotic intervention: a randomized controlled trial – Zhe Li – Frontiers in Nutrition

Effectiveness of probiotic- and fish oil-loaded water-in-oil-in-water (W1/O/W2) emulsions at alleviating ulcerative colitis – Qingzhao Gu – Food & Function

Plant, root, and soil microbiome

Competition mode and soil nutrient status shape the role of soil microbes in the diversity–invasibility relationship – Haokun Li – Ecology and Evolution

Dynamics and drivers of fungal communities in a multipartite ant-plant association – Veronica Barrajon-Santos – BMC Biology

Quorum sensing related activities of beneficial and pathogenic bacteria have important implications for plant and human health – Anton Hartmann – FEMS Microbiology Ecology

Impacts of vegetable processing and cheese making effluent on soil microbial functional diversity, community structure, and denitrification potential of land treatment systems – Geoffrey S. Siemering – Water Environment Research

Role of Bacillus subtilis exopolymeric genes in modulating rhizosphere microbiome assembly – Caroline Sayuri Nishisaka – BMC Environmental Microbiome

The predominant lactic acid bacteria and yeasts involved in the spontaneous fermentation of millet during the production of the traditional porridge Hausa koko in Ghana – Amy Atter – BMC Microbiology

Bioinformatics & Tools

Multi-class boosting for the analysis of multiple incomplete views on microbiome data – Andrea Simeon – BMC Bioinformatics

PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome – Lara Vázquez-González – BMC Bioinformatics

Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches – Ryan Kuster – BMC Bioinformatics

March 13, 2024

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Human gut microbiome

Gut microbiota–tryptophan metabolism–GLP-1 axis participates in β-cell regeneration induced by dapagliflozin – Yafei Jiang et al – Diabetes

Inhibition of inosine metabolism of the gut microbiota decreases testosterone secretion in the testis – Lei Tang et al – mSystems

[REVIEW] Exploring the gut microbiota and its potential as a biomarker in gliomas – Dana Aljarrah et al – Biomedicine & Pharmacotherapy

Comparative prebiotic potential of galacto- and fructo-oligosaccharides, native inulin and acacia gum in Kenyan infant gut microbiota during iron supplementation – Paula Momo Cabera et al – ISME Communications

A bacterial sialidase mediates early-life colonization by a pioneering gut commensal – Ekaterina Buzun et al – Cell Host and Microbe

Animal Microbiome

Dietary carbohydrate sources differently prime the microbial ecosystem but not the epithelial gene expression profile along the complete gut of young calves – Thomas Hartinger et al – BMC Animal Microbiome

Multi-omics reveals that alkaline mineral water improves the respiratory health and growth performance of transported calves – Jiancheng Qi et al – BMC Microbiome

Efficacy of a novel multi-enzyme feed additive on growth performance, nutrient digestibility and gut microbiome of weanling pigs fed corn-wheat or wheat-barley based diet – Ayodeji S Aderibigbe et al – Journal of Animal Science

Plant and soil microbiome

Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition – Jia Wang et al – mSystems

Plasma Treatment Modifies Element Distribution in Seed Coating and Affects Further Germination and Plant Growth through Interaction with Soil Microbiome – Tetiana Kalachova et al – Journal of Agricultural and Food Chemistry

Soil Microbiomes and their Arsenic Functional Genes in Chronically High-Arsenic Contaminated Soils – Prinpida Sonthiphand et al – Bulletin of Environmental Contamination and Toxicology

Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria – Katarina Hrovat et al – ISME Communications

Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process – Liqun Jiang et al – Microbiology Spectrum

Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes – Ziguo Zhang et al – mSystems

Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis – Eliza P.-I. Loo et al – Cell Host and Microbe

Built environment microbiome

Microbiome analysis of the restricted bacteria in radioactive element-containing water at the Fukushima Daiichi Nuclear Power Station – Tomoro Warashina et al – Applied and Environmental Microbiology

Bioinformatics and Techniques

The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes – Thibaut Dumas et al – BMC Microbiome

Proportion-based normalizations outperform compositional data transformations in machine learning applications – Aaron Yerke et al – BMC Microbiome

A method to correct for local alterations in DNA copy number that bias functional genomics assays applied to antibiotic-treated bacteria – Geraldine J. Sullivan et al – mSystems

[PREPRINT] Bacterial strain nomenclature in the genomic era: Life Identification Numbers using a gene-by-gene approach – Federica Palma et al – bioRXiv

July 10, 2023

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Last week’s highlights

Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial – Bertrand Routy – Nature Medicine

Top-down identification of keystone taxa in the microbiome – Guy Amit – Nature Communications

Sources of gut microbiota variation in a large longitudinal Finnish infant cohort – Roosa Jokela – EBioMedicine

Events

11th Microbiome R&D and Business Collaboration Forum and 5th Probiotics & Prebiotics Congress: USA – San Diego, CA – October, 19 – 20, 2023

Human and General Microbiome

Essay: A microbiome exercise – Christoph A Thaiss – Science

Mendelian randomisation analysis reveals the possible causal relationship between infections, microbiota and clinical disease – Shifang Li – Gut

Microbiome variance of the small bowel in Crohn’s disease – Lucas Wauters – Gut

Metagenomics analysis of the neonatal intestinal resistome – Stefano Leo – Frontiers in Pediatrics

Development of the intestinal microbiome in cystic fibrosis in early life – Courtney E Price – mSphere

Overexpression of human alpha-Synuclein leads to dysregulated microbiome/metabolites with ageing in a rat model of Parkinson disease – Yogesh Singh – Molecular Neurodegeneration

Male-Biased Gut Microbiome and Metabolites Aggravate Colorectal Cancer Development – Ling Wang – Advanced Science

Review: Systematic review: Autism spectrum disorder and the gut microbiota – Jenni Korteniemi – Acta Psychiatrica Scandinavica

Review: Early-life respiratory infections and developmental immunity determine lifelong lung health – Clare M Lloyd – Nature Immunology

Microbiome and Evolution

Ecoevolutionary processes structure milk microbiomes across the mammalian tree of life – Mia M Keady – PNAS

Shared evolutionary path in social microbiomes – Nelson Frazão – Molecular Biology and Evolution

Beneficial Microbes and Compounds

Review: Use of probiotics, prebiotics, and synbiotics in non-alcoholic fatty liver disease: A systematic review and meta-analysis – Lim Rong – Journal of Gastroenterology and Hepatology

Akkermansia muciniphila and Bifidobacterium bifidum Prevent NAFLD by Regulating FXR Expression and Gut Microbiota – Fulin Nian – Journal of Clinical and Translational Hepatology

Limosilactobacillus reuteri inhibits the acid tolerance response in oral bacteria – Gabriella Boisen – Biofilm

Animal Microbiome

Using the collaborative cross to identify the role of host genetics in defining the murine gut microbiome – Aravindh Nagarajan – Microbiome

Selection for environmental variance shifted the gut microbiome composition driving animal resilience – Cristina Casto-Rebollo – Microbiome

Plant Microbiome

Metabolic interaction models recapitulate leaf microbiota ecology – Martin Schäfer – Science

Environmental Microbiome

Microeukaryotic predators shape the wastewater microbiome – Nils Heck – Water Research

Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples – Cátia Santos-Pereira – Applied Microbiology and Biotechnology

Analysis of the microbiome of the Bolivian high-altitude Lake Pastos Grandes – Jeanett Daga-Quisbert – FEMS Microbiology Ecology

Built Environment

Metagenomic Analysis of a Concrete Bridge Reveals a Microbial Community Dominated by Halophilic Bacteria and Archaea – E Anders Kiledal – Microbiology Spectrum

Microbiome Research: Resources, Tools and Techniques

A catalog of bacterial reference genomes from cultivated human oral bacteria – Wenxi Li – NPJ Biofilms and Microbiomes

Gene-based microbiome representation enhances host phenotype classification – Thomas Deschênes – mSystems

Integrative meta-omics in Galaxy and beyond – Valerie C Schiml – Environmental Microbiome

Preprint: Compositional analysis of microbiome data using the linear decomposition model (LDM) – Yi-Juan Hu – bioRxiv

Preprint: Processing and Storage Methods Affect Oral and Gut Microbiome Composition – Dorothy K Superdock – bioRxiv

Preprint: A genome catalog of the early-life human skin microbiome – Zeyang Shen – bioRxiv

Review: In vitro models as a tool to study the role of gut microbiota in obesity – Abigail González – Critical Reviews in Food Science and Nutrition

January 18, 2022

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Today’s digest contains interesting gut-brain axis articles, developments in bioinformatic multi-omic analyses, and some recent developments in long COVID research highlighted under non microbiome picks below. 

General microbiome

Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states – Adu oppong et al. – Microbiome 

Human gut microbiome

Gut Ruminococcaceae levels at baseline correlate with risk of antibiotic-associated diarrhea – Gu et al. – iScience

Home or hospital birth: the neonatal microbiota perspective – Stojanov et al. – The Lancet Microbe

A pilot exploration of multi-omics research of gut microbiome in major depressive disorders – Zhao et al – Translational Psychiatry

Post-ischemic protein restriction induces sustained neuroprotection, neurological recovery, brain remodeling, and gut microbiota rebalancing – de Carvalho et al. – Brain Behavior and Immunity

Bifidobacterium breve CCFM1025 attenuates major depression disorder via regulating gut microbiome and tryptophan metabolism: A randomized clinical trial – Tian et al.  – Brain Behavior and Immunity

Gestational insulin resistance is mediated by the gut microbiome-indoleamine 2,3-dioxygenase axis – Priyadarshini et al. – Gastroenterology

A natural polyphenol exerts antitumor activity and circumvents anti-PD-1 resistance through effects on the gut microbiota – Messaoudene et al. – Cancer Discovery

Virome

[Research Highlight] Virome holds back a vaccine – York – Nature Reviews Microbiology

Plant & Soil microbiome

Genome-Resolved Metagenomics Reveals Distinct Phosphorus Acquisition Strategies between Soil Microbiomes – Wu et al. – mSystems

Bioinformatics

M&Ms: a versatile software for building microbial mock communities – García-García et al. – Bioinformatics

GraphOmics: an interactive platform to explore and integrate multi-omics data – Wandy & Daly – BMC Bioinformatics

Aristotle: stratified causal discovery for omics data – Mansouri et al.  – BMC Bioinformatics

Non Microbiome Picks

The last few weeks has seen several big studies of ‘long COVID’ published, as well as a letter in The Guardian, which I wanted to highlight

Immunological dysfunction persists for 8 months following initial mild-to-moderate SARS-CoV-2 infection – Phetsouphanh et al. – Nature Immunology

Long-term perturbation of the peripheral immune system months after SARS-CoV-2 infection – Ryan et al. BMC Medicine

Post-acute neurological consequences of COVID-19: an unequal burden – Nolen et al. – Nature Medicine 

Long COVID in children – Gurdasani et al. – The Lancet Child Adolescent Health
I’m leading a long Covid trial – it’s clear Britain has underestimated its impact – Amitava Banerjee – The Guardian

March 13, 2020

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Good moring y’all!

Today’s digest is relatively short, but rather diverse- from the potential characteristics of scientific tweets readers, through cancer microbiome and horses fecal transplants, as well as endophytes microbiomes in different biomes and plants. Also, if you’re still unfaimilar with the ‘Talking about Biotech’ podcast (by Kevin Folta), I highly recommend to add it to your list. The latest episode talks, of course, about the Corona outbreak, and if you’ll go a bit earlier you will find plenty interesring and insightful episodes.

And lastly- pls stay safe! in Israel, as in other parts of the world, conferences are being cancelled, group meetings are rescheduled and we were highly encouraged to work from home (go bioinformatics!). Remember- there is not a single experiment that is more important than your and your love ones health.

General microbiology

Quantifying and contextualizing the impact of bioRxiv preprints through social media audience segmentation, Jedidiah Carlson , bioRxiv

An optimised saliva collection method to produce high-yield, high-quality RNA for translational research, Roisin Sullivan, PLOS ONE

The Vibrio cholerae Type VI Secretion System: Toxins, Regulators and Consequences, Cristian V. Crisan, Env. Micro.

Human microbiome

Microbiome analyses of blood and tissues suggest cancer diagnostic approach, Gregory D. Poore , Nature

Changes in key vaginal bacteria among postpartum African women initiating intramuscular depot-medroxyprogesterone acetate, Bridget M. Whitney ,PLOS ONE

Animal microbiome

The fecal microbiota of healthy donor horses and geriatric recipients undergoing fecal microbial transplantation for the treatment of diarrhea, Caroline A. McKinney , PLOS ONE

Low mutational load and high mutation rate variation in gut commensal bacteria, Ricardo S. Ramiro, PLOS Biology

Marine microbiome

Diel, daily, and spatial variation of coral reef seawater microbial communities, Laura Weber , PLOS ONE

Short‐term changes in polysaccharide utilization mechanisms of marine bacterioplankton during a spring phytoplankton bloom, Greta Reintjes, Env. Micro.

Plant and Soil microbiome

The diversity and distribution of endophytes across biomes, plant phylogeny, and host tissues—how far have we come and where do we go from here?, Joshua G. Garrison, Env. Micro.

Tissue age, orchard location and disease management influence the composition of fungal and bacterial communities present on the bark of apple trees, Elena Arrigoni , Env. Micro.

Salmonella persistence in soil depends on reciprocal interactions with indigenous microorganisms, Jasper Schierstaedt , Env. Micro.

Bioinformatics

Random sampling in metagenomic sequencing leads to overestimated spatial scaling of microbial diversity, Qichao Tu , Env. Micro.

November 2, 2019

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Good Weekend morning for all!

Today’s digest is highly rich with plant and soil microbiome papers (notice a great Science paper regarding soil suppressiveness phenomena), as well as bacterial metabolism papers and more. Have a great and peaceful weekend!

Human and animal microbiome

Studying the gut virome in the metagenomic era: challenges and perspectives, Sanzhima Garmaeva, BMC Biology

Cortisol-induced signatures of stress in the fish microbiome, Tamsyn M Uren Webster, bioRxiv

Influence of pig gut microbiota on Mycoplasma hyopneumoniae susceptibility, Meera Surendran Nair, Veterinary Research

Natural variation in the contribution of microbial density to inducible immune dynamics, Derrick Jent, Molecular Ecology

Metabolism

The ecology and evolution of microbial metabolic strategies, Djordje Bajic & Alvaro Sanchez, Curr. Opin. In. Biotechnology

Is the enzymatic hydrolysis of soil organic phosphorus compounds limited by enzyme or substrate availability?, K.A. Jarosch ,SBB

Plant and Soil microbiome

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome, Victor J. Carrio, Science

Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands, Selma Vieira, ISME

Analysis of soil bacterial communities associated with genetically modified drought-tolerant corn, Jose G. Ibaraa ,Applid Soil Ecology

Phyllosphere of Submerged Plants in Bathing Lakes as a Reservoir of Fungi Potential Human Pathogens, Anna Biedunkiewicz, Microbial Ecology

Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada, Jorge Cordero, Can. J. of Microbiology

Comparative metagenomics of two distinct biological soil crusts in the Tengger Desert, China, Jin-Yu Li , SBB

In planta bacterial multi-omics analysis illuminates regulatory principles underlying plant-pathogen interactions, Tatsuyas Nobori, bioRxiv

Air microbiome

Microbial communities in the tropical air ecosystem follow a precise diel cycle, Elena S. Gusareva, PNAS

Bioinformatics

Evaluating Bioinformatic Pipeline Performance for Forensic Microbiome Analysis, Kierra F. Kaszubinski, J. o. Forensic Sci.

Microbiome digest, September 25, 2014

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Asbestos and microbiome, human gut microbiome during a long stay in the hospital, gut microbiome of 15 mammals, Wolbachia in insects, microbiome of plant roots, and eukaryotes in Norwegian waters.

Human respiratory microbiome

Airways microbiota: Hidden Trojan horses in asbestos exposed individuals? – Dimitrios E. Magouliotis – Medical Hypotheses

“Here, we propose and discuss that certain proteins secreted by airways symbiotic microbiota create membrane pores to the airway epithelial cells, through which asbestos fibers can penetrate the lung parenchyma and reach the sub-pleural areas.”

Human gut microbiome

Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness – Alexander Zaborin – mBio

“We analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients.”

Mammal microbiome

Convergence of gut microbiomes in myrmecophagous mammals – Frederic Delsuc – Molecular Ecology

“Here, we expand upon previous mammalian gut microbiome studies … to characterize the composition of gut microbiota in 15 species representing all placental myrmecophagous lineages and their close relatives from zoo- and field-collected samples.

Insect microbiome

Symbionts Commonly Provide Broad Spectrum Resistance to Viruses in Insects: A Comparative Analysis of Wolbachia Strains – Julien Martinez – PLOS Pathogens

“We have investigated antiviral protection in 19 Wolbachia strains originating from 16 Drosophila species after transfer into the same genotype of Drosophila simulans. “

Plant microbiome

Niche and host-associated functional signatures of the root surface microbiome – Maya Ofek-Lalzar – Nature Communications

“Metagenomic (genetic potential) analysis identifies a core set of functional genes associated with root colonization in both plant hosts, and metatranscriptomic (functional expression) analysis revealed that most genes enriched in the root zones are expressed. “

Water microbiome

Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing – Elianne S. Egge – Journal of Eukaryotic Microbiology

“Nano- and picoplanktonic subsurface samples were collected monthly for 2 yr, and the haptophytes were targeted by amplification of RNA/cDNA with Haptophyta-specific 18S ribosomal DNA V4 primers. “

Microbes in the news

Intensive Loss of Gut Bacteria Diversity – Molly Sharlach – The Scientist

In a study published today (September 23) in mBio, researchers also fed ICU patients’ “ultra-low-diversity” gut microbes to C. elegans roundworms.

How Termites Evolved to Decompose Plant Matter: Gut Bacteria and Fungus – Catherine Griffin – Science World Report

“In order to better understand this interaction, the researchers analyzed plant decomposition genes in the first genome sequencing of a fungus-farming termite and its fungal crop, and bacterial gut communities.”

Science and Career

Scientists Are Not Trusted By Americans – Here’s Why – Science 2.0

“A paper in PNAS finds that Americans seem wary of researchers because they get grant funding and do not trust scientists pushing political and cultural agendas. “

Read The Nasty Comments Women In Science Deal With Daily – Macrina Cooper-White – Huffington Post

“Every day you’re faced with some comment, some snide remark, some inability to get a name on a research paper. “

Bik’s Picks

Water on Earth is older than the sun, scientists say – Deborah Netburn – Los Angeles Times

“Some of the water molecules in your drinking glass were created more than 4.5 billion years ago, according to new research.”

Science Graphic of the Week: Three Ways to Visualize Our Melting Northern Ice Cap – Nick Stockton – Wired.com

“These three visualizations, by NASA’s Scientific Visualization Studio, illustrate this steadily unfolding situation, which has nightmarish implications..“

Healthy food might be bad for patients – here’s why – Amanda Squire – The Conversation

“The truth is that healthy food as we think of it may not be what patients really need.”

Brazil releases ‘good’ mosquitoes to fight dengue fever – BBC News

“Brazilian researchers in Rio de Janeiro have released thousands of mosquitoes infected with bacteria that suppress dengue fever.”

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