Category Archives: Phages and viruses

June 01, 2022

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General microbiome

[REVIEW]Akkermansia muciniphila: paradigm for next-generation beneficial microorganisms – Cani et al. – Nature Reviews Gastroenterology & Hepatology

[REVIEW]Role of Microbiota in Viral Infections and Pathological Progression – Mizutani et al. – Viruses

Fitness effects of plasmids shape the structure of bacteria–plasmid interaction networks – Newbury et al. – PNAS

Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales – Martinez-Gutierrez & Aylward – PLOS Genetics

Interspecies commensal interactions have nonlinear impacts on host immunity – Rice et al. – Cell Host & Microbe

Human skin myco-/microbiome

Distinct skin microbiome community structures in congenital ichthyosis – Tham et al. – British Journal of Dermatology

Biodiversity of mycobial communities in health and onychomycosis – Olbrich et al. – Scientific Reports

Human gut microbiome

Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study – Jiang et al. – Genome Medicine

Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes – Guthrie et al. – Cell Host & Microbe

Discovery of bioactive microbial gene products in inflammatory bowel disease – Zhang et al. – Nature

Animal microbiome (for animals in the wild)

The functional evolution of termite gut microbiota – Arora et al. – Microbiome

Oral Microbiota Populations of Adult Dogs Consuming Wet or Dry Foods – Oba et al. – Journal of Animal Science

Mating Leads to a Decline in the Diversity of Symbiotic Microbiomes and Promiscuity Increased Pathogen Abundance in a Moth – Zhang et al. – Front. Microbiol.

Plant, root, and soil microbiome

Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships – Schäfer et al. – Nature Microbiology

Polyploidy and microbiome associations mediate similar responses to pathogens in Arabidopsis – Mehlferber et al. – Current Biology

May 25, 2022

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General microbiome

Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness – Ørsted et al. – PLOS Genetics

Human skin microbiome/virome

[PREPRINT]Diversity, abundance, and host specificity of the human skin associated circular and single stranded DNA virome – Graham et al. – bioRxiv

[REVIEW]Climate change, the cutaneous microbiome and skin disease: implications for a warming world – Isler et al. – International Journal of Dermatology

Species- and strain-level assessment using rrn long-amplicons suggests donor’s influence on gut microbial transference via fecal transplants in metabolic syndrome subjects – Benitez-Paez et al. – Gut Microbes

Human gut microbiome

[PREPRINT]Greater alteration of gut microbiota occurs in childhood obesity than adulthood obesity – Yu et al. – bioRxiv

Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet – Dahlin et al. – eBioMedicine

Towards Strain-Level Complexity: Sequencing Depth Required for Comprehensive Single-Nucleotide Polymorphism Analysis of the Human Gut Microbiome – Liu et al. – Front. Microbiol.

Animal microbiome (for animals in the wild)

Comparative Gut Microbiome in Trachypithecus leucocephalus and Other Primates in Guangxi, China, Based on Metagenome Sequencing – Que et al. – Front. Cell. Infect. Microbiol.

Bacterial Adaptation to Venom in Snakes and Arachnida – Esmaeilishirazifard et al. – Microbiology Spectrum

Plant, root, and soil microbiome

Recent advances in understanding of fungal and oomycete effectors – Wilson & McDowell – Current Opinion in Plant Biology

Fungi associated with the potato taste defect in coffee beans from Rwanda – Hale et al. – Botanical Studies

Delineating the Bacteriome of Packaged and Loose Smokeless Tobacco Products Available in North India – Srivastava et al. – Applied Microbiology and Biotechnology

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

Diversity, distribution and ecology of fungal communities present in Antarctic lake sediments uncovered by DNA metabarcoding – de Souza et al. – Scientific Reports

May 11, 2022

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General microbiome

[REVIEW]Cross-talk between the microbiome and chronic inflammation in esophageal cancer: potential driver of oncogenesis – Sharma et al. – Cancer and Metastasis Reviews

Systematic and quantitative view of the antiviral arsenal of prokaryotes – Tesson et al. – Nature Communications

Pregnancy and early life

A randomized controlled trial of the effects of whole grains versus refined grains diets on the microbiome in pregnancy – Sun et al. – Scientific Reports

Should we modulate the neonatal microbiome and what should be the goal? – van Best – Microbiome

[Commentary]Space travel and early childhood gut microbiome: is space dirty enough to raise a child? – Loh, Henriques & Tang – Future Microbiology

Human skin microbiome

[PREPRINT]On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis – Key et al. – bioRxiv

Human oral microbiome

Oral microbiome of Crohn’s Disease patients with and without oral manifestations – Hu et al. – Journal of Crohn’s and Colitis

Integrating the salivary microbiome in the forensic toolkit by 16S rRNA gene: potential application in body fluid identification and biogeographic inference – Liang et al. – International Journal of Legal Medicine

Human gut microbiome

An approach for evaluating the effects of dietary fiber polysaccharides on the human gut microbiome and plasma proteome – Delannoy-Bruno et al. – PNAS

A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota – Sommer et al. – PLOS Computational Biology

Microbiota and gastric cancer – Bessede & Megraud – Seminars in Cancer Biology

[REVIEW]Host—microbial interactions in metabolic diseases: from diet to immunity – Lee & Park – Journal of Microbiology

A randomized controlled trial for response of microbiome network to exercise and diet intervention in patients with nonalcoholic fatty liver disease – Cheng et al. – Nature Communications

Animal experiments

Sex-dependent host-microbiome dynamics in zebrafish: Implications for toxicology and gastrointestinal physiology – Martyniuk et al. – Comparative Biochemistry and Physiology Part D: Genomics and Proteomics

Comprehensive 16S rRNA and metagenomic data from the gut microbiome of aging and rejuvenation mouse models – Shin et al. – Scientific data

A total infectome approach to understand the etiology of infectious disease in pigs – Huang et al. – Microbiome

Synergistic interaction of gut microbiota enhances the growth of nematode through neuroendocrine signaling – Lo et al. – Current Biology

Plant, root, and soil microbiome

Unraveling global and diazotrophic bacteriomes of boreal forest floor feather mosses and their environmental drivers at the ecosystem and at the plant scale in North America – Renaudin, Laforest-Lapointe & Bellenger – Science of The Total Environment

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

Antimicrobial resistance in Antarctica: is it still a pristine environment? – Hwengwere et al. – Microbiome

[PREPRINT]Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps – Dong et al. – bioRxiv

Bioinformatics

Evaluating metagenomic assembly approaches for biome-specific gene catalogues – Delgado & Andersson – Microbiome

Compare the performance of multiple binary classification models in microbial high-throughput sequencing datasets – Xu et al. – Science of The Total Environment

May 5, 2022

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Today’s digest features a review on the role of bacterial translocation (especially oral-gut axis) in health and disease, a proof-of-concept study on probiotics on processing of negative emotions in humans, and more. Happy reading!

Let’s talk microbiome science at the next #MVIF!

Sterile (?) environment

Comprehensive human amniotic fluid metagenomics supports the sterile womb hypothesis – HanChen Wang – Scientific Reports

Probiotics

Lactobacillus acidophilus, L. plantarum, L. rhamnosus, and L. reuteri Cell-Free Supernatants Inhibit Candida parapsilosis Pathogenic Potential upon Infection of Vaginal Epithelial Cells Monolayer and in a Transwell Coculture System In Vitro – Luca Spaggiari – Microbiology Spectrum

*Probiotic Mixture Containing Lactobacillus helveticus, Bifidobacterium longum and Lactiplantibacillus plantarum Affects Brain Responses Toward an Emotional Task in Healthy Subjects: A Randomized Clinical Trial – Julia Rode – Frontiers in Nutrition

Vaginal microbiome

Identification and characterization of novel endolysins targeting Gardnerella vaginalis biofilms to treat bacterial vaginosis – Sara Arroyo-Moreno – npj Biofilms and Microbiomes

Gut microbiome

*Review: Deciphering mechanisms and implications of bacterial translocation in human health and disease – Shen Jin – Current Opinion in Microbiology

Two Competing Guilds as a Core Microbiome Signature for Chronic Diseases – Guojun Wu – bioRxiv

Neonatal Immune Challenge influences the Microbiota and Behaviour in a Sexually Dimorphic Manner – A. Cuskelly – Brain, Behavior, and Immunity

Review: Diet- and microbiota-related metabolite, 5-aminovaleric acid betaine (5-AVAB), in health and disease – Retu Haikonen – Trends in Endocrinology & Metabolism

Gut mycobiome

Review: “Molding” immunity—modulation of mucosal and systemic immunity by the intestinal mycobiome in health and disease – Mackenzie W. Gutierrez – Nature Mucosal Immunology

Animal experiments

Evolution of the murine gut resistome following broad-spectrum antibiotic treatment – Laura de Nies – Nature Communications & Behind the paper here.

Plant, root/soil microbiome

*Sugars dominate the seagrass rhizosphere – E. Maggie Sogin – Nature Ecology & Evolution

Viruses

A snapshot of the global drinking water virome: Diversity and metabolic potential vary with residual disinfectant use – Bridget Hegarty – Water Research

Techniques

Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification – Charlotte C. van de Velde – ISME Communications

Bioinformatics

A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments – Shaojun Pan – Nature Communications

HiFine: integrating Hi-c-based and shotgun-based methods to reFine binning of metagenomic contigs – Yuxuan Du and Fengzhu Sun – Bioinformatics

happi: a Hierarchical Approach to Pangenomics Inference – Pauline Trinh – bioRxiv

Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome – Rebecca H. Smit – bioRxiv

TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles – Varuni Sarwal – bioRxiv

April 20, 2022

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General microbiome

How the gut talks to the brain – Adamantidis – Science

Pregnancy and early life

Relationship between gut microbiome characteristics and the effect of nutritional therapy on glycemic control in pregnant women with gestational diabetes mellitus – Chen et al. – PLOS One

Dynamics of the infant gut microbiota in the first 18 months of life: the impact of maternal HIV infection and breastfeeding – Grant-Beurmann et al. – Microbiome

Human respiratory microbiome

The diagnostic value of nasal microbiota and clinical parameters in a multi-parametric prediction model to differentiate bacterial versus viral infections in lower respiratory tract infections – Li et al. – PLOS One

Human skin microbiome

The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes – Verbanic, Deacon & Chen – Microbiology Spectrum

Human vaginal microbiome

Vaginal microbiota as an unusual cause of spondylodiscitis – Kolakowska et al. – Archives of Gynecology and Obstetrics

Human gut microbiome

Environmental factors shaping the gut microbiome in a Dutch population – Gacesa et al. – Nature

Predictive Role of Gut Microbiota in Weight Loss Achievement after Bariatric Surgery – Gutierrez-Repiso et al. – Journal of the American College of Surgeons

Intestinal Blautia may protect against neutropenic fever in allogeneic transplant patients by augmenting the intestinal epithelium – Rashidi et al. – Clinical Infectious Diseases

Clinical Observation of the Effects of Oral Opioid on Inflammatory Cytokines and Gut Microbiota in Patients with Moderate to Severe Cancer Pain: A Retrospective Cohort Study – Wang et al. – Pain and Therapy

The human gut microbiota contributes to type-2 diabetes non-resolution 5-years after Roux-en-Y gastric bypass – Debedat et al. – Gut Microbes

The gut microbial metabolite formate exacerbates colorectal cancer progression – Ternes et al. – Nature Metabolism

Drinking water chlorination has minor effects on the intestinal flora and resistomes of Bangladeshi children – Nadimpalli et al. – Nature Microbiology

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

The microbiota-gut-brain axis participates in chronic cerebral hypoperfusion by disrupting the metabolism of short-chain fatty acids – Xiao et al. – Microbiome

Effect of gluten-free diet and antibiotics on murine gut microbiota and immune response to tetanus vaccination – Kihl et al. – PLOS One

Hawk tea prevents high-fat diet-induced obesity in mice by activating the AMPK/ACC/SREBP1c signaling pathways and regulating the gut microbiota – Tao et al. – Food & Function

Changes in gut microbiota, metabolite SCFAs, and GPR43 expression in obese diabetic mice after sleeve gastrectomy – Guo et al. – Journal of Applied Microbiology

The gut microbiome influences host diet selection behavior – Trevelline & Kohl – PNAS

High-fat diet disrupts REG3γ and gut microbial rhythms promoting metabolic dysfunction – Frazier et al. – Cell Host & Microbe

Animal microbiome (for animals in the wild)

Intrinsic and extrinsic factors influence on an omnivore’s gut microbiome – Trujillo et al. – PLOS One

Effects of Schyzocotyle acheilognathi (Yamaguti, 1934) infection on the intestinal microbiota, growth and immune reactions of grass carp (Ctenopharyngodon idella) – Fu et al. – PLOS One

Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses – Shan et al. – Microbiome

Interspecies microbiome transplantation recapitulates microbial acquisition in mosquitoes – Coon, Hedge & Hughes

Gut microbiota promote biotransformation and bioaccumulation of arsenic in tilapia – Environmental Pollution

Plant, root, and soil microbiome

Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species – Vandepol et al. – PLOS One

Bacterial and fungal microbiota of total mixed ration silage stored at various temperatures – Wali et al. – Journal of Applied Microbiology

Bioinformatics

Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community – Lyalina – PLOS One

Techniques

THOR’s Hammer: the Antibiotic Koreenceine Drives Gene Expression in a Model Microbial Community – Hurley et al. – mBio

Microbes in the news

Bacteria generate electricity from methane

April 04, 2022

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General microbiome

[REVIEW]Types and functions of heterogeneity in mycobacteria – Chung, Johnson & Aldridge – Nature Reviews Microbiology

Human breast tissue microbiome

The breast tissue microbiome, stroma, immune cells and breast cancer – Hieken et al. – Neoplasia

Human gut microbiome

Intestinal virome in patients with alcohol use disorder and after abstinence – Hsu et al. – Hepatology Communications

Sexual Dimorphism in the Gut Microbiome: Microgenderome or Microsexome? – Mulak, Larauche & Tache – J Neurogastroenterol Motil

Worms and bugs of the gut: the search for diagnostic signatures using barcoding, and metagenomics–metabolomics – Papaiakovou et al. – Parasites & Vectors

[REVIEW]Connecting the Human Microbiome and Pancreatic Cancer – Sexton et al. – Cancer and Metastasis Reviews

Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota – Ostrowski et al. – Nature Microbiology

Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis – Smith et al. – Scientific Reports

[PREPRINT]Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes – Merrill et al. – bioRxiv

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

Light-Sensitive Lactococcus lactis for Microbe–Gut–Brain Axis Regulating via Upconversion Optogenetic Micro-Nano System – Pan et al. – ACS Nano

Biogeography, succession, and origin of the chicken intestinal mycobiome – Robinson et al. – Microbiome

Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis – Forster et al. – Nature Microbiology

Growth promotion and antibiotic induced metabolic shifts in the chicken gut microbiome – Plata et al. – Communications Biology

Animal microbiome (for animals in the wild)

Microplastics impact the accumulation of metals in earthworms by changing the gut bacterial communities – Yang, Xu & Yu – Science of The Total Environment

Plant, root, and soil microbiome

Microbial communities in sandy beaches from the three domains of life differ by microhabitat and intertidal location – Okamoto et al. – Molecular Ecology

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

[REVIEW]Microbial metabolites in the marine carbon cycle – Moran et al. – Nature Microbiology

Bioinformatics

[PREPRINT]Controlling taxa abundance improves metatranscriptomics differential analysis – Ji & Ma – bioRxiv

March 23, 2022

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General microbiome

Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance – Yu et al. – Nature Microbiology

Human skin microbiome

Skin microbiota diversity among genetically unrelated individuals of Indian origin – Pothbhare et al. – PeerJ

Human gut microbiome

[REVIEW]Gut microbiota and allergic diseases in children – Akagawa & Kaneko – Allergology International

[REVIEW]Gut microbiome: New biomarkers in early screening of colorectal cancer – Zhou et al. – Journal of Clinical Laboratory Analysis

Can gut microbiota throughout the first 10 years of life predict executive functioning in childhood? – Eckermann et al. – Developmental Psychobiology

[PREPRINT]Meta-analysis of the autism gut microbiome identifies factors influencing study discrepancies and machine learning classification – Chavira, Wang & Mills – bioRxiv

Changes of Intestinal Microflora in Colorectal Cancer Patients after Surgical Resection and Chemotherapy – Huang et al. – Computational and Mathematical Methods in Medicine

Animal microbiome

Captivity and Animal Microbiomes: Potential Roles of Microbiota for Influencing Animal Conservation – Dallas & Warne – Microbial Ecology

Changes in gut microbiota composition with age and correlations with gut inflammation in rats – Meng et al. – PLOS One

[REVIEW]Translational multi-omics microbiome research for strategies to improve cattle production and health – Wang & Guan – Emerging Topics in Lefe Sciences

Multi-omics reveals host metabolism associated with the gut microbiota composition in mice with dietary ε-polylysine – Zhang et al. – Food & Function

Soil causes gut microbiota to flourish and total serum IgE levels to decrease in mice – Zhou et al. – Environmental Microbiology

Microbiome-metabolomics deciphers the effects of Cistanche deserticola polysaccharides on agedconstipated rats – Liu et al. – Food & Function

Plant, root, and soil microbiome

[PREPRINT]Plant Virus Database: a resource for exploring the diversity of plant viruses and their interactions with hosts – Wu et al. – bioRxiv

Waste microbiome

[PREPRINT]Identification of Microbial Flora and Isolation of Functional Strains Related to the Degradation of Domestic Waste – Huang, Liu & Zong – bioRxiv

Food microbiology

Comprehensive characterization of the bacterial community structure and metabolite composition of food waste fermentation products via microbiome and metabolome analyses – Li et al. – PLOS One

Bioinformatics

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations – Gregory et al. – Microbiome

HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities – Kalmar et al. – PLOS Genetics

Techniques

[PREPRINT]Vaginal microbiome-host interactions modeled in a human vagina-on-a-chip – Mahajan et al. – bioRxiv

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

Florence tomb by Michelangelo restored with aid of bacteria – The Guardian

March 3, 2022

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Today’s digest is heavy on studies focused on the gut and soil microbiomes. It also includes articles focused on microbial indoor air quality as well as bacterial vaginosis and aerobic vaginitis among pregnant women. If you’d still like more, I’ve also included several preprints.

Happy reading!


Human vaginal microbiome

Prevalence of bacterial vaginosis and aerobic vaginitis and their associated risk factors among pregnant women from northern Ethiopia: A cross-sectional study – Yalew et al. – PLOS One

Human gut microbiome

Systematically assessing microbiome–disease associations identifies drivers of inconsistency in metagenomic research – Tierney et al. – PLOS Biology

Preprint: Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation – Venzon et al. – bioRxiv

Hydrogen-producing small intestinal bacterial overgrowth is associated with hepatic encephalopathy and liver function – Yokoyama et al. – PLOS One

Plant, root, and soil microbiome

Preprint: Deciphering the potential niche of two novel black yeast fungi from a biological soil crust based on their genomes, phenotypes, and melanin regulation – Carr et al. – bioRxiv

Bacterial age distribution in soil—Generational gaps in adjacent hot and cold spots – Borer & Or – PLOS Computational Biology

Deciphering the influence of Bacillus subtilis strain Ydj3 colonization on the vitamin C contents and rhizosphere microbiomes of sweet peppers – Liang et al. – PLOS One

Antimicrobial effect and mechanism of bovine lactoferrin against the potato common scab pathogen Streptomyces scabiei – Nakamura et al. – PLOS One

Preprint: Arbuscular mycorrhizal fungal composition across US citrus orchards, management strategies, and disease severity spectrum – Xi et al. – bioRxiv

Built environment

Comprehensive health risk assessment of microbial indoor air quality in microenvironments – Kumar et al. – PLOS One

Phages and viruses

Preprint: Modelling the synergistic effect of bacteriophage and antibiotics on bacteria: killers and drivers of resistance evolution – Leclerc et al. -bioRxiv

Bioinformatics

Preprint: Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution – Kiefl et al. – bioRxiv

March 02, 2022

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General microbiome

Bacterial-Fungal Interactions and Their Impact on Microbial Pathogenesis – MacAlpine, Robbins & Cowen – Molecular Ecology

Pregnancy and early life

Influence of timing of maternal antibiotic administration during caesarean section on infant microbial colonisation: a randomised controlled trial – Dierikx et al. – Gut

Human skin microbiome

Predominance of Staphylococcus correlates with wound burden and disease activity in dystrophic epidermolysis bullosa: a prospective case-control study – Reimer-Taschenbrecker et al. – Journal of Investigative Dermatology

[REVIEW]Towards standardized and reproducible research in skin microbiomes – Ruuskanen et al. – Environmental Microbiology

Human oral microbiome

Comparability of microbiota of swabbed and spit saliva – Kaan et al. – Oral Sciences

Human gut microbiome

A multiple-dimension model for microbiota of patients with colorectal cancer from normal participants and other intestinal disorders – Shen et al. – Applied Microbial and Cell Physiology

Associations between Drinking Water Source and Gut Microbiota Composition in the American Gut Project Database – Vanhaecke – Annals of Nutrition and Metabolism

Rethinking Parkinson Disease: Exploring Gut-Brain Interactions and the Potential Role of Exercise – Zapanta et al. – Physical Therapy & Rehabilitation Journal

[PREPRINT]Mucosal microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients – Tran et al. – bioRxiv

How to Maintain a Healthy Gut Microbiome in Children with Cancer? Gut Microbiome Association with Diet in Children with Solid Tumors Postchemotherapy – Zhou et al. – OMICS: A Journal of Integrative Biology

[REVIEW]The potential utility of fecal (or intestinal) microbiota transplantation in controlling infectious diseases – Ghani et al. – Gut Microbes

Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma – Lee et al. – Nature Medicine

Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1 – McCulloch et al. – Nature Medicine

Establishing the role of the gut microbiota in susceptibility to recurrent urinary tract infections – Worby et al. – JCI

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

High environmental temperature: Insights into behavioural, neurodevelopmental and gut microbiome changes following gestational exposure in rats – Adebiyi – Neuroscience

Animal microbiome (for animals in the wild)

Unraveling the microbiota of the fish parasite Pseudoterranova decipiens in codfish (Gadus morhua) reveals a fish-related bacterial community – Saelens & Houf – International Journal of Food Microbiology

Microbial biogeography of the wombat gastrointestinal tract – Eisenhofer et al. – PeerJ

Intrinsic variation in the vertically transmitted core virome of the mosquito Aedes aegypti – Coatsworth et al. – Molecular Ecology

Plant, root, and soil microbiome

Multiomics Reveals the Effect of Root Rot on Polygonati Rhizome and Identifies Pathogens and Biocontrol Strain – Pang et al. – Microbiology Spectrum

Long-term effect of epigenetic modification in plant–microbe interactions: modification of DNA methylation induced by plant growth-promoting bacteria mediates promotion process – Chen et al. – Microbiome

Bioinformatics

[PREPRINT]Achieving pan-microbiome biological insights via the dbBact knowledge base – Amir et al. – bioRxiv

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