Category Archives: General Microbiome

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 28, 2022

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Highlights!

Recently, Science released a special issue about microbiomes, with the following articles:

Human and General Microbiome  

Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes – Adair L Borges – Nature Microbiology

Characteristics of the gut microbiota in women with premenstrual symptoms: A cross-sectional study – Takashi Takeda – PloS ONE

Dynamic colonization of gut microbiota and its influencing factors among the breast-feeding infants during the first two years of life – Ping Li – Journal of Microbiology

Metabolomics analysis reveals molecular linkages for the impact of vitamin D on childhood allergic airway diseases – Yu-Ho Chang – Pediatric Allergy and Immunology

Lysophosphatidylserines derived from microbiota in Crohn’s disease elicit pathological Th1 response – Yuriko Otake-Kasamoto – Journal of Experimental Medicine 

Tumor tissue-specific bacterial biomarker panel for colorectal cancer: Bacteroides massiliensis, Alistipes species, Alistipes onderdonkii, Bifidobacterium pseudocatenulatum, Corynebacterium appendicis – Rizwana Hasan – Archives of Microbiology

Lung Microbiota of Critically Ill COVID-19 Patients are Associated with Non-Resolving Acute Respiratory Distress Syndrome – Robert F J Kullberg – American Journal of Respiratory and Critical care Medicine

Altered Gut Microbiome in Patients With Dermatomyositis – Sangmee Sharon Bae – ACR Open Rheumatology

Review: Importance of crosstalk between the microbiota and the neuroimmune system for tissue homeostasis – Kunyu Li – Clinical & Translational Immunology

Review: Dietary influences on symptomatic and non-symptomatic toxicities during cancer treatment: A narrative review – Alan J Kim – Cancer Treatment Reviews

Review: How can patients with Clostridioides difficile infection on concomitant antibiotic treatment be best managed? – Fidelma Fitzpatrick – The Lancet. Infectious Diseases

Model Animal Microbiome

Protocol: Mouse Model to Study Salmonella-Induced Colitis – Katrin Ehrhardt – Methods in Molecular Biology

Amino acid-balanced diets improved DSS-induced colitis by alleviating inflammation and regulating gut microbiota – Sen Li – European Journal of Nutrition

Excess growth hormone alters the male mouse gut microbiome in an age-dependent manner – Elizabeth A Jensen – Endocrinology

Non-Model Animal Microbiome

Metagenomic Analysis of the Gastrointestinal Microbiota of Gadus morhua callarias L. Originating from a Chemical Munition Dump Site – Wojciech Wilczynski – Toxics

Bacterial Symbionts in Ceratitis capitata – Alessia Cappelli – Insects

Egg microbiota is the starting point of hatchling gut microbiota in the endangered yellow-spotted Amazon river turtle – Ana Sofia Carranco – Molecular Ecology

Unveiling the egg microbiota of the loggerhead sea turtle Caretta caretta in nesting beaches of the Mediterranean Sea – Luca Vecchioni – PloS ONE

Comparative Analyses of Scylla olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis – Nyok-Sean Lau – Microbial Ecology

Global landscape of gut microbiome diversity and antibiotic resistomes across vertebrates – Guangping Huang – The Science of the Total Environment

Beneficial Microbes and Compounds

Review: Functional fermented probiotics, prebiotics and synbiotics from non-dairy products: A perspective from nutraceutical – Dharmendra Kumar – Molecular Nutrition & Food Research

Bifidobacterium longum CCFM752 prevented hypertension and aortic lesion, improved antioxidative ability, and regulated the gut microbiome in spontaneously hypertensive rats – Wenwei Lu – Food & Function

Intestinal Flora Mediates Antiobesity Effect of Rutin in High-Fat-Diet Mice – Xu Yan – Molecular Nutrition & Food Research

Multi-Probiotics ameliorate Major depressive disorder and accompanying gastrointestinal syndromes via serotonergic system regulation – Peijun Tian – Journal of Advanced Research

Butyrate, a postbiotic of intestinal bacteria, affects pancreatic cancer and gemcitabine response in in vitro and in vivo models – Concetta Panebianco – Biomedicine & Pharmacotherapy

Plant and Fungi Microbiome

Deciphering core phyllomicrobiome assemblage on rice genotypes grown in contrasting agroclimatic zones: implications for phyllomicrobiome engineering against blast disease – Kuleshwar Prasad Sahu – Environmental Microbiome

Fusarium fruiting body microbiome member Pantoea agglomerans inhibits fungal pathogenesis by targeting lipid rafts – Sunde Xu – Nature Microbiology

Other studies

Indoor microbiome, microbial and plant metabolites, chemical compounds and asthma symptoms in junior high school students: a multicentre association study in Malaysia – Yu Sun – The European Respiratory Journal

Comparative Analysis of Metagenomics and Metataxonomics for the Characterization of Vermicompost Microbiomes – Marcos Pérez-Losada – Frontiers in Microbiology

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 20, 2022

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General microbiome

[Review]Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation – Liu et al. Microbiome

Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter – Hoarfost et al. – Nature Communications

Covid19 and Metabolome

Sex differences in global metabolomic profiles of COVID-19 patients – Escarcega et al. – Cell Death & Disease

Pregnancy and early life

Does the uterine microbiota affect the reproductive outcomes in women with recurrent implantation failures? – Keburiya et al. – BMC Women’s Health

Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies – Lebeaux et al. – Pediatric Research

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

Human respiratory microbiome

The respiratory microbiome associated with chronic obstructive pulmonary disease comorbidity in non-small cell lung cancer – Shimizu et al. – Thoacic Cancer

Human skin microbiome

SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata – Agostinetto et al. – Databases

Human gut microbiome

Dynamic microbiome and metabolome analyses reveal the interaction between gut microbiota and anti-PD-1 based immunotherapy in hepatocellular carcinoma – Wu et al. – International Journal of Cancer

[Review]Exploring the multifactorial aspects of Gut Microbiome in Parkinson’s Disease – Pavan et al. – Folia Microbiologica

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

[Preprint]Gut microbiota of homing pigeons shows summer-winter variation under constant diet indicating a substantial effect of temperature – Dietz et al. – bioRxiv

Animal microbiome (for animals in the wild)

[Review]Bumblebees with the socially transmitted microbiome: A novel model organism for gut microbiota research – Zhang & Zheng – Insect Science

Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats – Xiao et al. – The ISME Journal

Comparative Analysis of Gut Microbiota Between Healthy and Diarrheic Horses – Li et al. – Front. Vet. Sci.

Large Comparative Analyses of Primate Body Site Microbiomes Indicate that the Oral Microbiome Is Unique among All Body Sites and Conserved among Nonhuman Primates – Microbiology Spectrum

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

Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats – Liu et al. – Microbiome

Bioinformatics

CBEA: Competitive balances for taxonomic enrichment analysis – Nguyen, Hoen & Frost – PLOS Computational Biology

Clustering compositional data using Dirichlet mixture model – Pal & Heumann – PLOS One

Techniques

Generation and application of pseudo–long reads for metagenome assembly – Sim et al. – Giga Science

[Preprint]A comparison of six DNA extraction protocols for 16S, ITS, and shotgun metagenomic sequencing of microbial communities – Shaffer et al. – bioRxiv

[Preprint]Estimating Microbial Population Data from Optical Density – Mira, Yeh & Hall – bioRxiv

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 7, 2022

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Human and General Microbiome

Signature of Alzheimer’s Disease in Intestinal Microbiome: Results From the AlzBiom Study – Christoph Laske – Frontiers in Neuroscience

The Fungal Gut Microbiome Exhibits Reduced Diversity and Increased Relative Abundance of Ascomycota in Severe COVID-19 Illness and Distinct Interconnected Communities in SARS-CoV-2 Positive Patients – Johanna Reinold – Frontiers in Cellular and Infection Microbiology

The associations between low abundance of Mycoplasma hominis and female fecundability: a pregnancy-planning cohort study – Xiang Hong – BMC Microbiology

Insights into the Profile of the Human Expiratory Microbiota and Its Associations with Indoor Microbiotas – Yin Zhang – Environmental Science & Technology

Oral microbiome of Crohn’s Disease patients with and without oral manifestations – Shijia Hu – Journal of Crohn’s & Colitis

Systematic Review: SARS-CoV-2 and Prevotella spp.: friend or foe? A systematic literature review – Zohreh Tamanai-Shacoori – Journal of Medical Microbiology

Review: The Game for Three: Salmonella-Host-Microbiota Interaction Models – Krzysztof Grzymajlo – Frontiers in Microbiology

Review: Host gene effects on gut microbiota in type 1 diabetes – Keyu Guo – Biochemical Society Transactions

Minireview: Host-microbial interactions in metabolic diseases: from diet to immunity – Ju-Hyung Lee – Journal of Microbiology

Preprint: Bacterial association with metals enables in vivo tracking of microbiota using magnetic resonance imaging – Sarah C Donnelly – bioRxiv

Beneficial Microbes and Compounds

Natural Garlic Organosulfur Compounds Prevent Metabolic Disorder of Lipid and Glucose by Increasing Gut Commensal Bacteroides acidifaciens – Keyu Chen – Journal of Agricultural and food Chemistry

Animal Model Microbiome

Circulating gut microbiota-related metabolites influence endothelium plaque lesion formation in ApoE knockout rats – Hsiao-Li Chuang – PloS ONE

Depletion of the gut microbiota enhances the blood pressure-lowering effect of captopril: implication of the gut microbiota in resistant hypertension – Jun Kyoung – Hypertension Research

Non-Model Animal Microbiome

Fecal microbiota and diets of muskox female adults and calves – Ji-Yeon Cheon – Ecology and Evolution

Temporal Changes in Gut Microbiota Composition and Pollen Diet Associated with Colony Weakness of a Stingless Bee – Karen Luisa Haag – Microbial Ecology

Interaction between MHC diversity and constitution, gut microbiota and Astrovirus infections in a neotropical bat – Ramona Fleischer – Molecular Ecology

Review: Symbiont transmission in marine sponges: reproduction, development, and metamorphosis – Tyler J Carrier – BMC Biology

Preprint: A new microbiological weapon against lepidopteran pests – Vyacheslav Martemyanov – bioRxiv

Environmental Microbiome

Associations between bacterial communities and microplastics from surface seawater of the Northern Patagonian area of Chile – Patricia Aguila-Torres – Environmental Pollution

Plant and Soil Microbiome

Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons – Mingsheng Qi – The ISME Journal

A metagenomic study of the bacteria in snow algae microbiomes – Kurt Michael Yakimovich – Canadian Journal of Microbiology

Soil microbial diversity and functional profiling of a tropical rainforest of a highly dissected low hill from the upper Itaya river basin revealed by analysis of shotgun metagenomics sequencing data – Marianela Cobos – Data in Brief

Bioinformatics and Data Analysis

Accessible analysis of longitudinal data with linear mixed effects models – Jessica I Murphy – Disease Models & Mechanisms

Scalable in-memory processing of omics workflows – Vadim Elisseev – Computational and Structural Biotechnology Journal

DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation – Rui Gan – Frontiers in Genetics

A New Approach to Testing Mediation of the Microbiome at Both the Community and Individual Taxon Levels – Ye Yue – Bioinformatics

May 6, 2022

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Happy Friday! Today’s microbiome digest is a grab bag of articles on topics such as antibiotic cycling and bacterial contamination in surgery, phage isolated from diseased seafood, and microbial communities in snuff. I was particularly interested to see the article focused on degradation genes found in steel industrial soil communities. Finally, I enjoyed checking out two preprints on oral microbiota in Agta, a group of hunter-gatherers from the Philippines.

General microbiome

Preprint: The making of the oral microbiome in Agta hunter-gatherers – Dobon et al. – bioRxiv

Preprint: Microbial population dynamics decouple nutrient affinity from environmental concentration – Fink et al. – bioRxiv

Beneath the surface: Amino acid variation underlying two decades of dengue virus antigenic dynamics in Bangkok, Thailand – Huang et al. – PLOS Pathogens

Preprint: Hunter-gatherer oral microbiomes are shaped by contact network structure – Muscitto et al. – bioRxiv

Which vaccine attributes foster vaccine uptake? A cross-country conjoint experiment – Stöckli et al. – PLOS ONE

Associations between microbial communities and key chemical constituents in U.S. domestic moist snuff – Tyxobert et al. – PLOS ONE

Multi-site human microbiome

Mycobacterium tuberculosis infection, immune activation, and risk of HIV acquisition – Bender Ignacio et al. – PLOS ONE

The effects of antibiotic cycling and mixing on acquisition of antibiotic resistant bacteria in the ICU: A post-hoc individual patient analysis of a prospective cluster-randomized crossover study – van Duijin et al. – PLOS ONE

Human gut microbiome

Efficacy of laparotomy sponges to reduce bacterial contamination using an in vitro gastrointestinal surgery model – Bezhentseva et al. – PLOS ONE

Animal experiments

Virulence and antimicrobial resistance gene profiles of Staphylococcus aureus associated with clinical mastitis in cattle – Neelam et al. – PLOS ONE

Preexisting Trichinella spiralis infection attenuates the severity of Pseudomonas aeruginosa-induced pneumonia – Rong Long et al. – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Metagenomic analysis for taxonomic and functional potential of Polyaromatic hydrocarbons (PAHs) and Polychlorinated biphenyl (PCB) degrading bacterial communities in steel industrial soil – Sandhu et al. – PLOS ONE

Water and extremophile microbiome

Transcriptomic analysis of chloride tolerance in Leptospirillum ferriphilum DSM 14647 adapted to NaCl – Rivera-Araya et al. – PLOS ONE

Food microbiology

Sole and combined effect of foliar zinc and arbuscular mycorrhizae inoculation on basmati rice growth, productivity and grains nutrient – Mehmood et al. – PLOS ONE

Characterization and complete genome sequence analysis of a newly isolated phage against Vibrio parahaemolyticus from sick shrimp in Qingdao, China – Tian et al. – PLOS ONE

Techniques

Financial incentives to increase stool collection rates for microbiome studies in adult bone marrow transplant patients – Thompson et al. – PLOS ONE

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

May 3, 2022

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General microbiome

Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women – Worby et al. Nature Microbiology. 2022

Human gut microbiome

Unfavourable intrauterine environment contributes to abnormal gut microbiome and metabolome in twins – Yang et al. Gut

Dosing a synbiotic of human milk oligosaccharides and B. infantis leads to reversible engraftment in healthy adult microbiomes without antibiotics – Button et al. Cell Host & Microbe

Gut microbial similarity in twins is driven by shared environment and aging – Vilchez-Vargas et al. eBioMedicine

Gut Microbiome Alterations Associated with Diabetes in Mexican Americans in South Texas. Kwan et al. mSystems

Human respiratory & oral microbiome

Metagenomic sequencing reveals time, host, and body compartment-specific viral dynamics after lung transplantation – Widder et al. Microbiome

Polymicrobial Interactions of Oral Microbiota: a Historical Review and Current Perspective – Zhang et al. mBio

Animal experiments

Effects of ‘Healthy’ Fecal Microbiota Transplantation against the Deterioration of Depression in Fawn-Hooded Rats – Hu et al. mSystems

Water/Extremophile microbiome

Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans – Duncan et al. Microbiome

Bioinformatics

Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype – Martino et al. mSystems

BiomeHorizon: Visualizing Microbiome Time Series Data in R – Fink et al. mSystems

Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies. Yarmosh et al. mSphere

Non microbiome picks

Ancestry-inclusive dog genomics challenges popular breed stereotypes – Morrill et al. Science. 

Dietary fibre in hypertension and cardiovascular disease management: systematic review and meta-analyses – Reynolds et al. BMC Medicine

April 30, 2022

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Human Microbiome

Three-dimensional imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa – Octavio Mondragón-Palomino – PNAS

Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans – Samuel M Lancaster – Cell Host & Microbe

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

Disordered development of gut microbiome interferes with the establishment of the gut ecosystem during early childhood with atopic dermatitis – Min-Jung Lee – Gut Microbes

A starch- and sucrose-reduced dietary intervention in irritable bowel syndrome patients produced a shift in gut microbiota composition along with changes in phylum, genus, and amplicon sequence variant abundances, without affecting the micro-RNA levels – Clara Nilholm – United European Gastroenterology Journal

Alterations in intestinal microbiota in ultramarathon runners – Mika Sato – Scientific Reports

Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity – Sabine Hazan – BMJ Open Gastroenterology

Gut microbiota alterations in critically ill older patients: a multicenter study – Mesa Victoria – BMC Geriatrics

Bone marrow transplantation induces changes in the gut microbiota that chronically increase the cytokine response pattern of splenocytes – Saeed Katiraei – Scientific Reports

Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome – Adam L Edwinson – Nature Microbiology

Review: Communication between the gut microbiota and peripheral nervous system in health and chronic disease – Tyler M Cook – Gut Microbe

Systematic Review: Adverse events in fecal microbiota transplantation: a systematic review and meta-analysis – Eliot A Rapoport – Annals of Gastroenterology

Review: Eco-evolutionary impact of ultraviolet radiation (UVR) exposure on microorganisms, with a special focus on our skin microbiome – Sandhya Rai – Microbiological Research

Beneficial Microbes and Compounds

Review: The huge clinical potential of microbiota in the treatment of pancreatic cancer: The next frontier – Zhilin Zhang – Biochimica et Biophysica Acta. Reviews on Cancer

Oral Administration of Lactobacillus paracasei N1115 on Neonatal Mice Prevents the Intestinal Inflammation in Adulthood – Yiping Xun – Letters in Applied Microbiology

Animal Model Microbiome

ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs – Hui Yang – Nature

External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells – Chi-Chan Lee – EMBO Reports

Non-Model Animal Microbiome

Host-Associated Bacterial Communities Vary Between Daphnia galeata Genotypes but Not by Host Genetic Distance – Amruta Rajarajan – Microbial Ecology

Faecal Microbiota Divergence in Allopatric Populations of Podarcis lilfordi and P. pityusensis, Two Lizard Species Endemic to the Balearic Islands – Iris Alemany – Microbial Ecology

Gut microbiota of ring-tailed lemurs (Lemur catta) vary across natural and captive populations and correlate with environmental microbiota – Sally L Bornbusch – Animal Microbiome

Mechanisms of fungal community assembly in wild stoneflies moderated by host characteristics and local environment – Yu-Xi Zhu – NPJ Biofilms and Microbiomes

Changes to the gut microbiota of a wild juvenile passerine in a multidimensional urban mosaic – Öncü Maraci – Scientific Reports

Comparative study on gut microbiota in three Anura frogs from a mountain stream – Zhuo Chen – Ecology and Evolution

Plant Microbiome

Insights into the microbiome assembly during different growth stages and storage of strawberry plants – Expedito Olimi – Environmental Microbiome

More Microbes, Genes, and Proteins

Hypothesis: Does Lactobacillus reuteri influence ergothioneine levels in the human body? – Irwin K Cheah – FEBS Letters

Type VI secretion systems of pathogenic and commensal bacteria mediate niche occupancy in the gut – Antonio Serapio-Palacios – Cell Reports

Review: Utilization of glycosaminoglycans by the human gut microbiota: participating bacteria and their enzymatic machineries – Parkash Singh Rawat – Gut Microbes

Bioinformatics

DEPP: Deep Learning Enables Extending Species Trees using Single Genes – Yueyu Jiang – Systematic Biology

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

Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype – Cameron Martino – mSystems

Review: Could Artificial Intelligence/Machine Learning and Inclusion of Diet-Gut Microbiome Interactions Improve Disease Risk Prediction? Case Study: Coronary Artery Disease – Baiba Vilne – Frontiers in Microbiology

Review: Microbial dark matter: from discovery to applications – Yuguo Zha – Genomics, Proteomics & Bioinformatics