Category Archives: Animal microbiome

September 06, 2021

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General microbiome

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

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

Pregnancy and early life

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

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

Multi-site human microbiome

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

Human respiratory microbiome

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

Human oral microbiome

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

Human gut microbiome

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

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

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

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

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

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

Bioinformatics

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

September 01, 2021

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General microbiome

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

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

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

Pregnancy and early life

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

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

Human oral microbiome

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

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

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

Human gut microbiome

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

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

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

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

Animal/Insect microbiome

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

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

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

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

Plant, root, and soil microbiome

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

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

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

Bioinformatics/Techniques

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

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

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

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

August 25, 2021

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General microbiome

[REVIEW]The longitudinal and cross-sectional heterogeneity of the intestinal microbiota – Miller et al. – Current Opinion in Microbiology

Pregnancy and early life

Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California – Alderete et al. – Gut Microbes

Human respiratory microbiome

Characterization of the Human Oropharyngeal Microbiomes in SARS-CoV-2 Infection and Recovery Patients – Gao et al. – Advanced Science

Human gut microbiome

Metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in Japanese – Tomofuji et al. – Annals of the Rheumatic Diseases

Gut microbes participate in food preference alterations during obesity – d’Oplinter et al. – Gut Microbes

Altered gut microbiome compositions are associated with the severity of asthma – Wang et al. – Journal of Thoracic Disease

Evolution in a Community Context: towards Understanding the Causes and Consequences of Adaptive Evolution in the Human Gut Microbiota over Short Time Scales – Scanlan – mSystems

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

Propamocarb exposure has the potential to accelerate the formation of atherosclerosis in both WT and ApoE−/− mice accompanied by gut microbiota dysbiosis – Jin et al. – Science of The Total Environment

Inflammation-relevant microbiome signature of the stroke brain, gut, spleen, and thymus and the impact of exercise – Kingsbury et al. – Journal of Cerebral Blood Flow & Metabolism

Animal microbiome (for animals in the wild)

Comparative Analysis of Skin Bacterial Diversity and Its Potential Antifungal Function Between Desert and Pine Forest Populations of Boreal Toads Anaxyrus boreas – Basanta et al. – Host Microbe Interactions

Plant, root, and soil microbiome

Herbivory shapes the rhizosphere bacterial microbiota in potato plants – Malacrino et al. – Environmental Microbiology Reports

[PREPRINT]Teasing apart the host-related, nutrient-related and temperature-related effects shaping the phenology and microbiome of the tropical seagrass Halophila stipulacea – Szitenberg et al. – bioRxiv

Techniques/Bioinformatics

The Effect of Common Viral Inactivation Techniques on 16S rRNA Amplicon-Based Analysis of the Gut Microbiota – McAdams et al. – Cells

Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies – Ammer-Herrmenau et al. – mSystems

August 18, 2021

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Call for Papers

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

General microbiome

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

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

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

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

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

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

Multi-site human microbiome

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

Human skin microbiome

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

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

Human oral microbiome

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

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

Human gut microbiome

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

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

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

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

Plant, root, and soil microbiome

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

Bioinformatics

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

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

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

Techniques

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

August 11, 2021

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General microbiome

[REVIEW]Spot-light on microbiota in obesity and cancer – Marzullo et al. – International Journal of Obesity

Microbiome analysis, the immune response and transplantation in the era of next generation sequencing – Kanangat & Skaljic – Human Immunology

Pregnancy and early life

Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome – Roth-Schulze et al. – Microbiome

Human gut microbiome

[PREPRINT]Metataxonomic review to elucidate the role of the microbiome in Celiac disease across the gastrointestinal tract – Arcila et al. – bioRxiv

Microbiota and sleep: awakening the gut feeling – Sen et al. – Trends in Molecular Medicine

Effects of Smoking on Inflammatory Markers in a Healthy Population as Analyzed via the Gut Microbiota – Yan et al. – Front. Cell. Infect. Microbiol.

[REVIEW]The link between the gut microbiota and Parkinson’s Disease: A systematic mechanism review with focus on α-synuclein transport – Nielsen, Pearson & Seidler – Brain Research

[REVIEW]Gut brain axis: an insight into microbiota role in Parkinson’s disease – Moustafa et al. – Metabolic Brain Disease

Describing the intestinal microbiota of Holstein Fasciola-positive and -negative cattle from a hyperendemic area of fascioliasis in central Colombia – Ramirez et al. – PLOS Neglected Tropical Diseases

The gut microbiome of healthy Vietnamese adults and children is a major reservoir for resistance genes against critical antimicrobials – Pereira-Dias et al. – Journal of Infectious Diseases

Characteristics of gut microbiota in people with obesity – Duan et al. – PLOS One

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

Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes – Gaio et al. – Microbial Genomics

Effects of dietary rosemary extract supplementation on growth performance, nutrient digestibility, antioxidant capacity, intestinal morphology and microbiota of weaning pigs – Yang et al. – Journal of Animal Science

Changes in the gut microbiota: a possible factor influencing peripheral blood immune indexes in non-obese diabetic mice – Wu et al. – Antonie van Leeuwenhoek

Animal microbiome (for animals in the wild)

[PREPRINT]The gut bacteria of an invasive amphibian respond to the dual challenges of range-expansion and parasite attack – Zhou et al. – bioRxiv

Fishing for the Virome of Tropical Tuna – Gadoin et al. – Viruses

Plant, root, and soil microbiome

Colonization by the Red Imported Fire Ant, Solenopsis invicta, Modifies Soil Bacterial Communities – Travanty et al. – Host Microbe Interactions

Techniques

[PREPRINT]Shotgun proteomic profiling of dormant, ‘non-culturable’ Mycobacterium tuberculosis – Nikitushkin et al. – bioRxiv

[PREPRINT]A clinically validated human saliva metatranscriptomic test for global systems biology studies – Toma et al. – bioRxiv

Sample Preparation for Detection of Different Bacterial Strains by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry – Chac et al. – Current Protocols

July 23, 2021

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Happy Friday!

It’s an exciting day here because I’m packing for fieldwork! In just a few short days I’ll be sampling from a saline aquifer in Illinois. For those of you who aren’t lucky enough to be going into the field, today’s digest is packed with a wide range of articles. Topics covered include the wild spider gut microbiome, the presence of antibiotic resistance genes in an Ohio river, the mosquito virome, the plant rhizosphere, and more.

Happy reading!

Human gut microbiome

Preprint: Phenotypic and genomic diversification in complex carbohydrate degrading human gut bacteria – Pudlo et al. – bioRxiv

Animal experiments

Effect of biochanin A on the rumen microbial community of Holstein steers consuming a high fiber diet and subjected to a subacute acidosis challenge – Harlow et al. – PLOS ONE

Ear wound healing in MRL/MpJ mice is associated with gut microbiome composition and is transferable to non-healer mice via microbiome transplantation – Velasco et al. – PLOS ONE

Animal microbiome

Preprint: Increased microbial diversity and decreased prevalence of common pathogens in the gut microbiomes of wild turkeys compared to domestic turkeys – Craft et al. – bioRxiv

Interspecific variation and functional traits of the gut microbiome in spiders from the wild: The largest effort so far – Tyagi et al. – PLOS ONE

Plant, root, and soil microbiome

Preprint: Tillage intensity and plant rhizosphere selection shape bacterial-archaeal assemblage diversity and nitrogen cycling genes – Cloutier et al. – bioRxiv

Water and extremophile microbiome

Preprint: An Ohio State Scenic River Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent – Murphy – bioRxiv

Biogeochemistry of the Antrim Shale Natural Gas Reservoir – Stemple et al. – ACS Earth and Space Chemistry

Built environment

Preprint: Novel municipal sewage-associated bacterial genomes and their potential in source tracking – Linder et al. – bioRxiv

Preprint: Structure of bacterial communities in Japanese-style bathrooms: Comparative sequencing of bacteria in shower water and showerhead biofilms using a portable nanopore sequencer – Fujiyoshi et al. – bioRxiv

Phages and viruses

Preprint: Dynamic surveillance of mosquitoes and their viromes in Wuhan during 2020 – Ren et al. – bioRxiv

Techniques

Simple mapping-based quantification of a mock microbial community using total RNA-seq data – Moriya – PLOS ONE

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

July 16, 2021

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

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

Human microbiome

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

Gut microbiome

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

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

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

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

Resistome

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

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

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

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

Animal microbiome

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

Animal experiment

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

Bioinformatics

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

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

Webinars &c

Microbiome Virtual International Conference #MVIF – September 14

July 14, 2021

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General microbiome

Bacteriophage-Bacteria Interactions in the Gut: From Invertebrates to Mammals – Kirsch et al. – Annual Review of Virology

Helicobacter pylori infection has a detrimental impact on the efficacy of cancer immunotherapies – Oster et al. – Gut

Pregnancy and early life

Cervicovaginal microbiota and metabolome predict preterm birth risk in an ethnically diverse cohort – Flaviani et al. – JCI Insight

[REVIEW][Early-life gut microbiota and its connection to metabolic health in children: Perspective on ecological drivers and need for quantitative approach – Jian et al. – EBBioMedicine

Associations of air pollution and greenness with the nasal microbiota of healthy infants: A longitudinal study – Gisler et al. – Environmental Research

Human respiratory microbiome

Multi-omics profiling predicts allograft function after lung transplantation – Watzenböck et al. – European Respiratory Journal

Metagenomic Analysis Reveals A Possible Association Between Respiratory Infection and Periodontitis – Liu et al. – Genomics, Proteomics & Bioinformatics

Human skin microbiome

[REVIEW]Novel mechanisms of microbial crosstalk with skin innate immunity – Chinnappan & Harris-Tyron – Experimental Dermatology

Shifts in the skin bacterial and fungal communities of healthy children transitioning through puberty – Park et al. – Journal of Investigative Dermatology

Human gut microbiome

Gut-microbiota-targeted diets modulate human immune status – Wastyk et al. – Cell

[REVIEW]Silent hypoxia in COVID-19: a gut microbiota connection – Gopal et al. – Current Opinion in Physiology

[REVIEW]The Athlete and Gut Microbiome: Short-chain Fatty Acids as Potential Ergogenic Aids for Exercise and Training – Bongiovanni, Yin & Heaney

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

Kefir Ameliorates Specific Microbiota-Gut-Brain Axis Impairments in a Mouse Model Relevant to Autism Spectrum Disorder – van de Wouw et al. – Brain, Behavior, and Immunity

Animal microbiome

Comparative analysis of oral-gut microbiota between captive and wild long-tailed macaque in Thailand – Sawaswong et al. – Scientific Reports

Impact of the dietary inclusion of dried food residues on the apparent nutrient digestibility and the intestinal microbiota of dogs – Paßlack et al. – Archives of Animal Nutrition

Triphenyltin exposure causes changes in health-associated gut microbiome and metabolites in marine medaka – He et al. – Environmental Pollution

The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota – Bermudez-Martin et al. – Microbiome

Microbes in space

Seven years of Progress in Determining Fungal Diversity and Characterization of Fungi Isolated from the Japanese Experiment Module KIBO, International Space Station – Satoh et al. – Microbiology and Immunology

Food microbiology

[REVIEW]Virome studies of food production systems: time for ‘farm to fork’ analyses – Mahony & van Sinderen – Current Opinion in Biotechnology

Bioinformatics

D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies – Chen & Zhang – Bioinformatics

Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model – Hosoda, Fukunaga & Hamada – Bioinformatics

[PREPRINT]Stool Studies Don’t Pass the Sniff Test: A Systematic Review of Human Gut Microbiome Research Suggests Widespread Misuse of Machine Learning – Quinn – arXiv

Techniques

Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost – Harrison, Randolph & Buerkle – mSystems

Two-Target Quantitative PCR To Predict Library Composition for Shallow Shotgun Sequencing – Cho et al. – mSystems

Statistical approaches for differential expression analysis in metatranscriptomics – Zhang et al. – Bioinformatics

Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1–V2 and V3–V4 primer sets – Kameoka et al. – BMC Genomics

In vitro models of gut digestion across childhood: current developments, challenges and future trends – Fournier et al. – Biotechnology Advances

July 07, 2021

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General microbiome

Cross-Scale Analyses of Animal and Human Gut Microbiome Assemblies from Metacommunity to Global Landscape – Ma – mSystems

Multi-site human microbiome

Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation – Ingham et al. – Microbiome

Human gut microbiome

Early melanoma invasivity correlates with gut fungal and bacterial profiles – Vitali et al. – British Journal of Dermatology

The Interplay between fasting, gut microbiota, and lipid profile – Mohammadzadeh et al. – IJCP

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

Effect of Differences in the Microbiome of Cyp17a1-Deficient Mice on Atherosclerotic Background – Künstner et al. – Cells

Telmisartan induces a specific gut microbiota signature which may mediate its antiobesity effect – Beckmann et al. – Pharmacological Research

Novel insights into the genetically obese (ob/ob) and diabetic (db/db) mice: two sides of the same coin – Suriano et al. – Microbiome

Animal microbiome (for animals in the wild)

Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal – Stothart & Newman – Animal Microbiome

Untargeted fecal metabolome analysis in obese dogs after weight loss achieved by feeding a high-fiber-high-protein diet – Bermudez Sanches et al. – Metabolomics

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

Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico – Moguel et al. – Scientific Reports

Bioinformatics

ORFograph: search for novel insecticidal protein genes in genomic and metagenomic assembly graphs – Dvorkina et al. – Microbiome

Techniques

Measuring and mitigating PCR bias in microbiota datasets – Silverman et al. PLOS Computational Biology

July 6, 2021

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Several great papers today including a very interesting Cell paper on how Bifidobacterium interacts with the immune system and an mBio article on how different types of dietary fibre shape the gut microbiota.

To our Australian readers I’d like to wish a happy NAIDOC week, which is a time to celebrate the history, culture and achievements of Aboriginal and Torres Strait Islander peoples.

General microbiome

Microbiota regulate social behaviour via stress response neurons in the brain – Wu et al. Nature. 

Defining the resilience of the human salivary microbiota by a 520-day longitudinal study in a confined environment: the Mars500 mission – Bacci et al. Microbiome

A MicroRNA Gene Panel Predicts the Vaginal Microbiota Composition. Cheng et al. mSystems

Human gut microbiome

Gut microbiota mediate the FGF21 adaptive stress response to chronic dietary protein-restriction in mice – Martin et al. Nature Communications. 

Gut microbes impact stroke severity via the trimethylamine N-oxide pathway – Zhu et al. Cell Host & Microbe

Dietary Fiber Hierarchical Specificity: the Missing Link for Predictable and Strong Shifts in Gut Bacterial Communities – Centu-Jungles et al. mBio

Pregnancy and Early-Life

Bifidobacteria-mediated immune system imprinting early in life – Henrick et al. Cell

Animal microbiome

Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions – Lejal et al. Microbiome

Water Microbiome

Microbiome diversity and host immune functions influence survivorship of sponge holobionts under future ocean conditions – Posadas et al. ISME

Soil microbiome

A Community Effort: Combining Functional Amplicon Sequencing and Metagenomics Reveals Potential Biosynthetic Gene Clusters Associated with Protective Phenotypes in Rhizosphere Microbiomes – Winter. mSystems.

Bioinformatics

METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses – Milani et al. mSystems