Category Archives: Animal microbiome

October 11, 2023

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General microbiome

Major data analysis errors invalidate cancer microbiome findings – Gihawi et al. – mBio

Relative abundance data can misrepresent heritability of the microbiome – Bruihning et al. – Microbiome

Human gut microbiome

Discrimination exposure impacts unhealthy processing of food cues: crosstalk between the brain and gut – Zhang et al. – Nature Mental Health

[REVIEW]The impact of acute and chronic stress on gastrointestinal physiology and function: a microbiota–gut–brain axis perspective – Leigh et al. – The Journal of Physiology

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

Vertical transmission of gut bacteria in commercial chickens is limited – Shterzer et al. – Animal Microbiome

Animal microbiome (for animals in the wild)

[PREPRINT]The role of family and environment in determining the skin microbiome of captive aquatic frogs, Xenopus laevis – Chapman et al. – bioRxiv

Vertical transmission of gut bacteria in commercial chickens is limited – Shterzer et al. – Animal Microbiome

Bioinformatics/Techiques

[PREPRINT]MetaQuad: Shared Informative Variants Discovery in Metagenomic Samples – Xu et al. – bioRxiv

[PREPRINT]Insertion sequence driven evolution of the microbiota revealed by a novel metagenomics pipeline – Kirsch, Hryckowian & Duerkop

[PREPRINT]A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics – Eisenhofer et al. – bioRxiv

The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling – Zhang et al. – Applied and Environmental Microbiology

[PERSPECTIVE]Challenges and opportunities in sharing microbiome data and analyses – Huttenhower, Finn & McHardy – Nature Microbiology

October 4, 2023

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General microbiome

[OPINION]Toward an integrative framework for microbial community coalescence – Custer, Bresciani & Dini-Andreote – Trends in Microbiology

Statistically learning the functional landscape of microbial communities – Skwara et al. – Nature Ecology & Evolution

Human skin microbiome

Skin microbiota secretomes modulate cutaneous innate immunity against Borrelia burgdorferi s.s – Baquer et al. – Scientific Reports

Human gut microbiome

Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort – Galperine et al. – BMC Infectious Diseases

Association Between Bowel-Movement Pattern and Cognitive Function: Prospective Cohort Study and a Metagenomic Analysis of the Gut Microbiome – Ma et al. – Neurology

[REVIEW]The gut microbiome tango in the progression of chronic kidney disease and potential therapeutic strategies – Tang, Yu & Pan – Journal of Translational Medicine

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

Microbiota-gut-brain axis drives overeating disorder – Fan et al. – Cell Metabolism

Animal microbiome (for animals in the wild)

Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics – Wang et al. – Animal Microbiome

Plant, root, and soil microbiome

Using wasps as a tool to restore a functioning vine grape mycobiota and preserve the mycobial “terroir” – Di Paola et al. – Scientific Reports

Soil microbes mediate the effects of resource variability on plant invasion – Zhang et al. – Ecology

Bioinformatics

[PREPRINT]Deepurify: a multi-modal deep language model to remove contamination from metagenome-assembled genomes – Zou et al. – bioRxiv

[PREPRINT]BATTER: Accurate Prediction of Rho-dependent and Rho-independent Transcription Terminators in Metagenomes – Jin et al. – bioRxiv

[PREPRINT]Gut Microbiome Wellness Index 2 for Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles – Chang et al. – bioRxiv

Techniques

INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level resolution – Nino et al. – Nature Protocols

September 20, 2023

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General microbiome

Frequency of change determines effectiveness of microbial response strategies – Li et al. – The ISME Journal

Human gut microbiome

Social and psychological adversity are associated with distinct mother and infant gut microbiome variations – Warner et al. – Nature Communications

Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua – Mills et al. – Microbiome

Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts – Hansen et al. – Scientific Reports

The Impacts of Fecal Microbiota Transplantation from Same Sex on the Symptoms of Ulcerative Colitis Patients – Shang et al. – Polish Journal of Microbiology

Animal microbiome (for animals in the wild)

Transcriptomic, 16S ribosomal ribonucleic acid and network pharmacology analyses shed light on the anticoccidial mechanism of green tea polyphenols against Eimeria tenella infection in Wuliangshan black-boned chickens – Song et al. – Parasites & Vectors

Dityrosine Aggravates Hepatic Insulin Resistance in Obese Mice by Altering Gut Microbiota and the LPS/TLR4/NF-κB Inflammatory Pathway – Ding et al. – Molecular Nutrition & Food Research

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

[REVIEW]Microbiome-assisted restoration of degraded marine habitats: a new nature-based solution? – Corinaldesi et al. – Frontiers in Marine Science

Bioinformatics

[PREPRINT]Comparison of computational methods for host removal and classification of mycobacteria from clinical metagenomic data – Hall & Coin – bioRxiv

September 13, 2023

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General microbiome

[Resource]BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures – Geistlinger et al. – Nature Biotechnology

Human oral microbiome

[REVIEW]The oral microbiome: diversity, biogeography and human health – Baker et al. – Nature Reviews Microbiology

Dysbiosis of oral microbiome persists after dental treatment-induced remission of periodontal disease and dental caries – Yama et al. – mSystems

Human nearly-sterile sites (blood, organs, brain)

Proton pump inhibitor treatment aggravates bacterial translocation in patients with advanced cirrhosis and portal hypertension – Sturm et al. – mBio

Human gut microbiome

A faecal metabolite signature of impaired fasting glucose: results from two independent population-based cohorts – Nogal et al. – Diabetes

Composition and functional profiles of gut microbiota reflect the treatment stage, severity, and etiology of acute pancreatitis – Wang et al. – Microbiology Spectrum

Animal microbiome

Langerhans cells shape postnatal oral homeostasis in a mechanical-force-dependent but microbiota and IL17-independent manner – Jaber et al. – Nature Communications

Specific pathway abundances in the neonatal calf faecal microbiome are associated with susceptibility to Cryptosporidium parvum infection: a metagenomic analysis – Hares et al. – Animal Microbiome

Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety – Wortelboer et al. – Nature Communications

Gut microbiota of old mice worsens neurological outcome after brain ischemia via increased valeric acid and IL-17 in the blood – Zeng et al. – Microbiome

Plant, root, and soil microbiome

Different bacterial and fungal community patterns in restored habitats in coal-mining subsidence areas – Wang et al. – Environmental Science and Pollution Research

July 19, 2023

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General microbiome

RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities – Wang et al. – Microbiome

Human oral microbiome

[PREPRINT]The prevalence of motility within the human oral microbiota – Rocha et al. – bioRxiv

Human gut microbiome

A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis – McGregor et al. – Parasites & Vectors

Microbiome-derived cobalamin and succinyl-CoA as biomarkers for improved screening of anal cancer – Serrano-Villar et al. – Nature Medicine

[PREPRINT]Host-microbiota interactions contributing to the heterogeneous tumor microenvironment in colorectal cancer – Li et al. – bioRxiv

Diversity of plant DNA in stool is linked to dietary quality, age, and household income – Petrone et al. – PNAS

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

Alterations in fecal β-defensin-3 secretion as a marker of instability of the gut microbiota – Saqib et al. – Gut Microbes

The effect of prenatal stress on offspring depression susceptibility in relation to the gut microbiome and metabolome – Li et al. – Journal of Affective Disorders

[PROTOCOL]Gastrointestinal and Microbiome Profiling in Rodent Models of Neurological and Psychiatric Disorders – Kong et al. – Schizophrenia

Animal microbiome (for animals in the wild)

[PREPRINT]Persistent effects of intramammary ceftiofur treatment on the gut microbiome and antibiotic resistance in dairy cattle – Vasco et al. – bioRxiv

Bioinformatics

A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses – Elek et al. – Microbioal Genomics

[PREPRINT]Learning a deep language model for microbiomes: the power of large scale unlabeled microbiome data – Pope et al. – bioRxiv

MBECS: Microbiome Batch Effects Correction Suite – Olbrich, Künstner and Busch – BMC Bioinformatics

Techniques

[PREPRINT]High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific amplicons and long-read sequence – Stalder, Maurhofer and Croll – bioRxiv

June 16, 2023

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Thank you for answering my question above.

Today’s digest features indigenous chicken in Ethiopia, drug effects on gut microbiome, beach water microbial risk assessment, and more. See you at #MVIF next week!

Microbial ecology

Guild and Niche Determination Enable Targeted Alteration of the Microbiome – Oriane Moyne – bioRxiv

Genital microbiome

Interaction of genital microbiota in infertile couples – David Baud – bioRxiv

Gut microbiome

Emergence of community behaviors in the gut microbiota upon drug treatment – Sarela Garcia-Santamarina – bioRxiv

Skin microbiome

Skin microbiome differentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons – Marcus H. Y. Leung – Microbiome

Animal microbiome

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia – Laura Glendinning – bioRxiv

Animal experiments

Effects of fenbendazole on fecal microbiome in BPH/5 mice, a model of hypertension and obesity, a brief report – Kalie F. Beckers – Plos One

Gut microbiota and cognitive development in infant mice: Quantity and source of potable water – Chong-Su Kim and Dong-Mi Shin – Plos One

Plant microbiome

Globally consistent response of plant microbiome diversity across hosts and continents to soil nutrients and herbivores – Eric W. Seabloom – Nature Communications

Methodology

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

QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification – Yu Yang – Water Research

Bioinformatics

ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics – Rémi Gschwind – Nucleic Acids Research

June 13, 2023

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Today’s microbiome digest includes quite a few host-microbe studies, including one published by my colleague and highlighted below which focuses on the hindgut microbiome of the American cockroach.

Human gut microbiome

Gut microbiota interspecies interactions shape the response of Clostridioides difficile to clinically relevant antibiotics – Hromada – and Venturelli – PLOS Biology

Construction of model animals to explore intestinal microbiome for detection of breast cancer – Ji et al. – PLOS One

Animal experiments

**Disentangling hindgut metabolism in the American cockroach through single-cell genomics and metatranscriptomics – Dukes et al. – Frontiers in Microbiology

Evaluation of microbial and vancomycin treatments in ulcerative colitis in murine models – Hasan and Yang – PLOS One

Animal microbiome

Geography, not lifestyle, explains the population structure of free-living and host-associated deep-sea hydrothermal vent snail symbionts – Hauer et al. – Microbiome

Insect phylogeny structures the bacterial communities in the microbiome of psyllids (Hemiptera: Psylloidea) in Aotearoa New Zealand – Martoni et al. – PLOS One

Water and extremophile microbiome

In the right place, at the right time: the integration of bacteria into the Plankton Ecology Group model – Park et al. – Microbiome

Phages and viruses

Beyond pathogenesis: Detecting the full spectrum of ecological interactions in the virosphere – Jurburg et al. – PLOS Biology

Phage therapy and the public: Increasing awareness essential to widespread use – McCammon et al. – PLOS One

May 12, 2023

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Today’s digest features studies on human respiratory tract, mouse models, bovine milk microbiome, and more. See you at #MVIF next week!

Respiratory tract microbiome

Review: Ecology of the respiratory tract microbiome – Ana Elena Pérez-Cobas – Trends in Microbiology

Cervicovaginal microbiome

The cervical microbiota of Hispanics living in Puerto Rico is highly volatile and dominated by Lactobacillus iners regardless of HPV status – Daniela Vargas-Robles – bioRxiv

Gut microbiome

Key determinants of success in fecal microbiota transplantation: From microbiome to clinic – Serena Porcari – Cell Host & Microbes

Profiling the human intestinal environment under physiological conditions – Dari Shalon – Nature

Interaction between gut microbiota and sex hormones and their relation to sexual dimorphism in metabolic diseases – Jose Antonio Santos-Marcos – Biology of Sex Differences

Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis – Paige Salerno – bioRxiv

Animal microbiome

Metagenomic analysis of milk microbiota in the bovine subclinical mastitis – Giulia Alessandri – bioRxiv

Animal experiments

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice – Paolo Manghi – Cell Reports

Bioinformatics

ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning – Olga Mineeva – Plos Computational Biology

Technique

Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing – David Calderón-Franco – Antonie van Leeuwenhoek

Built environment

The microbiome of an outpatient rehabilitation clinic and predictors of contamination: A pilot study – Gabriella Brigando – PlosOne

May 5, 2023

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Today’s microbiome digest is a grab bag that includes ten simple rules for working with other people’s code, an article examining Wolbachia infections in native cockroach populations, and an article examining the role in lactic acid in shaping the human microbiome. Also highlighted is an article focused on human viruses residing within our cells and tissues, which demonstrated a unique virome in nine different human organs through targeted-enrichment viral metagenomics and virus specific qPCRs.

Happy reading!

General microbiome

The structure of prevacuolar compartments in Neurospora crassa as observed with super-resolution microscopy – Bowman – PLOS One

Phylogenetic trees of closely related bacterial species and subspecies based on frequencies of short nucleotide sequences – Nakano et al. – PLOS One

***Unmasking the tissue-resident eukaryotic DNA virome in humans – Pyöriä et al. – Nucleic Acids Research

Predicting partner fitness based on spatial structuring in a light-driven microbial community – Sakkos et al. – PLOS Computational Biology

Multi-site human microbiome

Evaluation of alcohol-free mouthwash for studies of the oral microbiome – Yano et al. – PLOS One

A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome – Zhang et al. – Microbiome

Human gut microbiome

Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the “Lunar Palace 365” experiment – Hao et al. – Microbiome

Animal microbiome

Wolbachia infection in native populations of Blattella germanica and Periplaneta americana – Choubdar et al. – PLOS One

Plant, root, and soil microbiome

Bacterial and fungal community composition and community-level physiological profiles in forest soils – Kunito et al. – PLOS One

Water and extremophile microbiome

Predicting microbial community compositions in wastewater treatment plants using artificial neural networks – Liu et al. – Microbiome

Open ocean and coastal strains of the N2-fixing cyanobacterium UCYN-A have distinct transcriptomes – Muñoz-Marín et al. – PLOS One

Meta-organism gene expression reveals that the impact of nitrate enrichment on coral larvae is mediated by their associated Symbiodiniaceae and prokaryotic assemblages – Tong et al. – Microbiome

Bioinformatics

Ten simple rules for working with other people’s code – Pilgrim et al. – PLOS Computational Biology

Predicting microbe organisms using data of living micro forms of life and hybrid microbes classifier – Raza et al. – PLOS One

iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria – Roux et al. – PLOS Biology

April 26, 2023

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General microbiome

[PREPRINT]Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance? – Klümper et al. – bioRxiv

Pregnancy and early life

First-Day-of-Life Rectal Swabs Fail To Represent Meconial Microbiota Composition and Underestimate the Presence of Antibiotic Resistance Genes – Graspeuntner et al. – Microbiology Spectrum

Human gut microbiome

Mucin-microbiome signatures shape the tumor microenvironment in gastric cancer – Oosterlinck et al. – Microbiome

[REVIEW]Fecal microbiota transplantation for recurrent C. difficile infection in patients with inflammatory bowel disease: A systematic review and meta-analysis – Porcari et al. – Journal of Autoimmunity

[REVIEW]Alcohol, the gut microbiome, and liver disease – Jew & Hsu – JGH

[REVIEW]Microbial metabolites in colorectal tumorigenesis and cancer therapy – Liu et al. – Gut Microbes

Human biliary microbiome

Neoadjuvant therapy does not impact the biliary microbiome in patients with pancreatic cancer – Behrens et al. – Journal of Surgical Oncology

Animal microbiome (for animals in the wild)

Indirect maternal effects via nest microbiome composition drive gut colonization in altricial chicks – Diez-Mendez et al. – Molecular Ecology

The gut microbiome of solitary bees is mainly affected by pathogen assemblage and partially by land use – de Landa et al. – Environmental Microbiome

Spatial Succession Underlies Microbial Contribution to Food Digestion in the Gut of an Algivorous Sea Urchin – Masasa et al. – Microbiology Spectrum

The microbiota in feces of domestic pigeons in Seoul, Korea – Oh et al. – Heliyon

Plant, root, and soil microbiome

Characterization of the Rhizosphere Bacterial Microbiome and Coffee Bean Fermentation in the Castillo-Tambo and Bourbon Varieties in the Popayán-Colombia Plateau – Solis Pino et al. – BMC Plant Biology

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

Hydrochemical and Seasonally Conditioned Changes of Microbial Communities in the Tufa-Forming Freshwater Network Ecosystem – Cackovic et al. – mSphere

Bioinformatics

[PREPRINT]ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization – Yang et al. – arXiv