January 27, 2023

General Microbiome

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies – Kennedy et al. Nature

Microbial foods for improving human and planetary health – Jahn et al. Cell

A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy – Mayer et al. Science Advances

Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults – Larson et al. Nature Aging

Bacteriophage / Virome

Phage therapy: From biological mechanisms to future directions – Strathdee et al. Cell

Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs – Lee et al. Cell

Water and extremophile microbiome

High-resolution metagenomic reconstruction of the freshwater spring bloom – Kavagutti et al. Microbiome

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria – Sereika et al. ISME

Bioinformatics

Enhanced correlation-based linking of biosynthetic gene clusters to their metabolic products through chemical class matching – Louwen et al. Microbiome

PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data – Wang & Cao. Briefings in Bioinformatics

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine – Heinken et al. Nature Biotechnology

Non-Microbiome picks

Infection infidelities drive innate immunity – Kagan. Science

Functional T cells are capable of supernumerary cell division and longevity – Soerens et al. Nature

Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe – Kerner et al. Cell Genomics

January 25, 2023

Human oral microbiome

Microbiological profile of peri-implantitis: Analyses of microbiome within dental implants – Kensara et al. – Journal of Prosthodontics

Human gut microbiome

Integrated Multi-Cohort Analysis of the Parkinson’s Disease Gut Metagenome – Boktor et al. – Movement Disorders

Gut microbiota and microbiota-derived metabolites promotes endometriosis – Chadchan et al. – Cell Death Discovery

Immune communication between the intestinal microbiota and the cardiovascular system – Ren et al. – Immunology Letters

Animal microbiome

The structure and diversity of microbial communities in Paederus fuscipes (Coleoptera: Staphylinidae): from ecological paradigm to pathobiome – Chamanakar et al. – Microbiome

The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet – Lin et al. – Microbiome

Fecal Microbiota Was Reshaped in UCP1 Knock-In Pigs via the Adipose-Liver-Gut Axis and Contributed to Less Fat Deposition – Pan et al. – Microbiology Spectrum

Gut microbiota of skywalker hoolock gibbons (Hoolock tianxing) from different habitats and in captivity: Implications for gibbon health – Lan et al. – American Journal of Primatology

Housing temperature plays a critical role in determining gut microbiome composition in research mice: Implications for experimental reproducibility – Hylander et al. – Biochimie

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

The biogeography and co-occurrence network patterns of bacteria and microeukaryotes in the estuarine and coastal waters – Wu et al. – Marine Environmental Research

Bioinformatics

[PREPRINT]Capturing the dynamics of microbiomes using individual-specific networks – Yousefi et al. – bioRxiv

PhaTYP: predicting the lifestyle for bacteriophages using BERT – Shang, Tang & Sun – Briefings in Bioinformatics

January 18, 2023

Human oral microbiome

[PRIMER]A possible role for taste receptor cells in surveying the oral microbiome – Heisey & McCluskey – PLOS Biology

Type II taste cells participate in mucosal immune surveillance – Qin et al. – PLOS One

Human gut microbiome

[NEWS]How our microbiome is shaped by family, friends and even neighbours – Callaway – Nature

The person-to-person transmission landscape of the gut and oral microbiomes – Valles-Colomer et al. – Nature

[REVIEW]The gut microbiota in obesity and weight management: microbes as friends or foe? – van Hul & Cani – Nature Reviews Endocrinology

Dynamics of the gut microbiome, IgA response, and plasma metabolome in the development of pediatric celiac disease – Girdhar et al. – Microbiome

Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes – Jacobs et al. – Microbiome

Microbiome Features Differentiating Unsupervised-Stratification-Based Clusters of Patients with Abnormal Glycometabolism – Xu et al. – mBio

Gut Bacterial Dysbiosis in Irritable Bowel Syndrome: a Case-Control Study and a Cross-Cohort Analysis Using Publicly Available Data Sets – Kim, Lee & Shim – Microbiology Spectrum

Harnessing gut microbes for glycan detection and quantification – Modesto, Pearce & Townsend Il – Nature Communications

The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles – Malan – Müller et al. – Gut Microbes

Animal microbiome

Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse – Li et al. – Microbiome

The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions – Bay et al. – Microbiome

Plant, root, and soil microbiome

A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data – Merihu et al. – Microbiome

Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle – Kibegwa et al. – PLOS One

Bioinformatics

Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and pre-processing bias in classification of mock bacterial community samples – Maki et al. – PLOS One

January 13, 2023

The very first 2023 digest features HMOs, antimicrobials and the neonatal gut microbiota, cheese community, cow rumen microbiome, SemiBin2, and more. Happy Friday and see you next week at #MVIF!

Food microbiome

*Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities – Christina C. Saak – mSystems

Gut microbiome

*Human milk oligosaccharides, antimicrobial drugs, and the gut microbiota of term neonates: observations from the KOALA birth cohort study – D.J.M Barnett – Gut microbes

The gut microbiota in multiple sclerosis varies with disease activity – Florence Thirion – Genome Medicine

Review: Intestinal gas production by the gut microbiota: A review – Erasme Mutuyemungu – Journal of Functional Foods

Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis – Yishay Pinto – Gut

Review: The gut microbiota is an emerging target for improving brain health during ageing – Marcus Boehme – Gut microbiome

Vaginal microbiome

Commensal Lactobacilli Metabolically Contribute to Cervical Epithelial Homeostasis in a Species-Specific Manner – Nicole R. Jimenez – mSphere

Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome – William F. Kindschuh – Nature Microbiology

Animal experiment

Gut microbiota of the young ameliorates physical fitness of the aged in mice – Kwang H. Kim – Microbiome

Catheterization of mice triggers resurgent urinary tract infection seeded by a bladder reservoir of Acinetobacter baumannii – Jennie E. Hazen – Science Translational Medicine

Prebiotic intervention with HAMSAB in untreated essential hypertensive patients assessed in a phase II randomized trial – Hamdi A. Jama – Nature Cardiovascular Research

Akkermansia muciniphila protects mice against an emerging tick-borne viral pathogen – Jinyan Xie – Nature Microbiology

Animal microbiome

Beehives possess their own distinct microbiomes – Lorenzo A. Santorelli – Environmental Microbiome

*Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome – Cameron R. Strachan – Nature Microbiology

Bioinformatics

Ecological landscapes guide the assembly of optimal microbial communities – Ashish B. George and Kirill S. Korolev – Plos Computational Biology

Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering – Theresa Ullmann – Plos Computational Biology

Ten simple rules for using public biological data for your research – Vishal H. Oza – Plos Computational Biology

*SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing – Shaojun Pan – bioRxiv

December 30, 2022

Happy New Year from the Microbiome Digest Team!

Human and General Microbiome

Microbiome Characteristics in Early Threatened Miscarriage Study (MCETMS): a study protocol for a prospective cohort investigation in China – Xiaofeng Chen – BMJ Open

Mapping the early life gut microbiome in neonates with critical congenital heart disease: multiomics insights and implications for host metabolic and immunological health – Yuan Huang – Microbiome

Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut – Ran Li – Nature Communications

Fecal level of butyric acid, a microbiome-derived metabolite, is increased in patients with severe carotid atherosclerosis – Kristine Stø – Scientific Reports

Transition in vaginal Lactobacillus species during pregnancy and prediction of preterm birth in Korean women – Young-Ah You – Scientific Reports

Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study – Freida Blostein – Microbiome

Systematic Review: The effects of microbiota abundance on symptom severity in Parkinson’s disease: A systematic review – Eliša Papić – Frontiers in Aging Neuroscience

Systematic Review: A systematic review of microbiome-derived biomarkers for early colorectal cancer detection – Florine H Zwezerijnen-Jiwa – Neoplasia

Review: Current insights into skin lipids and their roles in cutaneous health and disease – Anna Nicolaou – Current Opinion in Clinical Nutrition and Metabolic Care

Beneficial Microbes and Compounds

Akkermansia supplementation reverses the tumor-promoting effect of the fecal microbiota transplantation in ovarian cancer – Zizhuo Wang – Cell Reports

Review: A novel approach to Lactiplantibacillus plantarum: From probiotic properties to the omics insights – Noemí Echegaray – Microbiological Research

Animal Microbiome

Prokaryotic and eukaryotic microbial communities associated with coral species have high host specificity in the South China Sea – Keke Cheng – The Science of the Total Environment

Assessing the causes and consequences of gut mycobiome variation in a wild population of the Seychelles warbler – Sarah F Worsley – Microbiome

Gut microbe Lactiplantibacillus plantarum undergoes different evolutionary trajectories between insects and mammals – Elisa Maritan – BMC Biology

Environmental Microbiome

Permafrost in the Cretaceous supergreenhouse – Juan Pedro Rodríguez-López – Nature Communications

Degradation pathways for organic matter of terrestrial origin are widespread and expressed in Arctic Ocean microbiomes – Thomas Grevesse – Microbiome

Temporary establishment of bacteria from indoor plant leaves and soil on human skin – Gwynne Á Mhuireach – Environmental Microbiome

Microbiome Analysis

Stochastic variational variable selection for high-dimensional microbiome data – Tung Dang – Microbiome

December 23, 2022

Happy Holidays from the Microbiome Digest Team!

Human and General Microbiome

Analysis of the oral microbiome during hormonal cycle and its alterations in menopausal women: the AMICA project – A Tramice – Scientific Reports

Diversity and Prevalence of Clostridium innocuum in the Human Gut Microbiota – Disha Bhattacharjee – mSphere

A multiomics analysis of direct interkingdom dynamics between influenza A virus and Streptococcus pneumoniae uncovers host-independent changes to bacterial virulence fitness – Maryann P Platt – PLoS Pathogens

Butyrate Ameliorates Insufficient Sleep-Induced Intestinal Mucosal Damage in Humans and Mice – Ting Gao – Microbiology Spectrum

Prediction model of poorly differentiated colorectal cancer (CRC) based on gut bacteria – Zhang Qi – BMC Microbiology

Multidisciplinary Perinatal Care in IBD – Lihi Godny – Journal of Crohn’s & Colitis

Review: A multi-omic brain gut microbiome signature differs between IBS subjects with different bowel habits – Rachel P Sarnoff – Neuropharmacology

Review: From fecal microbiota transplantation toward next-generation beneficial microbes: The case of Anaerobutyricum soehngenii – Koen Wortelboer – Frontiers in Medicine

Beneficial Microbes and Compounds

Final Results from a Phase 2b Randomized, Placebo-Controlled Clinical Trial of RBX2660: A Microbiota-Based Drug for the Prevention of Recurrent Clostridioides difficile Infection – Erik R Dubberke – Infectious Diseases and Therapy

Systematic Review: The effect of probiotic and synbiotic supplementation on appetite-regulating hormones and desire to eat: a systematic review and meta-analysis of clinical trials – Morvarid Noormohammadi – Pharmacological Research

Animal Microbiome

Experimental Infection with Mycoplasma hyopneumoniae Strain 232 in Swine Influences the Lower Respiratory Microbiota – Henrique Meiroz de Souza Almeida – Veterinary Sciences

Functional Diversification of Oyster Big Defensins Generates Antimicrobial Specificity and Synergy against Members of the Microbiota – Noémie De San Nicolas – Marine Drugs

Gut microbiota modulates lung fibrosis severity following acute lung injury in mice – Ozioma S Chioma – Communications Biology

Effects of enhanced insect feeding on the faecal microbiota and transcriptome of a family of captive common marmosets (Callithrix jacchus) – Yumiko Yamazaki – PloS ONE

Review: The Mechanism of Important Components in Canine Fecal Microbiota Transplantation – Kerong Li – Veterinary Sciences

Food Microbiome

In vitro selection and characterization of probiotic properties in eight Lactobacillus strains isolated from cocoa fermentation – Milena E DE Almeida – Anais da Academia Brasileira de Ciencias

Microbiome Analysis Techniques

RIAM: A Universal Accessible Protocol for the Isolation of High Purity DNA from Various Soils and Other Humic Substances – Alexander G Pinaev – Methods and Protocols

Review: Compositionality, sparsity, spurious heterogeneity, and other data-driven challenges for machine learning algorithms within plant microbiome studies – Sebastiano Busato – Current Opinion in Plant Biology

December 19, 2022

Highlights!

Multi-omic interactions in the gut of children at the onset of islet autoimmunity – Patrick G Gavin – Microbiome

“Here, we apply an integrative approach to combine comprehensive fecal virome, microbiome, and metaproteome data sampled before and at the onset of islet autoimmunity in 40 children at increased risk of T1D […] We show a functional remodeling of the gut microbiota accompanies both islet autoimmunity and viral infection with a switch in function in Faecalibacterium occurring at the onset of islet autoimmunity.”

Human and General Microbiome

Review: The microbiota-gut-brain axis in pathogenesis of depression: a narrative review – Hui Yao – Physiology & Behavior

Review: Environmental enteric dysfunction: gut and microbiota adaptation in pregnancy and infancy – Carrie A Cowardin – Nature Reviews. Gastroenterology & Hepatology

Review: Gastrointestinal Tract, Microbiota and Multiple Sclerosis (MS) and the Link Between Gut Microbiota and CNS – Bahman Yousefi – Current Microbiology

Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort – Nele Brusselaers – Gut Pathogens

Endodontic microbial communities in apical periodontitis – Alessio Buonavoglia – Journal of Endodontics

Gut Microbiota-Generated Phenylacetylglutamine and Heart Failure – Kymberleigh A Romano – Circulation. Heart Failure

Animal Microbiome

Midgut Bacterial Microbiota of 12 Fish Species from a Marine Protected Area in the Aegean Sea (Greece) – Konstantinos Kormas – Microbial Ecology

Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host – Ankur Midha – Microbiome

Plant Microbiome

Multifaceted roles of flavonoids mediating plant-microbe interactions – Lanxiang Wang – Microbiome

Microbiome Analysis and Techniques

An economic and robust TMT labeling approach for high throughput proteomic and metaproteomic analysis – Marybeth Creskey – Proteomics

Machine learning-derived gut microbiome signature predicts fatty liver disease in the presence of insulin resistance – Baeki E Kang – Scientific Reports

Pseudomonas-specific 16S rRNA insect gut-microbiome profiling using next-generation sequencing – Ayushi Gupta – STAR Protocols

December 16, 2022

Highlights!

A microbiome-dependent gut-brain pathway regulates motivation for exercise – Lenka Dohnalová – Nature 

Here, we report on the discovery of a gut–brain connection in mice that enhances exercise performance by augmenting dopamine signalling during physical activity. We find that microbiome-dependent production of endocannabinoid metabolites in the gut stimulates the activity of TRPV1-expressing sensory neurons and thereby elevates dopamine levels in the ventral striatum during exercise.

Gut microbiota in the early stage of Crohn’s disease has unique characteristics – Xianzong Ma – Gut Pathogens

The present study aimed to identify dysbacteriosis in patients with early Crohn’s Disease (CD) and explore specific gut bacteria related to the progression of CD.

Human and General Microbiome

Longitudinal multi-omics analyses of the gut-liver axis reveals metabolic dysregulation in hepatitis C infection and cirrhosis – Rabab O Ali – Nature Microbiology

Impact of HIV infection and integrase strand transfer inhibitors-based treatment on the gut virome – Pablo Villoslada-Blanco – Scientific Reports

Consequences of collagen induced inflammatory arthritis on circadian regulation of the gut microbiome – Devin Amanda Simpkins – FASEB Journal

Isolation and characterization of a novel choline degrading Citrobacter amalonaticus strain from the human gut – Jyoti Kashyap – Current Research in Microbial Sciences

HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome – Jingjing Meng – Microbiology Spectrum

Gut dysbiosis and bacterial translocation in the aneurysmal wall and blood in patients with abdominal aortic aneurysm – Ken Nakayama – PloS One

Review: Female reproductive tract microbiome and early miscarriages – Olga Lebedeva – APMIS

Review: Emerging roles of intratumor microbiota in cancer metastasis – Aikun Fu – Trends in Cell Biology

In Brief: Urine microbiota differ in bladder cancer – Louise Stone – Nature Reviews. Urology

Animal Microbiome

Characterization of the bacterial microbiome of Amblyomma scalpturatum and Amblyomma ovale collected from Tapirus terrestris and Amblyomma sabanerae collected from Chelonoidis denticulata, Madre de Dios- Peru – Jesús Rojas-Jaimes – BMC Microbiology

Increased Proportion of Fiber-Degrading Microbes and Enhanced Cecum Development Jointly Promote Host To Digest Appropriate High-Fiber Diets – Guang Pu – mSystems

Review: Involvement of Microbiota in Insect Physiology: Focus on B Vitamins – Javier Serrato-Salas – mBio

Plant Microbiome

The Endophytic Root Microbiome Is Different in Healthy and Ralstonia solanacearum-Infected Plants and Is Regulated by a Consortium Containing Beneficial Endophytic Bacteria – Yiting Li – Microbiology Spectrum

Microbiome Analysis and Methods

Interpreting tree ensemble machine learning models with endoR – Albane Ruaud – PLoS Computational Biology

Analysis of Ancient Microbial DNA – Olivier Gorgé – Methods in Molecular Biology (Book)

Confocal Laser Scanning Microscopy Approach to Investigate Plant-Fungal Interactions – F Fracchia – Methods in Molecular Biology (Book)

December 12, 2022

Today’s digest has the kind of articles I like best–they are all focused on the unique relationship between microbial communities and their niche environments. These environments span everything from rice seeds to the Mariana Trench to the gut microbiome and even Appalachian coalbeds. Happy reading!


Human gut microbiome

Gut microbiome of helminth-infected indigenous Malaysians is context dependent – Tee et al. – Microbiome

Animal experiments

Taurine metabolism is modulated in Vibrio-infected Penaeus vannamei to shape shrimp antibacterial response and survival – Wang et al. – Microbiome


Plant, root, and soil microbiome

Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome – Mataigne et al. – Microbiome

Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes – Zhang et al. – Microbiome


Water and extremophile microbiome

Comparison of prokaryotes between Mount Everest and the Mariana Trench – Liu et al. – Microbiome


Built environment

Predominance of Methanomicrobiales and diverse hydrocarbon-degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome-resolved metabolisms – Ross et al. – Environmental Microbiology

Evaluation of the Microbial Community and Geochemistry in Produced Waters Collected from CO2 EOR in the Niagaran Pinnacle Reef – Stemple et al. – ACS Earth Space Chem

December 12, 2022

Human and General Microbiome

Dental calculus microbiome correlates with dietary intake – Gabriel Innocenti – Molecular Oral Microbiology

Ruminococcus gnavus plays a pathogenic role in diarrhea-predominant irritable bowel syndrome by increasing serotonin biosynthesis – Lixiang Zhai – Cell Host & Microbe

The gut microbiome and child mental health: a population-based study – Robert Kraaij – Brain, Behavior, and Immunity

Gut microbiota profile of COVID-19 patients: Prognosis and risk stratification (MicroCOVID-19 study) – José Guilherme Nobre – Frontiers in Microbiology

Systematic Review: Gut microbiota diversity and composition in predicting immunotherapy response and immunotherapy-related colitis in melanoma patients: A systematic review – Oliver Oey – World Journal of Clinical Oncology

Review: Scientometric analysis of kidney disease and gut microbiota from 2001 to 2020 based on Web of Science – Ran Zhang – Medicine

Review: Crosstalk between liver macrophages and gut microbiota: An important component of inflammation-associated liver diseases – Ziyuan Zhou – Frontiers in Cell and Developmental Biology

Review: Dental calculus – oral health, forensic studies and archaeology: a review – Roger Forshaw – British Dental Journal

Animal Microbiome

Inputs don’t equal outputs: Bacterial microbiomes of the ingesta, gut, and feces of the keystone deposit feeder Ilyanassa obsoleta – Craig J Plante – FEMS Microbiology Ecology

Urinary neopterin reflects immunological variation associated with age, helminth parasitism, and the microbiome in a wild primate – India A Schneider-Crease – Scientific Reports

Dark-purple rice extract modulates gut microbiota composition in acetic acid- and indomethacin-induced inflammatory bowel disease in rats – Kornsuda Thipart – International Microbiology

Review: Nasonia-microbiome associations: a model for evolutionary hologenomics research – Zhengyu Zhu – Trends in Parasitology

Microbiome Analysis

Rapid separation of bacteria from primary nasal samples using inertial microfluidics – Jesus Shrestha – Lab on a Chip