Category Archives: Plant Root Soil microbiome

April 30, 2022

Posted on by

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

April 20, 2022

Posted on by

General microbiome

How the gut talks to the brain – Adamantidis – Science

Pregnancy and early life

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

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

Human respiratory microbiome

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

Human skin microbiome

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

Human vaginal microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Animal microbiome (for animals in the wild)

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

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

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

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

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

Plant, root, and soil microbiome

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

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

Bioinformatics

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

Techniques

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

Microbes in the news

Bacteria generate electricity from methane

April 8, 2022

Posted on by

Good morning! Today’s microbiome digest is brought to you by mild insomnia induced by a mid-afternoon coffee. It includes two food related studies, one on pathogenic E. coli found in ready-to-eat foods and the other focused on a antifungal lipopeptide produced by B. velezensis isolated from honey, and an an article focused on a new approach for processing frozen lung and lavage samples for use in microbiome studies. Also included are several articles focused on the gut microbiome, and several preprints focused on soil microbiome studies. Finally, I want to highlight a piece that details the positive outcomes associated with the National Summer Undergraduate Research Project (NSURP). Registration for this year’s program is still open until April 15th, and the organizers are looking for both mentors, mentees, and donors!


Pregnancy and early life

Group B Streptococcus colonization at delivery is associated with maternal peripartum infection – Brigtsen et al. – PLOS ONE

Human gut microbiome

Mycobacterium avium subsp. paratuberculosis and microbiome profile of patients in a referral gastrointestinal diseases centre in the Sudan – Elmagzoub et al. – PLOS ONE

Animal experiments

Vertical transmission of attaching and invasive E. coli from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life – Brand et al. – PLOS ONE

Sex differences in the fecal microbiome and hippocampal glial morphology following diet and antibiotic treatment – Saxena et al. – PLOS ONE

Animal microbiome

Preprint: Anthropogenic disturbance impacts gut microbiome homeostasis in a Malagasy primate – Wasimuddin et al. – bioRxiv

Plant, root, and soil microbiome

Preprint: Microclimate is a strong predictor of the native and invasive plant-associated soil microbiota on San Cristóbal Island, Galápagos archipelago – Schoenborn et al. bioRxiv

Preprint: The activity and functions of soil microbial communities in the Finnish sub-Arctic vary across vegetation types – Vitamaki et al. – bioRxiv

Preprint: Tracing carbon metabolism with stable isotope metabolomics reveals the legacy of diverse carbon sources in soil – Wilhelm et al. – bioRxiv

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

Preprint: Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments – Kohtz et al. – bioRxiv

Food microbiology

Processed ready-to-eat (RTE) foods sold in Yenagoa Nigeria were colonized by diarrheagenic Escherichia coli which constitute a probable hazard to human health – Beshiru et al. – PLOS ONE

Purification and characterization of antifungal lipopeptide produced by Bacillus velezensis isolated from raw honey – Ziong et al. – PLOS ONE

Techniques

An optimized approach for processing of frozen lung and lavage samples for microbiome studies – Wiscovitch-Russo et al. – PLOS ONE

Science, publishing, and career

***National Summer Undergraduate Research Project (NSURP): A Virtual Research Experience to Deliver REAL (Retention, Equity, Access, and Life-Changing) Outcomes for Underrepresented Minorities in STEM – Johnson & Knox – JMBE

April 6, 2022

Posted on by

Today’s digest features studies on microbial genes of unknown function, oral microbiome of smokeless tobacco consumers, non-industrialized infant microbiome, and more news. Happy reading!

Microbiome Forum FOR EVERYONE
Each event is replicated shortly thereafter to reach a global audience.
ALL microbiome research & career levels welcome!
Free registration.

Global microbiome

Global Distribution of mcr Gene Variants in 214K Metagenomic Samples – Hannah-Marie Martiny – mSystems

Symposium Review: After the storm—Perspectives on the taxonomy of Lactobacillaceae – Nanzhen Qiao – JDS Communications

Oral microbiome

Assessing the Effect of Smokeless Tobacco Consumption on Oral Microbiome in Healthy and Oral Cancer Patients – Rituja Saxena – Frontiers in Cellular and Infection Microbiology

Gut microbiome

Unravelling specific diet and gut microbial contributions to inflammatory bowel disease – Gabriel Vasconcelos Pereira – bioRxiv

Effects of caloric restriction on the gut microbiome are linked with immune senescence – Julia Sbierski-Kind – Microbiome

Tap water as a natural vehicle for microorganisms shaping the human gut microbiome – Gabriele Andrea Lugli – Environmental Microbiology

Review: Diet-gut microbiota interactions on cardiovascular disease – Xufei Zhang and Philippe Gérard – Computational and Structural Biotechnology Journal

*Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles – Matthew R Olm – bioRxiv

Animal microbiome

Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance – Yunyan Zhou – Microbiome

Animal experiment

Modulation of the gut microbiome by novel synthetic glycans for the production of propionate and the reduction of cardiometabolic risk factors – Yves A Millet – bioRxiv

Plant microbiome

The phyllosphere microbiome shifts toward combating melanose pathogen – Pu-Dong Li – Microbiome

Wastewater microbiome

Near-neutral pH increased n-caprylate production in a microbiome with product inhibition of methanogenesis – Rodolfo Palomo-Briones – bioRxiv

Techniques

Review: Next-generation sequencing: insights to advance clinical investigations of the microbiome – Caroline R. Wensel – The Journal of Clinical Investigations

Metagenomics-enabled microbial surveillance – Karrie K. K. Ko – Nature Microbiology

Bioinformatics

Software testing in microbial bioinformatics: a call to action – Boas C.L. van der Putten – Microbial Genomics

Review: Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation – Alban Mathieu – Frontiers in Microbiology

*Unifying the known and unknown microbial coding sequence space – Chiara Vanni – eLife

NSURP is a community-driven initiative to create rewarding remote summer research opportunities for BIPOC and Latinx undergraduate students in the Microbiology, Immunology, and Cancer Biology Sciences.

April 04, 2022

Posted on by

General microbiome

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

Human breast tissue microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

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

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

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

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

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

Animal microbiome (for animals in the wild)

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

Plant, root, and soil microbiome

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

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

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

Bioinformatics

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

March 31, 2022

Posted on by

General microbiome

Whole genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming – Peng et al. – PLOS Computational Biology

[PREPRINT]Superfast Evolution of Multi-drug Antibiotic Resistance – Zhang et al. – bioRxiv

Pregnancy and early life

Identification of the specific microbial community compositions in saliva associated with periodontitis during pregnancy – Narita & Kodama – Clinical Oral Investigations

Vaginal microbiome

Impact of Topical Interventions on the Vaginal Microbiota and Metabolome in Postmenopausal Women – Srinivasan et al. – JAMA Network Open

Human gut microbiome

[REVIEW]The interplay between anticancer challenges and the microbial communities from the gut – Hobson et al. – European Journal of Clinical Microbiology & Infectious Diseases

[EDITORIAL]Unraveling disease pathways involving the gut microbiota: the need for deep phenotyping and longitudinal data – Meyer et al. – The American Journal of Clinical Nutrition

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

The Effects of Stevia Consumption on Gut Bacteria: Friend or Foe? – Kasti et al. – Microorganisms

Jejunoileal mucosal growth in mice with a limited microbiome – Shaughnessy – PLOS One

Plant, root, and soil microbiome

Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation – Causevic et al. – mSystems

Built environment (subways, indoor surfaces)

A quantitative microbial risk assessment for touchscreen user interfaces using an asymmetric transfer gradient transmission mode – di Battista – PLOS One

Forensics

Postmortem Skeletal Microbial Community Composition and Function in Buried Human Remains – Emmons et al. – mSystems

Bioinformatics

Microbial Identification Using rRNA Operon Region: Database and Tool for Metataxonomics with Long-Read Sequence – Seol et al. – Microbiology Spectrum

Techniques

Long-Term Incubation of Lake Water Enables Genomic Sampling of Consortia Involving Planctomycetes and Candidate Phyla Radiation Bacteria – Jaffe et al. – mSystems

March 23, 2022

Posted on by

General microbiome

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

Human skin microbiome

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

Human gut microbiome

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

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

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

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

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

Animal microbiome

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

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

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

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

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

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

Plant, root, and soil microbiome

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

Waste microbiome

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

Food microbiology

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

Bioinformatics

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

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

Techniques

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

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

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

March 09, 2022

Posted on by

General microbiome

Public human microbiome data are dominated by highly developed countries – Abdill, Adamowicz & Blekhman – PLOS Biology

Beyond the Microbiome: Germ-ganism? An Integrative Idea for Microbial Existence, Organization, Growth, Pathogenicity, and Therapeutics – Kambouris et al. – OMICS

Quantifying and Cataloguing Unknown Sequences within Human Microbiomes – Modha et al. – mSystems

Human respiratory microbiome

Alterations of lung microbiota in patients with non-small cell lung cancer – Zeng et al. – Bioengineered

Human vaginal microbiome

Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore’s adaptive sequencing – Marquet et al. – Scientific Reports

Human gut microbiome

[REVIEW]Personal diet–microbiota interactions and weight loss – Roager & Christensen

Integrated analysis of gut microbiome and host immune responses in COVID-19 – Xu et al. – Frontiers in Medicine

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

Gut microbiome modifications over time when removing in-feed antibiotics from the prophylaxis of post-weaning diarrhea in piglets – Cremonesi et al. – PLOS One

Complete Genome Sequences of Three Staphylococcus haemolyticus Strains Isolated from the Lung of a TGFβ1 Transgenic Mouse with Lung Fibrosis – Abdel-Hamid et al. – Microbiology Resource Announcements

Colitis-associated microbiota drives changes in behaviour in male mice in the absence of inflammation – Vicentini et al. – Brain, Behaviour, and Immunity

Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart – Kieser, Zdobnov & Trajkovski – PLOS Comp Biol

Plant, root, and soil microbiome

The microbiome and resistome of apple fruits alter in the post-harvest period – Wassermann et al. – Environmental Microbiome

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

Effects of Ocean Warming on the Underexplored Members of the Coral Microbiome – Maire et al. – Integrative and Comparative Biology

Techniques

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

[PREPRINT]A comparison of hard and soft direct methods for DNA extraction from soil – Hill et al. – bioRxiv

March 3, 2022

Posted on by

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

Happy reading!


Human vaginal microbiome

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

Human gut microbiome

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

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

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

Plant, root, and soil microbiome

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

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

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

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

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

Built environment

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

Phages and viruses

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

Bioinformatics

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

March 02, 2022

Posted on by

General microbiome

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

Pregnancy and early life

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

Human skin microbiome

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

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

Human oral microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

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

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

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

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

Animal microbiome (for animals in the wild)

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

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

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

Plant, root, and soil microbiome

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

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

Bioinformatics

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