Category Archives: Plant Root Soil microbiome

May 7, 2022

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Human and General Microbiome

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

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

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

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

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

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

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

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

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

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

Beneficial Microbes and Compounds

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

Animal Model Microbiome

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

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

Non-Model Animal Microbiome

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

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

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

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

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

Environmental Microbiome

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

Plant and Soil Microbiome

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

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

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

Bioinformatics and Data Analysis

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

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

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

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

May 6, 2022

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

General microbiome

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

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

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

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

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

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

Multi-site human microbiome

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

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

Human gut microbiome

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

Animal experiments

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

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

Plant, root, and soil microbiome

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

Water and extremophile microbiome

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

Food microbiology

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

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

Techniques

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

May 5, 2022

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Today’s digest features a review on the role of bacterial translocation (especially oral-gut axis) in health and disease, a proof-of-concept study on probiotics on processing of negative emotions in humans, and more. Happy reading!

Let’s talk microbiome science at the next #MVIF!

Sterile (?) environment

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

Probiotics

Lactobacillus acidophilus, L. plantarum, L. rhamnosus, and L. reuteri Cell-Free Supernatants Inhibit Candida parapsilosis Pathogenic Potential upon Infection of Vaginal Epithelial Cells Monolayer and in a Transwell Coculture System In Vitro – Luca Spaggiari – Microbiology Spectrum

*Probiotic Mixture Containing Lactobacillus helveticus, Bifidobacterium longum and Lactiplantibacillus plantarum Affects Brain Responses Toward an Emotional Task in Healthy Subjects: A Randomized Clinical Trial – Julia Rode – Frontiers in Nutrition

Vaginal microbiome

Identification and characterization of novel endolysins targeting Gardnerella vaginalis biofilms to treat bacterial vaginosis – Sara Arroyo-Moreno – npj Biofilms and Microbiomes

Gut microbiome

*Review: Deciphering mechanisms and implications of bacterial translocation in human health and disease – Shen Jin – Current Opinion in Microbiology

Two Competing Guilds as a Core Microbiome Signature for Chronic Diseases – Guojun Wu – bioRxiv

Neonatal Immune Challenge influences the Microbiota and Behaviour in a Sexually Dimorphic Manner – A. Cuskelly – Brain, Behavior, and Immunity

Review: Diet- and microbiota-related metabolite, 5-aminovaleric acid betaine (5-AVAB), in health and disease – Retu Haikonen – Trends in Endocrinology & Metabolism

Gut mycobiome

Review: “Molding” immunity—modulation of mucosal and systemic immunity by the intestinal mycobiome in health and disease – Mackenzie W. Gutierrez – Nature Mucosal Immunology

Animal experiments

Evolution of the murine gut resistome following broad-spectrum antibiotic treatment – Laura de Nies – Nature Communications & Behind the paper here.

Plant, root/soil microbiome

*Sugars dominate the seagrass rhizosphere – E. Maggie Sogin – Nature Ecology & Evolution

Viruses

A snapshot of the global drinking water virome: Diversity and metabolic potential vary with residual disinfectant use – Bridget Hegarty – Water Research

Techniques

Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification – Charlotte C. van de Velde – ISME Communications

Bioinformatics

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

HiFine: integrating Hi-c-based and shotgun-based methods to reFine binning of metagenomic contigs – Yuxuan Du and Fengzhu Sun – Bioinformatics

happi: a Hierarchical Approach to Pangenomics Inference – Pauline Trinh – bioRxiv

Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome – Rebecca H. Smit – bioRxiv

TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles – Varuni Sarwal – bioRxiv

April 30, 2022

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Human Microbiome

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

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

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

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

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

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

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

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

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

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

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

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

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

Beneficial Microbes and Compounds

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

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

Animal Model Microbiome

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

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

Non-Model Animal Microbiome

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

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

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

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

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

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

Plant Microbiome

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

More Microbes, Genes, and Proteins

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

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

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

Bioinformatics

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

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

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

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

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

April 20, 2022

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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

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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

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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

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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

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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

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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