Category Archives: General Microbiome

April 10, 2021

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Have a nice weekend! Today, in this (late) Digest: articles about gut microbiome and COVID19 and neurological disorders, as well as other studies with skin, respiratory and vaginal microbiomes. We have also: wine microbiome, rumen eukaryotome, hydrocarbon degraders, some bioinformatic pipelines and more!

Human and General Microbiome

Faecalibacterium prausnitzii increases following fecal microbiota transplantation in recurrent Clostridioides difficile infection – Olle Björkqvist – PLoS ONE

Comprehensive profiling of the gut microbiota in patients with chronic obstructive pulmonary disease of varying severity – Yu-Chi Chiu –  PLoS ONE

Nutrition and the microbiota post-COVID-19 – G. G. F. Alberca – The Saudi Journal of Gastroenterology

Book Chapter: From “Leaky Gut” to Impaired Glia-Neuron Communication in Depression – Leszek Rudzki – Major Depressive Disorder

Skin microbiome of patients with interdigital tinea pedis: Corynebacterium striatum is more abundant in the patients – Mayumi Miyamoto – The Journal of Dermatology 

Selected Clostridia Strains from The Human Microbiota and their Metabolite, Butyrate, Improve Experimental Autoimmune Encephalomyelitis – Laura Calvo-Barreiro – Neurotherapeutics

Gut Microbiota Composition and Epigenetic Molecular Changes Connected to the Pathogenesis of Alzheimer’s Disease – Priyanka Nagu – Journal of Molecular Neuroscience 

Global climate change, diet, and the complex relationship between human host and microbiome: Towards an integrated picture – Francesco Catania – BioEssays

Global research trends in the microbiome related to irritable bowel syndrome: A bibliometric and visualized study – Sa’ed H Zyoud – World Journal of Gastroenterology

Coronavirus disease-2019 and the intestinal tract: An overview – Gabriela Gama Freire Alberca – World Journal of Gastroenterology

Comparison of Argentinean microbiota with other geographical populations reveals different taxonomic and functional signatures associated with obesity – Susana A. Pesoa – Scientific Reports 

Six-month follow-up of gut microbiota richness in patients with COVID-19 – Yanfei Chen – Gut (BMJ)

The combined therapy of fecal microbiota transplantation and laxatives for functional constipation in adults: A systematic review and meta-analysis of randomized controlled trials – Fang, Sijia MM – Medicine

Vaginal metabolic profiles during pregnancy: Changes between first and second trimester – Luca Laghi – PLoS ONE

Microbiome profiling of uncinate tissue and nasal polyps in patients with chronic rhinosinusitis using swab and tissue biopsy – Sung-Woo Cho – PLoS ONE

Patient attitudes towards faecal sampling for gut microbiome studies and clinical care reveal positive engagement and room for improvement – Laura A. Bolte – PLoS ONE

Microbes in the Media

Microbiome research in general and business newspapers: How many microbiome articles are published and which study designs make the news the most? – Andreu Prados-Bo – PLoS ONE

Food Microbiome

Minireview: The ecology of wine fermentation: a model for the study of complex microbial ecosystems – CG Conacher – Applied Microbiology and Biotechnology

Animal Microbiome

The rumen eukaryotome is a source of novel antimicrobial peptides with therapeutic potential – Lucy A. Onime – BMC Microbiology

The skin microbiota in equine pastern dermatitis: a case-control study of horses in Switzerland – Sarah Kaiser‐Thom – Veterinary Dermatology

Association between aging-dependent gut microbiome dysbiosis and dry eye severity in C57BL/6 male mouse model: a pilot study – Chang Ho Yoon – BMC Microbiology

Environmental Microbiome

Black Yeast Genomes Assembled from Plastic Fabric Metagenomes Reveal an Abundance of Hydrocarbon Degradation Genes – Osman Radwan – Microbiology Resource Annoucements

Effects of supplemental feeding on the fecal bacterial communities of Rocky Mountain elk in the Greater Yellowstone Ecosystem – Claire E. Couch – PLoS ONE

Bioinformatics

A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota – Yafei Chang – Briefings in Bioinformatics

DisBalance: a platform to automatically build balance-based disease prediction models and discover microbial biomarkers from microbiome data – Fenglong Yang – Briefings in Bioinformatics

Review: Metagenomic Data Assembly – The Way of Decoding Unknown Microorganisms – Alla L. Lapidus – Frontiers in Microbiology

Built Environments

Analyzing indoor mycobiomes through a large-scale citizen science study in Norway – Sarah Kaiser‐Thom – Veterinary Dermatology

Forensic Microbiomes

Review: Microbiomes in forensic botany: a review – Sarah Ishak – Forensic Science, Medicine and Pathology 

Other papers

Untargeted Stable Isotope Probing of the Gut Microbiota Metabolome Using 13 C-Labeled Dietary Fibers – Pan Deng – Journal of Proteome Research

Metaproteomic sample preparation methods bias the recovery of host and microbial proteins according to taxa and cellular compartment – Patrick G.Gavin – Journal of Proteomics

April 07, 2021

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General microbiome

Primate phageomes are structured by superhost phylogeny and environment – Gogarten et al. – PNAS

Fungal‐induced glycolysis in macrophages promotes colon cancer by enhancing innate lymphoid cell secretion of IL‐22 – Zhu et al. – The EMBO Journal

A method for detection of SARS-CoV-2 RNA in healthy human stool: a validation study – Coryell et al. – The Lancet Microbe

The Ocular Microbiome and Microbiota and their Effects on Ocular Surface Pathophysiology and Disorders – Aragona et al. – Survey of Ophthalmology

Human oral microbiome

Multi-dimensional study of the oral microbiome, metabolite, and immunologic environment in peanut allergy – Ho et al. – Journal of Allergy and Clinical Immunology

Human skin microbiome

Temporal Variation in Staphylococcus aureus Protein A Genotypes from Nose and Skin in Atopic Dermatitis Patients – van Mierlo et al. – Dermatology

Sex‐Based Differences in Fecal Short‐Chain Fatty Acid and Gut Microbiota in Irritable Bowel Syndrome Patients – Sun et al. – Journal of Digestive Diseases

Human gut microbiome

[REVIEW]Ecological and evolutionary responses to antibiotic treatment in the human gut microbiota – Pennycook & Scanlan – FEMS Microbiology Reviews

Animal microbiome (for animals in the wild)

The Fecal and Serum Metabolomics of Giant Pandas Based on Untargeted Metabolomics – Yang et al. – Zoological Scienc

Microbes in space

Astrobiology of life on Earth – Hallsworth et al. – Environmental Microbiology
Mars’ surface is not universally biocidal – Hallsworth – Environmental Microbiology

Bioinformatics

Draft Genome Sequences and Antimicrobial Profiles of Three Staphylococcus epidermidis Strains from Neonatal Blood Samples – Afeke et al. – Microbiology Resource Announcements

CoCoNet: An Efficient Deep Learning Tool for Viral Metagenome Binning – Arisdakessian et al. – Bioinformatics

Techniques

Rank normalization empowers a t-test for microbiome differential abundance analysis while controlling for false discoveries – Davis, Huang & Wang – Briefings in Bioinformatics

Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing – Tourancheau et al. – Nature Methods

April 3, 2021

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Have a nice weekend! Today we want to highlight a new podcast about Microbiome and Health, available in Spotify. We also have today a set of studies, covering aspects of the urinary microbiome, drug-microbiome dynamics, and cancer microbiota.

Microbes in the Media

Biomes Podcast with Dr. Ruairi Robertson (Available in Spotify)

Human and General Microbiome

Microbiome and Metabolome Analyses Reveal Novel Interplay Between the Skin Microbiota and Plasma Metabolites in Psoriasis – Dongmei Chen – Frontiers in Microbiology

Microreview: Organ-on-chip to investigate host-pathogens interactions – Thomas Feaugas – Cellular Microbiology

Investigating colonization patterns of the infant gut microbiome during the introduction of solid food and weaning from breastmilk: A cohort study protocol – Sara Dizzell – PLoS One

Urinary Microbiota; Which Non-Invasive Urine Collection Method Should We Use? – Muhammed Selcuk Ozer – IJCP

A specific association between laxative misuse and suicidal behaviours in patients with anorexia nervosa and bulimia nervosa – Aiste Lengvenyte – Eating and Weight Disorders – Studies on Anorexia, Bulimia and Obesity

Bile Microbiota in Liver Transplantation: Proof of Concept Using Gene Amplification in a Heterogeneous Clinical Scenario – Francesco D’Amico – Frontiers in Surgery

The Unique Impact of COVID-19 on Human Gut Microbiome Research – Ella Burchill – Frontiers in Medicine

Modeling of Urinary Microbiota Associated With Cystitis – Marina Ceprnja – Frontiers in Cellular and Infection Microbiology

Identification of Microbiome Etiology Associated With Drug Resistance in Pleural Empyema – Zhaoyan Chen – Frontiers in Cellular and Infection Microbiology

Analysis of Gut Microbiome Using Explainable Machine Learning Predicts Risk of Diarrhea Associated With Tyrosine Kinase Inhibitor Neratinib: A Pilot Study – Chi Wah Wong – Frontiers in Oncology 

Antitumor efficacy of a neoantigen cancer vaccine delivered by electroporation is influenced by microbiota composition – Lucia Lione – OncoImmunology 

Associations between dysbiosis-inducing drugs, overall survival and tumor response in patients treated with immune checkpoint inhibitors – Louis Gaucher – Therapeutic Advances in Medical Oncology

The Hygiene Hypothesis – Learning From but Not Living in the Past – Petra I. Pfefferle – Frontiers in Immunology

Strength Exercise Confers Protection in Central Nervous System Autoimmunity by Altering the Gut Microbiota – Hao Chen – Frontiers in Immunology

Beneficial Microbes and Compounds

Enrichment of Food With Tannin Extracts Promotes Healthy Changes in the Human Gut Microbiota – Silvia Molino – Frontiers in Microbiology

Bifidobacterium Lactis Probio-M8 regulates gut microbiota to alleviate Alzheimer’s disease in the APP/PS1 mouse model – Jianing Cao – European Journal of Nutrition 

Animal Microbiome

Re-Analysis of 16S rRNA Gene Sequence Data Sets Uncovers Disparate Laboratory-Specific Microbiomes Associated with the Yellow Fever Mosquito (Aedes aegypti) – Jonas Frankel-Bricker – Microbial Ecology 

FOXO regulates the expression of antimicrobial peptides and promotes phagocytosis of hemocytes in shrimp antibacterial immunity – Cang Li – PLoS Pathogens

Environmental Microbiome

Microbial characteristics response to the soil quality of newly created farmland on the Loess Plateau – Chen Xu – Environmental Science and Pollution Research

Bioinformatics

Human microbiome privacy risks associated with summary statistics – Jae-Chang Cho – PLoS One

ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data – Achal Dhariwal – NAR Genomics and Bioinformatics

April 2, 2021

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Good morning and happy Friday!

In my last blog post I requested reader contributions and many of you reached out! Below are some of the highlights which include a commentary on phylogenetic core groups, a preprint on viral RNA methylation in Wolbachia, a database for the murine oral bacterial community, and a research article on fungal modification in the leaf-cutter ant fungal garden ecosystem.

Events and jobs

Biological Sciences Laboratory Instructor Position at Smith College in Northampton, MA

General microbiome

***Commentary: Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework – Pascual-García – Microbiome

Animal microbiome

***Preprint: Differential viral RNA methylation contributes to pathogen blocking in Wolbachia-colonized arthropod – Bhattacharya et al. – bioRxiv

Preprint: Isolation and characterization of a novel Wolbachia bacteriophage from Allonemobius socius crickets in Missouri – Fischer et al. – bioRxiv

***From plants to ants: Fungal modification of leaf lipids for nutrition and communication in the leaf-cutter ant fungal garden ecosystem – Khadempour et al. – mSystems

Plant, root, and soil microbiome

Preprint: Experimental evolution-driven identification of Arabidopsis rhizosphere competence genes in Pseudomonas protegens – Zhang et al. – bioRxiv

Built environment

Metagenomic profile of microbial communities in a drinking water storage tank sediment after sequential exposure to monochloramine, free chlorine, and monochloramine – Gomez-Alvarez et al. – ACS EST Water

Bioinformatics

***A 16S rRNA gene and draft genome database for the murine oral bacterial community – Joesph et al. – mSystems

April 1, 2021

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General microbiome

Viral genomic, metagenomic and human transcriptomic characterization and prediction of the clinical forms of COVID-19 – Rodrigez et al. – PLOS Pathogens

A multiomics approach to identify host-microbe alterations associated with infection severity in diabetic foot infections: a pilot study – Radzieta – et al. – NPJ Biofilms and Microbiomes

Pregnancy and early life

Interactions between gut microbiota and metabolites modulate cytokine network imbalances in women with unexplained miscarriage – Liu et al. – NPJ Biofilms and Microbiomes

Developmental trajectory of the healthy human gut microbiota during the first 5 years of life – Roswall et al. – Cell Host & Microbiome

Human gut microbiome

Compositional change of gut microbiome and osteocalcin expressing endothelial progenitor cells in patients with coronary artery disease – Toya et al. – PLOS One

Stool metabolome-microbiota evaluation among children and adolescents with obesity, overweight, and normal-weight using 1H NMR and 16S rRNA gene profiling – Jaimes et al. – PLOS One

Gut dysbiosis and mortality in hemodialysis patients – Lin et al. – NPJ Biofilms and Microbiomes

[REVIEW]The Interplay between Diet, Gut Microbes, and Host Epigenetics in Health and Disease – Shock et al. – The Journal of Nutritional Biochemistry

[REVIEW]Circadian rhythms and the gut microbiome synchronize the host’s metabolic response to diet – Lopez et al. – Cell Metabolism

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

Meta-analysis identifies the effect of dietary multi-enzyme supplementation on gut health of pigs – Ramani et al. – Scientific Reports

Silicon-containing water intake confers antioxidant effect, gastrointestinal protection, and gut microbiota modulation in the rodents – Wu et al. – PLOS One

Animal microbiome (for animals in the wild)

[PREPRINT]16S rRNA Amplicon Sequencing of Bagworm Metisa plana Walker (Lepidoptera: Psychidae) – Ting et al. – bioRxiv

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

Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake – Ahmad et al. – PLOS One

Geochemical and metagenomics study of a metal-rich, green-turquoise-coloured stream in the southern Swiss Alps – Buetti-Dinh – PLOS One

Phages and viruses

[REVIEW]The human virome: assembly, composition and host interactions – Liang & Bushman – Nature Reviews Microbiology

[PREPRINT]Diverse viruses carrying genes for microbial extremotolerance in the Atacama Desert hyperarid soil – Hwang et al. – bioRxiv

Bioinformatics

MCPdb: The bacterial microcompartment database – Ochoa et al. – PLOS One
[Twitter]97% identity cutoff applied on humans and related species – Matthew Hahn

Techniques

Single strain control of microbial consortia – Fedorec et al. – Nature Communications

Microbes and Art

A Cultural Triumph: Microbiology Student Makes A Petri Dish Masterpiece – McCammon – npr

March 30, 2021

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Good morning!

Today’s digest is fairly light, with just a few preprints, so I’d like to do something a bit different today! If you have a recent microbiome-related publication (or have read one that’s particularly exciting) send me a direct message on Twitter (@KaraAnnTinker) or comment on this blog post. If it hasn’t been included on the blog yet, I’ll either update today’s post or cover it on my next blog post later this week.

General microbiome

Preprint: Sulfate adenylyl transferase kinetics and mechanisms of metabolic inhibitors of microbial sulfate respiration – Carlson et al. – bioRxiv

Preprint: Paraburkholderia edwinii protects Aspergillus sp. from phenazines by acting as a toxin sponge – Dahlstrom and Newman – bioRxiv

Plant, root, and soil microbiome

Preprint: Strain diversity of plant-associated Lactiplantibacillus plantarum – Yu et al. – bioRxiv

Water and extremophile microbiome

Preprint: Microbial helpers allow cyanobacteria to thrive in ferruginous waters – Szeinbaum et al. – bioRxiv

March 27, 2021

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Have a nice weekend! Today, in this Digest, we have an interesting review published in Science about microbiome and cancer. We have also articles about different conditions and the effect of the microbiome in the COVID19 vaccine-based immunity. More papers about: microbiome of wild animals,  cow microbiome and glyphosate,  anorexia microbiome in a mice model, and more!

Human and General Microbiome

Review: The microbiome and human cancer – Gregory D. Sepich-Poore – Science

Alterations in mucosa-associated microbiota in the stomach of patients with gastric cancer – Yilin Deng – Cellular Oncology 

Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease – Menghan Liu – eLife

The gut microbiome in subclinical atherosclerosis: a population-based multi-phenotype analysis – Sibo Zhu – Rheumatology

The microbiome in atopic patients and potential modifications in the context of the severe acute respiratory syndrome coronavirus 2 pandemic – Euna Lee – Current Opinion in Allergy and Clinical Immunology

An observational study of anaerobic bacteria in cystic fibrosis lung using culture dependant and independent approaches – Claudie Lamoureux – Scientific Reports

The Role of Mucosal Immunity and Recombinant Probiotics in SARS-CoV2 Vaccine Development – Shima Moradi-kalbolandi – Probiotics and Antimicrobial Proteins

Propionate catabolism by CD-associated adherent-invasive E. coli counteracts its anti-inflammatory effect – Allison Agus – Gut Microbes

Metabolic Syndrome Cannot Mask the Changes of Fecal Microbiota Compositions Caused by Primary Hepatocellular Carcinoma – Jiajia Ni – Letters in Applied Microbiology

Mendelian Randomization Analysis Reveals Causal Effects of the Human Gut Microbiota on Abdominal Obesity – Qian Xu – The Journal of Nutrition

Animal Microbiome

Diversity and functional landscapes in the microbiota of animals in the wild – Doron Levin – Science

Preliminary functional analysis of the subgingival microbiota of cats with periodontitis and feline chronic gingivostomatitis – Marjory Xavier Rodrigues – Scientific Reports

No hints at glyphosate-induced ruminal dysbiosis in cows – Fabian Billenkamp – npj Biofilms and Microbiomes 

Animal Models

Gut microbial communities from patients with anorexia nervosa do not influence body weight in recipient germ-free mice – Elaine M. Glenny – Gut Microbes

Environmental Microbiome

Invasive freshwater snails form novel microbial relationships – Laura Bankers – Evolutionary Applications

Preprint: Diversity and metagenome analysis of a hydrocarbon-degrading bacterial consortium from asphalt lakes located in Wietze, Germany – Michael O. Eze – Biorxiv

Built Environment

The Impacts of the Occupants on the Bacterial Communities of Classrooms – Zhou Feng – Current Microbiology 

Other

Meta-analysis methods for multiple related markers: Applications to microbiome studies with the results on multiple α-diversity indices – Hyunwook Koh – Statistics in Medicine

March 20, 2021

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Have a nice weekend! Today we have to remark a Free webinar to be online next March 24. We also have a bunch of articles about different beneficial compounds, microbes, or interventions on the microbiome (from human milk to dietary supplements). Today we also highlight articles about the potential effect of resident bacteria on opportunistic respiratory infections, a set of papers about insect microbiome, and a review about the use of Machine Learning in microbiome studies.

Webinars

Free webinar: The One You Feed: Identifying Specific Interactions Of Dietary Fiber Structures And The Microbiota That Ferment Them. March 24, 1:30-2:30 ET

Human and General Microbiome

Parasites, niche modification, and the host microbiome: A field survey of multiple parasites – Kayleigh R. O’Keeffe – Molecular Ecology

Large-scale functional network connectivity mediate the associations of gut microbiota with sleep quality and executive functions – Huanhuan Cai – Human Brain Mapping

Early Life Microbiome

Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial – Clara Yieh Lin Chong – Frontiers in Cellular and Infection Microbiology

Respiratory Tract Microbiome

Resident bacteria contribute to opportunistic infections of the respiratory tract – Yifan Wu – PLoS Pathogens

The influence of nasal microbiome diversity and inflammatory patterns on the prognosis of nasal polyps – Weigang Gan – Scientific Reports

Animal Microbiome

Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation – Anita Silver – PLoS One

Pollinators mediate floral microbial diversity and network under agrochemical disturbance – Na Wei – Molecular Ecology

Assessment of bacterial and fungal populations in urine from clinically healthy dogs using next-generation sequencing – Tonatiuh Melgarejo – Journal of Veterinary Internal Medicine

Immunosuppressive effect of mesenchymal stem cells on lung and gut CD8 + T cells in lipopolysaccharide-induced acute lung injury in mice – Yanping Xu – Cell Proliferation

Environmental Microbiome

Aerobiological study of bacterial and fungal community composition in the atmosphere of Mexico City throughout an annual cycle – María del Carmen Calderón-Ezquerro – Environmental Pollution

Beneficial Microbes and Compounds

Bio-therapeutics from Human Milk: Prospects and Perspectives – Kumar Siddharth Singh – Journal of Applied Microbiology

Low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols diet compared with traditional dietary advice for diarrhea-predominant irritable bowel syndrome: a parallel-group, randomized controlled trial with analysis of clinical and microbiological factors associated with patient outcomes – Yawen Zhang – The American Journal of Clinical Nutrition

Synergistic Protective Effects of Different Dietary Supplements Against Type 2 Diabetes via Regulating Gut Microbiota – Leilei Yu – Journal of Medicinal Food

Characterization of antibacterial activity of a N-acetylmuramoyl-L-alanine amidase produced by Latilactobacillus sakei isolated from salami – Adriana Lopez-Arvizu – World Journal of Microbiology and Biotechnology 

Administration of β-lactam antibiotics and delivery method correlate with intestinal abundances of Bifidobacteria and Bacteroides in early infancy, in Japan – Naruaki Imoto – Scientific Reports

Lactobacillus acidophilus LA5 improves saturated fat-induced obesity mouse model through the enhanced intestinal Akkermansia muciniphila – Thunnicha Ondee – Scientific Reports

Plant Microbiome

Review: Linking Plant Secondary Metabolites and Plant Microbiomes: A Review – Zhiqiang Pang – Frontiers in Plant Science

Bioinformatics

Review: Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment – Laura Judith Marcos-Zambrano – Frontiers in Microbiology

March 18, 2021

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Greetings from Pittsburgh!

Today’s digest has a lot of food and agriculture associated articles. Several articles focus on the effects of various pathogens on dairy cows, beef steers, and poultry breeds! For those of us who are more interested in plants, there is an article on biogas production from tomato waste and a preprint on how the microbial community of food waste changes during the composting process. Finally, I included a research article about social media during the pandemic since I’m sure I’m not the only one who has relied on it a little too heavily over the last year…

Happy reading!

General microbiome

Preprint: Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations – Conrad et al. – bioRxiv

BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE – Demo et al. – PLOS ONE

Review: The gut microbiota–brain axis in behaviour and brain disorders – Morais et al. – Nature Reviews Microbiology

Preprint: Cross-species evolutionary rewiring in the enteric bacterium Campylobacter – Taylor et al. – bioRxiv

Human gut microbiome

Gut microbiota profiles in diarrheic patients with co-occurrence of Clostridioides difficile and Blastocystis – Vega et al. – PLOS ONE

Animal experiments

Preprint: Low pathogenic avian influenza virus infection retards colon microbiome diversification in two different chicken lines – Chrzastek et al. – bioRxiv

Preprint: Borrelia infection in rodent host has dramatic effects on the microbiome of ticks – Hamilton et al. – bioRxiv

Animal microbiome

Preprint: The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe – Wallace et al. – bioRxiv

Plant, root, and soil microbiome

Effects of precipitation change and nitrogen addition on the composition, diversity, and molecular ecological network of soil bacterial communities in a desert steppe – Jia et al. – PLOS ONE

Preprint: Changes and composition of microbial community during aerobic composting of household food waste – Jin et al. – bioRxiv

Preprint: What’s under the Christmas tree? Soil acidification alters fir tree rhizosphere bacterial and eukaryotic communities, their interactions, and functional traits – Steven et al. – bioRxiv

A comparative analysis of biogas production from tomato bio-waste in mesophilic batch and continuous anaerobic digestion systems – Szilágyi et al. – PLOS ONE

Food microbiology

Red seaweed (Asparagopsis taxiformis) supplementation reduces enteric methane by over 80 percent in beef steers – Roque et al. – PLOS ONE

Prevalence and distribution of multilocus sequence types of Staphylococcus aureus isolated from bulk tank milk and cows with mastitis in Pennsylvania – Thomas et al. – PLOS ONE

Multidrug-resistant enterobacteria in newborn dairy calves in Germany – Waade et al. – PLOS ONE

Phages and viruses

Review: Viral and host heterogeneity and their effects on the viral life cycle – Jones et al. – Nature Review Microbiology

Bioinformatics

Dcmd: Distance-based classification using mixture distributions on microbiome data – Shestopaloff et al. – PLOS Computational Biology

Kara’s non-microbiology pick

Don’t put all social network sites in one basket: Facebook, Instagram, Twitter, TikTok, and their relations with well-being during the COVID-19 pandemic – Masciantonio et al. – PLOS ONE

March 16, 2021

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Human gut microbiome

Strain-level functional variation in the human gut microbiota based on bacterial binding to artificial food particles – Patnode et al. Cell Host & Microbe. 

Debaryomyces is enriched in Crohn’s disease intestinal tissue and impairs healing in mice – Jain et al. Science.

Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn’s Disease – Dubinsky et al. mSystems

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

Early life 

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

Human oral microbiome

Tonsillar Microbiota: a Cross-Sectional Study of Patients with Chronic Tonsillitis or Tonsillar Hypertrophy – Wu et al. mSystems

Animal experiments 

Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice – Yilmaz et al. Cell Host & Microbe

Bioinformatics

ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data – Deng & Delart. BMC Bioinformatics