July 31, 2020

Today’s digest features studies on hospital-associated bacterial communities on window components, the effect of urbanization on the vaginal microbiota of Amerindians, nitrate as a potential prebiotic for oral health, and the latest news in bioinformatics. Happy reading!

General microbiome

Microbial species interactions determine community diversity in fluctuating environments – Shota Shibasaki – bioRxiv

Review: The host-associated archaeome – Guillaume Borrel – Nature Reviews Microbiology

Oral microbiome

*Nitrate as a potential prebiotic for the oral microbiome – Bob T. Rosier – Scientific Reports

Skin microbiome

Deep skin dysbiosis in vitiligo patients: link with mitochondrial and immune changes – Hanene Bzioueche – medRxiv

Gut microbiome

Review: The microbiome: An emerging key player in aging and longevity– Minhoo Kim and Bérénice A. Benayoun – Translational Medicine of Aging

Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study – Kelsey E. Huus – Microbiome

Vaginal microbiome

*Changes in the vaginal microbiota across a gradient of urbanization – Daniela Vargas-Robles – Scientific Reports

Comparison between a novel molecular tool and conventional methods for diagnostic classification of bacterial vaginosis: is integration of the two approaches necessary for a better evaluation? – Margherita Scapaticci – New Microbiologica

Genome-wide mutagenesis identifies factors involved in Enterococcus faecalis vaginal adherence and persistence – Norhan Alhajjar – bioRxiv

Association between Vaginal Bacterial Microbiota and Vaginal Yeast Colonization – McKenna C Eastment – The Journal of Infectious Diseases

Urinary microbiome

Review: The microbiome in urological diseases – Kwang Woo Lee – Investigive and Clinical Urology

Review: FimH and Anti-Adhesive Therapeutics: A Disarming Strategy Against Uropathogens – Meysam Sarshar – Antibiotics

Characterization of urinary microbiome in patients with bladder cancer: Results from a single-institution, feasibility study – Juan Chipollini – Urologic Oncology: Seminars and Original Investigations

Animal microbiome

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage – Jolinda Pollock – Scientific Reports

Vaginal Microbiota Changes During Estrous Cycle in Dairy Heifers – Juan J. Quereda – Frontiers in Veterinary Science

Animal experiment

The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic – Eliran Kadosh – Nature

An Enteric Pathogen Subverts Colonization Resistance by Evading Competition for Amino Acids in the Gut – Gustavo Caballero-Flores – Cell Host & Microbe

Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin – Damien J. Cabral – mSystems

Water and extremophile microbiome

Determining the primary sources of fecal pollution using microbial source tracking assays combined with land-use information in the Edwards Aquifer – Jessica Hinojosa – Water Research

Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities – Tyler J. Arbour – Frontiers in Microbiology

Food microbiome

Discovering microbiota and volatile compounds of surströmming, the traditional Swedish sour herring – Luca Belleggia – Food Microbiology

Built environment

*Viable bacterial communities on hospital window components in patient rooms – Patrick F. Horve – PeerJ

Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation – Ganesh Babu Malli Mohan – mSystems

Phages and viruses

Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone – Anastasia Tsiola – Viruses

Bioinformatics

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets – Yi Yue – BMC Bioinformatics

Untangling Species-Level Composition of Complex Bacterial Communities through a Novel Metagenomic Approach – Christian Milani – mSystems

Automated prediction and annotation of small proteins in microbial genomes– Matthew G Durrant and Ami S Bhatt – bioRxiv

Accurate and sensitive detection of microbial eukaryotes from metagenomic shotgun sequencing data – Abigail L. Lind – bioRxiv

MicrobeAnnotator: a user-friendly, comprehensive microbial genome annotation pipeline – Carlos A. Ruiz-Perez – bioRxiv

Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra – Caroline Weis – Bioinformatics

NetCoMi: Network Construction and Comparison for Microbiome Data in R – Stefanie Peschel – bioRxiv

Review: Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses – Ana Elena Pérez-Cobas – Microbial Genomics

Podcast

Machine learning for drug development with Marinka Zitnik – Jacob Schreiber – The Bioinformatics Chat

July 7, 2020

Today’s digest features the mighty sourdough microbiome, AGNOSTOS (a computational workflow for genes annotation using clustering and remote homology detection, contextualizing them with genomic and environmental information), and a new episode of the Bioinformatics Chat podcast about reproducible pipelines and NGLess (a user-friendly domain-specific programming language for NGS data processing), and more. Happy reading/listening!

General microbiome

Microbiome definition re-visited: old concepts and new challenges – Gabriele Berg – Microbiome

Positive interactions are common among culturable bacteria – Jared Kehe – bioRxiv

Gut microbiome

An emerging role of Prevotella histicola on estrogen-deficiency induced bone loss through the gut microbiota-bone axis – Zhongxiang Wang – bioRxiv

Identifying novel high-impact rare disease-causing mutations, genes and pathways in exomes of Ashkenazi Jewish inflammatory bowel disease patients – Yiming Wu – medRxiv

Early prediction of liver disease using conventional risk factors and gut microbiome-augmented gradient boosting – Yang Liu – medRxiv

GWAS of stool frequency reveals genes, pathways, and cell types relevant to human gastrointestinal motility and irritable bowel syndrome – Ferdinando Bonfiglio – medRxiv

Relationships of gut microbiota, short-chain fatty acids, inflammation, and the gut barrier in Parkinson’s disease – Velma Aho – medRxiv

Lung microbiome

Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung – Adrian Kordes – Nature Communications

Genitourinary microbiome

Architecture and function of human uromodulin filaments in urinary tract infections – Gregor L. Weiss – Science

The structure and diversity of strain level variation in vaginal bacteria – Brett A. Tortelli – bioRxiv

Synchronous genitourinary lichen sclerosus signals a distinct urinary microbiome profile in men with urethral stricture disease – Andrew J. Cohen – World Journal of Urology

Human urine 1H NMR metabolomics reveals alterations of the protein and carbohydrate metabolism when comparing habitual Average Danish diet vs. healthy New Nordic diet – Alessia Trimigno – Nutrition

Animal experiments

Lactobacillus rhamnosus probiotic prevents airway function deterioration and promotes gut microbiome resilience in a murine asthma model – Irina Spacova – Gut Microbes

Food microbiome

*The Sourdough Microbiome – Justine Dees – ASM

Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function – Brittany A. Niccum – mSystems

Bioinformatics

*Light into the darkness: Unifying the known and unknown coding sequence space in microbiome analyses – Chiara Vanni – bioRxiv

Welcome to the dark side of genomes and metagenomes – a blog post about the above mentioned study – Antonio Fernandez-Guerra

GraphBin: refined binning of metagenomic contigs using assembly graphs – Vijini Mallawaarachchi – Bioinformatics

Podcast

*Reproducible pipelines and NGLess with Luis Pedro Coelho – Roman Cheplyaka – The Bioinformatics Chat

June 5, 2020

Today’s digest features a review on genetic variability within species in microbiomes, a study on Lactobacilli in the human nose, a new episode of Microbiology Lab Pod with the latest science news on functional metagenomics, a novel resistance gene called GAR, and more. Happy reading/listening!

General microbiome

*Diversity within species: interpreting strains in microbiomes – Thea Van Rossum – Nature Reviews

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes – Bin Ma – Microbiome

Oral and nasal microbiome

Local oral and nasal microbiome diversity in age-related macular degeneration – Jacob Rullo – Scientific Reports

*Lactobacilli Have a Niche in the Human Nose – Ilke De Boeck – Cell Reports

Gut microbiome

Resistant maltodextrin intake reduces virulent metabolites in the gut environment: randomized control study in a Japanese cohort – Yuichiro Nishimoto – MedRxiv

Pregnancy and early life

One year cross-sectional study in adult and neonatal intensive care units reveals the bacterial and antimicrobial resistance genes profiles in patients and hospital surfaces – Ana Paula Christoff – PlosOne

Animal microbiome

Cecal microbiome composition and metabolic function in probiotic treated broilers – Denise R. Rodrigues – PlosOne

Characterization of native Escherichia coli populations from bovine vagina of healthy heifers and cows with postpartum uterine disease – Candelaria Gonzalez Moreno – PlosOne

Animal experiments

Structural and Functional Changes of Gut Microbiota in Ovariectomized Rats and Their Correlations With Altered Bone Mass – Sicong Ma – Aging

Plant, root, and soil microbiome

Dissecting the effect of continuous cropping of potato on soil bacterial communities as revealed by high-throughput sequencing – Jing Zhao – Plos One

Water microbiome

Increasing flow rate reduces biofouling and colonization by filamentous bacteria in drippers fed with reclaimed wastewater – Kevin Lequette – bioRxiv

Phages and viruses

Integration of phage and yeast display platforms: A reliable and cost effective approach for binning of peptides as displayed on-phage – Priyanka Pandya – PlosOne

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes – Kira Moon – Microbiome

Bioinformatics

Estimating Microbial Interaction Network: Zero-inflated Latent Ising Model Based Approach– Jie Zhou – bioRxiv

Assessment of statistical methods from single cell, bulk RNA-seq and metagenomics applied to microbiome data – Matteo Calgaro – bioRxiv

Metabolomics

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power– Jasmin Hafner – Synthetic Biology

Inferring Active Metabolic Pathways from Proteomics and Essentiality Data – Ariadna Montero-Blay – Cell Reports

Podcast

*May 2020 Pod: Discovering novel resistance genes and how bacteria become virulent – Bengtsson-Palme Lab and Marlies Böhm – Microbiology Lab Pod

March 10, 2020

Today’s digest features a study on the fecal microbiota transplantation and obesity, a comprehensive overview of the diversity and abundance of antibiotic resistance genes in migratory birds, and more. Happy reading!

Gut microbiome

*Fecal microbiota transplantation for the improvement of metabolism in obesity: The FMT-TRIM double-blind placebo-controlled pilot trial – Elaine W. Yu – PlosMedicine

Diet influences the functions of the human intestinal microbiome – Maria De Angelis — Scientific Reports

Bacillus coagulans SANK 70258 suppresses Enterobacteriaceae in the microbiota of ulcerative colitis in vitro and enhances butyrogenesis in healthy microbiota – Kengo Sasaki – Applied Microbiology and Biotechnology

Mini review: Gut epithelial metabolism as a key driver of intestinal dysbiosis associated with noncommunicable diseases – Catherine D. Shelton and Mariana X. Byndloss – Infection and Immunity

Etiologic features of diarrheagenic microbes in stool specimens from patients with acute diarrhea in Thailand – Kazuhisa Okad – Scientific reports

Raman‐activated sorting of antibiotic‐resistant bacteria in human gut microbiota – Yi Wang – Environmental Microbiology

Animal microbiome

*Metagenomic analysis reveals the microbiome and resistome in migratory birds – Jian Cao – Microbiome

Lack of evidence for microbiota in the placental and fetal tissues of rhesus macaques – Kevin R. Theis – bioRxiv

Animal experiment

Diarrhoeal events can trigger long-term Clostridium difficile colonization with recurrent blooms – David VanInsberghe – Nature Microbiology

Plant/root/soil microbiome

Long-Term Phytoremediation of Coastal Saline Soil Reveals Plant Species-Specific Patterns of Microbial Community Recruitment – Xiaogai Wang – mSystems

Impact of Soil Microbial Amendments on Tomato Rhizosphere Microbiome and Plant Growth in Field Soil – Andrea Nuzzo – Microbial Ecology

Bioinformatics

DeepMAsED: Evaluating the quality of metagenomic assemblies– Olga Mineeva – Bioinformatics

A method for achieving complete microbial genomes and better quality bins from metagenomics data – Lauren M. Lui – bioRxiv

Estimating relative biomasses of organisms in microbiota using “phylopeptidomics” – Olivier Pible – Microbiome

February 21, 2020

This Friday, read about the potential influence of microbiomes in hominin evolution, gut microbiome in patients with Sjögren’s syndrome, new antibiotics discovered through comparative genomics, and more. Happy reading!

General microbiome

*The Internal, External and Extended Microbiomes of Hominins – Robert R. Dunn – Front. Ecol. Evol.

A Deep Learning Approach to Antibiotic Discovery– Jonathan M. Stokes – Cell

Review: Next-generation physiology approaches to study microbiome function at single cell level – Roland Hatzenpichler – Nature Reviews Microbiology

Patterns of partnership: surveillance and mimicry in host-microbiota mutualisms – Travis J Wiles & Karen Guillemin – Current Opinion in Microbiology

Review: Innovative and rapid antimicrobial susceptibility testing systems – Alex van Belkum – Nature Reviews Microbiology

Gut microbiome

*Gut dysbiosis is prevailing in Sjögren’s syndrome and is related to dry eye severity– Jayoon Moon – PlosOne

Review: Healthy Human Gastrointestinal Microbiome: Composition and Function After a Decade of Exploration – Wenly Ruan – Digestive Diseases and Sciences

Review: Gut microbiota-derived metabolites as key actors in inflammatory bowel disease– Aonghus Lavelle & Harry Sokol – Nature Reviews Gastroenterology & Hepatology

Review: Microbiome in Colorectal Cancer: How to Get from Meta-omics to Mechanism?–Dominik Ternes – Trends in Microbiology

Urinary microbiome

Review: Urinary tract infections: microbial pathogenesis, host–pathogen interactions and new treatment strategies – Roger D. Klein & Scott J. Hultgren – Nature Reviews Microbiology

Vaginal microbiome

The microbiome and gynaecological cancer development, prevention and therapy – Paweł Łaniewski – Nature Reviews Urology

Animal microbiome

Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion – Carolyn A. Miller – The ISME Journal

Animal experiment

*Evolution-guided discovery of antibiotics that inhibit peptidoglycan remodelling – Elizabeth J. Culp – Nature

The Gene Expression Profile of Uropathogenic Escherichia coli in Women with Uncomplicated Urinary Tract Infections Is Recapitulated in the Mouse Model – Arwen E. Frick-Cheng – bioRxiv

Sustained IFN-I stimulation impairs MAIT cell responses to bacteria by inducing IL-10 during chronic HIV-1 infection – X. Tang – Science Advance

Bioinformatics

Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data– Kyle D. Brumfield – PlosOne

Viruses & Phages

Respiratory viruses in mechanically ventilated patients: a pilot study – Raquel Nazareth – BMC Pulmonary Medicine

February 12, 2020

This Wednesday, read about the microbiome in “flammable ice”, gastric bypass surgery in a rat model, virulence genes of the coral reef phage, and more. Happy reading!

Gut microbiome

Changes in microbiome and metabolomic profiles of fecal samples stored with stabilizing solution at room temperature: a pilot study– Mi Young Lim — Scientific Reports

Fecal microbiota transplantation to maintain remission in Crohn’s disease: a pilot randomized controlled study – Harry Soko – Microbiome

Identification of Clostridioides difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly – Sudeep Ghimire – mySystems

Neonatal microbiota development and the effect of early life antibiotics are determined by two distinct settler types – Anat Eck – plosOne

Oral Microbiome

Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study – Zachary M. Burcham – Scientific Reports

Sub-species niche specialization in the oral microbiome is associated with nasopharyngeal carcinoma risk – Justine W. Debelius – bioRxiv

Animal experiments

*Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss – Sven-Bastiaan Haange – Microbiome

Growth phase-dependent responses of an in vitro gut microbiome to metformin – Zikai Hao – bioRxiv

Ursolic acid improves the bacterial community mapping of the intestinal tract in liver fibrosis mice – Sizhe Wan – bioRxiv

Animal microbiome

Beef cattle that respond differently to fescue toxicosis have distinct gastrointestinal tract microbiota – Lucas R Koester – bioRxiv

Variation in gut bacterial composition is associated with Haemonchus contortus parasite infection of sheep – Md. Abdullah Al Mamun – Animal microbiome

Water microbiome

Microbial diversity, ecological networks and functional traits associated to materials used in drinking water distribution systems – Isabel Douterelo – Water Research

Diverse Arctic lake sediment microbiota shape methane emission temperature sensitivity – Joanne B. Emerson – bioRxiv

Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities – Eslam O. Osman – Microbiome

Extremophile microbiome

*Evidence in the Japan Sea of microdolomite mineralization within gas hydrate microbiomes – Glen T. Snyder – Scientific Reports

Textile waste and microplastic induce activity and development of unique hydrocarbon-degrading marine bacterial communities – Elsa B. Girard – bioRxiv

Plant/root/soil microbiome

Maize (Zea mays L. Sp.) varieties significantly influence bacterial and fungal community in bulk soil, rhizosphere soil, and phyllosphere – Xiao Kong – FEMS Microbiology Ecology

A Small Effort for Researchers, a Big Gain for Soil Metaproteomics– Marco Chiapello – Frontiers in Microbiology

Viruses and phages

*Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes – Cynthia B. Silveira – BMC Genomics

Profiling of Human Gut Virome with Oxford Nanopore Technology – Jiabao Cao – bioRxiv

Bioinformatics

MICHELINdb: a web-based tool for mining of helminth-microbiota interaction datasets, and a meta-analysis of current research – Riccardo Scotti – Microbiome

January 22, 2020

In today’s digest read about Lactobacillus mulieris sp. nov. isolated from healthy female urinary tract, diversity of Escherichia coli phages in the Danish wastewater, PLate Coverage Algorithm (PLCA) in culture-enriched metagenomics, and more. Happy reading!

General microbiome

Microbiomes Reduce Their Host’s Sensitivity to Interspecific Interactions – Sara L. Jackrel – mBio

Gut microbiome

Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition – Rita A. Oliveira – Nature Microbiology

Long-term impact of fecal transplantation in healthy volunteers – Oleg V. Goloshchapov – BMC Microbiology

Efficacy of faecal microbiota transplantation in Crohn’sdisease: a new target treatment?– Liyuan Xiang – Microbial Biotechnology

Resident microbial communities inhibit growth and antibiotic resistance evolution of Escherichia coli in human gut microbiome samples – Michael Baumgartner – bioRxiv

Microreview: Causalities of war: The connection between type VI secretion system and microbiota – Luke P. Allsopp – Cellular Microbiology

Urinary microbiome

*Lactobacillus mulieris sp. nov., a new species of Lactobacillus delbrueckii group – Joana Rocha – International Journal of systematic and evolutionary microbiology

Vaginal microbiome

Vaginal Microbiota Transplantation: The Next Frontier – Kevin DeLong – The Journal of Law, Medicine, & Ethics

Respiratory microbiome

*Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota – Fiona J. Whelan – Nature Microbiology

A Refined View of Airway Microbiome in Chronic Obstructive Pulmonary Disease at Species and Strain-levels– Zhang Wang – bioRxiv

Eye microbiome

The closed eye harbors a unique microbiome in dry eye disease – Kent A. Willis – medRxiv

Plant/root/soil microbiome

Root ethylene mediates rhizosphere microbial community reconstruction when chemically detecting cyanide produced by neighbouring plants – Yan Chen – Microbiome

Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community– Jiajie Feng – Microbiome

Microbiome composition differs in hybrid and inbred maize – Maggie R. Wagner – bioRxiv

Diversity and plant growth-promoting functions of diazotrophic/N-scavenging bacteria isolated from the soils and rhizospheres of two species of Solanum – Zuluaga Mya – PlosOne

Water microbiome

Molecular Characteristics of Dissolved Organic Nitrogen and Its Interaction with Microbial Communities in a Prechlorinated Raw Water Distribution System – Hang Xu – Environmental Science and Technology

Effects of geographic location and water quality on bacterial communities in full-scale biofilters across North America – Ben Ma – FEMS Microbiology Ecology

Phages and viruses

*Exploring the remarkable diversity of Escherichia coli Phages in the Danish Wastewater Environment, Including 91 Novel Phage Species – Nikoline S. Olsen – bioRxiv

Bioinformatics

Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences – Nicole R. Narayan – BMC Genomics

Network-Based Prediction of Novel CRISPR-Associated Genes in Metagenomes – Jake L. Weissman and Philip L. F. Johnson – mSystems

Review: Integrating Computational Methods to Investigate the Macroecology of Microbiomes – Rilquer Mascarenhas – Frontiers in Genetics

Assessment of single cell RNA-seq statistical methods on microbiome data – Matteo Calgaro – bioRxiv

January 8, 2020

Today’s digest features a retrospective mini-review of mothur, study on gut microbiomes of over 900 vertebrate species [Spoiler alert: birds and bats share similarities in their microbiome], findings of fifteen-thousand-year-old viruses in glacier ice, and more. Happy reading!

Gut microbiome

Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform – Christian Munck – Nature Communications

Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels – Mohammad Tauqeer Alam – Gut Pathogens

Gut dysbiosis induces the development of pre-eclampsia through bacterial translocation– Xia Chen – Gut

Analysis of gut microbiota of obese individuals with type 2 diabetes and healthy individuals – Aftab Ahmad – PlosOne

Alterations of human lung and gut microbiome in non-small cell lung carcinomas and distant metastasis – Hui Lu – bioRxiv

The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for human complex diseases – Fengzhe Xu – bioRxiv

Oral microbiome

Acquisition of Oral Microbiota is Driven by Environment, Not Host Genetics – Chiranjit Mukherjee – bioRxiv

Animal microbiome

*Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats– Se Jin Song – mBio

Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities – Nikola Palevich – Applied and Environmental Microbiology

Inside out: microbiota dynamics during host-plant adaptation of whiteflies – Diego Santos-Garcia – The ISME Journal

Blood Loss Leads to Increase in Relative Abundance of Opportunistic Pathogens in the Gut Microbiome of Rabbits – Junjie Yang – Current Microbiology

Probiotics

In Vitro Probiotic Potential of Hemophilin-producing Strains of Haemophilus haemolyticus – Brianna Atto – bioRxiv

Quantifying and engineering mucus adhesion of probiotics – Zachary J. S. Mays – bioRxiv

Plant/root/soil microbiome

Temporal and spatial changes in phyllosphere microbiome of acacia trees growing in super arid environments – Ashraf Al-Ashhab – bioRxiv

Secreted metabolite-mediated interactions between rhizosphere bacteria and Trichoderma biocontrol agents – Ningxiao Li – PlosOne

Water microbiome

Quantification of nosZ genes and transcripts in activated sludge microbiomes with novel group-specific qPCR methods validated with metagenomic analyses – Daehyun Daniel Kim – bioRxiv

Viruses

*Glacier ice archives fifteen-thousand-year-old viruses – Zhi-Ping Zhong – bioRxiv

Meeting report: Viruses in the Built Environment (VIBE) meeting report – Aaron J. Prussin – Microbiome

Bioinformatics

*Minireview: Reintroducing mothur: 10 Years Later – Patrick D. Schloss – Applied and Environmental Microbiology

FunGeCo : A web based tool for estimation of Functional potential of bacterial genomes and microbiomes using Gene Context information – Swadha Anand – Bioinformatics

December 23, 2019

In today’s digest read about the subway microbiome (from surface and air samples collected at 16 subway stations in Oslo, Norway), role of Staphylococcus epidermidis in healthy maturation of the nasal microbiome, effect of storage and time on urinary microbiome, and more. Happy Holidays!

General microbiome

The emergence of microbiome centres – Jennifer B. H. Martiny – Nature Microbiology

Subway microbiome

*The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities– Jostein Gohli – Microbiome

Gut microbiome

Engineered E. coli Nissle 1917 for the delivery of matrix-tethered therapeutic domains to the gut– Pichet Praveschotinunt – Nature Communications

Urinary microbiome

*The urinary microbiota composition remains stable over time and under various storage conditions – Caspar Bundgaard-Nielsen – bioRxiv

Vaginal microbiome

Review: Genetic Heterogeneity and Taxonomic Diversity among Gardnerella Species – Joana Castro – Trends in Microbiology

Nasal microbiome

*Staphylococcus epidermidis Contributes to Healthy Maturation of the Nasal Microbiome by Stimulating Antimicrobial Peptide Production – Qian Liu – Cell Host & Microbes

Animal microbiome

Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China – Chunlai Wang – mSystems

Animal experiments

Altered microbiota composition reflects enhanced communication in 15q11-13 CNV mice– Dian Eurike Septyaningtrias – Neuroscience Research

Plant/root/soil microbiome

Time after Time: Temporal Variation in the Effects of Grass and Forb Species on Soil Bacterial and Fungal Communities – S. Emilia Hannula – mBio

Habitat filtering shapes the differential structure of microbial communities in the Xilingol grassland– Jie Yang – Scientific Reports

Water microbiome

Metagenomic Insights into the Effects of Seasonal Temperature Variation on the Activities of Activated Sludge– Chenbing Ai – Microorganisms

Viruses

Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves – Victor Golyaev – Scientific Reports

Bioinformatics

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise – Valentina Peona – bioRxiv

Transcriptome assembly from long-read RNA-seq alignments with StringTie2– Sam Kovaka – Genome Biology

Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework – Guo Liang Gan – BMC Bioinformatics

The Generalized Matrix Decomposition Biplot and Its Application to Microbiome Data – Yue Wang – mSystems

November 23, 2019

In today’s digest read about the Darobactin (a new antibiotic that selectively kills Gram-negative pathogens by binding to the BamA protein, located in the external membrane of Gram-negative bacteria), temporal stability of the rumen microbiota, and Gardnerella species (Gardnerella leopoldii, G. swidsinskii, G. piotii, and G. vaginalis) in the vaginal microbiome. And, check out 2019 Holiday Gift Guide For Microbe Lovers. Happy weekend!

General microbiome

*A new antibiotic selectively kills Gram-negative pathogens – Yu Imai – Nature

Read the story behind the paper by Roberto Molar Candanosa, Northeastern University.

Gut microbiome

Review: The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health – Jillian L. Waters & Ruth E. Ley – BMC Biology

The gut microbiota influences how circulating immune cells in humans change from one day to the next – Jonas Schluter – bioRxiv

Vaginal microbiome

*Resolution and Cooccurrence Patterns of Gardnerella leopoldii, G. swidsinskii, G. piotii, and G. vaginalis within the Vaginal Microbiome – Janet E. Hill – Infection and Immunity

Clinical validation of the Aptima Bacterial Vaginosis and Aptima Candida/Trichomonas Vaginitis Assays: results from a prospective multi-center clinical study – Jane R. Schwebke – Journal of Clinical Microbiology

Review: Understanding and interpreting community sequencing measurements of the vaginal microbiome – HL Berman – BJOG : an International Journal of Obstetrics and Gynaecology

Endocervical microbiome

Diversity of endocervical microbiota associated with genital Chlamydia trachomatis infection and infertility among women visiting obstetrics and gynecology clinics in Malaysia – Heng Choon Cheong – PlosOne

Uterine microbiome

Does dysbiotic endometrium affect blastocyst implantation in IVF patients? – Tomoko Hashimoto & Koichi Kyono – Journal of Assisted Reproduction and Genetics

Oral microbiome

Oral microbial community composition is associated with pancreatic cancer: A case‐control study in Iran – Emily Vogtmann – Cancer Medicine

Animal microbiome

*Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements – Timothy J. Snelling – Animal Microbiome

Development of the duodenal, ileal, jejunal and caecal microbiota in chickens – Laura Glendinning – Animal Microbiome

Mammary microbiome of lactating organic dairy cows varies by time, tissue site, and infection status – Tucker Andrews – PlosOne

Inulin improves the egg production performance and affects the cecum microbiota of laying hens – Hongmei Shang – International Journal of Biological Macromolecules

Animal experiments

Effects of Debaryomyces hansenii treatment on intestinal mucosa microecology in mice with antibiotic-associated diarrhea – Ao Zeng – PlosOne

Microbe-metabolite associations linked to the rebounding murine gut microbiome post-colonization with vancomycin resistant Enterococcus faecium – Andre Mu – bioRxiv

Hepatitis B Virus Infection Alters Gut Microbiota Composition in Mice – Qingfeng Zhu – Front. Cell. Infect. Microbiol.

Human Gut Microbiome Transplantation in Ileitis Prone Mice: A Tool for the Functional Characterization of the Microbiota in Inflammatory Bowel Disease Patients – Abigail R Basson – Inflammatory Bowel Diseases

Effects of an Escherichia coli exopolysaccharide on human and mouse gut microbiota in vitro – Baiyuan Li – International Journal of Biological Macromolecules

Ion Transport Basis of Diarrhea in a Mouse Model of Adoptive T Cell Transfer Colitis – Dulari Jayawarden – Digestive Diseases and Sciences

Water microbiome

Rewetting of three drained peatlands drives congruent compositional changes in pro- and eukaryotic microbiomes through environmental filtering – Micha Weil – bioRxiv

Phages and viruses

Herpes Simplex Virus Infection, Acyclovir and IVIG Treatment All Independently Cause Gut Dysbiosis – Chandran Ramakrishna – bioRxiv

Svetlana’s pick

Gift guide for this holiday season!
by Justine Dees