April 1, 2020

Hello Everyone, I am excited for my first post here. Continuing the trend the first few papers are on COVID-19 : first one talks about its classification and nomenclature. I hope everyone is staying safe and healthy. Last but not the least, keep up the hand washing.

COVID-19

* The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2- Coronaviridae Study – Group of the International Committee on Taxonomy of Viruses – Nature Microbiology

Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses – Letko et al. – Nature Microbiology

General microbiome
Variation in prostaglandin metabolism during growth of the diatom Thalassiosira rotula – Dato et al. – Scientific Reports

Pregnancy and early life
Factors affecting early-life intestinal microbiota development – Vandenplas et al. – Nutrition

Multi-site human microbiome
Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age – Chaudhari et al. – Scientific Reports

Human gut microbiome
Implication of the gut microbiome composition of type 2 diabetic patients from northern China – Li et al. – Scientific Reports

The microbiota programs DNA methylation to control intestinal homeostasis and inflammation– Ansari et al. – Nature Microbiology

Animal microbiome
The Contest of Microbial Pigeon Neighbors: Interspecies Competition Between Serratia marcescens and the Human Pathogen Cryptococcus neoformans – Haleva et al. – Fungal Biology

Plant, root, and soil microbiome
Pseudomonas PS01 Isolated from Maize Rhizosphere Alters Root System Architecture and Promotes Plant Growth – Chu et al. – Microorganisms

Phages and viruses
Viruses with different genome types adopt a similar strategy to pack nucleic acids based on positively charged protein domains – Requião et al. – Scientific Reports

*Review: 5 challenges in understanding the role of the virome in health and disease – Wang David – PLOS Pathogens

Bioinformatics
Whole-genome sequencing of Burkholderia pseudomallei from an urban melioidosis hot spot reveals a fine-scale population structure and localised spatial clustering in the environment – Rachlin et al. – Scientific Reports

Techniques
Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture – Cummings et al. – Scientific Reports

Review: Potential of proteomics to probe microbes – Matilda et al. – Journal of Basic Microbiology

March 31st, 2020

Hello all, this is my first post on the blog. Following earlier trends, I will begin with news on COVID-19. Stay safe, everyone.

COVID – 19

Preprint: Ocular conjunctival inoculation of SARS-CoV-2 can cause mild COVID-19 in Rhesus macaques – Deng. et al

Preprint: Comparative Genomic Analysis of Rapidly Evolving SARS CoV-2 Viruses Reveal Mosaic Pattern of Phylogeographical Distribution – Kumar et al. 

Human Gut Microbiome

Gut Microbial Metabolites Induce Changes in Circadian Oscillation of Clock Gene Expression in the Mouse Embryonic Fibroblasts – Ku et al. – Molecules and Cells

Plant, Root, and Soil Microbiome

Ochraceocephala foeniculi gen. et sp. nov., a new pathogen causing crown rot of fennel in Italy – Aiello et al. – MycoKeys

Food Microbiology

The impact of hybrid yeasts on the aroma profile of cool climate Riesling wines – Kanter et al. – Food Chemistry: X

Phages and Viruses

Preprint: A novel antiviral formulation inhibits a range of enveloped viruses – Fletcher et al. 

March 20, 2020

Good morning! I hope this post finds you well. There are lots of new microbiome papers to share, including work on the disruption of E. coli biofilms, inconsistent diets used in Drosophila microbiome studies, and the effects of pollution on soil microbial communities.

General microbiome

Biosynthesis of silver nanoparticles by Fusarium scirpi and its potential as antimicrobial agent against uropathogenic Escherichia coli biofilms, Candelario Rodríguez-Serrano et al., PLOS ONE


Human gut microbiome

Targeted inhibition of gut bacterial β-glucuronidase activity enhances anticancer drug efficacy, Aadra P. Bhatt et al., PNAS

Gut Microbiome Pattern Reflects Healthy Aging and Predicts Extended Survival in Humans (preprint), Tomasz Wilmanski et al., bioRxiv

Propionic Acid Shapes the Multiple Sclerosis Disease Course by an Immunomodulatory Mechanism, Alexander Duscha et al., Cell

Adjusting for age improves identification of gut microbiome alterations in multiple diseases, Tarini S Ghosh et al., eLife

Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms, Jian Sun et al., Nature Communications

Review – Altering Routine Intensive Care Unit Practices to Support Commensalism, Hamilton and Behal, Nutrition in Clinical Practice

Household Pet Ownership and the Microbial Diversity of the Human Gut Microbiota, Ashley E. Kates et al., Frontiers in Cellular and Infection Microbiology

Meta-analysis – Assessing the efficacy and safety of fecal microbiota transplantation and probiotic VSL#3 for active ulcerative colitis: A systematic review and meta-analysis, Xiaofei Dang et al., PLOS ONE


Other human microbiome

Subgingival Host-Microbial Interactions in Hyperglycemic Individuals, P.S. Kumar et al., Journal of Dental Research

Investigating Bifidobacteria and Human Milk Oligosaccharide Composition of Lactating Mothers, Gabriele Andrea Lugli et al., FEMS Microbiology Ecology


Animal experiments

Effects of intestinal flora on the pharmacokinetics and pharmacodynamics of aspirin in high-altitude hypoxia, Sun and Zhang et al., PLOS ONE

Meta-analysis of diets used in Drosophila microbiome research and introduction of the Drosophila Dietary Composition Calculator (DDCC) (preprint), Broderick and Lesperance, bioRxiv

The Carnivorous Digestive System and Bamboo Diet of Giant Pandas May Shape Their Low Gut Bacterial Diversity, Wei Gui et al., Conservation Physiology


Animal microbiome

Non-invasive evaluation of the equine gastrointestinal mucosal transcriptome, Coleman and Whitfield-Cargile et al., PLOS ONE

Dietary substitution of soybean oil with coconut oil in the absence of dietary antibiotics supports growth performance and immune function in nursery and grower pigs, Andrea G. Braundmeier-Fleming et al., Journal of Animal Science and Biotechnology

Isoflavone supplementation, via red clover hay, alters the rumen microbial community and promotes weight gain of steers grazing mixed grass pastures, Brittany E. Harlow et al., PLOS ONE

Domesticated equine species and their derived hybrids differ in their fecal microbiota, J.E. Edwards et al., Animal Microbiome

Integrative analysis of gut microbiome and metabolites revealed novel mechanisms of intestinal Salmonella carriage in chicken, Khin K.Z. Mon et al., Scientific Reports


Plant, root, and soil microbiome

Acute effects of PAH contamination on microbial community of different forest soils, Enrica Picariello et al., Environmental Pollution

Context-dependent Dynamics Lead to the Assembly of Functionally Distinct Microbial Communities, Leonora S Bittleston et al., Nature Communications

Lifting the veil on arid-to-hyperarid Antarctic soil microbiomes: a tale of two oases, Eden Zhang et al., Microbiome

Perspective – Toward Comprehensive Plant Microbiome Research, Kari Saikkonen et al., Frontiers in Ecology and Evolution


Water and extremophile microbiome

Deep-sea corals provide new insight into the ecology, evolution, and the role of plastids in widespread apicomplexan symbionts of anthozoans, Samuel A. Vohsen et al., Microbiome


Food microbiology

Lactic Acid Bacteria Isolated From Korean Kimchi Activate the Vitamin D Receptor–autophagy Signaling Pathways, Rong Lu et al., Inflammatory Bowel Diseases

Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome, Bryn C. Taylor et al., mSystems

Differential Microbial Composition of Monovarietal and Blended Extra Virgin Olive Oils Determines Oil Quality During Storage, Zullo and Ciafardini, Microorganisms


Phages and viruses

Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota, Germán Bonilla-Rosso et al., PNAS


Bioinformatics

FORENSIC: an Online Platform for Fecal Source Identification, Adélaïde Roguet et al., mSystems

Review – Accurate and complete genomes from metagenomes, Lin-Xing Chen et al., Genome Research

Powmic: An R Package for Power Assessment in Microbiome Case-Control Studies, Li Chen, Bioinformatics


Techniques

RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs, Leyuan Li et al., Microbiome


Non-microbiology picks

Marketplace shrimp mislabeling in North Carolina, Morgan L. Korzik et al., PLOS ONE

March 14, 2020

Events

NYSCC Microbiome Program Postponed – Happi

General microbiome

Weakest link dynamics predict apparent antibiotic interactions in a model cross-feeding community – EM Adamowicz – bioRxiv

Simultaneous copper removal and electricity production and microbial community in microbial fuel cells with different cathode catalysts – Y Wu – Bioresource Technology

Multi-site human microbiome

Disrupted tongue microbiota and detection of nonindigenous bacteria on the day of allogeneic hematopoietic stem cell transplantation – S Oku – PLoS Pathogens

Human vaginal microbiome

Changes in key vaginal bacteria among postpartum African women initiating intramuscular depot-medroxyprogesterone acetate – BM Whitney – PLoS One

Human gut microbiome

Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach – S Pan – Microorganisms

A Story of Liver and Gut Microbes: How Does the Intestinal Flora Affect Liver Disease? A Review of the Literature – M Giuffrè – American Journal of Physiology

Fecal microbiota transplantation for the improvement of metabolism in obesity: The FMT-TRIM double-blind placebo-controlled pilot trial – EW Yu – PLoS Medicine

Animal experiments 

Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis – J Miyoshi – bioRxiv

Low mutational load and high mutation rate variation in gut commensal bacteria – RS Ramiro – PLoS Biology

Response to mechanical loading in rat Achilles tendon healing is influenced by the microbiome – F Dietrich-Zagonel – PLoS One

Plant, root, and soil microbiome

Testing the two-step model of plant root microbiome acquisition under multiple plant species and soil sources – HR Barajas – bioRxiv

A survey of invasive plants on grassland soil microbial communities and ecosystem services – JK Bell – Scientific Data

Host identity is more important in structuring bacterial epiphytes than endophytes in a tropical mangrove forest – H Yao – FEMS Microbiology Ecology

Water and extremophile microbiome 

Metagenomic Insights into Microbial Metabolisms of a Sulfur-Influenced Glacial Ecosystem – CB Trivedi – bioRxiv

Diel, daily, and spatial variation of coral reef seawater microbial communities – L Weber – PLoS One

Food microbiology

Shotgun Metagenomic Analysis Reveals New Insights on Bacterial Community Profiles in Tempeh – A Yulandi – bioRxiv

Phages and viruses

Identification of viruses belonging to the family Partitiviridae from plant transcriptomes – Y Jo – bioRxiv

The Restrictome of Flaviviruses – L Berthoux – Virologica Sinica

Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus – E Fahsbender – PLoS One

Techniques

Intestinal Organoids: A Tool for Modelling Diet–Microbiome–Host Interactions – J Rubert – Trends in Endocrinology and Metabolism

Microbes in the news

Microbiome studies may require correction for PPI use – MD edge

As You Age, So Does Your Microbiome – Technology Networks

DuPont Nutrition & Biosciences and APC Microbiome Ireland on infant gut health project – Nutra Ingredients

The Role of Zinc: It’s More Important than You Think –  UMass Lowell

Microbiome Therapeutics Market to Make Great Impact in near Future by 2026 – Nyse News Times

Mapping Bacterial Neighborhoods in Gut – Mirage News

Non-microbe picks

Sorry, we’re open: Golden Open Access and inequality in the natural sciences – RJ Gray – bioRxiv

Quantifying and contextualizing the impact of bioRxiv preprints through automated social media audience segmentation – J Carlson – bioRxiv

Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature – CFD Carneiro – bioRxiv

Studying the dynamics of the gut microbiota using metabolically stable isotopic labeling and metaproteomics – P Smyth – bioRxiv

March 5, 2020

Today’s Digest is heavy, so you might want to pace yourself. It’s hard to pick the highlights, but I’m biased towards fungal research, so first about a wake-up call to look at the fungi seriously. The insects might provide for remedy against antibiotic resistance and is the dust settled on the sparse fetal intestinal microbiota? Stay healthy and keep reading.

Event

Call for papers – Global Outbreaks and Responses – BMC Medicine

General microbiology

** Viewpoints: Fungal diseases as neglected pathogens: A wake-up call to public health officials – Marcio L. Rodrigues & Joshua D. Nosanchuk – PLoS NTD

Inducible cell-to-cell signaling for tunable dynamics in microbial communities – Arianna Miano et al. – Nature Communications

Antimicrobial resistance

** The insect antimicrobial peptide cecropin A disrupts uropathogenic Escherichia coli biofilms – Miriam Kalsy et al. – npj Biofilms and Microbiomes

Using comparative genomics to understand molecular features of carbapenem-resistant Acinetobacter baumannii from South Korea causing invasive infections and their clinical implications – Min Hyung Kim – PLoS One

Factors associated with sufficient knowledge of antibiotics and antimicrobial resistance in the Japanese general population – Shinya Tsuzuki et al. – Scientific Reports

Faeces and vaccines could be the key to tackling antimicrobial resistance – Elisabeth Mahase – BMJ

A survey of extended-spectrum beta-lactamase-producing Enterobacteriaceae in urban wetlands in southwestern Nigeria as a step towards generating prevalence maps of antimicrobial resistance – Olawale Olufemi Adelowo et al. – PLoS One

Pregnancy and early life

** Viable bacterial colonization is highly limited in the human intestine in utero – E. Rackaityte et al. – Nature Medicine

Perinatal Antibiotic Exposure Affects the Transmission between Maternal and Neonatal Microbiota and Is Associated with Early-Onset Sepsis – Ping Zhou et al. – mSphere

Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut – Yonatan Sher et al. – PLoS One

Human skin microbiome

A microbiome and metabolomic signature of phases of cutaneous healing identified by profiling sequential acute wounds of human skin: An exploratory study – Mohammed Ashrafi et al. – PLoS One

Human oral microbiome

Review: Single-Cell Genomics and the Oral Microbiome – M. Balachandran et al. – Journal of Dental Research

Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts – B. Bor et al. – Journal of Dental Research

Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection – Smruti Pushalkar et al. – iScience

Press: Oral Microbiome Changes Implicated in Gum Inflammation in E-Cigarette Users – GenomeWeb

In vitro: A salivary metabolite signature that reflects gingival host-microbe interactions: instability predicts gingivitis susceptibility – Marcela M. Fernandez-Gutierrez et al. – Scientific Reports

Human respiratory microbiome

Review: The Role of Lung and Gut Microbiota in the Pathology of Asthma – Weronika Barcik et al. – Immunity

Cancer and microbiome

Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth – Elena Zagato et al. – Nature Microbiology

Escherichia coli adhesion portion FimH functions as an adjuvant for cancer immunotherapy – Wei Zhang et al. – Nature Communications

Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy – Ling Ling Chua et al. – BMC Cancer

Review: Interplay between Dietary Polyphenols and Oral and Gut Microbiota in the Development of Colorectal Cancer – Carolina Cueva & Mariana Silva – Nutrients

Human gut microbiome

In vitro: Short-term supplementation of celecoxib-shifted butyrate production on a simulated model of the gut microbial ecosystem and ameliorated in vitro inflammation – Emma Hernandez-Sanabria et al. – npj Biofilms and Microbiomes

Review: Crosstalk Between Gut Microbiota and Innate Immunity and Its Implication in Autoimmune Diseases – Yuhao Jiao et al. – Frontiers in Immunology

An empirically derived method for measuring human gut microbiome alpha diversity: Demonstrated utility in predicting health-related outcomes among a human clinical sample – Sarah L. Hagerty et al. – PLoS One

Proof-of-concept study of the efficacy of a microbiota-directed complementary food formulation (MDCF) for treating moderate acute malnutrition – Ishita Mostafa et al. – BMC Public Health

Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation – Jonathan U. Peled et al. – New England Journal of Medicine

Human multi-site microbiome

Age-Related Variation of Bacterial and Fungal Communities in Different Body Habitats across the Young, Elderly, and Centenarians in Sardinia – Lu Wu et al. – mSphere

Response of the human gut and saliva microbiome to urbanization in Cameroon – Ana Lokmer et al. – Scientific Reports

The gut-microbiota-brain axis

Therapeutic Effects of the In Vitro Cultured Human Gut Microbiota as Transplants on Altering Gut Microbiota and Improving Symptoms Associated with Autism Spectrum Disorder – Kainan Chen et al. – Microbial Ecology

Built environment microbiome

A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes – Anders B. Nygaard et al. – Scientific Reports

Metabolomics

Spatial metabolomics of in situ host–microbe interactions at the micrometre scale – Benedikt Geier et al. – Nature Microbiology

Global chemical effects of the microbiome include new bile-acid conjugations – Robert A. Quinn et al. – Nature

Animal experiments

PM2.5 exposure perturbs lung microbiome and its metabolic profile in mice – Jingli Li et al. – Science of the Total Environment

Growth hormone deficiency and excess alter the gut microbiome in adult male mice – Elizabeth A Jensen et al. – Endocrinology

Dissociation of Adaptive Thermogenesis from Glucose Homeostasis in Microbiome-Deficient Mice – Tibor L. Krisko et al. – Cell Metabolism

Fecal IgA Levels Are Determined by Strain-Level Differences in Bacteroides ovatus and Are Modifiable by Gut Microbiota Manipulation – Chao Yang et al. – Cell Host & Microbe

Animal microbiome

Can rumen bacteria communicate to each other? – Mi-Young Won et al. – Microbiome

Entomopathogenic nematode-associated microbiota: from monoxenic paradigm to pathobiome – Jean-Claude Ogier et al. – Microbiome

The canine oral microbiome: variation in bacterial populations across different niches – Avika Ruparell et al. – BMC Microbiology

Evolutionary analysis of Mycobacterium bovis genotypes across Africa suggests co-evolution with livestock and humans – Osvaldo Frederico Inlamea et al. – PLoS NTD

Nanopore sequencing of microbial communities reveals the potential role of sea lice as a reservoir for fish pathogens – Ana Teresa Gonçalves et al. – Scientific Reports

Plant, root and soil microbiome

Insights on aquatic microbiome of the Indian Sundarbans mangrove areas – Paltu Kumar Dhal et al. – PLoS One

Ganoderma lucidum cultivation affect microbial community structure of soil, wood segments and tree roots – Fei Ren et al. – Scientific Reports

Effect of long-term destocking on soil fungal functional groups and interactions with plants – Jie Wang et al. – Plant and Soil

Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters – Zachary Liechty et al. – mSystems

Fungal diversity and community composition of wheat rhizosphere and non-rhizosphere soils from three different agricultural production regions of South Africa – Magalane Pheladi Gqozo et al. – Applied Soil Ecology

Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat – Adam Ossowicki & Vittorio Tracanna et al. – Proceedings of the Royal Society B

Industrial development as a key factor explaining variances in soil and grass phyllosphere microbiomes in urban green spaces – Zhen-Zhen Yan et al. – Environmental Pollution

Plant communities mediate the interactive effects of invasion and drought on soil microbial communities – Catherine Fahey et al. – The ISME Journal

Water and extremophile microbiome

Methyl t-butyl ether-degrading bacteria for bioremediation and biocontrol purposes – Giada d’Errico et al. – PLoS One

Uncovering microbial responses to sharp geochemical gradients in a terrace contaminated by acid mine drainage – Rui Xu et al. – Environmental Pollution

Snapshot: Microbial Extremophiles – Amy K. Schmid et al. – Cell

Denitrification performance and microbial communities of solid-phase denitrifying reactors using poly (butylene succinate)/bamboo powder composite – Wanhe Qi et al. – Bioresource Technology

Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning – Johanne Aubé et al. – Microbial Ecology

Role of microbial diversity for sustainable pyrite oxidation control in acid and metalliferous drainage prevention – Omy T. Ogbughalu et al. – Journal of Hazardous Materials

Phages and viruses

** Coronavirus research highlights – BMC

Fecal Viral Community Responses to High-Fat Diet in Mice – Anjelique Schulfer et al. – mSphere

Technology

Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens – Richard M. Leggett et al. – Nature Microbiology

Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities – John Beaulaurier et al. – Genome Research

Bioinformatics

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing – Karel Břinda et al. – Nature Microbiology

Microbes in the news

Tough microbe’s DNA could be a lasting archive – Steve Nadis – Science

How Bacteria Can ‘Sculpt The Gut’ – Maya Trabulsi – KPBS

The bee microbiome can fight back against fungi that cause Colony Collapse Disorder – Lauren Sara McKee – Massive Science

Ancient gut microbiomes shed light on human evolution – Newswise

Launch of the Marine Microbiome Roadmap – NIOZ

Understanding Microbiome Resilience on a Changing Planet – Michigan State University

Adaptations in gut microbes helped our ancestors thrive in new geographical territories: Study – New Kerala

Scientists Announce VIRGO, First Comprehensive Gene Catalog To Decode the Vaginal Microbiome – PR Newswire

Metabolomics Reveals Connection Between Gut Microbiome and Blood – Metabolon

Study shows universally positive effect of cover crops on soil microbiome – Phys.org

New Center of Microbiome Science is in the works at Ohio State – Emily Caldwell – Ohio State University News

Common diseases may be communicable through microbiome, says UBC researcher – Stephanie Blain – The Ubyssey

The microbes in your mouth, and a reminder to floss and go to the dentist – Science Daily

For Your Microbiome, How You Eat Could Be As Important As What You Eat – Technology Networks

Study: Infectious gut bacteria may predict UTI risk – Sue Treiman – Cornell Chronicle

The Best Way to Avoid Getting Sick Is to Wash Your Hands — But You’re Probably Doing It Wrong – Bojana Galic – Live Strong

Microbes on the market

DuPont carries on microbiome momentum with metabolic disease collaboration – Will Chu – Nutraingredients

Non-microbiology picks

Invest 5% of research funds in ensuring data are reusable – Barend Mons – Nature

 

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 18, 2020

Highlights for today’s Digest: a study takes us deep into bacterial community of the dermal compartment of the skin, skin microbiota predicts chronological age most accurately, and a review on network analyses using multi-omics data. Enjoy!

General microbiology

A biphasic growth model for cell pole elongation in mycobacteria – Mélanie T. M. Hannebelle et al. – Nature Communications

Press: Bacteria under the microscope: A new growth model for tuberculosis – Lionel Pousaz, Ecole Polytechnique Federale de Lausanne – Phys.org

Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem – Xinyu Zhu et al. – Microbiome

Antimicrobial resistance

Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli – afael Patiño-Navarrete et al. – Genome Medicine

Pregnancy and early life

The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months – M Isabel Ordiz et al. – The American Journal of Clinical Nutrition

Human skin microbiome

** Universal Dermal Microbiome in Human Skin – Lene Bay et al. – mBio

Human cancer microbiome

Opinion: The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View – Joao B. Xavier et al. – Trends in Cancer

Human gut microbiome

Interactions between the gut microbiome and host gene regulation in cystic fibrosis – Gargi Dayama et al. – Genome Medicine

Human multi-site microbiome

Review: Blood Microbiota and Circulating Microbial Metabolites in Diabetes and Cardiovascular Disease – Ganesan Velmurugan et al. – Trends in Endocrinology & Metabolism

** Human Skin, Oral, and Gut Microbiomes Predict Chronological Age – Shi Huang et al. – mSystems

Press: Human Skin, Oral Microbiomes Can Estimate People’s Ages to Within Few Years – GenomeWeb

Animal experiments

Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine – Said R. Bogatyrev et al. – Microbiome

Mouse: It’s the fiber, not the fat: significant effects of dietary challenge on the gut microbiome – Kathleen E. Morrison et al. – Microbiome

Animal microbiome

Trait-Based Comparison of Coral and Sponge Microbiomes – Cara L. Fiore et al. – Scientific Reports

Plant, root and soil microbiome

Functional relationships between aboveground and belowground spinach (Spinacia oleracea L., cv. Racoon) microbiomes impacted by salinity and drought – A. Mark Ibekwe et al. – Science of the Total Environment

Water and extremophile microbiome

Constraints on microbial communities, decomposition and methane production in deep peat deposits – Laurel A. Kluber et al. – PLoS One

Machine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes – Lin Ye et al. – Microbiome

Phages and viruses

Pearls: Virus interactions with bacteria: Partners in the infectious dance – Ursula Neu & Bernardo A. Mainou – PLoS Pathogens

Coronavirus: hospitals must learn from past pandemics – Nahid Bhadelia – Nature

Review: Phage diversity, genomics and phylogeny – Moïra B. Dion et al. – Nature Reviews Microbiology

Technology

Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil – Pauline C. Göller et al. – Microbiome

Review: Combining omics technologies with CRISPR-based genome editing to study food microbes – Meichen Pan & Rodolphe Barrangou – Current Opinion in Biotechnology

Complete, closed bacterial genomes from microbiomes using nanopore sequencing – Eli L. Moss et al. – Nature Biotechnology

Press: Closing bacterial genomes from the human gut microbiome using long-read sequencing – Dylan Maghini – Nature Bioengineering Community

Bioinformatics

A pipeline for targeted metagenomics of environmental bacteria – Anissa Grieb et al. Microbiome

** Review: Network analyses in microbiome based on high-throughput multi-omics data – Zhaoqian Liu et al. – Briefings in Bioinformatics

Microbes in the news

Getting the Band (of Microbes) Back Together – Jessica Messier – Worcester Polytechnic Institute

Gut microbe imbalance may stunt CF babies’ growth – Leila Gray – University of Washington

The Big Idea: The Microbiome – Purdue University

Moscow’s Subway Microbiome Looks Similar to that of New York’s – GenEngNews

A guide to caring for the Indian gut – Cherylann Mollan – Hindustan Times