March 24, 2020

Today’s Digest features a study to use engineered Acinetobacter to boost host immunity against bacterial pneumonia, and a review on the relationship between plant-microbe symbiosis and agriculture.The coronavirus is probably on the mind of all of us. Listen to Dr. Blaser talk about it. Stay well and keep reading.

Job

Research Tech II – CHOP Microbiome Center

COVID-19

Editorial: Coronavirus: three things all governments and their science advisers must do now – Nature

World View: Don’t rush to deploy COVID-19 vaccines and drugs without sufficient safety guarantees – Shibo Jiang – Nature

Q&A: The novel coronavirus outbreak causing COVID-19 – Dale Fisher & David Heymann – BMC Medicine

** Dr. Martin Blaser answers coronavirus questions from Twitter (full video available) – mlive.com

General microbiology

Regulation of fungal decomposition at single-cell level – Michiel Op De Beeck et al. – The ISME Journal

Antimicrobial resistance

** Broad-spectrum suppression of bacterial pneumonia by aminoglycoside-propagated Acinetobacter baumannii – M. Indriati Hood-Pishchany et al. – PLoS Pathogens

Vulnerability and resistance in the spatial heterogeneity of soil microbial communities under resource additions – Kelly Gravuer et al. – PNAS

Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities – Maria-Elisabeth Böhm et al. – Microbiome

Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection – Lingdi Zhang et al. – Microbiome

Human gut microbiome

The role of gut microbiota in bone homeostasis – Jyotirmaya Behera et al. – Bone

Animal experiments

Docosahexaenoate-enriched fish oil and medium chain triglycerides shape the feline plasma lipidome and synergistically decrease circulating gut microbiome-derived putrefactive postbiotics – Matthew I. Jackson & Dennis E. Jewell – PLoS One

Animal microbiome

The rodent vaginal microbiome across the estrous cycle and the effect of genital nerve electrical stimulation – Micah Levy et al. – PLoS One

The different dietary sugars modulate the composition of the gut microbiota in honeybee during overwintering – Hongfang Wang et al. – BMC Microbiology

Most dominant roles of insect gut bacteria: digestion, detoxification, or essential nutrient provision? – Tian-Zhong Jing et al. – Microbiome

Predictive ability of host genetics and rumen microbiome for subclinical ketosis – Grum Gebreyesus et al. – Journal of Dairy Science

Plant, root and soil microbiome

** Review: Agriculture and the Disruption of Plant–Microbial Symbiosis – Stephanie S. Porter & Joel L. Sachs – Trends in Ecology & Evolution

Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil – Steven J. Blazewicz et al. – The ISME Journal

Reusing oil and gas produced water for agricultural irrigation: Effects on soil health and the soil microbiome – Hannah Miller et al. – Science of the Total Environment

Network analysis reveals the strengthening of microbial interaction in biological soil crust development in the Mu Us Sandy Land, northwestern China – Hong Zhou et al. – Soil Biology and Biochemistry

Water and extremophile microbiome

Performance and functional microbial communities of denitrification process of a novel MFC-granular sludge coupling system – Qiujin Deng et al. – Bioresource Technology

Microbial community structure and functional properties in permanently and seasonally flooded areas in Poyang Lake – Yang Liu et al. – Scientific Reports

Associations between redox-sensitive trace metals and microbial communities in a Proterozoic ocean analogue – Kathryn I. Rico et al. – Geobiology

Reactor configuration influences microbial community structure during high-rate, low-temperature anaerobic treatment of dairy wastewater – Paul G McAteer et al. – Bioresource Technology

Bioinformatics

Multiple-Disease Detection and Classification across Cohorts via Microbiome Search – Xiaoquan Su et al. – mSystems

Microbes in the news

How the mi­cro­biome is in­volved in the de­vel­op­ment of can­cer – Christian Urban – MedicalXpress

How a Fiber-Rich Plant-Based Diet Keeps Your Gut Microbiome Happy and Healthy – Chelsea Debret – One Green Planet

Gerhart: Keeping well during a pandemic – Timothy Gerhart – Your Valley

Study shows positive effect of cover crops on soil microbiome – AgriNews

Microbiome search engine can increase efficiency in disease detection and diagnosis – Chinese Academy of Sciences – EurekAlert

7 Ways A Gastroenterologist Supports His Microbiome & Overall Health – Marvin Singh – mbg Health

Infliximab Helps Gut Microbiome in Children with Crohn’s, Study Finds – Ana Pena – IBD News Today

Microbes on the market

DuPont, APC Microbiome Ireland link up for babies – Melody M. Bomgardner – C&EN

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 16, 2020

To all the work-from-home researchers (like me!), today’s digest covers microbiome in memory recognition, enteric neuropathy and neurodevelopmental disorder in rodent models. Gut microbiome in cardiovascular disease, a dual mechanism antibiotic and shifts in human gut microbiome and metabolome following gastric bypass. An important preprint that Covid-19 could not induce reinfection in infected rhesus macaques and that Ibuprofen may aggravate Covid-19 infection.

General microbiome

Gut microbiota and cardiovascular disease: opportunities and challenges – Negin Kazemian – Microbiome

Human microbiome
Pharmacomicrobiomics in inflammatory arthritis: gut microbiome as modulator of therapeutic response – Jose U. Scher – Nature Reviews Rheumatology

Long-term metal exposure changes gut microbiota of residents surrounding a mining and smelting area – Mengmeng Shao – Scientific Reports

Temporospatial shifts in the human gut microbiome and metabolome after gastric bypass surgery – Zehra Esra Ilhan – NPJ biofilms and microbiomes

Animal experiments

Habitat and seasonality shape the structure of tench (Tinca tinca L.) gut microbiome – Tomasz Dulski – Scientific Reports

Microecological Koch’s postulates reveal that intestinal microbiota dysbiosis contributes to shrimp white feces syndrome – Zhijian Huang – Microbiome

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

Gut microbiota manipulation during the prepubertal period shapes behavioral abnormalities in a mouse neurodevelopmental disorder model – Justin M. Saunders – Scientific Reports

Minocycline-induced microbiome alterations predict cafeteria diet-induced spatial recognition memory impairments in rats – Sarah-Jane Leigh – Translational Psychiatry

A purified membrane protein from Akkermansia muciniphila or the pasteurised bacterium blunts colitis associated tumourigenesis by modulation of CD8+ T cells in mice – Lijuan Wang – Gut

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

High‐fat diet–induced alterations to gut microbiota and gut‐derived lipoteichoic acid contributes to the development of enteric neuropathy – Yvonne Nyavor – Neurogastroenterology and Motility

Plant, root and soil microbiome

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil – L. V. Alteio – mSystems

Impact of plants on the diversity and activity of methylotrophs in soil – Michael C. Macey – Microbiome

Conserved bacterial genomes from two geographically distinct peritidal stromatolite formations shed light on potential functional guilds – Samantha C. Waterworth – BioRxiv

Techniques

A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures – Nathan D. Olson – Microbiome

Antibiotic resistance

A dual-mechanism antibiotic targets Gram-negative bacteria and avoids drug resistance – James K. Martin – BioRxiv

Non microbiology picks

Reinfection could not occur in SARS-CoV-2 infected rhesus macaques – Linlin Bao – BioRxiv

Anti-inflammatories may aggravate Covid-19, France advises – The Guardian

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

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 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
 

Antibiotic resistance- can reducing outpatient prescription help?

Antibiotic resistance is increasing at a rapid rate making pathogens and other bacterial species resistant to currently available antibiotics. Its impact is already visible globally and clock is ticking faster than ever pushing scientists all over the world to develop better antibiotics with higher specificity (only!) for pathogens. Antibiotic consumption is directly related to antibiotic resistance and policies across the continents are underway to control the consumption and prescription of antibiotics.

A recent article in elife introduces the problem of unnecessary antibiotic use and provides data to avert it.

Inappropriate antibiotic use leads to increased risk of adverse events, disruption of colonization resistance and other benefits of the microbial flora, and bystander selection for antibiotic resistance, with little to no health gains for the patient.”

To address the problem, Christine et al. used publically available data (NAMCS/NHAMCS) and mathematical models to find what would happen if antibiotic consumption is averted in hypothetical scenarios.

What they did?
The analysis included sixteen antibiotics that are frequently prescribed in the outpatient setting and nine potentially pathogenic bacterial species that are commonly carried in the normal human microbiome. For each antibiotic-species pair, they estimated the proportion of antibiotic exposures experienced by that species that could be averted under four hypothetical scenarios.

1) Eliminate unnecessary antibiotic use across all outpatient conditions.
2) Eliminate all antibiotic use for outpatient respiratory conditions for which antibiotics are not indicated.
3) Eliminate all antibiotic use for acute sinusitis.
4) Prescribe nitrofurantoin* for all cases of cystitis in women.”

“*Nitrofurantoin- a recommended first-line therapy with good potency against common uropathogens, low levels of resistance, and decreased risk of collateral damage to the intestinal microbiome”

Results

Picture1

Heatmaps showing the estimated percentage of species exposures to each antibiotic or antibiotic class that could be averted if A: unnecessary antibiotic prescriptions across all outpatient conditions, B: all antibiotic use for outpatient respiratory conditions for which antibiotics are not indicated, C: all antibiotic use for acute sinusitis, or D: non-nitrofurantoin treatment of cystitis in women was eliminated. Drug class results include prescriptions of all antibiotics in that class, as identified by the Lexicon Plus classification system.
Abbreviations: Antibiotics (y-axis): AMX-CLAV=amoxicillin-clavulanate,, MACR/LINC=macrolides/lincosamides, TMP-SMX=sulfamethoxazole-trimethoprim;

Organisms (x-axis): EC=E. coli, HI=H. influenzae, KP=K. pneumoniae, MC=M. catarrhalis, PA=P. aeruginosa, SA=S. aureus, SAg=S. agalactiae, SP=S. pneumoniae, SPy=S. pyogenes; PY=person-years


The darker shades in panel A (scenario 1) clearly indicated that “elimination of unnecessary antibiotic prescriptions across all outpatient conditions would prevent 6 to 48% (IQR: 17 to 31%) of antibiotic-species exposures. If all unnecessary antibiotic use could be prevented, over 30% of exposures to amoxicillin-clavulanate, penicillin, azithromycin, clarithromycin, levofloxacin, and doxycycline across most potential pathogens of interest could be averted.

In panel D (scenario 4), they found that prescribing nitrofurantoin not only averted antibiotic exposure in non-causative bacterial species (bystanders) but also in causative species for cystitis in women.
Overall, 27% of ciprofloxacin use is associated with acute cystitis in women. Organisms that are not causative pathogens of cystitis have proportions of avertable exposures close to or less than 27%, but a substantially higher proportion of exposures could be averted among causative pathogens – 33%, 36%, and 44% of ciprofloxacin exposures to E. coli, K. pneumoniae, and P. aeruginosa, respectively.

The study addresses the limitations with regard to data availability and reporting in public database. Authors are cautious and point out,

It is important to note that the reduction in antibiotic exposures estimated here does not translate to the same reduction in the prevalence of resistance or in the morbidity and mortality attributable to resistance. Additionally, in this analysis, we give each exposure equal weight. However, the selective pressure imposed by a single exposure depends on a number of variables, including pharmacokinetics, pharmacodynamics, distribution of bacteria across body sites, and bacterial population size. For example, we might expect that the probability of resistance scales with population size, and thus that an exposure received by an individual with higher bacterial load will have a larger impact on resistance.

Overall, this study indeed provides evidence that “improved prescription of antibiotics has the potential to prevent antibiotic exposure experienced by bacterial species throughout microbiome.