March 26th, 2020

This is my first post on the site! There weren’t a lot of alerts today, so I dug around for other papers I can find. Today’s digest includes mostly human microbiome research, most notably a study identifying a staph peptide that induces acute exacerbation of pulmonary fibrosis, as well as a very diverse epidemiological study of the impact of diet on the gut microbiome in the United States.

General Human Microbiome

US nativity and dietary acculturation impact the gut microbiome in a diverse US population  – Peters, B.A., Yi, S.S., Beasley, J.M. et al. – ISME

Microbiome in Pregnancy and Birth

Maternal carriage of Prevotella during pregnancy associates with protection against food allergy in the offspring – Vuillermin, P.J., O’Hely, M., Collier, F. et al. – Nature Communications

Vaginal Microbiome of Pregnant Indian Women: Insights into the Genome of Dominant Lactobacillus Species – Mehta, O., Ghosh, T.S., Kothidar, A. et al. – Microbial Ecology

Translational human microbiome research

A Staphylococcus pro-apoptotic peptide induces acute exacerbation of pulmonary fibrosis – D’Alessandro-Gabazza, C.N., Kobayashi, T., Yasuma, T. et al. – Nature Communications

Effect of probiotics during vonoprazan‐containing triple therapy on gut microbiota in Helicobacter pylori infection: A randomized controlled trial – Kakiuchi et al. – Helicobacter

Rosuvastatin alters the genetic composition of the human gut microbiome – Kummen, M., Solberg, O.G., Storm-Larsen, C. et al. – Scientific Reports

Microbiome and Cancer

Metaproteomics characterizes human gut microbiome function in colorectal cancer – Long, S., Yang, Y., Shen, C. et al. – npj Biofilms and Microbiomes

Plant microbiome

Genome‐resolved metagenomics to study co‐occurrence patterns and intraspecific heterogeneity among plant pathogen metapopulations – Newberry et al. – Environmental Microbiology

Symbiotic nitrogen fixation and endophytic bacterial community structure in Bt-transgenic chickpea (Cicer arietinum L) – Alok, D., Annapragada, H., Singh, S. et al. – Scientific Reports

Soil microbiome

Soil Microbial Diversity Affects the Plant-Root Colonization by Arbuscular Mycorrhizal Fungi – Ferreira et al. – Microbial Ecology

Bioinformatics/Sequencing analysis methods

Joining Illumina paired-end reads for classifying phylogenetic marker sequences – Liu et al. – BMC Bioinformatics

M2IA: a Web Server for Microbiome and Metabolome Integrative Analysis – Ni et al. – Bioinformatics

Culturomics

Alcohol pretreatment of stools effect on culturomics – Afouda, P., Hocquart, M., Pham, T. et al. – Scientific Reports

Pre-prints on bioRxiv to look forward to

Infant gut microbiome

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics – West et al. (Side note: The Banfield lab produces a lot of good work!)

Laboratory work on bacterial motility in the gut

Bacterial Swarmers exhibit a Protective Response to Intestinal Stress – Chen et al.

Long-read sequencing of gut mycobiome

Assessing anaerobic gut fungal (Neocalliamstigomycota) diversity using PacBio D1/D2 LSU rRNA amplicon sequencing and multi-year isolation – Hanafy et al.

Databases

HumGut: A comprehensive Human Gut prokaryotic genomes collection filtered by metagenome data

 

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 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 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

February 1, 2020

Today’s Digest brings you an Outlook collection on human gut microbiome by Nature, a Hi-C investigation of the evolution of the gut microbiota, and be careful with the dust, there’s transferrable antimicrobial genes within!

Events

Reshaping the Microbiome through Nutrition – Nature Conference – San Diego, CA

General microbiology

Commensal Bacteroidetes protect against Klebsiella pneumoniae colonization and transmission through IL-36 signalling – Richard P. Sequeira et al. – Nature Microbiology

** The gut microbiome – Nature Outlook

Antimicrobial resistance

The negative cofactor 2 complex is a key regulator of drug resistance in Aspergillus fumigatus – Takanori Furukawa et al. – Nature Communications

Plasmid-mediated metronidazole resistance in Clostridioides difficile – Ilse M. Boekhoud et al. – Nature Communications

A Common Practice of Widespread Antimicrobial Use in Horse Production Promotes Multi-Drug Resistance – S. Álvarez–Narváez et al. – Scientific Reports

Surveys of knowledge and awareness of antibiotic use and antimicrobial resistance in general population: A systematic review – PLoS One

Antimicrobial resistance patterns and molecular resistance markers of Campylobacter jejuni isolates from human diarrheal cases – Mohamed Elhadidy et al. – PLoS One

Review: Antibiotic resistance: turning evolutionary principles into clinical reality – Dan I Andersson et al. – FEMS Microbiology Reviews

Antibiotic resistome associated with microbial communities in an integrated wastewater reclamation system – Kaifeng Yu et al. – Water Research

Human gut microbiome

** Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation – Eitan Yaffe & David A. Relman – Nature Microbiology

Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease – Nadine Fornelos et al. – Nature Microbiology

Human cancer microbiome

The Influence of Lung Microbiota on Lung Carcinogenesis, Immunity, and Immunotherapy – Ariel G. Ramírez-Labrada et al. – Trends in Cancer

Built environment microbiome

** Mobilizable antibiotic resistance genes are present in dust microbial communities – Sarah Ben Maamar et al. – PLoS Pathogens

Indoor and outdoor airborne bacterial and fungal air quality in kindergartens: seasonal distribution, genera, levels, and factors influencing their concentration – Farhad Mirkhond Chegini et al. – Building and Environment

Metabolomics

Targeted metabolomics of pellicle and saliva in children with different caries activity – Annika Schulz et al. – Scientific Reports

Animal experiments

Review: The role of the microbiota in sedentary life style disorders and ageing: Lessons from the animal kingdom – P.W. O’Toole & P.G. Shiels – Journal of Internal Medicine

Animal microbiome

Dietary effects on gut microbiota of the mesquite lizard Sceloporus grammicus (Wiegmann, 1828) across different altitudes – Nina Montoya-Ciriaco et al. – Microbiome

Late weaning is associated with increased microbial diversity and Faecalibacterium prausnitzii abundance in the fecal microbiota of piglets – Francesca Romana Massacci et al. – Animal Microbiome

Plant, root and soil microbiome

Effects of soil chemical properties and fractions of Pb, Cd, and Zn on bacterial and fungal communities – Xiaomei Pan et al. – Science of the Total Environment

Resilience of the microbial communities of semiarid agricultural soils during natural climatic variability events – Lumarie Pérez-Guzmán et al. – Applied Soil Ecology

Effects of microbial inoculants on the fermentation characteristics and microbial communities of sweet sorghum bagasse silage – Miaoyin Dong et al. – Scientific Reports

Water and extremophile microbiome

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing – Genevieve L. Fernandes et al. – Frontiers in Microbiology

Ionic Liquid Enriches the Antibiotic Resistome, Especially Efflux Pump Genes, Before Significantly Affecting Microbial Community Structure – Xiaolong Wang et al. – Environmental Science & Technology

Methane yield enhancement of mesophilic and thermophilic anaerobic co-digestion of algal biomass and food waste using algal biochar: Semi-continuous operation and microbial community analysis – Le Zhang et al. – Bioresource Technology

Characterization and co-occurrence of microbial community in epiphytic biofilms and surface sediments of wetlands with submersed macrophytes – Yuansi Liu et al. – Science of the Total Environment

Phages and viruses

** Giant virus diversity and host interactions through global metagenomics – Frederik Schulz et al. – Nature

Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China – Bingqian Qu et al. – PLoS One

Outbreak of Pneumonia of Unknown Etiology in Wuhan China: the Mystery and the Miracle – Hongzhou Lu et al. – Journal of Medical Virology

Bioinformatics

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing – Andrei Prodan et al. – PLoS One

Microbes in the news

Walnuts May Benefit Gut Bacteria and Improve Heart Health – Karina Lichtenstein – Medicine Net

How to create living art with microbes – Eugenia Angulo – BBVA OpenMind

January 27, 2020

In today’s Monday morning post – establishing causality for gut microbiome using human microbiota associated rodents, gut microbiota profiling in pregnant women after bariatric surgery, proteomics changes in bacteria, discovery of core microbiome of common bean rhizosphere and many more.

General Microbiome

Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents – Jens Walter – Cell

Microbial Genomics and Metagenomics in India: Explorations and Perspectives– Princy Hira – Proceedings of Indian National Science Academy

Human Microbiome

Longitudinal metabolic and gut bacterial profiling of pregnant women with previous bariatric surgery – Kiana Ashley West – Gut

Identifying determinants of bacterial fitness in a model of human gut microbial succession – Lihui Feng – PNAS

16S rDNA microbiome composition pattern analysis as a diagnostic biomarker for biliary tract cancer – Huisong Lee – World Journal of Surgical Oncology

Faecal microbiota transplantations and urinary tract infections – Jean Christophe Lagier – Lancet

Animal Microbiome

Influences of a Prolific Gut Fungus (Zancudomyces culisetae) on Larval and Adult Mosquito (Aedes aegypti)-Associated Microbiota – Jonas Frankel-Bricker – Applied and Environmental Microbiology

Functional dynamics of bacterial species in the mouse gut microbiome revealed by metagenomic and metatranscriptomic analyses – Youn Wook Chung – PlosOne

Early life microbiome perturbation alters pulmonary responses to ozone in male mice – Traci A. Brown – Physiological Reports

Evolution and maintenance of microbe-mediated protection under occasional pathogen attack – Anke Kloock – BioRxiv

Plant, root and soil microbiome

Community sequencing on a natural experiment reveals little influence of host species and timing but a strong influence of compartment on the composition of root endophytes in three annual Brassicaceae – Jose G Macia-Vicente – BioRxiv

Discovery of a spatially and temporally persistent core microbiome of the common bean rhizosphere – Nejc Stopnisek – BioRxiv

Resident and phytometer plants host comparable rhizosphere fungal communities in managed grassland ecosystems – Ricardo Schöps – Scientific Reports

Evaluation of fatty acid derivatives in the remediation of aged PAH-contaminated soil and microbial community and degradation gene response – Qingling Wang – Chemosphere

Techniques

Proteomic changes in bacteria caused by exposure to environmental conditions can be detected by Matrix-Assisted Laser Desorption/Ionization – Time of Flight (MALDI-ToF) Mass Spectrometry – Denise Chac – BioRxiv

Probiotics, prebiotics

Beneficial bile acid metabolism from Lactobacillus plantarum of food origin – Roberta Prete – Scientific Reports

Microbes in the news

Could a kid’s microbiome alter their behaviour? – Health24

Microbiome Therapeutics Market Report Forecast by Capital Investment, Industry Outlook, Opportunities & Trends 2024 – Fusion Science Academy