November 2, 2018

Your Friday Digest features plentiful of soil/plant and gut microbiome papers. Highlights include correlation between infant metabolic functions and diet/gestational weight gain, profiling human gut microbiomes across India, and the absence of a placenta microbiota. There are many other more articles worth reading, enjoy!

General microbiology

Suboptimal community growth mediated through metabolite crossfeeding promotes species diversity in the gut microbiota – Michael A. Henson & Poonam Phalak – PLoS Computational Biology

A cohabiting bacterium alters the spectrum of short RNAs secreted by Escherichia coli – Olga V Alikina et al. – FEMS Microbiology Letters

Pregnancy and early life

Long-lasting effect of oral azithromycin taken by women during labour on infant nutrition: Follow-up cohort of a randomized clinical trial in western Gambia – Anna Roca et al. – PLoS One

** Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes – Aimee M. Baumann-Dudenhoeffer et al. – Nature Medicine

Antibiotic and acid-suppression medications during early childhood are associated with obesity – Christopher M Stark et al. – Gut

** Lack of detection of a human placenta microbiome in samples from preterm and term deliveries – Jacob S. Leiby et al. – Microbiome

Human oral microbiome

Multi-species oral biofilm promotes reconstructed human gingiva epithelial barrier function – Lin Shang et al. – Scientific Reports

Review: Administration of systemic antibiotics during non-surgical periodontal therapy—a consensus report – B. Pretzl et al. – Clinical Oral Investigations

Human repiratory microbiome

Sputum Microbiome is Associated with 1-Year Mortality Following COPD Hospitalizations – Fernando Sergio Leitao Filho et al. – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

The co-existence of elevated high sensitivity C-reactive protein and homocysteine levels is associated with increased risk of metabolic syndrome: A 6-year follow-up study – Jinkwan Kim & Sangshin Pyo – PLoS One

** LogMPIE, pan-India profiling of the human gut microbiome using 16S rRNA sequencing – Ashok Kumar Dubey et al. – Scientific Data

Association between Neutrophil-to-Lymphocyte Ratio and Gut Microbiota in a Large Population: a Retrospective Cross-Sectional Study – Hee-Young Yoon et al. – Scientific Reports

Microbial nitrogen limitation in the mammalian large intestine – Aspen T. Reese et al. – Nature Microbiology

Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles – Trishla Sinha et al. – Gut Microbes

Anti-Inflammatory Activities of Pentaherbs formula and Its Influence on Gut Microbiota in Allergic Asthma – Miranda Sin-Man Tsang et al. – Molecules

Identification of TMAO-producer phenotype and host–diet–gut dysbiosis by carnitine challenge test in human and germ-free mice – Wei-Kai Wu et al. – Gut

Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin – Zhen He et al. – Gut

Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers – Vanessa L. Hale et al. – Genome Medicine

Comment: Targeting the microbiome: from probiotics to fecal microbiota transplantation – Alexander Khoruts – Genome Medicine

Human vaginal microbiome

Review: Endometrial microbes and microbiome: Recent insights on the inflammatory and immune “players” of the human endometrium – Silvia D’Ippolito et al. – American Journal of Reproductive Immunology

Animal experiments

Effect of dietary fiber content on nutrient digestibility and fecal microbiota composition in growing-finishing pigs – Mathilde Le Sciellour et al. – PLoS One

Effects of ultraviolet radiation and nutrient level on the physiological response and organic matter release of the scleractinian coral Pocillopora damicornis following thermal stress – Lucile Courtial et al. – PLoS One

Dog: Balance of saccharolysis and proteolysis underpins improvements in stool quality induced by adding a fiber bundle containing bound polyphenols to either hydrolyzed meat or grain-rich foods – Matthew I. Jackson & Dennis E. Jewell – Gut Microbes

Ventilator-induced lung injury is aggravated by antibiotic mediated microbiota depletion in mice – Sandra-Maria Wienhold & Mario Macrì et al. – Critical Care

Mouse: Dioxin-like PCB 126 increases intestinal inflammation and disrupts gut microbiota and metabolic homeostasis – Michael C. Petriello et al. – Environmental Pollution

Review: Innate Immune Influences on the Gut Microbiome: Lessons from Mouse Models – Susan J. Robertson et al. – Trends in Immunology

Animal microbiome

Milk microbiome diversity and bacterial group prevalence in a comparison between healthy Holstein Friesian and Rendena cows – Paola Cremonesi & Camilla Ceccarani et al. – PLoS One

Comparing the bacterial communities of wild and captive golden mantella frogs: Implications for amphibian conservation – Luiza F. Passos et al. – PLoS One

Insect anal droplets contain diverse proteins related to gut homeostasis – Tianzhong Jing et al. – BMC Genomics

Plant, root and soil microbiome

Putative Nitrogen-fixing bacteria Associated with The Rhizosphere and Root Endosphere of wheat plants grown in an Andisol from southern Chile – Joaquin I. Rilling et al. – Frontiers in Microbiology

Land-use intensity rather than plant functional identity shapes bacterial and fungal rhizosphere communities – Ricardo Schöps et al. – Frontiers in Microbiology

Microbial expression profiles in the rhizosphere of two maize lines differing in N use efficiency – Shamina Imran Pathan et al. – Plant and Soil

The rhizosphere of the halophytic grass Sporobolus robustus Kunth hosts rhizobium genospecies that are efficient on Prosopis juliflora (Sw.) DC and Vachellia seyal (Del.) P.J.H. Hurter seedlings – Fatoumata Fall et al. – Systematic and Applied Microbiology

Rhizosphere responses to environmental conditions in Radix pseudostellariae under continuous monoculture regimes – Hongmiao Wu et al. – Agriculture, Ecosystems & Environment

Plant-microbe interactions endorse growth by uplifting microbial community structure of Bacopa monnieri rhizosphere under nematode stress – Rupali Gupta et al. – Microbiological Research

Review: Multifaceted interactions between endophytes and plant: Developments and Prospects – Naveen K. Arora et al. – Frontiers in Microbiology

Enhancing phytoextraction of HMs at real scale, by combining Salicaceae Trees with microbial consortia – CARMINE GUARINO et al. – Frontiers in Environmental Science

PhD Dissertation: Implications of land-use legacy on soil microbiomes of urban grasslands – Grant Lafayette Thompson – Cornell University

Body size determines soil community assembly in a tropical forest – Lucie Zinger et al. Molecular Ecology

Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes – Joshua Ladau et al. – mSystems

Water and extremophile microbiome

Microbial diversity and antibiotic resistance in a final effluent-receiving lake – Kinga Bondarczuk & Zofia Piotrowska-Seget – Science of The Total Environment

Non‐random processes determine the colonization of groundwater sediments by microbial communities in a pristine porous aquifer – Lucas Fillinger et al. – Environmental Microbiology

Food microbiome

Changes of microbial community and metabolite in kimchi inoculated with different microbial community starters – Seong-Eun Park et al. – Food Chemistry

Phages and viruses

Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow – A. Bal et al. – BMC Infectious Diseases


A high-throughput sequencing assay to comprehensively detect and characterize unicellular eukaryotes and helminths from biological and environmental samples – Matthew V. Cannon et al. – Microbiome


RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification – Daniel J. Nasko et al. – Genome Biology

* Species-level functional profiling of metagenomes and metatranscriptomes – Eric A. Franzosa et al. – Nature Methods

Striped UniFrac: enabling microbiome analysis at unprecedented scale – Daniel McDonald et al. – Nature Methods

Mechanistic microbiota models – Tal Nawy – Nature Methods

Microbes in the news

Club STEAM Powered students study bacteria, genetics – Cassie Gibb – The Southeast Sun

Media alert: New articles in The CRISPR Journal – MARY ANN LIEBERT, INC. – EurekAlert!

Electric shocks kill bacteria – Vienna University of Technology –

The Mad Science of Fermentation’s Funky Flavors – Joe Ray – Wired

How Nuclear Testing Transformed the Land in Nevada and New Mexico – Kealey Boyd – Hyperallergic

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