July 16, 2018

Today’s Digest is all about cows! Microbiome of healthy cows and cows developing postpartum endometritis, and metabolic pathways of rumen microbiota. Ok, almost. Find out whether anthropogenic radionuclides at Chernobyl (Ukraine) impact the gut microbiome of the bank vole. Also, there’s an interesting read on human microbiome and microbial metabolites that contribute to the accumulation of lipids in the liver. Happy week!

Animal microbiome

*Preprint: Delayed differentiation of vaginal and uterine microbiomes in dairy cows developing postpartum endometritis – Raúl Miranda-CasoLuengo – bioRxiv

Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria – E.H. Hart – Scientific Report

*Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus – Anton Lavrinienko – The ISME Journal

The maternal vaginal microbiome partially mediates the effects of prenatal stress on offspring gut and hypothalamus – Eldin Jašarević – Nature Neuroscience

Human microbiome

*Microbiome metabolomics reveals new drivers of human liver steatosis – Nathalie M. Delzenne – Nature Medicine

The gut–liver axis and the intersection with the microbiome – Anupriya Tripathi – Nature Reviews Gastroenterology & Hepatology

Longevity extension in Drosophila through gut-brain communication – Susan Westfall — Scientific Reports

Gut microbiota composition is related to cardiorespiratory fitness in healthy young adults – Ryan P. Durk – International Journal of Sport Nutrition and Exercise Metabolism

Microbes in the news

Data on transfer of gut microbiota from hen to chick can inform probiotic R&D [A Czech team’s research findings provide insights for the development of next generation probiotics for poultry production in the absence of antibiotics.] – Jane Byrne

*The future of the microbiome: A conversation with Michael Fischbach [Discussion on the growing knowledge of the bacteria in our bodies, their role in our health, and how researchers like Fischbach are shaping the future of microbiome-mediated disease therapy.] – Russ Altman

Advertisements

July 14, 2018

 

Editorial

Ediorial:The nasal microbiome: opening new clinical research avenues for allergic disease.Mahdavinia M.

Beyond Bacteria: Bacteriophage-Eukaryotic Host Interactions Reveal Emerging Paradigms of Health and Disease.Chatterjee A. Frontiers in Microbiology. Expert Rev Clin Immunol

Correction

Correction:Huddling remodels gut microbiota to reduce energy requirements in a small mammal species during cold exposure.Zhang XY. Microbiome.

General Microbiome

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life.Yassour M. Cell Host Microbe

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.Ferretti P. Cell Host Microbe

Reduced microbiome alpha diversity in young patients with ADHD.Prehn-Kristensen A. PLoS One.

Reducing healthcare-associated infections incidence by a probiotic-based sanitation system: A multicentre, prospective, intervention study. Caselli E. PLoS One

The Microbiome and Pancreatic Cancer: An Evidence-based Association?Archibugi L. Journal of  Clinical Gastroenterology

Testing the light:nutrient hypothesis: Insights into biofilm structure and function using metatranscriptomics.Veach AM. Molecular Ecology

Animal Experiments and Microbiome

Modulation of the honey bee queen microbiota: Effects of early social contact.Powell JE. PLoS One. 2018

Plants, Soil, and Water Microbiome

Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia. Garrido-Oter R

Biodiversity of cultivable Burkholderia species in Argentinean soils under no-till agricultural practices. Draghi WO.  PLoS One

Characterized non-transient microbiota from stinkbug (Nezara viridula) midgut deactivates soybean chemical defenses. Medina V. PLoS One.

Characterization of Actinobacterial Communities from Arauca River Sediments (Colombia) Reveals Antimicrobial Potential Presented in Low Abundant Isolates.Arango C, Open Microbiology Journal. Cell Host Microbe.

Predictive Modeling of Microbiome Data Using a Phylogeny-Regularized Generalized Linear Mixed Model. Xiao J.Frontier in Microbiology

Virome

Characterization of airborne viromes in cheese production plants. Colombo S.Journal of Applied Microbiology

 

 

 

July 13, 2018

Comparing affects of host physiology and diet on primate gut microbiomes, oral bacterial and fungal dysbiosis in people with HIV, contribution of non-fermentable dietary fiber to prevention of autoimmune neurological disease via the gut microbiota.

General microbiome

Tools for engineering coordinated system behaviour in synthetic microbial consortia – Nicolas Kylilis – Nature Communications

Human oral microbiome

Dysbiosis in the oral bacterial and fungal microbiome of HIV-infected subjects is associated with clinical and immunologic variables of HIV infection – Pranab K Mukherjee – PLOS ONE

Human gut microbiome

Dietary non-fermentable fiber prevents autoimmune neurological disease by changing gut metabolic and immune status – Kerstin Berer – Scientific Reports

Physiology and central carbon metabolism of the gut bacterium Prevotella copri – Thomas Franke – Molecular Microbiology

Chemotaxis of Escherichia coli to major hormones and polyamines present in human gut – Joana G Lopes – The ISME Journal

Stool Microbiota Composition Differs in Patients with Stomach, Colon, and Rectal Neoplasms – Omar Youssef – Digestive Diseases and Sciences

Animal experiments

Of Mice and Men . . . and Microbes: Conclusions and Cautions from a Murine Study of the Lung Microbiome and Microbiome-Immune Interactions – John E McGinniss – American Journal of Respiratory and Critical Care Medicine

Modulation of gut microbiota by mulberry fruit polysaccharide treatment of obese diabetic db/db mice – Chun Chen – Food & Function

Evidence for the Role of the Cecal Microbiome in Maintenance of Immune Regulation and Homeostasis – Preeti Chhabra – Annals of Surgery

Human Milk Fortification with Bovine Colostrum Is Superior to Formula‐Based Fortifiers to Prevent Gut Dysfunction, Necrotizing Enterocolitis, and Systemic Infection in Preterm Pigs – Jing Sun – Journal of Parenteral & Enteral Nutrition

Fecal Microbiota Transplantation Is Effective in Relieving Visceral Hypersensitivity in a Postinfectious Model – Tao Bai – BioMed Research International

Animal microbiome

First report of foregut microbial community in proboscis monkeys: Are diverse forests a reservoir for diverse microbiomes? – Takashi Hayakawa – Environmental Microbiology Reports

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes – Katherine R Amato – The ISME Journal

The composition of the perinatal intestinal microbiota in cattle – Mohammad Jaber Alipour – Scientific Reports

Metagenomic evaluation of the effects of storage conditions on the bacterial microbiota of oysters Crassostrea gasar (Adanson, 1757) – Antonio Ostrensky – Journal of Applied Microbiology

16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus – Inga Reich – Scientific Reports

A Robust Noninvasive Approach to Study Gut Microbiota Structure of Amphibian Tadpoles by Feces – Xiaowei Song – Herpetology Research

Plant, root, and soil microbiome

Isolation and characterization of two phosphate-solubilizing fungi from rhizosphere soil of moso bamboo and their functional capacities when exposed to different phosphorus sources and pH environments – Yang Zhang – PLOS ONE

Water and extremophile microbiome

Hydrothermal chimneys host habitat-specific microbial communities: analogues for studying the possible impact of mining seafloor massive sulfide deposits – Yuchen Han – Scientific Reports

Food microbiology

Changes in Quality and Microbial Succession of Lightly Salted and Sugar-Salted Blunt Snout Bream (Megalobrama amblycephala) Fillets Stored at 4°C – Yan Li – Journal of Food Protection

Review: Novel approaches for Chemical and Microbiological shelf life extension of cereal crops – Marcus Schmidt – Critical Reviews in Food Science and Nutrition

Probiotics/prebiotics

The short-term impact of probiotic consumption on the oral cavity microbiome – Erik Dassi – Scientific Reports

Bioinformatics

The evolutionary signal in metagenome phyletic profiles predicts many gene functions – Vedrana Vidulin – Microbiome

More microbes

Pre-print: Listeria monocytogenes cell-to-cell spread in epithelia is heterogeneous and dominated by rare pioneer bacteria – Fabian E Ortega – bioRxiv

Microbes in the news

Gut microbiota: a new way to take your vitamins – João Carlos Gomes-Neto – Nature Reviews Gastroenterology & Hepatology

July 12, 2018

Bacteria in desert soils, mycobacteria in showerhead biofilms, metabolic diversity of microbes from commercial probiotics.

Human gut microbiome

Pre-print: Evaluating bacterial and functional diversity of human gut microbiota by complementary metagenomics and metatranscriptomics – Ravi Ranjan – bioRxiv

Animal microbiome

Pre-print: Olive fruit fly rearing procedures affect the vertical transmission of the bacterial symbiont Candidatus Erwinia dacicola – Patrizia Sacchetti – bioRxiv

Pre-print: Survey of bacteria associated with western corn rootworm life stages reveals no difference between insects reared in different soils – Dalton C Ludwick – bioRxiv

Plant, root, and soil microbiome

Influences of fertilization on soil environment and microorganism in continuous cropping based on high-throughput sequencing – Zhang YiJie – Journal of Agricultural Science and Technology

Review: Consortia of cyanobacteria/microalgae and bacteria in desert soils: an underexplored microbiota – Isiri Perera – Applied Microbiology and Biotechnology

Effects of cover crop in an apple orchard on microbial community composition, networks, and potential genes involved with degradation of crop residues in soil – Wei Zheng – Biology and Fertility of Soils

Microbial Community Level Physiological Profiles of Active Mud Volcano Soils in Andaman and Nicobar Islands – N Amaresan – National Academy Science Letters

Water and extremophile microbiome

Pre-print: Interspecies interactions mediated by conductive minerals in the sediments of the ferruginous Lake La Cruz, Spain – Amelia-Elena Rotaru – bioRxiv

Pre-print: Microbial community structure and microbial networks correspond to nutrient gradients within coastal wetlands of the Laurentian Great Lakes – Dean J Horton – bioRxiv

Pre-print: Hidden in plain sight – highly abundant and diverse planktonic freshwater Chloroflexi – Maliheh Mehrshad – bioRxiv

Built environment

Pre-print: Ecological analyses of mycobacteria in showerhead biofilms and their relevance to human health – Matthew Gebert – bioRxiv

Probiotics/prebiotics

Pre-print: Metabolic diversity of bacteria and yeast from commercial probiotic products illustrated by phenotypic profiling – Juliana Mastronunzio Ansari – bioRxiv

Phages and viruses

Pre-print: Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow – Antonin Bal – bioRxiv

More microbes

Species-specific activity of antibacterial drug combinations – Ana Rita Brochado – Nature

Science, career, and publishing

Hot streaks in artistic, cultural, and scientific careers – Lu Liu – Nature

Amy’s non-microbiology picks

Reprogramming human T cell function and specificity with non-viral genome targeting – Theodore L Roth – Nature

11 July, 2018

Today’s digest is short but full of exciting research. Firstly, a look at how maternal diet can influence infant microbiome and a brilliant preprint highlighting the role women have played in science

General Microbiome

Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner. Lundgren SN. Microbiome.

Oral Microbiome

Dysbiosis of oral microbiota and its association with salivary immunological biomarkers in autoimmune liver disease.Kazumichi Abe. PLos ONE

Gut Microbiome

Gut microbiota-immune-brain interactions in chemotherapy-associated behavioral comorbidities.Jordan KR Cancer

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas. Das B. Scientific Reports

Commentary:Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis.Agustí G. Frontier in Cellular and Infection Microbiology .

Animal Experiments and Microbiome

Non-nutritive sweeteners possess a bacteriostatic effect and alter gut microbiota in mice.Wang. PLoS One

The spleen microbiota of small wild mammals reveals distinct patterns with tick-borne bacteria. Ge Y. PLoS Neglected Tropical Diseases

Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria.Pais IS. PLoS Biology

Plant, Soil, and Water Microbiome

Microbial community of tannery wastewater involved in nitrification revealed by Illumina MiSeq sequencing.Ma X. Journal of Microbiology and Biotechnology

Rhizosphere fungal community dynamics associated with Rehmannia glutinosa replant disease in a consecutive monoculture regime. Wu L Phytopathology.

Effects of soil erosion on agro-ecosystem services and soil functions: A multidisciplinary study in nineteen organically farmed European and Turkish vineyards. Costantini EAC. Journal of Environmental Management

Virome

Temporal dynamics of the lung and plasma viromes in lung transplant recipients Maia Segura-Wang. PLos ONE

Techniques

Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in <i>Escherichia coli</i>.Westmann CA. Frontier in Microbiology.

Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies.Lau MCY. Frontiers in Microbiology.

Preprint

Illuminating women’s hidden contribution to the foundation of theoretical population genetics. Samantha Dung. bioRxiv

July 10, 2018

A review on microbial connections to depression and anxiety, effects of anthocyanins and flavanoids on the gut, and a Nature Communications paper on  Gut microbiota associations with common diseases and prescription medications! Also included are some articles on Oliver Sacks who would have turned 85 yesterday.

General microbiome

Mechanisms of action of vitamin D in colon cancer – Ferrer-Mayorga G – Journal of  Steroid Biochemistry and Molecular Biology

A review of dietary and microbial connections to depression, anxiety, and stress. – Taylor AM – Nutritional Neuroscience

The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants-but not always. – Bengtsson-Palme J – Microbiome

Human respiratory microbiome

Aerodigestive dysbiosis in children with chronic cough. – Kazachkov M – Pediatric Pulmonology

Human gut microbiome

Shifts of Faecal Microbiota During Sporadic Colorectal Carcinogenesis. – Mori G – Scientific Reports

Gut microbiota associations with common diseases and prescription medications in a population-based cohort. -Jackson MA – Nature Communications

Disruption of maternal gut microbiota during gestation alters offspring microbiota and immunity. – Nyangahu DD – Microbiome

Animal experiments 

Delayed differentiation of vaginal and uterine microbiomes in dairy cows developing postpartum endometritis – Raúl Miranda-CasoLuengo – bioRxiv

Dietary fiber increases the butyrate-producing bacteria and improves growth performance of weaned piglets. – Zhao J – J Agric Food Chem

Early intervention with faecal microbiota transplantation: an effective means to improve growth performance and the intestinal development of suckling piglets. – Cheng CS – Animal

Plant, root, and soil microbiome

A common garden experiment with Porphyra umbilicalis (Rhodophyta) evaluates methods to study spatial differences in the macroalgal microbiome – Quigley CTC -Journal of Applied Phycology

Food Microbiology

Consumption of Black Legumes Glycine soja and Glycine max Lowers Serum Lipids and Alters the Gut Microbiome Profile in Mice Fed a High-Fat Diet. – Jing C – Journal of Agricultural Food Chemistry

A systematic literature review of the effect of anthocyanins on gut microbiota populations. – Igwe EO – Journal of Human Nutrition and Dietetics

*****************************

Probiotics / prebiotics

The Mechanisms behind the Biological Activity of Flavonoids. – Gonzalez-Paramas AM – Current Medicinal Chemistry

 

*****************************

Swathi’s non-microbiology picks

In honor of Oliver Sacks who would have been 85 yesterday:

 

 

July 9, 2018

Today’s Digest features new insights into the microbial communities associated with shisha (water pipe), microbial mats, and tropical marine ecosystems. In addition, there are some new techniques and benchmarks to read about, including domain intelligible models for mining ‘omics data and the potential of giant viruses to introduce errors into metagenomic binning. I also highlighted some non-microbiology picks about the potential role for robots in autism therapies and photographs of a brand new planet taken at the Max Planck Institute for Astronomy!

Human gut microbiome
Faecal microbiota transplantation alters gut microbiota in patients with irritable bowel syndrome: results from a randomised, double-blind placebo-controlled study – Sofie Ingdam Halkjær – Gut

Animal experiments
Early-life sickness may predispose Siberian hamsters to behavioral changes following alterations of the gut microbiome in adulthood – Kristyn E. Sylvia – Brain, Behavior, and Immunity

Deficiency in class III PI3-kinase confers postnatal lethality with IBD-like features in zebrafish – Shaoyang Zhao – Nature Communications

Plant, root, and soil microbiome
Shisha microbiota: the good, the bad and the not so ugly – Julia Hani – BMC Research Notes

Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes – Hon Lun Wong – The ISME Journal

Water and extremophile microbiome
A long-standing complex tropical dipole shapes marine microbial biogeography – Wei Yan – Applied and Environmental Microbiology

Probiotics / prebiotics
Probiotic Lactobacillus paracasei HII01 protects rats against obese-insulin resistance-induced kidney injury and impaired renal organic anion transporter 3 (Oat3) function – Keerati Wanchai – Clinical Science

Bioinformatics
Domain Intelligible Models – Sultan Imangaliyev – Methods

Techniques
Metagenomic binning reconstruction coupled with automatic pipeline annotation and giant viruses: a potential source of mistake in annotations – Julien Andreani – Virus Research

Does universal 16S rRNA gene amplicon sequencing of environmental communities provide an accurate description of nitrifying guilds? – Vaibhav Diwan – Journal of Microbiological Methods

Linking uncultivated microbial populations with benthic carbon turnover using quantitative stable isotope probing – Ömer K. Coskun – Applied and Environmental Microbiology

Determining lineage-specific bacterial growth curves with a novel approach based on amplicon reads normalization using internal standard (ARNIS) – Kasia Piwosz – The ISME Journal

Alyson’s non-microbiology picks
Personalized machine learning for robot perception of affect and engagement in autism therapy – Ognjen Rudovic – Science Robotics

Scientists Capture First Birth Of A Planet – M. Keppler – via NPR