November 19, 2017

A large number of papers overall, but especially in the plant/soil microbiome and animal experiments. For the former, one is from one of the MicrobiomeDigest contributors (in green) – congratulations!

General microbiome

Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities – Ali R. Zomorrodi – Nature Communications

Pregnancy and early life
Low dietary fiber intake increases Collinsella abundance in the gut microbiota of overweight and obese pregnant women – Luisa F. Gomez-Arango – Gut Microbes

Multi-site human microbiome
The Akkermansia-muciniphila is a gut microbiota signature in psoriasis – LiRong Tan – Experimental Dermatology

Human respiratory microbiome
Airway microbiota across age and disease spectrum in cystic fibrosis – Edith T. Zemanick – European Respiratory Journal

Human skin microbiome
Review: Skin barrier and microbiome in acne – M. A. Rocha – Archives of Dermatological Research

Fungi in the Wound Microbiome – Lindsay Kalan – Advances in Wound Care

Environmental influences on the skin microbiome of humans and cattle in rural Madagascar – Melissa B. Manus – Evolution, Medicine, and Public Health

Human gut microbiome
The Inuit gut microbiome is dynamic over time and shaped by traditional foods
Geneviève Dubois – Microbiome

Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment – Sepideh Pakpour – Microbiome

Gastrointestinal and Hepatic Disease in Spondyloarthritis – Liron Caplan – Rheumatic Disease Clinics of North America

Review: Gutsy Moves: The Amygdala as a Critical Node in Microbiota to Brain Signaling – Caitlin S. M. Cowan – BioEssays

Review: The Role of the Gut Microbiome in Multiple Sclerosis Risk and Progression: Towards Characterization of the “MS Microbiome” – Anne-Katrin Pröbstel – Neurotherapeutics

Review: The gut–brain interaction in opioid tolerance – Hamid I Akbarali – Current Opinion in Pharmacology

ReviewLipotoxicity and the gut-liver axis in NASH pathogenesis – Fabio Marra – Journal of Hepatology

ReviewEvidence of giant viruses of amoebae in the human gut – Philippe Colson -Human Microbiome Journal

Animal experiments
Evaluating the impact of domestication and captivity on the horse gut microbiome – Jessica L. Metcalf – Scientific Reports

Changes of gut microbiota structure and morphology in weaned piglets treated with fresh fermented soybean meal – Zhengjun Xie – World Journal of Microbiology and Biotechnology

Brown rice and retrograded brown rice alleviate inflammatory response in dextran sulfate sodium (DSS)-induced colitis mice – Kemika Praengam – Food and Function

Depletion of Stercobilin in Fecal Matter from a Mouse Model of Autism Spectrum Disorders – Emily R. Sekera – Metabolomics

Comparison of (R)-ketamine and lanicemine on depression-like phenotype and abnormal composition of gut microbiota in a social defeat stress model – Youge Qu – Scientific Reports

Beyond immunity: The Imd pathway as a coordinator of host defense, organismal physiology and behavior – Zongzhao Zhai – Developmental & Comparative Immunology
# This is a review on the Imd pathway in Drosophila, and its influence on their gut microbiome.

Dietary Fructo-Oligosaccharides Attenuate Early Activation of CD4+ T Cells Which Produce both Th1 and Th2 Cytokines in the Intestinal Lymphoid Tissues of a Murine Food Allergy Model – M. Tsuda – International Archives of Allergy and Immunology

Disorder of gut amino acids metabolism during CKD progression is related with gut microbiota dysbiosis and metagenome change – Yang Liu – Journal of Pharmaceutical and Biomedical Analysis

Animal microbiome
The sponge microbiome project – Lucas Moitinho-Silva – Gigascience

Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome – Natasha K. Dudek – Current Biology

Review: Gut Brain Axis and Its Microbiota Regulation in Mammals and Birds – Jan S. Suchodolski- Veterinary Clinics of North America: Exotic Animal Practice

Analysis of Bacterial and Fungal Nucleic Acid in Canine Sterile Granulomatous and Pyogranulomatous Dermatitis and Panniculitis – Fabio B. Rosa – Veterinary Pathology

Developmental and gut-related changes to microbiomes of the cultured juvenile spiny lobster Panulirus ornatus – MC Ooi – FEMS Microbial Ecology
# Pubmed linked since DOI not yet active

Illumina Based Analysis of Bacterial and Fungal Flora in Foreguts and Hindguts of Crucian Carp (Carassius Aumtus) in Retail Markets – Mingyue Wang – Open Journal of Bacteriology

16S rRNA gene amplicon sequencing reveals dominance of Actinobacteria in Rhodnius pallescens compared to Triatoma maculata midgut microbiota in natural populations of vector insects from Colombia – Luisa M. Montoya-Porras – Acta Tropica

Plant, root, and soil microbiome
Exploration, antifungal and antiaflatoxigenic activity of halophilic bacteria communities from saline soils of Howze-Soltan playa in Iran – Samaneh Jafari – Extremophiles

No single driver of biodiversity: divergent responses of multiple taxa across land use types – Jamie R. Wood – Ecosphere

Community evolution increases plant productivity at low diversity – Sofia J. van Moorse – Ecology Letters

Co-Variation of Bacterial and Fungal Communities in Different Sorghum Cultivars and Growth Stages is Soil Dependent – Thiago R. Schlemper – Microbial Ecology

Microbial communities in the native habitats of Agaricus sinodeliciosus from Xinjiang Province revealed by amplicon sequencing – Jiemin Zhou – Scientific Reports

Previous crop and rotation history effects on maize seedling health and associated rhizosphere microbiome – Maria-Soledad Benitez – Scientific Reports

Soil bacterial community response to altered precipitation and temperature regimes in an old field grassland are mediated by plants – A Koyama – FEMS Microbial Ecology
# Pubmed linked since DOI not yet active

The abundance of health-associated bacteria is altered in PAH polluted soils-Implications for health in urban areas? – Anirudra Parajuli – PLoS One

Effect of halotolerant methylotrophs isolated from saline soil rhizosphere on diminution of salt stress in wheat (Triticum aestivum l.) – Dmitry Y. Sharavin – Journal of Agriculture and Environment

Build your own soil: exploring microfluidics to create microbial habitat structures – Kristin Aleklett – ISMEJ

Influence of high-carbon basal fertiliser on the structure and composition of a soil microbial community under tobacco cultivation – Song-tao Zhang – Research in Microbiology

Impacts of environmental factors on the whole microbial communities in the rhizosphere of a metal-tolerant plant: Elsholtzia haichowensis Sun – Songqiang Deng – Environmental Pollution

Contrasting the microbiomes from forest rhizosphere and deeper bulk soil from an Amazon rainforest reserve – Jose Pedro Fonseca – Gene

Microplot long-term experiment reveals strong soil type influence on bacteria composition and its functional diversity – Jarosław Grządziel – Applied Soil Ecology

Bulk soil bacterial community mediated by plant community in Mediterranean ecosystem, Israel – I. Moroenyane – Applied Soil Ecology
# From fellow MicrobiomeDigest contributor!

Thesis: Characterisation of Metagenomic Bougainvillea Soil DNA Through rDNA PCR Amplification – Aruna Ganesan – INTI International University

Book: Endophytes: Crop Productivity and Protection
Book chapterEndophytes as Contender of Plant Productivity and Protection: An Introduction – Dinesh K. Maheshwari
Book chapterBeneficial Effects of Bacterial Endophytes on Forest Tree Species – Akshit Puri

Water and extremophile microbiome
Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change – Julia Kleinteich – Frontiers in Ecology and Evolution

Microbial pathway for anaerobic 5′-methylthioadenosine metabolism coupled to ethylene formation – Justin A. North – PNAS

Built environment
Droplet distribution and airborne bacteria in an experimental shower unit C.E. Estrada-Perez – Water Research

Mapping the ‘hospital microbiome’ and the spread of antimicrobial resistance and biofilm on the intensive care units from different regions – Khalid Johani – Infection, Disease, and Health

A study of microbial communities on terracotta separator and on biocathode of air breathing microbial fuel cells – Laura Rago – Bioelectrochemistry

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes – Irena Maus – Biotechnology of Biofuels

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites – Baknoon Ham – Frontiers in Microbiology (Extreme Microbiology)

Food microbiology
Evaluation of microbial consortia and chemical changes in spontaneous maize bran fermentation – Marilù Decimo – AMB Express

Novel insights into microbial community dynamics during the fermentation of Central European ice wine – Mária Bučková – International Journal of Food Microbiology

Probiotics / prebiotics / antibiotics
Treatment efficacy of a probiotic preparation for non-alcoholic steatohepatitis: a pilot trial – Elina Manzhalii – Journal of Digestive Diseases

ReviewA Meta-Analysis of the Use of Probiotics to Alleviate Depressive Symptoms – Qin Xiang Ng – Journal of Affective Disorders

Review: Identification of probiotic effector molecules: present state and future perspectives – Sarah Lebeer – Current Opinion in Biotechnology

Review: Association between prior antibiotic therapy and subsequent risk of community-acquired infections: a systematic review – Umer Malik – Journal of Antimicrobial Therapy

Phages and viruses
The gut virome of the protochordate model organism, Ciona intestinalis subtype A – Brittany A. Leigh – Virus Research

Bioinformatics and statistical methods
Statistical analysis of co-occurrence patterns in microbial presence-absence datasets – Kumar P. Mainali – PLoS One

A Sequence-Based Mesh Classifier for the Prediction of Protein-Protein Interactions – Edgar D. Coelho – arXiv

Techniques
Analysis of single-cell genome sequences of bacteria and archaea – Robert M. Bowers – Emerging Topics in Life Sciences

A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites – John L. Chodkowski – mSystems

The inputs of metagenomics in the diagnostic of infectious diseases – G. Durand – Journal des Anti-infectieux

Genome announcements
Complete Genome Sequence of a Novel Nonnodulating Rhizobium Species Isolated from Agave americana L. Rhizosphere – Víctor Manuel Ruíz-Valdiviezo – genome Announcements

Complete Genome Sequence of Bacillus cereus C1L, a Plant Growth-Promoting Rhizobacterium from the Rhizosphere of Formosa Lily in Taiwan – Chien-Jui Huang – genome Announcements

Nocardia rhizosphaerihabitans sp. nov., a novel actinomycete isolated from a coastal soil – Peng Ding – International Journal of Systematic and Evolutionary Microbiology

The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics – Mohammad Bahram – PeerJ

*****************************
Microbes in the news
Gut bacteria at young age can contribute to MS disease onset and progression, study suggests – News Medical

Microbes on the market
Patent: Methods for distinguishing inflammatory bowel diseases using microbial community signatures – Wolfgang F. Fricke and James Robert White

Global Microbiome Sequencing Services Market Forecast to 2022 with Key Companies Profile, Supply, Demand, Cost Structure – Maciej Heyman – MilTech

Know about Microbiology Testing Market Posting +11% CAGR By 2022- Newly Invented Strategies, Healthcare Trends, Growth Opportunities, Forecast, & Key Players like Biomerieux S.A., Danaher, Becton, Dickinson and Company, Cepheid, Abbott, Alere, Bio-Rad Laboratories, Hologic, Bruker, F.Hoffmann-La Roche Ltd – MedGadget

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