Category Archives: Microbial Ecology

June 5, 2018

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A model to study the effect of horizontal gene transfer on maintaining equilibrium in microbial communities, antimicrobial tolerance in brewery biofilms, the sperm whale microbiota.

General microbiome

Horizontal Gene Transfer Can Help Maintain the Equilibrium of Microbial Communities – Yuhang Fan – Journal of Theoretical Biology

Human gut microbiome

Review: Carcinogenesis as a Result of Multiple Inflammatory and Oxidative Hits: a Comprehensive Review from Tumor Microenvironment to Gut Microbiota – Floriana Morgillo – Neoplasia

Animal experiments

Extrathymically Generated Regulatory T Cells Establish a Niche for Intestinal Border-Dwelling Bacteria and Affect Physiologic Metabolite Balance – Clarissa Campbell – Immunity

Animal microbiome

Pre-print: Microbiome interaction networks and community structure from lab-reared and field-collected Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus mosquito vectors – Shivanand Hegde – bioRxiv

Pre-print: Metagenomics reveals diet-specific specialization in fungus gardens of grass- and dicot-cutter ants – Lily Khadempour – bioRxiv

Occurrence of anthropozoonotic parasitic infections and faecal microbes in free-ranging sperm whales (Physeter macrocephalus) from the Mediterranean Sea – Carlos Hermosilla – Parasitology Research

Plant, root, and soil microbiome

Root-associated bacteria influencing mycelial growth of Tricholoma matsutake (pine mushroom) – Seung-Yoon Oh – Journal of Microbiology

Determinants of Soil Bacterial and Fungal Community Composition Toward Carbon-Use Efficiency Across Primary and Secondary Forests in a Costa Rican Conservation Area – Katie M McGee – Microbial Ecology

Water and extremophile microbiome

Pre-print: Competition and Synergy Between Prochlorococcus and Synechococcus Under Ocean Acidification Conditions – James Jeffrey Morris – bioRxiv

Quantifying the Relative Contributions of Environmental Sources to the Microbial Community in an Urban Stream under Dry and Wet Weather Conditions – Darshan Baral – Applied and Environmental Microbiology

The deep continental subsurface: the dark biosphere – Cristina Escudero – International Microbiology

Food microbiology

Competitive inter-species interactions underlie the increased antimicrobial tolerance in multispecies brewery biofilms – Ilse Parijs – ISME Journal

Phages and viruses

Influence of gut microbiome on mucosal immune activation and SHIV viral transmission in naive macaques – Yongjun Sui – Mucosal Immunity

Techniques

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

June 3, 2018

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Today’s digest full of great and fun studies including a fungal survey of the atmosphere and links between gut microbiome and MS.

General Microbiome

RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions. Egert M. Methods

Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics.Cardona C. mSystems

Biohydrogen production from space crew’s waste simulants using thermophilic consolidated bioprocessing.Wang J. Bioresource Technology

Prevalence of <i>Trichomonas vaginalis</i> infection and protozoan load in South African women: a cross-sectional study.de Waaij DJ.BMJ Open

Time course metabolome of Roux-en-Y gastric bypass confirms correlation between leptin, body weight and the microbiome.Seridi L. PLoS One

Gut Microbiome

A gut feeling about multiple sclerosis.Quintana FJ. Proceedings of the National Academy of Sciences

Dietary fat and gut microbiota: mechanisms involved in obesity control.Coelho OGL. Critical Reviews in Food Science and Nutrition

Probiotic Species in the Modulation of Gut Microbiota: An Overview.Azad MAK J. Biomedical Research International.

The Relationship between Frequently Used Glucose-Lowering Agents and Gut Microbiota in Type 2 Diabetes Mellitus.Lv Y. Journal of Diabetes Research

The Gut Microbiome Profile in Obesity: A Systematic Review.Castaner O. International Journal of Endocrinology.

The <i>Lactobacillus</i> Bile Salt Hydrolase Repertoire Reveals Niche-Specific Adaptation.O’Flaherty S. mSphere

Skin Microbiome

Early-life skin microbiota in hospitalized preterm and full-term infants.Younge NE. Microbiome.

Oral Microbiome

Stimulated and unstimulated saliva samples have significantly different bacterial profiles.Gomar-Vercher S. PLoS

Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status.Presti RM. AIDS

Oral microbiota in youth with perinatally acquired HIV infection. Starr JR. Microbiome

Air and Water Microbiome

Biogeochemical probing of microbial communities in a basalt-hosted hot spring at Kverkfjöll volcano, Iceland.Cousins CR. Geobiology

Taxonomic diversity of fungi deposited from the atmosphere.Woo C. ISME Journal.

Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.Garcia SL. mSphere.

Animal Experiments and Microbiome

Thermal processing of food reduces gut microbiota diversity of the host and triggers adaptation of the microbiota: evidence from two vertebrates.Zhang Z. Microbiome

Longevity extension in Drosophila through gut-brain communication.Westfall S. Scientific Reports

Exploring the diversity-stability paradigm using sponge microbial communities.Glasl B. Scientific Reports

Exploring the Microbiome of Callinectes sapidus (Maryland Blue Crab).Ramachandran P. Genome Announcements

Effect of different types of olive oil pomace dietary supplementation on the rumen microbial community profile in Comisana ewes.Mannelli F. Scientific Reports

Variation in faecal microbiota in a group of horses managed at pasture over a 12-month period.Salem SE. Scientific Reports

Intestinal microbiota composition is altered according to nutritional biorhythms in the leopard coral grouper (Plectropomus leopardus).Mekuchi M. PLoS One

Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors.Herstad KMV.PLoS One

Fungal, Bacterial, and Archaeal Diversity in the Digestive Tract of Several Beetle Larvae (Coleoptera). Ziganshina EE. Biomedical Research International.

Plant and Soil Microbiomes

Antibiotic Resistance in Plant-Pathogenic Bacteria. Sundin GW. Annual Review of Phytopathology

Characterization of Microbial Communities in Pilot-Scale Constructed Wetlands with <i>Salicornia</i> for Treatment of Marine Aquaculture Effluents.Ma X. Archaea.

Fall Armyworm-Associated Gut Bacteria Modulate Plant Defense Responses.Acevedo FE. Molecular Plant-Microbe Interactions

Multifunctional potential of endophytic and rhizospheric microbial isolates associated with Butia purpurascens roots for promoting plant growth.da Silva CF. Antonie Van Leeuwenhoek

Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition.Gołębiewski M. Microbial Ecology

In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana.Bartoli C. ISME Journal.

 

May 31, 2018

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Metagenomic analysis of the endangered kakapo fecal microbiota, a role for the microbiota in the social interaction habits of mice, using fecal metabolomics to readout functions of the gut microbiome.

General microbiome

Pre-print: Measuring the archaeome: detection and quantification of archaea signatures in the human body – Manuela R Pausan – bioRxiv

Human skin microbiome

Short‐term direct contact with soil and plant materials leads to an immediate increase in diversity of skin microbiota – Mira Grönroos – Microbiology Open

Human oral microbiome

Preliminary esophageal microbiome studies prompt important scientific questions – Yash Choksi – Clinical and Translational Gastroenterology

Human urinary microbiome

Calcium Oxalate Urolithiasis: A Case of Missing Microbes? – Carlos Alfredo Batagello – Journal of Endourology

Animal experiments

Social interaction-induced activation of RNA splicing in the amygdala of microbiome-deficient mice – Roman M Stilling – eLIFE

Differences in cecal microbiome of selected high and low feather-pecking laying hens – P Birkl – Poultry Science

Digestive microbiota is different in pigs receiving antimicrobials or a feed additive during the nursery period – Cassandra Soler – PLOS ONE

Dietary supplementation with yeast hydrolysate in pregnancy influences colostrum yield and gut microbiota of sows and piglets after birth – Shah Hasah – PLOS ONE

Dietary sodium butyrate improves intestinal development and function by modulating the microbial community in broilers – Wei Wu – PLOS ONE

Animal microbiome

Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo – David W Waite – Scientific Reports

Bacterial diversity and community structure of the intestinal microbiome of Channel Catfish (Ictalurus punctatus) during ontogenesis – Francisca A Burgos – Systematic and Applied Microbiology

Plant, root, and soil microbiome

Pre-print: Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes – Hirokazu Toju – bioRxiv

The importance of phyllosphere on plant functional ecology: a phyllo trait manifesto – Bruno H P Rosado – New Phytologist

Biocatalytic potential of Streptomyces spp. isolates from rhizosphere of plants and mycorrhizosphere of fungi – Jelena Spasic – Biotechnology and Applied Biochemistry

Hosts do not simply outsource pathogen resistance to protective symbionts – Jan Hrček – Evolution

Water and extremophile microbiome

Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench – Takuro Nunoura – Microbes and Environments

Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes – Amit Kumar – Microbial Ecology

Bloom of a denitrifying methanotroph, “Candidatus Methylomirabilis limnetica”, in a deep stratified lake – Jon S Graf – Environmental Microbiology

Food microbiology

Microbiome dynamics during spontaneous fermentations of sound grapes in comparison with sour rot and Botrytis infected grapes – Jessica Lleixà – International Journal of Food Microbiology

Pre-print: Microbial Community Structure and Diversity of Shrimp Paste at Different Fermentation Stages – Dai Lingying – bioRxiv

Bioinformatics

MetaHMM: A webserver for identifying novel genes with specified functions in metagenomic samples – Balázs Szalkai – Genomics

Metabolomics

The fecal metabolome as a functional readout of the gut microbiome – Jonas Zierer – Nature Genetics

More microbes

Pre-print: Aggregation of Vibrio cholerae by cationic polymers enhances quorum sensing but over-rides biofilm dissipation in response to autoinduction – Nicolas Perez-Soto – bioRxiv

Microbes in the news

Virus genes from city pond rescue bacteria – ScienceDaily

May 29, 2018

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Today we have an interesting review discussing the best practices for performing a microbiome study by R. Knight, “Microbial wars” – a brief overview on microbial competition by M.A. Bauer. Check many other interesting papers, particularly “crowded” section of Soil microbes, while in news you can read how scientists tested bacteria’s power to boost broccoli growth in space. Enjoy!

General microbiome

Review: Best practices for analysing microbiomes – Rob Knight – Nature Reviews Microbiology

Microbial wars: Competition in ecological niches and within the microbiome – Maria A. Bauer – Microbial Cell

Review: Concepts and Methods to Access Novel Antibiotics from Actinomycetes – Joachim J. Hug  – Antibiotics

 

 

Human gut microbiome

Gut Microbiota and Human Health: Insights From Ecological Restoration – Matthew R. Orr – The Quarterly Review of Biology

Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota – Ruairi C. Robertson – Microbiome

Current Evidence for the Management of Inflammatory Bowel Diseases Using Fecal Microbiota Transplantation – Seong Ran Jeon – Current Infectious Disease Reports

The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species – Melhem Bilen – Microbiome

Animal experiments

Gut microbes contribute to variation in solid organ transplant outcomes in mice – Christine M. McIntosh – Microbiome

Animal microbiome 

Necessary Sequencing Depth and Clustering Method to Obtain Relatively Stable Diversity Patterns in Studying Fish Gut Microbiota – Fanshu Xiao – Current Microbiology

Microbial shifts in the swine nasal microbiota in response to parenteral antimicrobial administration – Mohamed Zeineldin – Microbial Pathogenesis

Photobacterium malacitanum sp. nov., and Photobacterium andalusiense sp. nov., two new bacteria isolated from diseased farmed fish in Southern Spain – Alejandro M. Labella – Systematic and Applied Microbiology

Plant, root, and soil microbiome

Effects of genetically modified Burkholderia pyrrocinia JK-SH007E1 on soil microbial community in poplar rhizosphere – L. He – Forest Pathology

Dynamics of soil nitrogen fractions and their relationship with soil microbial communities in two forest species of northern China – Dong Liu – PLOS One

Short-term transcriptional response of microbial communities to N-fertilization in a pine forest soil – Michaeline B.N. Albright – Applied and Environmental Microbiology

Spatial structuring of soil microbial communities in commercial apple orchards – Greg Deakin – Applied Soil Ecology

Dynamics of soil nitrogen fractions and their relationship with soil microbial communities in two forest species of northern China – Dong Liu – PLOS One

Effects of winter snowpack and nitrogen addition on the soil microbial community in a temperate forest in northeastern China – Guoyong Yan – Ecological Indicators

Responses of soil bacterial communities to Conyza canadensis invasion with different cover classes along a climatic gradient* – Congyan Wang – CLEAN Soil Water

Shifts in microbial community structure and soil nitrogen mineralization following short-term soil amendment with the ammonifier Bacillus amyloliquefaciens DT – Cai Hui – International Biodeterioration & Biodegradation

Restoration with pioneer plants changes soil properties and remodels the diversity and structure of bacterial communities in rhizosphere and bulk soil of copper mine tailings in Jiangxi Province, China – Xiaoyan Sun – Environmental Science and Pollution Research

Enhancer assisted-phytoremediation of mercury-contaminated soils by Oxalis corniculata L., and rhizosphere microorganism distribution of Oxalis corniculata L. – Zhongchuang Liu – Ecotoxicology and Environmental Safety

Draft Genome Sequence of the Plant Growth-Promoting Sphingobium sp. Strain AEW4, Isolated from the Rhizosphere of the Beachgrass Ammophila breviligulata – Abanoub E. Wanees – Genome Announcements

Cultivar-specific response of bacterial community to cadmium contamination in the rhizosphere of rice (Oryza sativa L.)  – Dandi Hou – Environmental Pollution

Elevated CO2 increases the abundance but simplifies networks of soybean rhizosphere fungal community in Mollisol soils – Zhenhua Yu – Agriculture, Ecosystems & Environment

Suppression of Alternaria blight disease and plant growth promotion of mustard (Brassica juncea L.) by antagonistic rhizosphere bacteria – R. Sharma – Applied Soil Ecology

Water and extremophile microbiome

Salipaludibacillus halalkaliphilus sp. nov., a moderately haloalkaliphilic bacterium from a coastal-marine wetland – Mohammad Ali Amoozegar – International Journal of Systematic and Evolutionary Microbiology

Insights into Brevibacillus borstelensis AK1 through Whole Genome Sequencing: A Thermophilic Bacterium Isolated from a Hot Spring in Saudi Arabia – Amjad B. Khalil – BioMed Research International

Seasonal dynamics of bacterioplankton community in a large, shallow, highly dynamic freshwater lake – Zhaoyu Kong – Canadian Journal of Microbiology

Sediment microbial communities influenced by cool hydrothermal fluid migration – Laura A. Zinke – Frontiers in Microbiology / Extreme Microbiology

Microbial interactions with dissolved organic matter drive carbon dynamics and community succession’ – Xiaoqin Wu – Frontiers in Microbiology / Microbiological Chemistry and Geomicrobiology

Metabolites change of Scenedesmus obliquus exerted by AgNPs – Pu Wang – Journal of Environmental Sciences

Built environment

Cultivable microbial diversity associated with cellular phones – Rashmi Kurli – Frontiers in Microbiology / Systems Microbiology

Food microbiology

A bioinformatics pipeline integrating predictive metagenomics profiling for the analysis of 16S rDNA/rRNA sequencing data originated from foods – Marios Mataragas – Food Microbiology

Phages and viruses

Identification of a bacteriophage from an environmental multidrug-resistant E. coli isolate and its function in horizontal transfer of ARGs – Qiang Wang – Science of The Total Environment

Metagenomic analysis of the RNA fraction of the fecal virome indicates high diversity in pigs infected by porcine endemic diarrhea virus in the United States – Qi Chen – Virology Journal

Bioinformatics

Evaluating the use of diversity indices to distinguish between microbial communities with different traits – Sergey Feranchuka – Research in Microbiology

Taxonomic and functional compositions impacted by the quality of metatranscriptomic assemblies – Maggie Lau – Frontiers in Microbiology – Microbiological Chemistry and Geomicrobiology

Biotechnology

Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples – Zhichao Zhou – Applied Microbiology and Biotechnology

Systems analysis of phosphate-limitation-induced lipid accumulation by the oleaginous yeast Rhodosporidium toruloides – Yanan Wang – Biotechnology for Biofuels

Review: A decade of understanding secondary metabolism in Pseudomonas spp. for sustainable agriculture and pharmaceutical applications – Izzah Shahid – Environmental Sustainability

Microbes in the news

Could we work together with our bacteria to stop infection?

Scientists test bacteria’s power to boost broccoli growth in space

May 26, 2018

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We have a big variety of topics covered in today’s posts, from built environment to bat microbiome to biolfilms!

Biofilms

Genomic identification of microbial species adhering to maxillofacial prostheses and susceptibility to different hygiene protocols – Juliana Barchelli, The Journal of Bioadhesion and Biofilm Research

Anti-biofilm effect of a butenolide/polymer coating and metatranscriptomic analyses – Wei Ding, The Journal of Bioadhesion and Biofilm Research

Microbial ecology

Keystone taxa as drivers of microbiome structure and functioning – Samiran Banerjee, Nature Reviews Microbiology

Diversity, Stability, and Reproducibility in Stochastically Assembled Microbial Ecosystems – Akshit Goya, Physical Review Letters

Pregnancy and early life

Iron supplementation has minor effects on gut microbiota composition in overweight and obese women in early pregnancy – Marloes Dekker Nitert, British Journal of Nutrition

Human respiratory microbiome

The concordance between upper and lower respiratory microbiota in children with Mycoplasma pneumoniae pneumonia – Wenkui Dai, Emerging Microbes & Infections

The lung microbiome in children with HIV-bronchiectasis: a cross-sectional pilot study – Refiloe Masekela, BMC Pulmonary Medicine

Human skin microbiome

Does Lindioil (Indirubin) treatment affect the composition of Malassezia species on psoriatic skin? – Y. K. Lin, British Journal of Dermatology

Shift in skin microbiota of Western European women across aging – Romain Jugé, Journal of Applied Microbiology

Human vaginal microbiome

Understanding mucosal and microbial functionality of the female reproductive tract by metaproteomics: Implications for HIV transmission – Alicia R. Berard, American Journal of Reproductive Immunology

Vaginal microbiome studies in pregnancy must also analyse host factors – S.S. Witkin, BJOG: An International Journal of Obstetrics & Gynaecology

Vaginal microbiome in early pregnancy and subsequent risk of spontaneous preterm birth: a case‐control study – Negar Tabatabaei, BJOG: An International Journal of Obstetrics & Gynaecology

Human gut microbiome

Structural Alteration of Gut Microbiota during the Amelioration of Human Type 2 Diabetes with Hyperlipidemia by Metformin and a Traditional Chinese Herbal Formula: a Multicenter, Randomized, Open Label Clinical Trial – Xiaolin Tong, mBio

The role of diet in the aetiopathogenesis of inflammatory bowel disease – Hamed Khalili, Nature Reviews Gastroenterology & Hepatology

Animal experiments

Ethanolamine enhances intestinal functions by altering gut microbiome and mucosal anti-stress capacity in weaned rats – Jian Zhou, British Journal of Nutrition

Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses – Zhongming Ge, Scientific Reports

Evaluation of the impact of glyphosate and its residues in feed on animal health – European Food Safety Authority (EFSA), EFSA Journal

Risks for animal health related to the presence of fumonisins, their modified forms and hidden forms in feed – EFSA Panel on Contaminants in the Food Chain (CONTAM), EFSA Journal

Plateau hypoxia attenuates the metabolic activity of intestinal flora to enhance the bioavailability of nifedipine – Juanhong Zhang, Drug Delivery

Animal microbiome

Fecal Microbiota Composition Changes after a Body Weight Loss Diet in Beagle Dogs – A Salas, Journal of Animal Sciences

The fecal bacterial microbiota of bats; Slovenia – Modest Vengust, PLOS One

Plant, root, and soil microbiome

Fertilization shapes a well-organized community of bacterial decomposers for accelerated paddy straw degradation – Yushan Zhan, Scientific Reports

Paddy-upland rotation for sustainable agriculture with regards to diverse soil microbial community – Ping-Fu Hou, Scientific Reports

Annual post‐market environmental monitoring report on the cultivation of genetically modified maize MON 810 in 2016 – European Food Safety Authority (EFSA), EFSA Journal

Conserved Responses in a War of Small Molecules between a Plant-Pathogenic Bacterium and Fungi – Joseph E. Spraker, mBio

Pseudomonads contribute to regulation of Pratylenchus penetrans (Nematoda) populations on apple – Tristan T. Watson, Canadian Journal of Microbiology

Water and extremophile microbiome

Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm – Jennifer M. Michaud, Nature Communications

Combined genotyping, microbial diversity and metabolite profiling studies on farmed Mytilus spp. from Kiel Fjord – Caroline Utermann, Scientific Reports

Bathyarchaeota: globally distributed metabolic generalists in anoxic environments – Zhichao Zhou, FEMS Microbiology Reviews

Probiotics / prebiotics

Dietary fibers, prebiotics, and exopolysaccharides produced by lactic acid bacteria: potential health benefits with special regard to cholesterol-lowering effects – E. Korcz, Food and Function

Pharmacomicrobiomics: exploiting the drug-microbiota interactions in anticancer therapies – Concetta Panebianco, Microbiome

Built environment

City-scale distribution and dispersal routes of mycobiome in residences – Xinzhao Tong, Microbiome

Unraveling bacterial fingerprints of city subways from microbiome 16S gene profiles – Alejandro R. Walker, Biology Direct

Bioinformatics

ASaiM: a Galaxy-based framework to analyze microbiota data – Bérénice Batut, GigaScience

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers – Alexa B. R. McIntyre, Genome Biology

Techniques

The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain – Elena A. Oniciuc, Genes

A microbial endocrinology-based simulated small intestinal medium for the evaluation of neurochemical production by gut microbiota – Daniel N Villageliú, FEMS Microbiology Ecology

May 24, 2018

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Pest gut microbiota indirectly effects plant defenses in corn, evolution of microbial social behavior from shearing in flow environments, a model to predict cytokine responses based on multi-comics data integration.

General microbiome

Shearing in flow environment promotes evolution of social behavior in microbial populations – Gurdip Uppal – eLIFE

Pregnancy and early life

Review: The Neonatal Microbiome and Its Partial Role in Mediating the Association between Birth by Cesarean Section and Adverse Pediatric Outcomes – D Montoya-Williams – Neonatology

Human respiratory microbiome

Chronic rhinosinusitis with nasal polyps is characterized by dysbacteriosis of the nasal microbiota – Thanit Chalermwatanachai – Scientific Reports

Human oral microbiome

Metagenomic study of bacterial microbiota in persistent endodontic infections using Next‐generation sequencing – G Sánchez-Sanhueza – International Endodontic Journal

Human gut microbiome

Iron Sequestration in Microbiota Biofilms As A Novel Strategy for Treating Inflammatory Bowel Disease – Jean-Paul Motta – Inflammatory Bowel Diseases

Temporal and long‐term gut microbiota variation in allergic disease: A prospective study from infancy to school age – Kotryna Simonyté Sjödin – European Journal of Allergy and Clinical Immunology

Bangladeshi children with acute diarrhea show fecal microbiomes with increased Streptococcus abundance, irrespective of diarrhea etiology – Silas Kieser – Environmental Microbiology

Animal experiments

Effects of a protease and essential oils on growth performance, blood cell profiles, nutrient retention, ileal microbiota, excreta gas emission, and breast meat quality in broiler chicks – J H Park – Poultry Science

Colonic Inhibition of Phosphatase and Tensin Homolog Increases Colitogenic Bacteria, Causing Development of Colitis in Il10-/- Mice – Jonathon Mitchell – Inflammatory Bowel Diseases

Review: Microbial Signatures as a Predictive Tool in IBD—Pearls and Pitfalls – Nadine Waldschmitt – Inflammatory Bowel Diseases

Oral hydroxysafflor yellow A reduces obesity in mice by modulating the gut microbiota and serum metabolism – Juan Liu – Pharmacological Research

Impact of commensal flora on periodontal immune response to lipopolysaccharide – Daiki Fukuhara – Journal of Periodontology

Animal microbiome

Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes – Rocky D Patil – Journal of Animal Science

Plant, root, and soil microbiome

Cadmium phytoextraction potential of king grass (Pennisetum sinese Roxb.) and responses of rhizosphere bacterial communities to a cadmium pollution gradient – Li Hu – Environmental Science and Pollution Research

Gut-Associated Bacteria of Helicoverpa zea Indirectly Trigger Plant Defenses in Maize – Jie Wang – Journal of Chemical Ecology

Water and extremophile microbiome

Microbial activity during a coastal phytoplankton bloom on the Western Antarctic Peninsula in late summer – María E Alcamán-Arias – FEMS Microbiology Letters

Effects of partially saturated conditions on the metabolically active microbiome and on nitrogen removal in vertical subsurface flow constructed wetlands – Catiane Pelissari – Water Research

Pre-print: Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines – Andrian P Gajigan – PeerJ

Food microbiology

Porous Silicon-Based Biosensors: Towards Real-Time Optical Detection of Target Bacteria in the Food Industry – Naama Massad-Ivanir – Scientific Reports

Probiotics/prebiotics

Survival of Planktonic and Sessile Cells of Lactobacillus rhamnosus and Lactobacillus reuteri upon Exposure to Simulated Fasting-State Gastrointestinal Conditions – Kyle B Klopper – Probiotics and Antimicrobial Proteins

Phages and viruses

Pre-print: A novel oceanic uncultured temperate cyanophage lineage – José Flores-Uribe – bioRxiv

Bioinformatics

Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses – Olivier B Bakker – Nature Immunology

More microbes

Pre-print: New sequential touch method for determining bacterial contact transfer rate from finger to surface – Pengcheng Zhao – bioRxiv

Amy’s non-microbiology picks

Restoration of paper artworks with microemulsions confined in hydrogels for safe and efficient removal of adhesive tapes – Nicole Bonelli – PNAS

May 21, 2018

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A long update to make up for the past few days, with extra emphasis on Plant/root/soil studies and water studies!

General microbiome

Why do microbes exhibit weak biogeographic patterns? – Kyle M. Meyer, ISME

Understanding and designing the strategies for the microbe-mediated remediation of environmental contaminants using omics approaches – Muneer A. Malla, Frontiers in Microbiology

Two-year microbial adaptation during hydrogen-mediated biogas upgrading process in a serial reactor configuration – L. Treu, Bioresource Technology

Microbial ecology

Grazer-induced transcriptomic and metabolomic response of the chain-forming diatom Skeletonema marinoi – Alberto Amato, ISME

Cooperation, competition and antibiotic resistance in bacterial colonies – Isabel Frost, ISME

Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities – Tyler P. Barnum, ISME

Diversity and Hidden Host Specificity of Chytrids infecting Colonial Volvocacean Algae – Silke Van den Wyngaert, Journal of Eukaryotic Microbiology

Human bone microbiome

Understanding the microbiome of diabetic foot osteomyelitis: insights from molecular and microscopic approaches – Khalid Johani, Clinical Microbiology and Infection

Human oral microbiome

Bacterial-derived exopolysaccharides enhance antifungal drug tolerance in a cross-kingdom oral biofilm – Dongyeop Kim, ISME

Human vaginal microbiome

Metabolomics as a clinical testing method for the diagnosis of vaginal dysbiosis – Emiley Watson, American Journal of Reproductive Immunology

Human gut microbiome

Design and rationale of the INSYTE study: A randomised, placebo controlled study to test the efficacy of a synbiotic on liver fat, disease biomarkers and intestinal microbiota in non-alcoholic fatty liver disease – Eleonora Scorletti, Contemporary Clinical Trials

Gastrointestinal Disorders Associated with Primary Immunodeficiency Diseases – Stella Hartono, Clinical Reviews in Allergy & Immunology

Impact on the quality of life of an episode of Clostridium difficileinfection in a hospital setting – A. Duburcq, Journal of Epidemiology and Public Health

Animal experiments

Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome – Ece A. Mutlu, Environmental Pollution

Effects of long-term intake of a yogurt fermented with Lactobacillus delbrueckii subsp.bulgaricus 2038 and Streptococcus thermophilus1131 on mice – Yuki Usui, International Immunology

Dietary mung bean protein reduces high-fat diet-induced weight gain by modulating host bile acid metabolism in a gut microbiota-dependent manner – Akiho Nakatani, Biochemical and Biophysical Research Communications

Dietary nitrate modulates gut microbiota profile and prevents the activation of mucosal inflammatory pathways induced by broad-spectrum antibiotics – Bárbara S. Rocha, Free Radical Biology and Medicine

Animal microbiome

Coral bleaching from a single cell perspective – Daniel Aagren Nielsen, ISME

Plant, root, and soil microbiome

Lack of thinning effects over inter-annual changes in soil fungal community and diversity in a Mediterranean pine forest – Carles Castaño, Forest Ecology and Management

Response of soil microbial communities to agroecological versus conventional systems of extensive agriculture – Diego N. Chavarria, Agriculture, Ecosystems & Environment

Intraspecific variation in indirect plant–soil feedbacks influences a wetland plant invasion – Warwick J. Allen, Ecology

Native bacteria promote plant growth under drought stress condition without impacting the rhizomicrobiome – Elisabeth Armada, FEMS Microbiology Ecology

Plant roots redesign the rhizosphere to alter the three‐dimensional physical architecture and water dynamics – Sheikh M. F. Rabbi, New Phytologist

The Invasive Brazilian Pepper Tree (Schinus terebinthifolius) Is Colonized by a Root Microbiome Enriched With Alphaproteobacteria and Unclassified Spartobacteria – Karim Dawkins, Frontiers in Microbiology

Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation – Marie-Francoise Noirot-Gros, Frontiers in Microbiology

The Emergence of Endophytic Microbes and Their Biological Promise – Gary Strobel, Journal of Fungi

Changes in soil nitrogen dynamics caused by prescribed fires in dense gorse lands in SW Pyrenees – Leire Múgica, Science of The Total Environment

Response of soil microbial communities to agroecological versus conventional systems of extensive agriculture – Diego N. Chavarria, Agriculture, Ecosystems & Environment

Application of biosolids drives the diversity of antibiotic resistance genes in soil and lettuce at harvest – Lu Yang, Soil Biology and Biochemistry

Mycorrhizal Status In Endemic Pipewort: Eriocaulon eurypeplon Körn (Fam: Eriocaulaceae) – Vishal R. Kamble, IOSR Journal of Pharmacy and Biological Sciences

Model formulation of microbial CO2production and efficiency can significantly influence short and long term soil C projections – Ford Ballantyne IV & Sharon A. Billings, ISME

Effect of endophytic fungus Piriformospora indica on yield and some physiological traits of millet (Panicum miliaceum) under water stress – Goudarz Ahmadvand, Crop and Pasture Science

Composition and functional genes analysis of bacterial communities from urban parks of Shanghai, China and their role in ecosystem functionality – Xin Wang, Landscape and Urban Planning

Plant, fungal, bacterial, and nitrogen interactions in the litter layer of a native Patagonian forest – Lucía Vivanco​, PeerJ

Root-exuded coumarin shapes the root microbiome – Derek S. Lundberg, PNAS

Deforestation decreases spatial turnover and alters the network interactions in soil bacterial communities – Jing Tian, Soil Biology and Biochemistry

Distinct nitrogen provisioning from organic amendments in soil as influenced by farming system and water regime – Martina Lori, Frontiers in Microbiology

Biodiversity of urban soils for sustainable cities – C. Guilland, Environmental Chemistry Letters

Predator–prey mass ratio drives microbial activity under dry conditions in Sphagnum peatlands – Monika K. Reczuga, Ecology and Evolution

Organic and Biofertilization on Crop Production in Semiarid Regions – Ayman M. Helmy, The Handbook of Environmental Chemistry

Prevalence of Botrytis cinerea at different phenological stages of table grapes grown in the northern region of South Africa – Patricia C. Carmichael, Scientia Horticulturae

Water and extremophile microbiome

Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast – Cene Gostinčar, BMC Genomics

Interactive effects of multiple stressors revealed by sequencing total (DNA) and active (RNA) components of experimental sediment microbial communities – Simone C. Birrer, Science of The Total Environment

Physicochemical drivers of microbial community structure in sediments of Lake Hazen, Nunavut, Canada – Matti O. Ruuskanen, Frontiers in Microbiology

Strains of the toxic and bloom-forming Nodularia spumigena (cyanobacteria) can degrade methylphosphonate and release methane – Jonna E. Teikari, ISME

Seasonal resource conditions favor a summertime increase in North Pacific diatom–diazotroph associations – Christopher L. Follett, ISME

Predator and prey biodiversity relationship and its consequences on marine ecosystem functioning—interplay between nanoflagellates and bacterioplankton – Jinny Wu Yang, ISME

Light and temperature control the seasonal distribution of thaumarchaeota in the South Atlantic bight – Qian Liu, ISME

Distributions of phytoplankton carbohydrate, protein and lipid in the world oceans from satellite ocean colour – Shovonlal Roy, ISME

Relationship between dissolved organic matter quality and microbial community composition across polar glacial environments – H J Smith, FEMS Microbiology Ecology

Sediment depth-dependent spatial variations of bacterial communities in mud deposits of the eastern China marginal seas – Yanlu Qiao, Frontiers in Microbiology

Food microbiology

Origin and varietal based proteomic and peptidomic fingerprinting of Theobroma cacao in non-fermented and fermented cocoa beans – Neha Kumari, Food Research International

Metagenomic and metatranscriptomic analysis of the microbial community in Swiss-type Maasdam cheese during ripening – Ilhan Cem Duru, International Journal of Food Microbiology

Combined effect of cold atmospheric plasma, intrinsic and extrinsic factors on the microbial behavior in/on (food) model systems during storage – C. Smet, Innovative Food Science & Emerging Technologies

Polyphenols from selected dietary spices and medicinal herbs differentially affect common food-borne pathogenic bacteria and lactic acid bacteria – Chak-Lun Chan, Food Control

Probiotics

Enhanced viability of probiotics (Pediococcus pentosaceusLi05) by encapsulation in microgels doped with inorganic nanoparticles – Mingfei Yao, Food Hydrocolloids

Dysbiosis of microbiome and probiotic treatment in a genetic model of autism spectrum disorders – Tabouy Laure, Brain, Behavior, and Immunity

Bioinformatics

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation – Han Zhang, Nucleic Acids Research

A Multi-Omics Database for Parasitic Nematodes and Trematodes – John Martin, Eukaryotic Genomic Databases

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis – Jasmine Chong, Nucleic Acids Research

AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination – Alan J Medlar, Nucleic Acids Research

Techniques

Mutant phenotypes for thousands of bacterial genes of unknown function – Morgan N. Price, Nature

Methods for Generating Microbial Cocultures that Grow in the Absence of Fixed Carbon or Nitrogen – Matthew J. Smith, Synthetic Biology

Development of a 16S rRNA-targeted fluorescence in situ hybridization probe for quantification of the ammonia-oxidizer Nitrosotalea devanaterra and its relatives – C.X. Restrepo-Ortiz, Systematic and Applied Microbiology

Creation of a fibre categories database to quantify different dietary fibres – Stacey Fuller, Journal of Food Composition and Analysis

May 17, 2018

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Genome engineering tools for non-model prokaryotes, microgravity and space radiation’s effects on microbes, an analysis of science podcasts.

General microbiome

Taking the technical microbiome into the next decade – Jo De Vrieze – Environmental Microbiology

Pre-print: Links between environment, diet, and the hunter-gatherer microbiome – Gabriela K Fragiadakis – bioRxiv

Human vaginal microbiome

The effect of vaginal microbial communities on colonization by Staphylococcus aureus with the gene for toxic shock syndrome toxin 1 (TSST-1): a case–control study – Jacob D Pierson – FEMS Pathogens and Disease

Human urinary microbiome

Lactobacillus and Urine Microbiome in Association with Urinary Tract Infections and Bacterial Vaginosis – Jun-Mo Kim – Urogenital Tract Infection

Human gut microbiome

Combination Antibiotics Improves Disease Activity and Alters Microbial Communities In Children with Ulcerative Colitis – Kattayoun Kordy – Journal of Pediatric Gastroenterology and Nutrition

Animal experiments

Postnatal colonization with human “infant-type” Bifidobacterium species alters behavior of adult gnotobiotic mice – Berkley Luk – PLOS ONE

A gene catalogue of the Sprague-Dawley rat gut metagenome – Hudan Pan – Gigascience

Animal microbiome

Changes in intestinal microbiota of Bufo gargarizans and its association with body weight during metamorphosis – Lihong Chai – Archives of Microbiology

Metagenomic analysis of Varroa-free Australian honey bees (Apis mellifera) shows a diverse Picornavirales virome – John M K Roberts – Journal of General Virology

Plant, root, and soil microbiome

Strong associations between plant genotypes and bacterial communities in a natural salt marsh – Gregory P Zogg – Ecology and Evolution

What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs – Julian Taffner – mSphere

Rhizosphere hydrophobicity limits root water uptake after drying and subsequent rewetting – Mohsen Zarebanadkouki – Plant and Soil

Crop rotational diversity increases disease suppressive capacity of soil microbiomes – Ariane L Peralta – Ecosphere

Water and extremophile microbiome

A thiotrophic microbial community in an acidic brine lake in Northern Chile – Lorena Escudero – Antonie van Leeuwenhoek

Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium – Andrew Hart – PLOS ONE

Microbes in space

Review: Effect of microgravity & space radiation on microbes – Giuliana Senatore – Future Microbiology

Food microbiology

Bacterial community analysis in three types of the fermented seafood, jeotgal, produced in South Korea – Eun-Ji Song – Bioscience, Biotechnology, and Biochemistry

Metabolomics

Transcriptomic and metabolomic analyses reveal that bacteria promote plant defense during infection of soybean cyst nematode in soybean – Wenshu Kang – BMC Plant Biology

Techniques

Review: Building a genome engineering toolbox in non‐model prokaryotic microbes – Emily Freed – Biotechnology and Bioengineering

Pre-print: Effective soil extraction method for cultivating previously uncultured soil bacteria – Tuan Manh Nguyen – bioRxiv

More microbes

Disentangling complex parasite interactions: Protection against cerebral malaria by one helminth species is jeopardized by co-infection with another – Jessica L Abbate – PLOS Neglected Tropical Diseases

Pre-print: Nanotube-mediated cross-feeding couples the metabolism of interacting bacterial cells – Shraddha Shitut – bioRxiv

Science, career, and publishing

Pre-print: Science podcasts: analysis of global production and output from 2004 to 2018 – Lewis E MacKenzie – bioRxiv

May 15, 2018

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Comparison of the cottage cheese and artisanal cheese microbiota, no microbes found in amniotic fluid from healthy term pregnancies, impacts of ocean warming on the oyster microbiome.

General microbiome

Molecular (Me)micry? – Orly Avni – Cell Host & Microbe

Pregnancy and early life

Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community – Efrem S Lim – Microbiome

Multi-site human microbiome

Data on the gut and saliva microbiota from a cohort of atherosclerosis patients determined by 16S rRNA gene sequencing – Gregory B Gloor – Data in Brief

Human skin microbiome

Antiseptic Agents Elicit Short-Term, Personalized and Body Site-Specific Shifts in Resident Skin Bacterial Communities – Adam J SanMiguel – The Journal of Investigative Dermatology

Human gut microbiome

Review: Systematic review assessing the effectiveness of dietary intervention on gut microbiota in adults with type 2 diabetes – David Houghton – Diabetologia

Animal experiments

Increased butyrate priming in the gut stalls microbiome associated-gastrointestinal inflammation and hepatic metabolic reprogramming in a mouse model of Gulf War Illness – Ratanesh Kumar Seth – Toxicology and Applied Pharmacology

Light exposure influences the diurnal oscillation of gut microbiota in mice – Guangyan Wu – Biochemical and Biophysical Research Communications

Early-Life Antibiotic-Driven Dysbiosis Leads to Dysregulated Vaccine Immune Responses in Mice – Miriam Anne Lynn – Cell Host & Microbe

The effect of the timing of exposure to Campylobacter jejuni on the gut microbiome and inflammatory responses of broiler chickens – Phillippa L Connerton – Microbiome

Animal microbiome

Potential impacts of hypoxia and a warming ocean on oyster microbiomes – Bushra Khan – Marine Environmental Research

Mixed-Mode Transmission Shapes Termite Gut Community Assemblies – Rafael R da Costa – Trends in Microbiology

Plant, root, and soil microbiome

Effect of compost application on the dynamics of carbon in a nectarine orchard ecosystem – E Baldi – Science of the Total Environment

Review: Current research trends on plastic pollution and ecological impacts on the soil ecosystem: A review – Yooeun Chae – Environmental Pollution

Community structure and plant growth-promoting potential of cultivable bacteria isolated from Cameroon soil – Gylaine Vanissa Tchuisseu Tchakounté – Microbiological Research

Characterisation of antagonistic yeasts for biocontrol applications on apples or in soil by quantitative analyses of synthetic yeast communities – Simon Gross – Yeast

Water and extremophile microbiome

Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry – Ishfaq Nabi Najar – Science of the Total Environment

Exploring abundance, diversity and variation of a widespread antibiotic resistance gene in wastewater treatment plants – Ziyan Wei – Environment International

Antimicrobial resistance and potential virulence of Vibrio parahaemolyticus isolated from water and bivalve mollusks from Bahia, Brazil – Irana Paim Silva – Marine Pollution Bulletin

Diversity and distribution of Archaea in global estuarine ecosystems – Xiaobo Liu – Science of the Total Environment

Microbes in space

Acute exposure to space flight results in evidence of reduced lymph Transport, tissue fluid Shifts, and immune alterations in the rat gastrointestinal system – W E Cromer – Life Sciences in Space Research

Food microbiology

Using PacBio sequencing to investigate the bacterial microbiota of traditional Buryatian cottage cheese and comparison with Italian and Kazakhstan artisanal cheeses – Hao Jin – Journal of Dairy Science

Salmonella Cold Stress Response: Mechanisms and Occurrence in Foods – Steven C Ricke – Advances in Applied Microbiology

Probiotics/prebiotics

Strategies to improve the functionality of probiotics in supplements and foods – Claude P Champagne – Current Opinion in Food Science

Phages and viruses

Pre-print: Diversity of active viral infections within the Sphagnum microbiome – Joshua M A Stough – bioRxiv

Review: Composition of gut microbiota and its influence on the immunogenicity of oral rotavirus vaccines – Cliff A Magwira – Vaccines

Metabolomics

Review: A Review on Human Fecal Metabolomics: Methods, Applications and the Human Fecal Metabolome Database – Naama Karu – Analytica Chimica Acta

More microbes

Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance – D G Joakim Larsson – Environment International

May 10, 2018

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Today we have quite a few interesting papers in “Water microbiome”, there you can read about: drift in the community structuring of bacteria and microbial eukaryotes by R.Logares; phylogeny‐based database “EukRef–Ciliophora” by V. Boscaro;  diverse bacterial and viral populations in agricultural freshwater pond by J. Chopyk. In a “Bioinformatics” section you can read about “MIMOSA: Algorithms for Microbial Profiling” (by O. U. Nalbantoglu) and about use of SplinectomeR package in longitudinal microbiome studies by R.R. Shields- Cutler. Enjoy!

Jobs

PhD position for anaerobic microbiology of the Black Sea, Netherlands

General microbiome

Cargo Transport Shapes the Spatial Organization of a Microbial Community – Abhishek Shrivastava – bioRxiv

The Effect of Berberine on the Transcriptome and Proteome of E. coli – Zhang Shilei – bioRxiv

Predator-by-Environment Interactions Mediate Bacterial Competition in the Dictyostelium discoideum Microbiome – R. Fredrik Inglis – Frontiers in Microbiology / Evolutionary and Genomic Microbiology

Diversity time-period and diversity-time-area relationships exemplified by the human microbiome – Zhanshan (Sam) Ma – Scientific Reports

Pregnancy and early life

Microbial Biomarkers of Intestinal Barrier Maturation in Preterm Infants – Bing Ma – bioRxiv

Influence of human milk oligosaccharides on adherence of bifidobacteria and clostridia to cell lines – Musilova Sarka  – Acta Microbiologica et Immunologica Hungarica

 

Oral microbiome

Research on oral microbiota of monozygotic twins with discordant caries experience – in vitro and in vivo study – Hongle Wu – Scientific Reports

Glycemic Status Affects the Subgingival Microbiome of Diabetic Patients – Priscila Larcher Longo – Journal of Clinical Periodontology

Research on oral microbiota of monozygotic twins with discordant caries experience – in vitro and in vivo study – Hongle Wu – Scientific Reports

Human gut microbiome

Fecal microbiota transplantation in experimental ulcerative colitis reveals associated gut microbial and host metabolic reprogramming – Zhixiang Yan – Applied and Environmental Microbiology

Fecal microbiota transplantation treatment for refractory ulcerative colitis with allergy to 5-aminosalicylic acid: A case report – Hong-Gang Wang – Medicine

Review: Influence of Commensal Microbiota on the Enteric Nervous System and Its Role in Neurodegenerative Diseases – Endres K. – Journal of Innate Immunology

Loss of Ethanolamine Utilization in Enterococcus faecalis Increases Gastrointestinal Tract Colonization – Karan Gautam Kavala – mBio

Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi – Yan Zhang – mBio

Animal experiments

Effects of gut microbiota and time of treatment on tissue levels of green tea polyphenols in mice – Anna B. Liu – BioFactors

Gastrointestinal microbiota and mucosal immune gene expression in neonatal pigs reared in a cross-fostering model – Nidia Maradiaga – Microbial Pathogenesis

Prolonged restraint stressor exposure in outbred CD-1 mice impacts microbiota, colonic inflammation, and short chain fatty acids – Ross M. Maltz – PLOS One

Review: Biomarkers for monitoring intestinal health in poultry: present status and future perspective – Richard Ducatelle – Veterinary Research

Animal microbiome 

Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae – Ania T. Deutscher – Microbiome

Crown-of-thorns sea star, Acanthaster cf. solaris, have tissue-characteristic microbiomes with potential roles in health and reproduction – Lone Høja – Applied and Environmental Microbiology

Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate – Pål Trosvik – Microbiome

Antimicrobial activity in culturable gut microbial communities of springtails – Valeria Agamennone  – Journal of Applied Microbiology

Diversity and antimicrobial potential in sea anemone and holothurian microbiomes – Elizabeth León-Palmero  – PLOS One

Plant, root, and soil microbiome

Niche partition of phenanthrene-degrading bacteria along a Phragmites australis rhizosphere gradient – Xiaofei Lv – Biology and Fertility of Soils

Core microbiomes for sustainable agroecosystems – Toju H -Nature Plants

Determination of agricultural impact on soil microbial activity using δ18OP HCl and respiration experiments – Katherine Polain – ACS Earth and Space Chemistry

Seasonal dynamics of bacterial communities in a Betula albosinensis forest – C. Du – European Journal of Soil Science

Niche partition of phenanthrene-degrading bacteria along a Phragmites australis rhizosphere gradient – Xiaofei Lv – Biology and Fertility of Soils

Water and extremophile microbiome

Effects of Xiantao sewage treatment on microbial community structure of shallow groundwater in wetland – Shu-Fen Song – bioRxiv

Unexpected versatility in the metabolism and ecophysiology of globally relevant nitrite-oxidizing Nitrotoga bacteria – Andrew Boddicker – bioRxiv

Long-term seasonality of marine photoheterotrophic bacteria reveals low cohesiveness within the different phylogroups – Adrià Auladell – bioRxiv

Molecular cloning of glutathione peroxidase gene of Antarctic ice microalga Chlamydomonas sp. ICE‐L and its expression changes under temperature and salinity stress – Jin Hui Wang – Phycological Research

Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes – Ramiro Logares – Environmental Microbiology

EukRef–Ciliophora: A manually curated, phylogeny‐based database of small subunit rRNA gene sequences of ciliates – Vittorio Boscaro – Environmental Microbiology

Novel human-associated Lachnospiraceae genetic markers improve detection of fecal pollution sources in urban waters – Shuchen Feng – Applied and Environmental Microbiology

Municipal wastewater treatment potential and metal accumulation strategies of Colocasia esculenta (L.) Schott and Typha latifolia L. in a constructed wetland – Vivek Rana – Environmental Monitoring and Assessment

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations – Jessica Chopyk – Frontiers in Microbiology / Aquatic Microbiology

Characterization of a Highly Enriched Microbial Consortium Reductively Dechlorinating 2,3-Dichlorophenol and 2,4,6-Trichlorophenol and the Corresponding cprA Genes from River Sediment – Wael S. El-Sayed – Polish Journal of Microbiology

Built environment

Characterization of fungi in office dust: comparing results of microbial secondary metabolites, fungal ITS region sequencing, viable culture, and other microbial indices – Ju Hyeong Park – Indoor Air

Investigation of the Active Biofilm Communities on Polypropylene Filter Media in a Fixed Biofilm Reactor for Wastewater Treatment – Iffat Naz – Journal of Chemical Technology and Biotechnology

Food microbiology

Characterization of the contaminant bacterial communities in sugarcane first-generation industrial ethanol production – Maria L. Bonatelli – FEMS Microbiology Letters

Probiotics / prebiotics

Phylotype-level profiling of lactobacilli in highly complex environments by means of an ITS-based metagenomic approach – Christian Milani – Applied and Environmental Microbiology

Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization – Aleksandr A. Arzamasov – Frontiers in Microbiology /Evolutionary and Genomic Microbiology

 

Bioinformatics

MIMOSA: Algorithms for Microbial Profiling – Ozkan Ufuk Nalbantoglu – IEEE/ACM Transactions on Computational Biology and Bioinformatics

SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies – Robin R. Shields-Cutler – Frontiers in Microbiology / Systems Microbiology

Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation – Alaine B.Guerra – Environmental Pollution

Biotechnology

Microbial co-culturing systems: butanol production from organic wastes through consolidated bioprocessing – Yujia Jiang – Applied Microbiology and Biotechnology

Techniques

Sensitive detection of Live Escherichia coli by bacteriophage amplification-coupled immunoassay on the Luminex® MAGPIX instrument – Tomotaka Mido – bioRxiv

Microbes in the news

Scientists use dietary seaweed to manipulate gut bacteria in mice

Microbes are savvy investors when contributing to the common good