December 12, 2018

Today’s digest features a citizen science project which describes the two compositional patterns (stomatotypes) in the oral microbiota of adolescents. The study also explores the role of different factors like hygeine, diet, drinking water in shaping the oral microbiota. Enjoy!

Human oral microbiome

*Citizen science charts two major “stomatotypes” in the oral microbiome of adolescents and reveals links with habits and drinking water composition – Jesse R. Willis – Microbiome

Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation – Anna Edlund – Microbiome

Human gut microbiome

Review: Gut microbiota and inflammation in chronic kidney disease and their roles in the development of cardiovascular disease – Emine M. Onal – Hypertension Research

Animal experiments 

Zinc-amino-acid supplementation alters yearling ram rumen bacterial communities but zinc sulfate supplementation does not – Suzanne L Ishaq – Journal of Animal Science

Administration of antibiotics contributes to cholestasis in pediatric patients with intestinal failure via the alteration of FXR signaling – Yongtao Xiao – Experimental & Molecular Medicine

Intestinal microbiota mediates the susceptibility to polymicrobial sepsis‐induced liver injury by granisetron generation in mice – Shenhai Gong – Hepatology

Rumen microbiome in dairy calves fed copper and grape-pomace dietary supplementations: Composition and predicted functional profile – Filippo Biscarini – PLOS ONE

Plant, root, and soil microbiome

Rhizosheath microbial community assembly of sympatric desert speargrasses is independent of the plant host – Ramona Marasco – Microbiome

Water and extremophile microbiome

Review: Petroleum Hydrocarbon-Degrading Bacteria for the Remediation of Oil Pollution Under Aerobic Conditions: A Perspective Analysis – Xingjian Xu – Frontiers in Microbiology

Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution – Priscila A. Calderoli – PLOS ONE

Gene probing reveals the widespread distribution, diversity and abundance of isoprene-degrading bacteria in the environment – Ornella Carrión – Microbiome

Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave – Lise Alonso – Micrtobiome

Deep-sea anthropogenic macrodebris harbours rich and diverse communities of bacteria and archaea – Lucy C. Woodall – PLOS ONE

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December 5, 2018

Today’s digest features study on Lactobacillus reuteri HCM2 (against Enterotoxigenic Escherichia coli), microbiome and virome of deep terrestrial biosphere, immunostimulatory potential of the earliest gut microbiome, and more. Happy reading!

Gut microbiome

*Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential – Linda Wampach – Nature Communications

Review: Bone and the gut microbiome: a new dimension – Carolina Medina-Gomez – Journal of Laboratory and Precision Medicine

Review: Simple organizing principles in microbial communities – Jeff Gore – Current Opinion in Microbiology

Soil microbiome

*Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India – Avishek Dutta – Scientific Reports

Organic carbon amendments affect the chemodiversity of soil dissolved organic matter and its associations with soil microbial communities – Xiaoming Li – Environmental Science and Technology

Microbial organic matter degradation potential in Baltic Sea sediments influenced by depositional conditions and in situ geochemistry – Laura A. Zinke – Applied and Environmental Microbiology

Water microbiome

Performance and dynamic characteristics of microbial communities in multi-stage anaerobic reactors treating gibberellin wastewater – Erming Ouyang – Journal of Bioscience and Bioengineering

Phages and viruses

Bioaerosol Sampling for Respiratory Viruses in Singapore’s Mass Rapid Transit Network – Kristen Coleman – Scientific Reports

Review: Future management of viral diseases: role of new technologies and new approaches in microbial interactions – Fabrizio Maggi – Clinical Microbiology and Infection

*Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing – Rebecca A. Daly – Nature Microbiology

Animal experiments

*Lactobacillus reuteri HCM2 protects mice against Enterotoxigenic Escherichia coli through modulation of gut microbiota – Tianwei Wang – Scientific Reports

Bioinformatics

Ultra-deep, long-read nanopore sequencing of mock microbial community standards – Samuel M. Nicholls – BioRxiv

December 2, 2018

Highlights: Colonocyte metabolism shapes the gut microbiota, skin and gut microbiome of wild mammals, bacterial diversity in waterholes of Kruger National Park, Yeast diversity of glaciers, Laser MICROSAMPLING of soil community, origin & evolution of global RNA virome, Lymphoma virome dynamics, PUMA-for processing 16S rRNA taxonomy data  for analysis and visualization and many more.

General microbiome

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations – Raphael Eisenhofer – Trends in Microbiology

Review: Gut microbiota – our new important organ  – Rositsa Sandeva – Albanian Journal of Agricultural Sciences

Human gut microbiome

Altered gut microbiota after traumatic splenectomy is associated with endotoxemia – Hua Zhu – Emerging Microbes & Infections

Review: Colonocyte metabolism shapes the gut microbiota – Yael Litvak – Science

Gut Microbiota Modulates Interactions Between Polychlorinated Biphenyls and Bile Acid Homeostasis – Sunny Lihua Cheng – Toxilogical Sciences

Animal experiments 

An intensive milk replacer feeding program benefits immune response and intestinal microbiota of lambs during weaning – Qian Zhang – BMC Veterinary Research

Animal microbiome 

Bacterial diversity in the waterholes of the Kruger National Park: an eDNA metabarcoding approach – Maxwell J Farrell – Genome

Skin and gut microbiomes of a wild mammal respond to different environmental cues – Anton Lavrinienko – BMC Microbiome

Meta-Omics Tools in the World of Insect-Microorganism Interactions – Antonino Malacrinò – MDPI

Land Use Influences Antibiotic Resistance in the Microbiome of Soil Collembolans Orchesellides sinensis – Dong Zhu – Environmental Science and Technology

The equine gastrointestinal microbiome: Impacts of age and obesity – Philippa K. Morrison – Systems Microbiology

Changes in gut bacterial communities in canaries infected by Macrorhabdus ornithogaster – Patrizia Robino – Journal of Avian Pathology

Plant, root, and soil microbiome

Laser MICROSAMPLING of soil microbial community – M. V. Gorlenko – Journal of Biological Engineering

Poplar phyllosphere harbors disparate isoprene-degrading bacteria – Andrew T. Crombie – PNAS

Changes in litter quality induced by N deposition alter soil microbial communitiesYingbin Li – Soil Biology and Biochemistry

Analysis of Bacterial Communities in White Clover Seeds via High-Throughput Sequencing of 16S rRNA Gene – Wenna Gao – Current Microbiology

Impact of Bactrocera oleae on the fungal microbiota of ripe olive drupes – Ahmed Abdelfattah – PLoS One

Water and extremophile microbiome 

Preprint: Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure Lauren Gillies Campbell – bioRxiv

Review: Microbiologically influenced corrosion and current mitigation strategies: A state of the art review – Bhavya Kachiprath – Data in Brief

Habitat-specificity and diversity of culturable cold-adapted yeasts of a cold-based glacier in the Tianshan Mountains, northwestern China – Baolong Luo – Applied Microbiology and Biotechnology

Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal  – Aleksandra S. Zakharenko – Microbial Ecology

Phages and viruses

Origins and Evolution of the Global RNA Virome – Yuri I. Wolf – mBio

Lymphoma Virome Dynamics Revealed By Cell-Free DNA Sequencing – Joseph G Schroers-Martin – Blood

Techniques

Inner Workings: Mapping the microbiome location helps elucidate its role – Marcus Woo – PNAS

Preprint: FDA-ARGOS: A Public Quality-Controlled Genome Database Resource for Infectious Disease Sequencing Diagnostics and Regulatory Science Research – Heike Sichtig – bioRxiv

Preprint: PUMA: A tool for processing 16S rRNA taxonomy data for analysis and visualization – Keith Mitchell – bioRxiv

EMA-amplicon-based taxonomic characterisation of the viable bacterial community present in untreated and SODIS treated roof-harvested rainwater – André Strauss  -Environmental Science: Water Research & Technology

 

November 28, 2018

Influence of bacterial biofilms from vats on cheese characteristics, the fecal virome of wild ducks, variation in fungal diversity associated with olive trees.

Pregnancy and early life

Review: Strategies for the Preservation, Restoration and Modulation of the Human Milk Microbiota. Implications for Human Milk Banks and Neonatal Intensive Care Units – Leónides Fernández – Frontiers in Microbiology

Human vaginal microbiome

Vaginal microbiome in pregnant women according to trimester and its association with preterm birth: critical appraisal of a cross-sectional study – Dimitrios Papoutsis – Obstetrics & Gynecology Science

Human gut microbiome

Microbial-Host Interactions in Inflammatory Bowel Disease, Functional Bowel Disease, Obesity and Obesity-Related Metabolic Disease – Shailja C Shah – Gastroenterology

Animal experiments

Bioactive Food Abates Metabolic and Synaptic Alterations by Modulation of Gut Microbiota in a Mouse Model of Alzheimer’s Disease – Tauqeerunnisa Syeda – Journal of Alzheimer’s Disease

Extract of the Microalga Nitzschia laevis Prevents High-Fat-Diet Induced Obesity in Mice by Modulating the Composition of Gut Microbiota – Bingbing Guo

Effects of Taste Signaling Protein Abolishment on Gut Inflammation in an Inflammatory Bowel Disease Mouse Model – Ya-Wen Du – Journal of Visualized Experiments

Animal microbiome

Use of next generation sequencing to investigate the microbiota of experimentally induced wounds and the effect of bandaging in horses – Louis J Kamus – PLOS ONE

Plant, root, and soil microbiome

The chirality of imazethapyr herbicide selectively affects the bacterial community in soybean field soil – Hao Wu – Environmental Science and Pollution Research

Genome‐Wide Association studies on the phyllosphere microbiome: embracing complexity in host‐microbe interactions – Kathleen Beilsmith – The Plant Journal

Invasive plants differentially affect soil biota through litter and rhizosphere pathways: a meta‐analysis – Pei Zhang – Ecology Letters

Analysis of the community composition and bacterial diversity of the rhizosphere microbiome across different plant taxa – Shaonan Lei – MicrobiologyOpen

Spatial and temporal variation of fungal endophytic richness and diversity associated to the phyllosphere of olive cultivars – Patrick Materatski – Fungal Biology

Water and extremophile microbiome

Pre-print: Metagenomic Insights Unveil the Dominance of Undescribed Actinobacteria in Pond Ecosystem of an Indian Shrine – Radhakrishnan Manikkam – bioRxiv

Built environment

A procedure for identifying chemical and biological risks for books in historic libraries based on microclimate analysis – Eva Schito – Journal of Cultural Heritage

Food microbiology

Influence of the early bacterial biofilms developed on vats made with seven wood types on PDO Vastedda della valle del Belìce cheese characteristics – Raimondo Gaglio – International Journal of Food Microbiology

Probiotics/prebiotics

Microbial consortia: promising probiotics as plant biostimulants for sustainable agriculture – Sheridan L Woo – Frontiers in Plant Science

Phages and viruses

Fecal virome composition of migratory wild duck species – Luis Alfonso Ramírez-Martínez – PLOS ONE

November 27, 2018

Microbial communities of IBS patients after fecal microbiota transplantation, the shipworm gill-associated microbiota, a profile of bioartist Ani Liu in our “bacteria art” section.

Human skin microbiome

The Microbiome in Atopic Dermatitis – Amy S Paller – The Journal of Allergy and Clinical Immunology

Human gut microbiome

Microbiome dynamics in obesity – Christoph A Thaiss – Science

The kinetics of gut microbial community composition in patients with irritable bowel syndrome following fecal microbiota transplantation – Tarek Mazzawi – PLOS ONE

Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential – Christopher Bulow – mSphere

Comparison of the gut microbiota of obese individuals from different geographic origins – Emmanouil Angelakis – New Microbes and New Infections

Review: Fire in the Forest: Adverse Effects of Antibiotics on the Healthy Human Gut Microbiome – Manosha Perera – International Journal of Medical Reviews

Animal experiments

Proteomic Analysis of Microbial Induced Redox-Dependent Intestinal Signaling – Jason D Matthews – Redox Biology

Population and Culture Age Influence the Microbiome Profiles of House Dust Mites – Jan Hubert – Microbial Ecology

Animal microbiome

Symbiotic microbes affect the expression of male reproductive genes in Glossina m. morsitans – Francesca Scolari – BMC Microbiology

The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei – Thais L Brito – PLOS ONE

Plant, root, and soil microbiome

Host-specific signatures of the cell wall changes induced by the plant parasitic nematode, Meloidogyne incognita – Refik Bozbuga – Scientific Reports

The effects of struvite and sewage sludge on plant yield and the microbial community of a semiarid Mediterranean soil – F Bastida – Geoderma

Review: Effects of elevated carbon dioxide on environmental microbes and its mechanisms: A review – Tong Yu – Science of the Total Environment

Water and extremophile microbiome

Combining fish and benthic communities into multiple regimes reveals complex reef dynamics – Mary K Donovan – Scientific Reports

Diversity and predictive metabolic pathways of the prokaryotic microbial community along a groundwater salinity gradient of the Pearl River Delta, China – Shilei Sang – Scientific Reports

Bioinformatics

Pre-print: Naught all zeros in sequence count data are the same – Justin D Silverman – bioRxiv

Microbes in the news

A bacterium’s enemy isn’t your friend – Michael S. Gilmore – Nature

Bacteria art

Portrait of the Artist as a Microbial Growth – Kevin Litman-Navarro – The Outline

November 19, 2018

Today’s digest features shallow shotgun sequencing as a useful alternative to 16S sequencing, soil metaproteomics, virus genomes from deep sea sediments, and more. And there’s an important news: the MicroMundo has been launched in Portugal! Happy reading!

Events and jobs

Open Rank Faculty Position in Microbiome or Microbial Systems Research, Baylor College of Medicine in Houston, TX

Physalia courses: 16S/ITS Metabarcoding of microbial communities (Berlin, 1-5 April 2019) Instructors: Anna Sandionigi, Antti Karkman, Bruno Fosso

Physalia courses: Metagenomics (Berlin, 27-31 May 2019) Instructors: Dr. Curtis Huttenhower, Melanie Schirmer, Cesar Arze

Gut microbiome

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn’s Disease Patient – Xin Fang – Front. Microbio.

Preprint: Microbial Dysbiosis and polyamine metabolism as predictive markers for early detection during progression of pancreatic adenocarcinoma in spontaneous mouse model – Roberto Mendez – bioRxiv

Oral microbiome

Preprint: Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study – Francesco Beghini – bioRxiv

Preprint: Sociodemographic patterning in the oral microbiome of a diverse sample of New Yorkers – Audrey Renson – bioRxiv

Soil microbiome

*Review: Using proteins to study how microbes contribute to soil ecosystem services: The current state and future perspectives of soil metaproteomics – Robert Starke – Journal of Proteomics

Phages and viruses

Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters  – Yanze Li – Viruses

*Preprint: Virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism – Disa Backstrom – bioRxiv

Bioinformatics

*Evaluating the Information Content of Shallow Shotgun Metagenomics – Benjamin Hillmann – MySystems

A novel method to accurately calculate statistical significance of local similarity analysis for high-throughput time series – Fang Zhang – Stat Appl Genet Mol Biol.

KrakenUniq: confident and fast metagenomics classification using unique k-mer counts – Breitwieser Florian – Genome Biol.

MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data –Simon Lucas – Gigascience

Svetlana’s microbiology pick

* Last week was World Antibiotic Awareness Week and the MicroMundo project has been launched in Portugal:
Initially created in the USA (2012) as Small World Initiative, the MicroMundo is an innovative Citizen Science project where professors and researchers from the University of Porto encourage students to pursue career in science while addressing a worldwide health threat – antibiotic resistance.

November 16, 2018

Happy Friday! Today’s digest includes the effects of chewing gum on the oral microbiome, the gill microbiome of mangrove shipworms, and the rumen microbiome of dairy cows. Enjoy!

Human oral microbiome

Effects of xylitol-containing chewing gum on the oral microbiota – Takeuchi – Journal of Oral Science

Human gut microbiome

Gut microbiome transition across a lifestyle gradient in Himalaya – Jha – PLoS Biology

Fecal chromogranins and secretogranins are linked to the fecal and mucosal intestinal bacterial composition of IBS patients and healthy subjects – Sundin – Scientific Reports

Animal experiments

Specific Members of the Gut Microbiota are Reliable Biomarkers of Irradiation Intensity and Lethality in Large Animal Models of Human Health – Carbonero – Radiation Research

Gut microbiota development in mice is affected by hydrogen peroxide produced from amino acid metabolism during lactation – Shigeno – FASEB Journal

Commensal bacteria contribute to insulin resistance in aging by activating innate B1a cells – Bodogai – Science Translational Medicine

Estrogen-mediated gut microbiome alterations influence sexual dimorphism in metabolic syndrome in mice – Kaliannan – Microbiome

Effects of Intraoperative Vagal Nerve Stimulation on the Gastrointestinal Microbiome in a Mouse Model of Amyotrophic Lateral Sclerosis – Haney – Comparative Medicine

Animal microbiome

Assessing the Microbiota of Black Soldier Fly Larvae (Hermetia illucens) Reared on Organic Waste Streams on Four Different Locations at Laboratory and Large Scale – Wynants – Microbial Ecology

The gill-associated microbiome is the main source of wood plant polysaccharide hydrolases and secondary metabolite gene clusters in the mangrove shipworm Neoteredo reynei – Brito – PLoS One

Illumina sequencing analysis of the ruminal microbiota in high-yield and low-yield lactating dairy cows – Tong – PLoS One

Plant, root, and soil microbiome

Rootstocks shape the rhizobiome: Rhizosphere and endosphere bacterial communities in the grafted tomato system – Poudel – Applied and Environmental Microbiology

Water and extremophile microbiome

Aquatic ecotoxicity of an antidepressant, sertraline hydrochloride, on microbial communities – Yang – Science of The Total Environment

Probing the ecological and evolutionary history of a thermophilic cyanobacterial population via statistical properties of its microdiversity – Rosen – PLoS One

Built environment

Activated sludge bacterial communities of typical wastewater treatment plants: distinct genera identification and metabolic potential differential analysis – Zhang – AMB Express

Analysis of bacteria stress responses to contaminants derived from shale energy extraction – Santos – Environmental Science: Processes & Impacts

Probiotics/prebiotics

Gut microbiota of preterm infants supplemented with probiotics: sub-study of the ProPrems trial – Plummer – BMC Microbiology