May 19, 2017

A short digest for Sunday morning. Few interesting gut microbiome articles and Time magazine cover story about the next pandemic and novel detection technologies.

General microbiome

Antibiotics in a general population: Relations with gender, body mass index (BMI) and age and their human health risks – Sisi Liu -Science of the Total Environment

Human gut microbiome

A Clostridium difficile-Specific, Gel-Forming Protein Required for Optimal Spore Germination – ML Donnelly – MBio

The intestinal microbiome and paediatric liver disease – Daniel H Leung, MD – The Lancet

Plant, root, and soil microbiome

Review: Communication in the Phytobiome – Jan E. Leach – Cell

Food microbiology

The impact of nutrition on intestinal bacterial communities – Harry J Flint – Current opinion in Microbiology

Large-scale targeted metagenomics analysis of bacterial ecological changes in 88 kimchi samples during fermentation – Moeun Lee – Food microbiology

Probiotics / prebiotics

Designer probiotics for the prevention and treatment of human diseases – Koon Jiew Chua – Current opinion in chemical biology

Microbes in the news

Time magazine: The world is not ready for the next pandemic

Researchers find link between gut microbiome, osteoarthritis pain

April 24, 2017

Posted on April 24, 2017 by JP Cardenas

General Microbiome

Review: Ecology of the Oral Microbiome: Beyond Bacteria – Jonathon L. Baker – Trends in Microbiology

Dietary High Zinc Oxide Modulates the Microbiome of Ileum and Colon in Weaned Piglets – Ting Yu – Frontiers in Microbiology

Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut environments – Matthew L Jenior – BioRxiv

Review: Strategies to promote abundance of Akkermansia muciniphila, an emerging probiotics in the gut, evidence from dietary intervention studies – Kequan Zhou – Journal of Functional Foods

Protective effects of milk fermented by Lactobacillus plantarum B7 from Brazilian artisanal cheese on a Salmonella enterica serovar Typhimurium infection in BALB/c mice – Journal of Functional Foods

Pathogens

Molecular Demonstration of a Pneumocystis Outbreak in Stem Cell Transplant Patients: Evidence for Transmission in the Daycare Center – Frontiers in Microbiology

A New Rabbit-skin Model to Evaluate Protective Efficacy of Tuberculosis Vaccines – Xun Liu – Frontiers in Microbiology

Molecular epidemiology and antibiotic resistance profiles of methicillin-resistant Staphylococcus aureus strains in a tertiary hospital in China – Haishen Kong – Frontiers in Microbiology

Environmental Microbiology

Microbial community assembly differs by mineral type in the rhizosphere – Thea Whitman – BioRxiv

Interaction between DAPG and HCN producing Pseudomonas brassicacearum LBUM300 and Clavibacter michiganensis subsp. michiganensis in the rhizosphere of tomato – Applied Environmental Microbiology

Nitrogen-Fixing Populations Of Planctomycetes And Proteobacteria Are Abundant In The Surface Ocean – Tom O. Delmont – BioRxiv

Bacterial communities in boreal forest mushrooms are shaped both by soil parameters and host identity – Mari Pent – Frontiers in Microbiology

Genomics

Isoprenoid Pyrophosphate-Dependent Transcriptional Regulation of Carotenogenesis in Corynebacterium glutamicum – Nadja A. Henke – Frontiers in Microbiology

Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements – Xavier Argemi – Genome Biology and Evolution

Pooled CRISPR interference screens enable high-throughput functional genomics study and elucidate new rules for guide RNA library design in Escherichia coli – Tianmin Wang – BioRxiv

Evolution

Tunneling through time: Horizontal gene transfer constrains the timing of methanogen evolution – Joanna M. Wolfe – BioRxiv

Bioinformatics

AliTV-interactive visualization of whole genome comparisons – Markus J. Ankenbrand – PeerJ (not peer-reviewed)

TaxaSE: Exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation – Ali Z Ijaz – PeerJ (not peer-reviewed)

Other

Preprinting Microbiology – Patrick D Schloss – BioRxiv

Non – Microbiology picks

News: Scientists across the world take to the streets to demand freedom from political interference – The Telegraph (via Yahoo News)

Human umbilical cord plasma proteins revitalize hippocampal function in aged mice – Joseph M. Castellano – Nature

April 16, 2017

Posted on April 16, 2017 by aalexiev

A post with an overgrowth of gut and skin microbiome papers. Talk about dysbiosis!

General microbiome

The ovarian cancer oncobiome – Sagarika Banerjee – Oncotarget

A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam – Saurav Das – Genomics Data

Applying the design-build-test paradigm in microbiome engineering – Hoang Long Pham – Current Opinion in Biotechnology

Microbiota and their affiliation with physiochemical characteristics of different subsurface petroleum reservoirs – Xiao-Xiao Li – International Biodeterioration & Biodegradation

Sampling, sequencing and the SAD – Sharon Bewick – Ecological Complexity

Pregnancy and early life

The Maternal Diet, Gut Bacteria, and Bacterial Metabolites during Pregnancy Influence Offspring Asthma – Lawrence E. K. Gray – Frontiers in Immunology

Deficiency Leads to Dysbiosis and Bacterial Translocation in the Newborn Intestine – Jason Fawley – Journal of Surgical Research

Human respiratory microbiome

The microbiome of the lung and its extracellular vesicles in nonsmokers, healthy smokers and COPD patients – Hyun Jung Kim – Experimental & Molecular Medicine

Human skin microbiome

The Molecular Revolution in Cutaneous Biology: Investigating the Skin Microbiome – Heidi H. Kong – Journal of Investigative Dermatology

Microbiome controls mast cell differentiation in the skin – Z. Wang – Journal of Investigative Dermatology

Inflammatory gene expression in keratinocytes is regulated by HDAC8 and HDAC9 and is modulated by metabolites from the microbiome – J. Sanford – Journal of Investigative Dermatology

Ultraviolet radiation alters the skin microbiome composition – H. Ahmed – Journal of Investigative Dermatology

Isolation and Identification of the follicular microbiome: Implications for acne research – Amanda Nelson – Journal of Investigative Dermatology

Role of the cutaneous microbiome in the pathogenesis of psoriasis – D. Yan – Journal of Investigative Dermatology

Skin microbiome and psoriasis: Staphylococcus induces robust biofilm formation by Aspergillus – Pranab Mukherjee – Journal of Investigative Dermatology

Microbiome-free fatty acid cross-talk in the human pilosebaceous gland – S. Singh – Journal of Investigative Dermatology

Changes of lesional and non-lesional skin microbiome in the treatment course of atopic dermatitis – J. Na – Journal of Investigative Dermatology

Human gut microbiome

Clinical, functional, behavioural and epigenomic biomarkers of obesity – Claudio L. Lafortuna – Frontiers in Bioscience

‘Collinsella phocaeensis’ sp. nov., ‘Clostridium merdae’ sp. nov., ‘Sutterella massiliensis’ sp. nov., ‘Sutturella timonensis’ sp. nov., ‘Enorma phocaeensis’ sp. nov., ‘Mailhella massiliensis’ gen. nov., sp. nov., ‘Mordavella massiliensis’ gen. nov., sp. nov. and ‘Massiliprevotella massiliensis’ gen. nov., sp. nov., 9 new species isolated from fresh stool samples of healthy French patients – S. Ndongo – New Microbes and New Infections

Editorial: Understanding Crohn’s Disease: Immunity, Genes and Microbes – Amelia Sarmento – Frontiers in Immunology

Human Derived Gut Microbiota Modulates Colonic Secretion in Mice by Regulating 5-HT3 Receptor Expression via Acetate Production – Yogesh Bhattarai – American Journal of Physiology: Gastrointestinal and Liver Physiology

Gastroparesis and lipid metabolism-associated dysbiosis in Wistar Kyoto rats – Julie E Dalziel – American Journal of Physiology: Gastrointestinal and Liver Physiology

How do they stick together? Bacterial adhesins implicated in the binding of bacteria to the human gastrointestinal mucins – Bélinda Ringot-Destrez – Biochemical Society Transactions

Relationships between gut microbiota, plasma metabolites, and metabolic syndrome traits in the METSIM cohort – Elin Org – BioMed Central Genome Biology

Gut microbiota plays a role in the development of alopecia areata – Lekha Nair – Journal of Investigative Dermatology

Dysbiosis of gut microbiota by ampicillin exacerbates vitiligo – S. Akhtar – Journal of Investigative Dermatology

More frequent hemodialysis does not effectively clear protein-bound azotemic solutes derived from gut microbiome metabolism – Andrew Davenport – Kidney International

Gut microbiota and Hepatitis B virus-Induced Chronic Liver Disease: implications for faecal microbiota transplantation therapy – Yongbo Kang – Journal of Hospital Infection

The effect of probiotics as a treatment for constipation in elderly people: a systematic review – Maria Isabel Martínez-Martínez – Archives of Gerontology and Geriatrics

Colonic microbiota encroachment correlates with dysglycemia in humans – Benoit Chassaing – Cellular and Molecular Gastroenterology and Hepatology

Animal microbiome

Liver microbiome of Peromyscus leucopus, a key reservoir host species for emerging infectious diseases in North America – Adrien André – Infection, Genetics and Evolution

Plant, root, and soil microbiome

Conversion of rainforest into agroforestry and monoculture plantation in China: Consequences for soil phosphorus forms and microbial community – Jinchuang Wang – Science of the Total Environment

Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii) – Qiang Li – PLoS ONE

Draft Genome Sequence of Chryseobacterium sp. JV274 Isolated from Maize Rhizosphere – Jordan Vacheron – Genome Anouncements

Wars between microbes on roots and fruits – Ben Lugtenberg – F1000Research

Food microbiology

Metagenomic assessment of the microbial diversity in ground pork products from markets in the North Central Region of South Korea – Ok-Kyung Koo – Journal
Journal of Environmental Science and Health

Growth of selected probiotic bacterial strains with fructans from Nendran banana and garlic – Ravichandran Shalini – LWT: Food Science and Technology

Techniques

Suitability of various DNA extraction methods for a traditional Chinese paocai system –
Nan Zhao – Bioengineered

Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies – William W. Greenwald – BioMed Central Genomics

Microbes in the news

IISc makes two potent molecules to fight TB – Ravindranath Prasad – The Hindu

Essential California: Inside UC Irvine hospital’s bacteria outbreak among infants – Benjamin Oreskes and Shelby Grad – Los Angeles Times

April 15, 2017

Posted on April 15, 2017 by galit_ms

Few interesting articles for your Saturday morning digest: Urbanization alters the physicochemical environment: A new study suggests that urban soil archaeal and bacterial communities are not vulnerable to biodiversity loss, whereas global diversity loss of ectomycorrhizal fungi was observed. Researchers believe they have found a method of hunting for buried landmines and explosive devices using a combination of engineered bacteria and lasers. And another reason to be engaged in sports activities: a study highlights differences of microbiota and secondary metabolites in elite athletes.

General microbiome

Remote detection of buried landmines using a bacterial sensor – Shimshon Belkin – Nature Biotech

Next-generation approaches to understand and combat the antibiotic resistome – Terence S. Crofts – Nature Reviews

Human Oral Microbiome

Microbiomes of the normal middle ear and ears with chronic otitis media – Shujiro B. Minami – Laryngoscope

Human gut microbiome

The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level– Wiley Barton – Gut

The MS-Associated Gut Microbiome – Sergio E Baranzini – Multiple Sclerosis Journal

Mental Health

Oral treatment with Lactobacillus rhamnosus attenuates behavioral deficits and immune changes in chronic social stress – Aadil Bharwani – BMC Medicine

Animal microbiome

Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut – Janneke P. Ouwerkerk – Genome Announcements

Water and extremophile microbiome

Spatial variation in bacterial community in natural wetland-river-sea ecosystems –
Hongxia Zhang – J. of Basic Microbiology

Built environment

Urbanization erodes ectomycorrhizal fungal diversity and may cause microbial communities to converge – Dietrich JE Schmidt -Nature Ecology & Evolution

Prebiotics

Prebiotic evaluation of red seaweed (Kappaphycus alvarezii) using in vitro colon model – DM Bajury – International Journal of Food Sciences and Nutrition

April 11, 2017

Posted on April 11, 2017 by TinaS

In today’s Microbiome Digest the first interesting study comes not from bacteria but from virus domain. Examining the genomes within a sample from a wastewater treatment plant in Austria, Schulz et al. assembled a previously undiscovered giant virus genome with more genes encoding components of the protein translation machinery than in other giant viruses. The second highlighted study introduces new oleaginous microalga as a new potential source of compounds for biotechnological applications.

Events and jobs

QC Microbiology Analyst – Dublin, Ireland

Assistant Lecturer in Microbiology – Sligo, Ireland

General microbiome

The genetics of human longevity: an intricacy of genes, environment, culture and microbiome – Serena Dato – Mechanisms of Ageing and Development

Pregnancy and early life

Correlation between early-life regulation of the immune system by microbiota and allergy development – Thomas Gensollen – Journal of Allergy and Clinical Immunology

Microbial Community Assembly And Metabolite Profile Of The Gut Microbiome In Extremely Low Birthweight Infants – Stephen Wandro – bioRxiv

Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum – Chihaya Yamada – Cell Chemical Biology

A Comparative Study of Oral Microbiota in Infants with Complete Cleft Lip and Palate or Cleft Soft Palate – Agnieszka Machorowska-Pieniążek – BioMed Research International

Effect of probiotics on digestibility and immunity in infants: A study protocol for a randomized controlled trial – Lingli Xiao – Medicine

Human respiratory microbiome

Airway microbial dysbiosis in asthmatic patients: A target for prevention and treatment? – Kian Fan Chung – Journal of Allergy and Clinical Immunology

Oral microbiome

Measuring nitrate reductase activity from human and rodent tongues – Khandaker Ahtesham Ahmed – Nitric Oxide

Streptococcal adhesin SspA/B analogue peptide inhibits adherence and impacts biofilm formation of Streptococcus mutans – Tatsuro Ito – PLOSOne

Characterization of growth inhibition of oral bacteria by sophorolipid using a microplate-format assay – Daniel K.Y. Solaiman – Journal of Microbiological Methods

Salivary microbiome of an urban Indian cohort and patterns linked to subclinical inflammation – Aneesha Acharya – Oral Diseases

Second Era of OMICS in Caries Research: Moving Past the Phase of Disillusionment – M.M. Nascimento – Journal of Dental Research

Human skin microbiome

Bacterial communities on facial skin of teenage and elderly Thai females – Naraporn Somboonna – Archives of Microbiology

Skin microbiome and mast cells – Satomi Igawa – Translational Research

Human vaginal microbiome
Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions – John J. Schellenberg – Journal of Microbiological Methods

‘Anaerococcus mediterraneensis’ sp. nov., a new species isolated from human female genital tract – K. Diop – New Microbes and New Infections

Human gut microbiome

Functional relevance of microbiome signatures: The correlation era requires tools for consolidation – Ludovica F. Buttó – Journal of Allergy and Clinical Immunology

Physiochemical Tuning of Potent Escherichia coli Anti-Adhesives by Microencapsulation and Methylene Homologation – Dimitri Alvarez Dorta – ChemMedChem

Gut microbiota functions: metabolism of nutrients and other food components – Ian Rowland – European Journal of Nutrition

Evaluation of the impact of gut microbiota on uremic solute accumulation by a CE-TOFMS–based metabolomics approach – Eikan Mishima – Kidney International

Animal experiments

Starch-enriched diet modulates the glucidic profile in the rat colonic mucosa – Maria Gabriella Gabrielli – European Journal of Nutrition

The influence of diet on the grass carp intestinal microbiota and bile acids – Jing Zhang – Aquaculture Research

Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves – D.E. Gomez – Journal of Veterinary Internal Medicine

Gut Microbiota Modulation Attenuated the Hypolipidemic Effect of Simvastatin in High-Fat/Cholesterol-Diet Fed Mice – Xuyun He – Journal of Proteome Research

Animal microbiome

Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut – Clayton M. Small – Genome Biology and Evolution

The structured diversity of specialized gut symbionts of the New World army ants – Piotr Łukasik – Molecular Ecology

Microbial composition of spiny ants (Hymenoptera: Formicidae: Polyrhachis) across their geographic range – Manuela Oliveira Ramalho – BMC Evolutionary Biology

Plant, root, and soil microbiome

Isolation, identification, and environmental adaptability of heavy-metal-resistant bacteria from ramie rhizosphere soil around mine refinery – Jie Jiang – Biotech

Autogenic succession and deterministic recovery following disturbance in soil bacterial communities – Stephanie D. Jurburg – Scientific Reports

Microbial community response to hydration-desiccation cycles in desert soil – Adam Šťovíček – Scientific Reports

Water and extremophile microbiome

Development of an economical, autonomous pHstat system for culturing phytoplankton under steady state or dynamic conditions – Rachel L. Golda – Journal of Microbiological Methods

Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods – Sarita Pudasaini – Frontiers in Microbiology

Subduction zone forearc serpentinites as incubators for deep microbial life – Oliver Plümper – PNAS

Ferrous iron- and ammonium-rich diffuse vents support habitat-specific communities in a shallow hydrothermal field off the Basiluzzo Islet (Aeolian Volcanic Archipelago) – G. Bortoluzzi – Geobiology

Microbial biotechnology

Characterization of a Chlorophyta microalga isolated from a microbial mat in Salar de Atacama (northern Chile) as a potential source of compounds for biotechnological applications – Gladys Hayashida – Phycological Research

Real-time iTRAQ-based proteome profiling revealed the central metabolism involved in nitrogen starvation induced lipid accumulation in microalgae – Vineeta Rai – Scientific Reports

Food microbiology

Microbial communities associated with the anthropogenic, highly alkaline environment of a saline soda lime, Poland – Agnieszka Kalwasińska – Antonie van Leeuwenhoek

Probiotics / prebiotics

Genome Sequences of Potential Probiotic Lactobacillus rhamnosus Isolates from Human Infants – Jason W. Arnold – Genome Announcements

Phages and viruses

Review: Phage injection establishes CRISPR immunity – Shimona Starling – Nature Reviews Microbiology

Giant viruses with an expanded complement of translation system components – Frederik Schulz – Science

Bioinformatics

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism – Garrett W. Birkel – BMC Bioinformatics

Techniques

Identification of microorganisms grown on chromogenic media by MALDI-TOF MS – Petra Lüthje – Journal of Microbiological Methods

The impact of fecal sample processing on prevalence estimates for antibiotic-resistant Escherichia coli – Sylvia Omulo – Journal of Microbiological Methods

Chapter in the book: New Generation DNA Sequencing (NGS): Mining for Genes and the Potential of Extremophiles – Bhagwan Rekadwad – Microbial Applications Vol.1

Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling – Stefan A. Boers – Scientific Reports
Microbes in the news

Bacteria to the Future – Mizzou News (University of Missouri)

April 9, 2017

Posted on April 9, 2017 by Itumeleng

Today’s digest features interesting research on how keystone microbial taxa regulate invasion of pathogens in agricultural systems. Also, interesting pre-print on how the gut microbiome influences the lifespan of fish.

Human gut microbiome

De novo assembly of microbial genomes from human gut metagenomes using barcoded short read sequences. Moss. E. Biorxiv

Review: Updating on Gut Microbiota and its Relationship with the Occurrence of Necrotizing Enterocolitis (Review). Hosny, M. Human Microbiome Journal

Supplementation of Diet with Galacto-oligosaccharides Increases Bifidobacteria, but not Insulin Sensitivity, in Obese Prediabetic Individuals. Canfora, E. Gastroenterology

Independence of Gut Bacterial Content and Neonatal Necrotizing Enterocolitis Severity Barron, LK. Journal of Pediatric Surgery

Evaluation of the impact of gut microbiota on uremic solute accumulation by a CE-TOFMS–based metabolomics approach. Mishima, E.Kidney International

Human skin microbiome

Semi-automated quantitative analysis of the human skin microbiome diversity Kumagai, C. Journal of Dermatological Science

Human Skin Is the Largest Epithelial Surface for Interaction with Microbes. Gallo, R. Journal of Investigative Dermatology

Human milk microbiome

Human milk microbiome in urban and rural populations of India Yati, H. Meta Gene

Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum.Yamada, C. Cell Chemical Biology

Food microbiome

Microbial metabolites derived from colonic fermentation of non-digestible compounds. Tabernero, M. Current Opinion in Food Science

High relative humidity pre-harvest reduces post-harvest proliferation of Salmonella in tomatoes . Devleesschauwer, B. Food Microbiology

Plant and soil microbiome

Keystone microbial taxa regulate the invasion of a fungal pathogen in agro-ecosystems. Trivedi, P. Soil Biology and Biochemistry

In-depth analysis of core methanogenic communities from high elevation permafrost-affected wetlands. Yang, S. Soil Biology and Biochemistry

Strigolactones in Plant Interactions with Beneficial and Detrimental Organisms: The Yin and Yang. López-Ráez, JA. Trends in Plant Science

Animal microbiome

Regulation of Life Span by the Gut Microbiota in The Short-Lived African Turquoise Killifish. Smith, P. Biorxiv

Factors influencing ruminal bacterial community diversity and composition and microbial fibrolytic enzyme abundance in lactating dairy cows with a focus on the role of active dry yeast. AlZahal, O. Journal of Dairy Science

Organochloride pesticides modulated gut microbiota and influenced bile acid metabolism in mice. Liu, Q. Environmental Pollution

Growth performance of the very small rotifer Proales similis is more dependent on proliferating bacterial community than the bigger rotifer Brachionus rotundiformis. Le, DVB. Aquaculture

Evidence of Campylobacter jejuni reduction in broilers with early synbiotic administration Baffoni, L. International Journal of Food Microbiology

Raspberry pomace alters cecal microbial activity and reduces secondary bile acids in rats fed a high-fat diet. Fotschki, B.The Journal of Nutritional Biochemistry

Rumen microbial and fermentation characteristics are affected differently by acarbose addition during two nutritional types of simulated severe subacute ruminal acidosis in vitro. Wang, Y. Anaerobe.

Metabolomics

Targeting aggression in severe mental illness: The predictive role of genetic, epigenetic, and metabolomic markers Manchia, M. Progress in Neuro-Psychopharmacology and Biological Psychiatry

Prebiotics/Probiotics

A three-stage continuous culture approach to study the impact of probiotics, prebiotics and fat intake on faecal microbiota relevant to an over 60 s population. Liu. Y.Journal of Functional Foods

April 8, 2017

Posted on April 8, 2017 by bergmaureen

General microbiome

Modeling The Consequences Of Heterogeneity In Microbial Population Dynamics – Helena Herrmann – BioRxiv

Human respiratory microbiome

16S rRNA Gene Sequencing Reveals Site-Specific Signatures Of The Upper And Lower Airways Of Cystic Fibrosis Patients – Sarah K. Lucas – BioRxiv

Review: Airway microbial dysbiosis in asthmatic patients: A target for prevention and treatment? – Kian Fan Chung – The Journal of Allergy and Clinical Immunology

Human skin microbiome

Toxification of polycyclic aromatic hydrocarbons by commensal bacteria from human skin – Juliane Sowada – Archives of Toxicology

Human gut microbiome

Long-term use of antibiotics and risk of colorectal adenoma – Yin Cao – Gut

Changes in Composition of the Gut Bacterial Microbiome after Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in a Pediatric Heart Transplant Patient – Kyle L. Flannigan – Frontiers in Cardiovascular Medicine

Animal experiments

Iron Supplements Modulate Colon Microbiota Composition and Potentiate the Protective Effects of Probiotics in Dextran Sodium Sulfate-induced Colitis – Marco Constante – Inflammatory Bowel Diseases

Animal microbiome

Intestinal microbiota of healthy and unhealthy Atlantic salmon Salmo salar L. in a recirculating aquaculture system – Chun Wang – Chinese Journal of Oceanology and Limnology

Identification and modes of action of endogenous bacteria in taphonomy of embryos and larvae – Justin L. Eagan – Palaios

Microbial community compositions in the gastrointestinal tract of Chinese Mongolian sheep using Illumina MiSeq sequencing revealed high microbial diversity – Yan Zeng – AMB Express

Skin microbiota differs drastically between co-occurring frogs and newts – Molly C. Bletz – The Royal Society Open Science

Amphibian skin microbiota exhibits temporal variation in community structure but stability of predicted Bd-inhibitory function – Molly C Bletz – ISME

Plant, root, and soil microbiome

Characterization of a metagenome-derived protease from contaminated agricultural soil microorganisms and its random mutagenesis – Chengjian Jiang – Folia Microbiologica

Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests – Luis E Castañeda – PeerJ

Initial nitrogen enrichment conditions determines variations in nitrogen substrate utilization by heterotrophic bacterial isolates – Suchismita Ghosh – BMC Microbiology

Sequential bioavailability of sedimentary organic matter to heterotrophic bacteria – Nagissa Mahmoudi – Environmental Microbiology

Seasonal and interannual dynamics of soil microbial biomass and available nitrogen in an alpine meadow in the eastern part of Qinghai-Tibet Plateau, China – Bo Xu – Biogeosciences

Microbial Functional Capacity Is Preserved Within Engineered Soil Formulations Used In Mine Site Restoration – Deepak Kumaresan – Scientific Reports

Keystone microbial taxa regulate the invasion of a fungal pathogen in agro-ecosystems – P. Trivedi – Soil Biology and Biochemistry

Water and extremophile microbiome

Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater – William B. Ludington – PLOS ONE

Hidden diversity revealed by genome-resolved metagenomics of iron-oxidizing microbial mats from Lō’ihi Seamount, Hawai’i – Heather Fullerton – ISME

Performance and microbial community analysis in a modified anaerobic inclining-baffled reactor treating recycled paper mill effluent – Haider M. Zwain – Environmental Science and Pollution Research

Microbial formation of labile organic carbon in Antarctic glacial environments – H. J. Smith – Nature Geoscience

Review: Cryospheric science: The power of glacial microbes – Elizabeth B. Kujawinski – Nature Geoscience

Taxonomic composition of Lake Baikal bacterioneuston communities – A. D. Galach’yants – Microbiology

Performance and microbial population dynamics during stable operation and reactivation after extended idle conditions in an aerobic granular sequencing batch reactor – Qiulai He – Bioresource Technology

Comparative metagenomics reveals insights into the deep-sea adaptation mechanism of the microorganisms in Iheya hydrothermal fields – Hai-liang Wang – Journal of Marine Systems

Built environment

Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City – Julia M. Maritz – PLOS ONE

Food microbiology

The Dynamic Microbiota Profile During Pepper (Piper nigrum L.) Peeling by Solid-State Fermentation – Qisong Hu – Current Microbiology

Molecular investigation of bacterial communities during the manufacturing and ripening of semi-hard Iranian Liqvan cheese – M. Ramezani – Food Microbiology

Identification of microbial communities, with a focus on foodborne pathogens, during kimchi manufacturing process using culture-independent and -dependent analyses – Hae-Won Lee – LWT – Food Science and Technology

Probiotics / prebiotics

Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial – Judit Villar-García – PLOS ONE

Phages and viruses

Taxonomic variability and functional stability in microbial communities infected by phages – Stilianos Louca – Environmental Microbiology

Bioinformatics

EzMap: A Simple Pipeline for Reproducible Analysis of the Human Virome – Patrick Czeczko – Bioinformatics

Microbes in the news

You Should Appreciate Germs – Bill Gates

Microbes on the market

The expanding ecosystem of microbiome startups – Juliet Preston – MedCity News

April 6, 2017

Posted on April 6, 2017 by JP Cardenas

Jobs

Microbial genomics expert : Basel, Switzerland via Nature Jobs

University Lecturer/University Senior Lecturer in Microbiology : Cambridge, United Kingdom via Nature Jobs

Microbiome Research

Review: Gut Microbiota Modulation and Its Relationship with Obesity Using Prebiotic Fibers and Probiotics: A Review – Dinesh K. Dahiya – Frontiers in Microbiology

Mini-Review: Linking Diet to Colorectal Cancer: The Emerging Role of MicroRNA in the Communication between Plant and Animal Kingdoms – Manuela Del Cornò – Frontiers in Microbiology

Comparative Analysis of the Gut Microbial Communities in Forest and Alpine Musk Deer Using High-Throughput Sequencing – Xiaolong Hu – Frontiers in Microbiology

Complex pectin metabolism by gut bacteria reveals novel catalytic functions – Didier Ndeh – Nature

State of the Art: The association of the skin microbiota with health, immunity and disease – Markus Egert – Clinical Pharmacology and Therapeutics

Human milk oligosaccharide composition predicts risk of necrotising enterocolitis in preterm infants – Chloe A Autran – Gut (BMJ)

Targeting the gut microbiota with inulin-type fructans: preclinical demonstration of a novel approach in the management of endothelial dysfunction – Emilie Catry – Gut (BMJ)

Exposure to household furry pets influences the gut microbiota of infant at 3–4 months following various birth scenarios – Hein M. Tun – Microbiome (BMC)

Probiotics – Prebiotics

Antimicrobial Compounds Produced by Vaginal Lactobacillus crispatus Are Able to Strongly Inhibit Candida albicans Growth, Hyphal Formation and Regulate Virulence-related Gene Expressions – Shuai Wang – Frontiers in Microbiology

Oral administration of Lactobacillus gasseri SBT2055 is effective in preventing Porphyromonas gingivalis-accelerated periodontal disease – R. Kobayashi – Scientific Reports

Commentary: Inulin prebiotic: is it all about bifidobacteria? – Sandrine Paule Claus – Gut (BMJ)

Extremophiles

Relative importance of chemoautotrophy for primary production in a light exposed marine shallow hydrothermal system – Gonzalo V. Gomez-Saez – Frontiers in Microbiology

The ecology of acidophilic microorganisms in the corroding concrete sewer environment – Xuan Li – Frontiers in Microbiology

Pathogen Research

A geographically widespread outbreak investigation and development of a rapid screening method using whole genome sequences of enterohemorrhagic Escherichia coli O121 – Ken-Ichi Lee – Frontiers in Microbiology

Comprehensive Diagnosis of Bacterial Infection Associated with Acute Cholecystitis using Metagenomic Approach – Manabu Kujiraoka – Frontiers in Microbiology

In vitro transfer of methicillin resistance determinants mecA from methicillin resistant Staphylococcus aureus (MRSA) to methicillin susceptible Staphylococcus aureus (MSSA) – Asinamai Athliamai Bitrus – BMC Microbiology

Effects of Pseudomonas aeruginosa and Streptococcus mitis mixed infection on TLR4-mediated immune response in acute pneumonia mouse model – Chao Song – BMC Microbiology

Mosquito Microbiome Dynamics, a Background for Prevalence and Seasonality of West Nile Virus – Eva Novakova – Frontiers in Microbiology

Supplemental invasion of Salmonella from the perspective of Salmonella enterica serovars Kentucky and Typhimurium – Kevin Howe – BMC Microbiology

Whole-genome comparative analysis of Salmonella enterica serovar Newport strains reveals lineage-specific divergence – Jie Zheng – Genome Biology and Evolution

Evolution

Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) – David W. Waite – Frontiers in Microbiology

Evolutionary dynamics of CRISPR gene drives – Charleston Noble – Science Advances

Methods

Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling – Stefan A. Boers – Scientific Reports

A Novel Ultra High-Throughput 16S rRNA Amplicon Sequencing Library Preparation Method On The Illumina HiSeq Platform – Eric J. de Muinck – BioRxiv

Improving ancient DNA genome assembly – Alexander Seitz – PeerJ (peer-reviewed)

Bioinformatic Tools

ATLAS (Automatic Tool for Local Assembly Structures) – a comprehensive infrastructure for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data – Richard Allen White III – PeerJ Preprints

News

Science Article Post: Ph.D. students face significant mental health challenges – Elisabeth Pain

News: A deep dive into the genomes of penicillin fungi reveals a trove of potential drugs via Cosmos Magazine

	Francis W on The Hetch Hetchy Railroad
	Best Practice Exchan… on June 1, 2018
	May 17, 2024 \| Micro… on May 15, 2024
	Kathy Brown on The Hetch Hetchy Railroad
	John Wilbur on The Hetch Hetchy Railroad

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Microbiome research

Pathogen microbiology

Probiotics – Prebiotics

Antimicrobials

Genomics

Microbiology – Other

non-Microbiology picks

Events and jobs

General microbiome

Human gut microbiome

Animal microbiome

Plant, root, and soil microbiome

Water and extremophile microbiome

Food microbiology

Techniques

Microbes in the news

Microbes on the market

Science, publishing, and career

General microbiome

Human gut microbiome

Plant, root, and soil microbiome

Food microbiology

Probiotics / prebiotics

Microbes in the news

General microbiome

Human Oral Microbiome

Human gut microbiome

Mental Health

Animal microbiome

Water and extremophile microbiome

Built environment

Prebiotics

General microbiome

Human respiratory microbiome

Human skin microbiome

Human gut microbiome

Animal experiments

Animal microbiome

Plant, root, and soil microbiome

Water and extremophile microbiome

Built environment

Food microbiology

Probiotics / prebiotics

Phages and viruses

Bioinformatics

Microbes in the news

Microbes on the market