Category Archives: Resistome

15 April, 2018

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Today’s digest features an interesting article on microbial resevoirs in an urban setting, and influence of sequencing depth in chareterising the resistome .

General Microbiome

Diversity of the midstream urine microbiome in adults with chronic kidney disease.Kramer H. International Urology and Nephrology

Oral/Gut Microbiome

Quantitative Assessment of Shotgun Metagenomics and 16S rDNA Amplicon Sequencing in the Study of Human Gut Microbiome.Laudadio I. OMICS

The role of the gut microbiota in the pathology and prevention of liver disease.Altamirano-Barrera A. Journal of Nutritional Biochemistry

Effects of green tea on miRNA and microbiome of oral epithelium.Adami GR. Scientific Reports

Plant, Soils, and Water Microbiome

High-throughput sequencing reveals microbial communities in drinking water treatment sludge from six geographically distributed plants, including potentially toxic cyanobacteria and pathogens.Xu H. Science of Total Environment

Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity.Charlop-Powers Z. PNAS

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience.Mandakovic D. Scientific Reports

Multivariate relationships between microbial communities and environmental variables during co-composting of sewage sludge and agricultural waste in the presence of PVP-AgNPs.Zhang L. Bioresources Technology

Animal Experiments and Microbiome

Gut microbiota recovery and immune response in ampicillin-treated mice.Castro-Mejía JL. Research in Veterinary Sciences

When the Nose Doesn’t Know: Canine Olfactory Function Associated With Health, Management, and Potential Links to Microbiota.Jenkins EK. Frontiers in Veterinary Sciences

Resistome

Microbiota transplantation and/or CRISPR-Cas in the battle against antimicrobial resistance.Vila J. Clinical Microbiology and Infection

Impact of sequencing depth on the characterization of the microbiome and resistome.Zaheer R. Scientific Reports

April 3, 2018

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Human Microbiome

Non-Ischemic Heart Failure With Reduced Ejection Fraction Is Associated With Altered Intestinal Microbiota – Themistoklis Katsimichas – Circulation Journal

The impact of antibiotics on the Intestinal microbiota needs to be re-defined in order to optimize the antibiotic usage – Bryan Coburn – Clinical Microbiology and Infection

The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia – Chaoting Zhang – Cancer Medicine

Review: The use of probiotics in different phases of diverticular disease – Veronica Ojetti – Reviews on Recent Clinical Trials

Fecal microbiota transplantation and its potential therapeutic uses in gastrointestinal disorders – Ryan D. Heath – Northern clinics of Istanbul

Dysbiosis of the salivary microbiota in pediatric-onset primary sclerosing cholangitis and its potential as a biomarker – Kentaro Iwasawa – Scientific Reports

Microbiota Composition May Predict Anti-Tnf Alpha Response in Spondyloarthritis Patients: an Exploratory Study – Thomas Bazin – Scientific Reports

Research Highlight: Obesity: ANGPTL4 — the link binding obesity and glucose intolerance – Alan Morris – Nature Reviews Endocrinology

Influence of intrauterine administration of Lactobacillus buchneri on reproductive performance and pro-inflammatory endometrial mRNA expression of cows with subclinical endometritis – S. Peter – Scientific Reports

Review: Overview of Current Concepts in Gastric Intestinal Metaplasia and Gastric Cancer – David S. Jencks – Gastroenterology & Hepatology

 

Animal Microbiome

Psychoneuroimmunology and immunopsychiatry of zebrafish – Murilo S.de Abreu – Psychoneuroendocrinology

Regulation of growth, intestinal microbiota, non-specific immune response and disease resistance of sea cucumber Apostichopus japonicus (Selenka) in biofloc systems – Jinghua Chen – Fish & Shellfish Immunology

Loss of microRNA-21 Influences the Gut Microbiota Causing Reduced Susceptibility in a Murine Model of Colitis – Daniel G W Johnston – Journal of Crohn’s and Colitis

Influence of Long-Term Feeding Antibiotics on the Gut Health of Zebrafish – Zhou Li – Zebrafish

Effects of Intestinal Microbiota on Brain Development in Humanized Gnotobiotic Mice – Jing Lu – Scientific Reports

Long-term Western diet fed apolipoprotein E-deficient rats exhibit only modest early atherosclerotic characteristics – Ida Rune – Scientific Reports

 

Methods

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing – Ayelet Di Segni – Journal Of Visualized Experiments (It includes a video)

 

Food Microbes

Tetracycline resistance in lactobacilli isolated from Serbian traditional raw milk cheeses – Tijana Ledina – Journal of Food Science and Technology

 

Pathogens

Case Report: Successful Fecal Microbiota Transplantation in a Patient with Severe Complicated Clostridium difficile Infection after Liver Transplantation – Schneider K.M. – Case Reports in Gastroenterology

Review: Significance of Streptococcus gallolyticus subsp. gallolyticus Association With Colorectal Cancer – Ewa Pasquereau-Kotula – Frontiers in Microbiology

Review: Helicobacter pylori the Latent Human Pathogen or an Ancestral Commensal Organism – Jackie Li –  Frontiers in Microbiology

Fungi-Induced Upper and Lower Respiratory Tract Allergic Diseases: One Entity – Aleksandra Barac – Frontiers in Microbiology

Genetic and Virulent Difference Between Pigmented and Non-pigmented Staphylococcus aureus – Jing Zhang – Frontiers in Microbiology

 

Environmental Microbes

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba – Patricia M. Valdespino-Castillo – Frontiers in Microbiology

Direct and Indirect Effects of Penguin Feces on Microbiomes in Antarctic Ornithogenic Soils – Yudong Guo – Frontiers in Microbiology

 

Other

Combination of peracetic acid and ultrasound reduces Salmonella Typhimurium on fresh lettuce (Lactuca sativa L. var. crispa) – Luiza Oliveira Silveira – Journal of Food Science and Technology

Recent advances in the physiopathology of IgA nephropathy – Renato C. Monteiro – Néphrologie & Thérapeutique

 

April 2, 2018

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Have a good monday! Today, in Microbiome Digest: interesting papers about Clostridium difficile, the use of Fecal Microbiota Transplant, studies in mice model, effect of Lactobacillus on Candida, antibiotic-resistant bacteria in sewerage biofilms, and more!

 

Human/General Microbiome

Diet, gut microbiota composition and feeding behavior – Jiyoung S. Kim – Physiology & Behavior

Fecal Microbiota Transplantation in Inflammatory Bowel Disease- a Primer for the Internists – Gaurav Syal – The American Journal of Medicine

Oral microbiota maturation during the first 7 years of life in relation to allergy development – Majda Dzidic – Allergy

The tangled web of interactions between host, pathogen and microbiota in C. difficile infection – Anna Maria Seekatz – Gastroenterology

Analysis of Treatment Outcomes for Recurrent Clostridium difficile Infections and Fecal Microbiota Transplantation in a Pediatric Hospital – Aileen Aldrich – The Pediatric Infectious Disease Journal

Role of microbiota in the autism spectrum disorders – Daniela Campion – Minerva Gastroenterologica e Dietologica

From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota – Eugen Bauer – mSystems

Developing a Bacteroides System for Function-Based Screening of DNA from the Human Gut Microbiome – Kathy N. Lam – mSystems

Is a Single Fecal Microbiota Transplant a Promising Treatment for Recurrent Clostridium difficile Infection? – Susy S Hota – Open Forum Infectious Diseases

Bronchoalveolar lavage fluid microbiota dysbiosis in infants with protracted bacterial bronchitis – Yanmin Bao – Journal of Thoracic Disease

Mother’s Milk: A Purposeful Contribution to the Development of the Infant Microbiota and Immunity – Kirsty Le Doare –  Frontiers in Immunology

Contributory Role of Gut Microbiota and Their Metabolites Toward Cardiovascular Complications in Chronic Kidney Disease – Daniel Y. Li – Seminars in Nephrology

Differential bacterial capture and transport preferences facilitate co-growth on dietary xylan in the human gut – Maria Louise Leth – Nature Microbiology

 

Animal Microbiome / Animal Experiments

Two new gene clusters involved in the degradation of plant cell wall from the fecal microbiota of Tunisian dromedary – Rihab Ameri – PLoS One

Honey Bee Antiviral Immune Barriers as Affected by Multiple Stress Factors: A Novel Paradigm to Interpret Colony Health Decline and Collapse – Francesco Nazzi – Viruses

Influence of Intestinal Microbiota Transplantation and NleH Expression on Citrobacter rodentium Colonization of Mice – Gaochan Wang – Pathogens

Shifts in the Gut Metabolome and Clostridium difficile Transcriptome throughout Colonization and Infection in a Mouse Model – Joshua R. Fletcher – mSystems

Akkermansia muciniphila is permissive to arthritis in the K/BxN mouse model of arthritis – Matthew L Stoll – Genes & Immunity

The Gut Microbiota Regulates Endocrine Vitamin D Metabolism through Fibroblast Growth Factor 23 – Stephanie A. Bora – Frontiers in Immunology

High diversity and variability in the bacterial microbiota of the coffee berry borer (Coleoptera: Curculionidae), with emphasis on Wolbachia – Yobana A Mariño – Journal of Applied Microbiology

Exercise prevents high fat diet-induced bone loss, marrow adiposity and dysbiosis in male mice – Laura R. McCabe – Bone

Protein- and RNA-Enhanced Fermentation by Gut Microbiota of the Earthworm Lumbricus terrestris – Lydia Zeibich – Applied and Environmental Microbiology

Canonical Wnt Signaling in CD11c+ APCs Regulates Microbiota-Induced Inflammation and Immune Cell Homeostasis in the Colon – Daniel Swafford – The Journal of Immunology

 

Beneficial Microbes

Culture Supernatants of Lactobacillus gasseri and L. crispatus Inhibit Candida albicans Biofilm Formation and Adhesion to HeLa Cells – Yuko Matsuda – Mycopathologia

 

Environmental and Water Microbiome

Prevalence of antibiotic resistant coliform bacteria, Enterococcus spp. and Staphylococcus spp. in wastewater sewerage biofilm – Kristína Lépesová – Journal of Global Antimicrobial Resistance

Occurrence of virulence-associated genes among Staphylococcus saprophyticus isolated from different sources – Weslley de Paiva-Santos – Microbial Pathogenesis

 

Other

Digest: Life history evolution in Darwin’s dream ponds – Foteini Spagopoulou – Evolution

Research Highlight: To grow, or not to grow – Ursula Hofer – Nature Reviews Microbiology

 

March 8, 2018

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A wide range of interesting articles today: the use of fungi communities in the production of gold nanoparticles, a link between dysbiosis of the oral microbiome and rheumatoid arthritis, a diet low in PKU decreases fecal butyrate, the bacterial diet of  C. elegans alters their proteome, and a functional metagenomic study of the gut microbiome of the giant panda.

Events and jobs

Postdoctoral Associate – School of Medicine/Surgery – University of Pittsburgh Health Sciences

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General microbiome

Review: Understanding the microbiome – Mark Buchanan – Nature Physics

Pregnancy and early life

Conference Proceedings: Biology and Science of Human Milk – Integrated Approaches to Analyze Big Data in the Perinatal/Neonatal Space – Rob Knight – Human Milk Science

PrePrint: Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles – Christopher T. Brown – bioRxiv

Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis – Martin Glatz – PLOSone

Human oral microbiome

*Dysbiotic subgingival microbial communities in periodontally healthy patients with rheumatoid arthritis – Isabel Lopez-Oliva – Arthritis and Rheumatology

Human gut microbiome

*Phenylketonuric diet negatively impacts on butyrate production – E. Verduci – Nutrition, Metabolism and Cardiovascular Diseases

Review: Microbiotes et rhumatismes inflammatoires – Matthias Jarlborg – Revue Medicale Suisse

Gut Microbiome Composition Predicts Infection Risk during Chemotherapy in Children with Acute Lymphoblastic Leukemia – Hana Hakim – Clinical Infectious Diseases

PrePrint: American Gut: an Open Platform for Citizen-Science Microbiome Research – Daniel McDonald – bioRxiv

Review: Bile acid–microbiota crosstalk in gastrointestinal inflammation and carcinogenesis: a role for bifidobacteria and lactobacilli? – Borja Sánchez – Gastroenterology and Hepatology

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Animal microbiome

Effect of urea-supplemented diets on the ruminal bacterial and archaeal community composition of finishing bulls – Zhenming Zhou – Applied Microbiology and Biotechnology

*Metagenomic Study Suggests That the Gut Microbiota of the Giant Panda (Ailuropoda melanoleuca) May Not Be Specialized for Fiber Fermentation – Wei Guo – Frontiers in Microbiology

*The C. elegans Proteome Response to Naturally Associated Microbiome Members of the Genus Ochrobactrum – Liam Cassidy – Proteomics

16S rRNA gene sequencing reveals effects of photoperiod on cecal microbiota of broiler roosters – Jun Wang – PeerJ

The Drosophila melanogaster Gut Microbiota Provisions Thiamine to Its Host – David R. Sannino – mBio

Host and aquatic environment shape the amphibian skin microbiome but effects on downstream resistance to the pathogen Batrachochytrium dendrobatidis are variable – Andrea J. Jani – Frontiers in Microbiology

A comparative analysis of microbial profile of Guinea fowl and chicken using metagenomic approach – Sarayu Bhogoju – PLOSone

Plant, root, and soil microbiome

Impact of wastewater effluent containing aged nanoparticles and other components on biological activities of the soil microbiome, Arabidopsis plants, and earthworms – Jia Liu – Environmental Research

Dissertation: The influence of intraspecific variation in host plants on arthropod and fungal endophyte communities – Joshua G. Harrison – University of Nevada

Soil Microbiology Research in the Coming Decades: Translational Research Opportunities – Tapan Kumar Adhya – Advances in Soil Microbiology: Recent Trends and Future Prospects

Divergence of dominant factors in soil microbial communities and
functions in forest ecosystems along a climatic gradient – Zhiwei Xu – Biogeosciences

Climate, but not trait, effects on plant–soil feedback depend on mycorrhizal type in temperate forests – Jonathan A. Bennett – Ecosphere

Arbuscular Mycorrhiza Alleviates Restrictions to Substrate Water Flow and Delays Transpiration Limitation to Stronger Drought in Tomato – Michael Bitterlich – Frontiers in Plant Science

Ecological responses to forest age, habitat, and host vary by mycorrhizal type in boreal peatlands – Peter G. Kennedy – Mycorrhiza

Microbial Ecology

Holobionts and their hologenomes: Evolution with mixed modes of inheritance – Karen Luisa Haag – Genetics and Molecular Biology

Resistome

PrePrint: Conjugation factors controlling F-plasmid antibiotic resistance transmission – Hanna Alalam – bioRxiv

Comparative Genomics of Staphylococcus Reveals Determinants of Speciation and Diversification of Antimicrobial Defense – Malcolm James Horsburgh – bioRxiv

Bioinformatics

PrePrint: MetaWRAP – a flexible pipeline for genome-resolved metagenomic data analysis
– Gherman V Uritskiy – bioRxiv

Biotechnology

*Green synthesis of gold nanoparticles by thermophilic filamentous fungi – Zsófia Molnár – Scientific Reports

Techniques

Evaluation of magnetic cellulose bead-based DNA extraction from faecal materials for high-throughput bacterial community analyses – Tanzila Afrin – Applied Entomology and Zoology

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Microbes in the news

How extremophiles flourish in stressful environments – Science Daily

Does a Microbiome Exist in the Womb? – Medical News Bulletin

IBS and the Developing Microbiome – David Carreon – Modern Medicine Network

Bacteria and Art

Finding Art in the Gut, and Other Unexpected Places – Patrician Olsen – The New York Times

This Psychedelic Art Made from Moldy Food Is Tripping Us Out – Artist Felix Kalmenson proves decay can be gorgeous – Anna Marks – Vice

Artist to offer presentation on ‘Living Light’ exhibit March 5 at MCC – Daily Herald

March 1, 2018

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Quite a few articles on viruses today: The identification of human-like hormones in viral genomes that can bind to human and murine receptors; identification of multiple Antarctic sea-ice bacteriophages that are only active in the cold; bacterial immunity loss explains bacteria/phage co-existence; and the plans for a global virome project.

Pregnancy and early life

The microbiome and metabolome of pre-term infant stool is personalized, and not driven by health outcomes including necrotizing enterocolitis and late-onset sepsis -Stephen Wandro – bioRxiv

Review: Relationships Between Perinatal Interventions, Maternal-Infant Microbiomes, and Neonatal Outcomes – Gregory Valentine – Clinics in Perinatology

Human respiratory microbiome

Review: The Respiratory Microbiome in COPD – Orla O’Carroll – COPD – An Update in Pathogenesis and Clinical Management

Human vaginal microbiome

Bacterial identification of the vaginal microbiota in Ecuadorian pregnant teenagers: an exploratory analysis – Ana María Salinas – PeerJ

Human gut microbiome

Dissertation: Multi-Omic Analysis of Complex Microbial Communities in Gastrointestinal Lavage Fluid and their Association with Pancreatic Ductal Adenocarcinoma – Brittany Ferguson-Williams – University of South Alabama

Gut microbiota diversity according to dietary habits and geographical provenance – Bruno Senghor – Human Microbiome Journal

Intestinal microbiota, metabolome and gender dimorphism in autism spectrum disorders – Rafail I.Kushak – Research in Autism Spectrum Disorders

Review: A gut feeling: Microbiome-brain-immune interactions modulate social and affective behaviors – Kristyn E.Sylvia – Hormones and Behavior

Gorillibacterium timonense sp. nov. and Vitreoscilla massiliensis sp. nov., two new bacterial species isolated from stool specimens of obese Amazonian patients – Sokhna Ndongo – New Microbes and New Infections

«Collinsella provencensis» sp. nov., «Parabacteroides bouchesdurhonensis» sp. nov., and «Sutterella seckii» sp. nov., three new bacterial species identified from human gut microbiota – Niokhor Dione – New Microbes and New Infections

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Animal experiments

Gastrointestinal colonisation and systemic spread of Candida albicans in mice treated with antibiotics and prednisolone – Michiyo Kobayashi-Sakamoto – Microbial Pathogenesis

Effects of non-purified and semi-purified commercial diets on behaviors, plasma corticosterone levels, and cecum microbiome in C57BL/6J mice – Atsushi Toyoda – Neuroscience Letters

Brain-derived neurotrophic factor preserves intestinal mucosal barrier function and alters gut microbiota in mice – Chen Li – The Kaohsiung Journal of Medical Sciences

Immunization with intestinal microbiota-derived Staphylococcus aureus and Escherichia coli reduces bacteria-specific recolonization of the intestinal tract – Julio Adrián Garfias-López – Immunology Letters

Commensal Microbes Induce Serum IgA Responses that Protect against Polymicrobial Sepsis – Joel R.Wilmore – Cell Host & Microbe

Animal microbiome

Effects of glyphosate herbicide on the gastrointestinal microflora of Hawaiian green turtles (Chelonia mydas) Linnaeus – Ronald P.Kittle – Marine Pollution Bulletin

Identification of Uncultured Bacterial Species from Firmicutes, Bacteroidetes and CANDIDATUS Saccharibacteria as Candidate Cellulose Utilizers from the Rumen of Beef Cows – Lee James Opdahl – Microorganisms

Microbial community dynamics during rearing of black soldier fly larvae (Hermetia illucens) and its impact on exploitation potential – Jeroen De Smet – Applied and Environmental Microbiology

Urea nitrogen induces changes in rumen microbial and host metabolic profiles in dairy cows – D.Jin – Livestock Science

Air Microbiome

Aeolian dispersal of bacteria in southwest Greenland: their sources, abundance, diversity and physiological states – Tina Šantl-Temkiv – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Shrub encroachment is associated with changes in soil bacterial community composition in a temperate grassland ecosystem – Xingjia Xiang – Plant and Soil

Effects of thinning intensity on understory vegetation and soil microbial communities of a mature Chinese pine plantation in the Loess Plateau – Peng Dang – Science of The Total Environment

Characterization of halotolerant, pigmented, plant growth promoting bacteria of groundnut rhizosphere and its in-vitro evaluation of plant-microbe protocooperation to withstand salinity and metal stress – Avishek Banik – Science of The Total Environment

Arbuscular mycorrhizal fungal and soil microbial communities in African Dark Earths – Tessa Camenzind – FEMS Microbiology Ecology

Effects of thinning intensity on understory vegetation and soil microbial communities of a mature Chinese pine plantation in the Loess Plateau – Peng Dang – Science of The Total Environment

Plant growth-promoting rhizobacteria inoculation and nitrogen fertilization increase maize (Zea mays L.) grain yield and modified rhizosphere microbial communities – Luciana P. Di Salvo – Applied Soil Ecology

Review: Understanding the impact of soil sodicity on mycorrhizal symbiosis: Some facts and gaps identified from cotton systems – Samieh Eskandari – Applied Soil Ecology

Morphological, biochemical and molecular characterization of culturable epilithic and endolithic bacteria from rocks of Ayubia (Murree), lower Himalaya, Pakistan – I. Khan –
Applied Ecology and Environmental Research

Impact of sugarcane bagasse-derived biochar on heavy metal availability and microbial activity: A field study – Chengrong Nie – Chemosphere

Water and extremophile microbiome

Unexpected fungal communities in the Rehai thermal springs of Tengchong influenced by abiotic factors – Kai-Hui Liu – Extremophiles

Marine microbes in 4D — using time series observation to assess the dynamics of the ocean microbiome and its links to ocean health – Pier Luigi Buttigieg – Current Opinion in Microbiology

The future of genomics in polar and alpine cyanobacteria – Nathan A M Chrismas – FEMS Microbiology Ecology

Unexpected fungal communities in the Rehai thermal springs of Tengchong influenced by abiotic factors – Kai-Hui Liu – Extremophiles

Actinobacterial community structure in the Polar Frontal waters of the Southern Ocean of the Antarctica using Geographic Information System (GIS): A novel approach to study Ocean Microbiome – P. Sivasankar – Data in Brief

Review: Actinobacterial community structure in the Polar Frontal waters of the Southern Ocean of the Antarctica using Geographic Information System (GIS): A novel approach to study Ocean Microbiome – P. Sivasankar – Data in Brief

Microbial Ecology

Symbiosis in the microbial world: from ecology to genome evolution – Jean-Baptiste Raina – Biology Open

Dissertation: Understanding Microbial Community Dynamics in High-Solids Lignocellulolytic Systems Using Bioinformatics Tools – Joshua Thomas Claypool – University of California, Davis

Review: Uncultivated microbes—in need of their own nomenclature? – Aharon Oren – The ISME Journal

Resistome

Diverse and abundant antibiotic resistance genes from mariculture sites of China’s coastline – Quanxin Gao – Science of The Total Environment

Evaluation of resistance gene transfer from heat-treated Escherichia coli – Laëtitia Le Devendec – International Journal of Food Microbiology

Phages and viruses

*The Global Virome Project – Dennis Carroll – Science

*Viral insulin-like peptides activate human insulin and IGF-1 receptor signaling: A paradigm shift for host–microbe interactions – Emrah Altindis – PNAS

*The first known virus isolates from Antarctic sea ice have complex infection patterns – Anne-Mari Luhtanen – FEMS Microbiology Ecology

*Immune loss as a driver of coexistence during host-phage coevolution
Jake L Weissman – The ISME Journal

PuLSE: Quality control and quantification of peptide sequences explored by phage display libraries – Steven Shave – PLOSone

Metabolomics

A quantitative metabolomics study of bacterial metabolites in different domains – Fanyi Zhong – Analytica Chimica Acta

Waste and Pollution

Ferric sulfate and proline enhance heavy-metal tolerance of halophilic/ halotolerant soil microorganisms and their bioremediation potential for spilled-oil under multiple stresses – Dina M. Al-Mailem – Frontiers in Microbiology

The divergence between fungal and bacterial communities in seasonal and spatial variations of wastewater treatment plants – Ziyan Wei – Science of The Total Environment

Techniques

Genome-scale metabolic models as platforms for identification of novel genes as antimicrobial drug targets – Bashir Sajo Mienda – Future Medicine

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Microbes in the news

Microbiota-gut-brain axis is at epicenter of new approach to mental health – Mary Ann Leibert – EurekAlert

Dietary Advice Based on the Bacteria in Your Gut – Charles Wallace – The Wall Street Journal

The silent microbiome crisis – Tobias Rees – The Washington Post

C-sections and gut bacteria increase risk of childhood obesity – Medical Press

Researchers film bacteria using melee combat to steal antibiotic resistance genes – Phys.org

February 28, 2018

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Have a good Wednesday! After few days of inactivity, we bring this digest with several reviews from different aspects of microbiome research. We included also some papers about microbiota and antibiotic resistance, microbiota and metabolism, and more.

 

Human and General microbiome

Review: Microbiota and Metabolism — What’s New in 2018 – Alexis Bretin – American Journal of Physiology-Endocrinology and Metabolism

Review: Eicosanoids in the GI Tract – John L Wallace – British Journal of Pharmacology

Review: Gut : liver : brain axis: the microbial challenge in the hepatic encephalopathy – Andrea Mancini – Food and Function

Meeting update: faecal microbiota transplantation–bench, bedside, courtroom? – Nik Sheng Ding – . Frontline Gastroenterology

Mini-Review: Involvement of Corticotropin-Releasing Factor and Receptors in Immune Cells in Irritable Bowel Syndrome – Mahanand Chatoo – Frontiers in Endocrinology

Gut microbiome composition in lean patients with NASH is associated with liver damage independent of caloric intake: A prospective pilot study – S.M.B.Duarte – Nutrition, Metabolism and Cardiovascular Diseases

Study protocol: Antifibrotic and molecular aspects of rifaximin in alcoholic liver disease: study protocol for a randomized controlled trial – Bjørn Stæhr Madsen – Trials

Gut microbiota characterisation in obese patients before and after bariatric surgery – G. Campisciano – Beneficial Microbes

Effect of sodium fluoride on oral biofilm microbiota and enamel demineralization – Thomas Thurnheer – Archives of Oral Biology

Review: Human Gut Microbiota in Health and Alzheimer’s Disease – Leszek Szablewski –  Journal of Alzheimer’s Disease

Fecal microbiota profile in atopic asthmatic adult patients – A.M. Okba – European annals of allergy and clinical immunology

Cervicovaginal microbiota composition correlates with the acquisition of high-risk human papillomavirus types – Xiaojie Huang – International journal of cancer

Review: Dysbiosis of gut microbiota in promoting the development of colorectal cancer – Shaomin Zou – Gastroenterology Report

In Brief: Microbiome: Principles of microbiota engraftment – Andrea Du Toit – Nature Reviews Microbiology

Clearance of Carbapenem-resistant Enterobacteriaceae versus Vancomycin-resistant enterococci carriage after fecal microbiota transplant: a prospective comparative study – Aurélien Dinh – The Journal of Hospital Infection

Alterations of the human gut Methanobrevibacter smithii as a biomarker for inflammatory bowel diseases – Shaghayegh Baradaran Ghavami – Microbial Pathogenesis

Forum: Inadequate Production of H2 by Gut Microbiota and Parkinson Disease – Sergej M.Ostojic – Trends in endocrinology and metabolism

Review: Brain Feeding Circuits after Roux-en-Y Gastric Bypass – Mohammed K.Hankir – Trends in endocrinology and metabolism

Temporal variability of oral microbiota over 10 months and the implications for future epidemiologic studies – Emily Vogtmann – Cancer Epidemiology, Biomarkers & Prevention

Review: Psoriatic arthritis: tissue-directed inflammation? – Giacomo Cafaro – Clinical Rheumatology

 

Animal Microbiome

Intestine farnesoid X receptor agonist and the gut microbiota activate G-protein bile acid receptor-1 signaling to improve metabolism – Preeti Pathak – Hepatology

Primary murine mucosal response during cephalosporin-induced intestinal colonization by Enterococcus faecium – Antoni P. A. Hendrickx – MicrobiologyOpen

Respiratory Disease following Viral Lung Infection Alters the Murine Gut Microbiota – Helen T. Groves – Frontiers in Immunology

Tartary buckwheat protein prevented dyslipidemia in high-fat diet-fed mice associated with gut microbiota changes – Xiao-Li Zhou – Food and chemical toxicology

When Darwin’s Special Difficulty Promotes Diversification in Insects – Frederic Legendre – Systematic Biology

Commensal Microbes Induce Serum IgA Responses that Protect against Polymicrobial Sepsis – Joel R.Wilmore – Cell host and microbe

Brain-derived neurotrophic factor preserves intestinal mucosal barrier function and alters gut microbiota in mice – Chen Li – The Kaohsiung Journal of Medical Sciences

Microbiota-mediated modulation of organophosphate insecticide toxicity by species-dependent lactobacilli interactions in a Drosophila melanogaster insect model – Brendan A. Daisley – Applied And Environmental Microbiology

Assessing bacterial community dynamics across the gastrointestinal tract of dairy calves during pre-weaning development – Juliana Dias – Applied And Environmental Microbiology

Microbial community dynamics during rearing of black soldier fly larvae (Hermetia illucens) and its impact on exploitation potential – Jeroen De Smet – Applied And Environmental Microbiology

Microbiota promote secretory cell determination in the intestinal epithelium by modulating host Notch signaling – Joshua V. Troll – Development

Hypoglycemic and hypolipidemic effect of S-allyl-cysteine sulfoxide (alliin) in DIO mice – Baiqiang Zhai – Scientific Reports

 

Pathogen research

Immunization with intestinal microbiota-derived Staphylococcus aureus and Escherichia coli reduces bacteria-specific recolonization of the intestinal tract – Julio Adrián Garfias-López – Immunology Letters

Salmonella-mediated inflammation eliminates competitors for fructose-asparagine in the gut – Jikang Wu – Infection and immunity

Treatment of Clostridium difficile infection with a small molecule inhibitor of toxin UDP-glucose hydrolysis activity – Ilana L. Stroke – Antimicrobial agents and chemotherapy

Review: Treatment of recurrent Clostridium difficile colitis: a narrative review – Roy J Hopkins – Gastroenterology Report

Review: Pseudomonas syringae: what it takes to be a pathogen – Xiu-Fang Xin – Nature Reviews Microbiology

 

Food Microbiome

Review: Seafood spoilage microbiota and associated volatile organic compounds at different storage temperatures and packaging conditions – Olumide A.Odeyemi – International journal of food microbiology

 

Water Microbiome

A closer look at the antibiotic-resistant bacterial community found in urban wastewater treatment systems – Amir H. Tehrani – MicrobiologyOpen

 

Extremophiles

Transitory microbial habitat in the hyperarid Atacama Desert – Dirk Schulze-Makuch – PNAS

 

Other papers

Microbial diversity in biodeteriorated Greek historical documents dating back to the 19th and 20th century: A case study – Kiriaki Karakasidou – MicrobiologyOpen

A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses – Mo Han – Microbiome

Identification of a highly active tannase enzyme from the oral pathogen Fusobacterium nucleatum subsp. polymorphum – Julen Tomás-Cortázar – Microbial Cell Factories

Effect of Bacillus subtilis C-3102 on loose stools in healthy volunteers – M. Hatanaka – Beneficial Microbes

In situ biomolecule production by bacteria; a synthetic biology approach to medicine – Yensi Flores Bueso – Journal of Controlled Release

February 23, 2018

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This Friday: A nice set of papers focused in pathogens such as Salmonella and C. difficile, several papers about soil/root microbiome and more…

Human Microbiome

Review: Skin microbiota and human 3D skin models – Franziska Rademacher – Experimental Dermatology

News and Views: Gut microbiota: Beyond metagenomics, metatranscriptomics illuminates microbiome functionality in IBD – Aonghus Lavelle – Nature Reviews Gastroenterology & Hepatology

Letter: Concomitant resolution through fecal microbiota transplantation of Clostridium difficile and OXA-48-producing Klebsiella pneumoniae –  Giovanni Bruno – Infectious Diseases

Oral cholera vaccination promotes homing of IgA+ memory B cells to the large intestine and the respiratory tract – M van Splunter – Mucosal Immunology

Review: Signalling from the periphery to the brain that regulates energy homeostasis – Ki-Suk Kim – Nature Reviews Neuroscience

Research Highlight: Colorectal cancer: Bacterial biofilms and toxins prompt a perfect storm for colon cancer – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Research Highlight: Metabolism: The small intestine — a new player in fructose metabolism – Ivone Leong – Nature Reviews Endocrinology

Akkermansia muciniphila-derived extracellular vesicles influence gut permeability through the regulation of tight junctions – Chaithanya Chelakkot – Experimental & Molecular Medicine

 

Animal Microbiome / Animal Experiments

Effects of a galacto-oligosaccharide-rich diet on fecal microbiota and metabolite profiles in mice – W. Cheng – Food and Function

Impact of oral fidaxomicin administration on the intestinal microbiota and susceptibility to Clostridium difficile colonization in mice – N. J. Ajami – Antimicrobial Agents and Chemotherapy

Interplay between gut microbiota and p66Shc affects obesity-associated insulin resistance – Stefano Ciciliot – The FASEB Journal

CD Obesity-Prone Rats, but not Obesity-Resistant Rats, Robustly Ferment Resistant Starch Without Increased Weight or Fat Accretion – Diana Obanda – Obesity

Dietary live yeast and increased water temperature influence the gut microbiota of rainbow trout – David Huyben – Journal of Applied Microbiology

Remodeling of the Candida glabrata cell wall in the gastrointestinal tract affects the gut microbiota and the immune response – Rogatien Charlet – Scientific Reports

Absence of receptor guanylyl cyclase C enhances ileal damage and reduces cytokine and antimicrobial peptide production during oral Salmonella Typhimurium infection – Shamik Majumdar – Infection and Immunity

Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato – Kelly Brener-Raffalli – Microbiome

Chitin Oligosaccharide Modulates Gut Microbiota and Attenuates High-Fat-Diet-Induced Metabolic Syndrome in Mice – Junping Zheng – Marine Drugs

Targeting the PXR–TLR4 signaling pathway to reduce intestinal inflammation in an experimental model of necrotizing enterocolitis – Kezhen Huang – Pediatric Research

Hypoglycemic and hypolipidemic effect of S-allyl-cysteine sulfoxide (alliin) in DIO mice – Baiqiang Zhai –  Scientific Reports

 

Human Pathogens

Clostridioides (Clostridium) difficile infection: current and alternative therapeutic strategies – Fernando Gil – Future Medicine

Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins – Elizabeth J. Klemm – mBio

Metronidazole-Loaded Polyethyleneimine and Chitosan-Based Liquid Crystalline System for Treatment of Staphylococcal Skin Infections – Francesca Damiani Victorelli –  Journal of Biomedical Nanotechnology

Cost-Effectiveness of Competing Treatment Strategies for Clostridium difficile Infection: A Systematic Review – Phuc Le – Infection Control & Hospital Epidemiology

 

Food Microbiome

Antibiotic Resistance Genetic Markers and Integrons in White Soft Cheese: Aspects of Clinical Resistome and Potentiality of Horizontal Gene Transfer –  Ana Caroline L. de Paula – Genes

Effect of the environment microbiota on the flavour of light-flavour Baijiu during spontaneous fermentation – Xiao-Na Pang – Scientific Reports

 

Plant and Environmental Microbiomes

Pseudomonas rhizophila S211, a New Plant Growth-Promoting Rhizobacterium with Potential in Pesticide-Bioremediation – Wafa Hassen – Frontiers in Microbiology

Indigenous Pseudomonas spp. Strains from the Olive (Olea europaea L.) Rhizosphere as Effective Biocontrol Agents against Verticillium dahliae: From the Host Roots to the Bacterial Genomes – Carmen Gómez-Lama Cabanás – Frontiers in Microbiology

Preprint: Network hubs in root-associated fungal metacommunities – Hirokazu Toju – BioRxiv

Preprint: Microbial Treatment of Soil Contaminated with Spent engine Oil / Biotreatment of Soil Contaminated with Spent Engine by Microorganisms – Abiodun A. Ayandele – BioRxiv

Bacterial Preferences for Specific Soil Particle Size Fractions Revealed by Community Analyses – Michael Hemkemeyer – Frontiers in Microbiology

Peatland Acidobacteria with a dissimilatory sulfur metabolism – Bela Hausmann – The ISME Journal

Systemic Homeostasis in Metabolome, Ionome, and Microbiome of Wild Yellowfin Goby in Estuarine Ecosystem – Feifei Wei – Scientific Reports

 

Microbes in General

Review: Ethanolamine Utilization in Bacteria – Karan Gautam Kavala – mBio

Review: The Genome-Scale Integrated Networks in Microorganisms – Tong Hao – Frontiers in Microbiology

 

February 22, 2018

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Events and jobs

Microbiology Adjunct Instructor – Diablo Valley College

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Pregnancy and early life

Review: Maternal Microbiota, Prepregnancy Weight, and Mode of Delivery
Intergenerational Transmission of Risk for Childhood Overweight and Obesity – Giulia Paolella – JAMA Pediatrics

 

Human ear, nose and throat microbiome

*A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera – Rachael Lappan – BMC Microbiology

The Tracheal Microbiota in Patients with a Tracheostomy Before, During, and After an Acute Respiratory Infection – Pérez-Losada, Marcos – The Pediatric Infectious Disease Journal

Human oral microbiome

Shift of microbial composition of peri-implantitis-associated oral biofilm as revealed by 16S rRNA gene cloning – Ali Al-Ahmad – Journal of Medical Microbiology

Human vaginal microbiome

Short- and long-term influence of the levonorgestrel-releasing intrauterine system (Mirena®) on vaginal microbiota and Candida – Gilbert Gerard Ghislain Donders – Journal of Medical Microbiology

Human gut microbiome

Transitional and temporal changes in the mucosal and submucosal intestinal microbiota in advanced Crohn’s disease of the terminal ileum – Rodrick J. Chiodini – Journal of Medical Microbiology

Gut microbiota trajectory in early life may predict development of celiac disease – Marta Olivares – BMC Microbiome

A comparison of the microbial community structure between inflamed and non-inflamed sites in patients with ulcerative colitis – Atsushi Hirano – Journal of Gastroenterology and Hepatology

The Impact of NOD2 Variants on Fecal Microbiota in Crohn’s Disease and Controls Without Gastrointestinal Disease – Nicholas A Kennedy – Inflammatory Bowel Diseases

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Animal experiments

Regulation of vitamin D metabolism following disruption of the microbiota using broad spectrum antibiotics – Stephanie A. Bora – The Journal of Nutritional Biochemistry

Soluble dietary fiber improves energy homeostasis in obese mice by remodeling the gut microbiota – Haiyuan Wang – Biochemical and Biophysical Research Communications

Lactobacillus and Bifidobacterium Ameliorate Memory and Learning Deficits and oxidative stress in Aβ (1-42) Injected Rats – Somayeh Athari Nik Azm – Applied Physiology, Nutrition, and Metabolism

*Chronic helminth infection perturbs the gut-brain axis, promotes neuropathology and alters behaviour – Paul R Giacomin – The Journal of Infectious Diseases

*Endometriosis induces gut microbiota alterations in mice – Ming Yuan – Human Reproduction

*Strain differences in the susceptibility to the gut–brain axis and neurobehavioural alterations induced by maternal immune activation in mice – Morais, Livia H – Behavioural Pharmacology

Specific synbiotics in early life protect against diet-induced obesity in adult mice
Mona Mischke – Diabetes, Obesity, and Metabolism

Transcriptomic and Proteomic Profiling Revealed High Proportions of Odorant Binding and Antimicrobial Defense Proteins in Olfactory Tissues of the House Mouse – Barbora Kuntová – Frontiers in Genetics

Lactobacillus accelerates ISCs regeneration to protect the integrity of intestinal mucosa through activation of STAT3 signaling pathway induced by LPLs secretion of IL-22 – Qihang Hou – Cell Death and Differentiation

Animal microbiome

Review: Gut barrier function: Effects of (antibiotic) growth promoters on key barrier components and associations with growth performance – Leon J Broom – Poultry Science

Fecal microbiota transplantation in puppies with canine parvovirus infection – Giorgio Q. Pereira – Journal of Veterinary Internal Medicine

Water and extremophile microbiome

Phylogeny and bioactivity of epiphytic Gram-positive bacteria isolated from three co-occurring antarctic macroalgae – Pamela Alvarado – Antonie van Leeuwenhoek

 

Resistome

The antibiotic resistome and microbiota landscape of refugees from Syria, Iraq and Afghanistan in Germany – Robert Häsler – BMC Microbiome

Transferable vancomycin resistance in clade B commensal-type Enterococcus faecium – François Lebreton – Journal of Antimicrobial Chemotherapy

 

Bioinformatics

Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach – Loo Wee Chia – Antonie van Leeuwenhoek

Biotechnology

*A 3D intestinal tissue model supports Clostridioides difficile germination, colonization, toxin production and epithelial damage – Lamyaa Shaban – Anaerobe

Design of synthetic bacterial communities for predictable plant phenotypes – Sur Herrera Paredes – PLOS Biology

Harnessing a Methane-Fueled, Sediment-Free Mixed Microbial Community for Utilization of Distributed Sources of Natural Gas – Jeffrey J. Marlow – Biotechnology and Bioengineering

Dissertation: Microbial Communities Involved in Carbon Monoxide and Syngas Conversion to Biofuels and Chemicals – Sofia Victoria Esquivel Elizondo – Arizona State University

 

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Microbes in the news

This Vibrant Bacteria Could Be Used to “Grow” Paint – Meilan Solly – Smithsonian

Bacteria-eaters to prevent food poisoning? Phages eliminate Yersinia from food – Science Daily

A ‘Grueling and Grotesque’ Biohacking Experiment – Kate McLean – The Atlantic

 

February 15, 2018

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An especially interesting article on engineered bacteria in the treatment of colon cancer today: Chun Loong Ho and colleagues engineered an E. coli strain to bind to colon cancer cells and constitutively secrete an enzyme that can turn dietary derived glucosinolates (from cruciferous vegetables) into cancer fighting isothiocynates. Mice exposed to carcinogens and fed both the engineered bacteria and broccoli developed fewer and smaller colorectal tumors than exposed mice who were fed 1) neither bacteria or brocoli, 2) only bacteria, or 3) only broccoli.  Engineered probiotics anyone?

Also : A cultured community developed from wastewater that can reduce the greenhouse gas N2O to N2 and help mitigate global warming; the majority of Daphnia microbiomes are not passed from parent to offspring but absorbed from the surrounding environment; and the impacts of CRISPR-Cas9 selection pressure on phage evolution.

Events and jobs

Postdoctoral Scholars of Microbiology, School of Life Sciences – University of Nevada Las Vegas

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General microbiome

Review: The genome, microbiome and evolutionary medicine – Robert C. Brunham – cmaj

Pregnancy and early life

Survey of Staphylococcus aureus in a general pediatric population and focus on isolates with three clinically relevant toxin-encoding genes – Anne Filleron – World Journal of Pediatrics

Human skin microbiome

Review: Impact of Skin Microbiome on Attractiveness to Arthropod Vectors and Pathogen Transmission – Niels O. Verhulst – Skin and Arthropod Vectors

Human gut microbiome

Intestinal Microbial Community Differs between Acute Pancreatitis Patients and Healthy Volunteers – Xi Mei Zhang – Biomedical and Environmental Sciences

The microbiome in chronic kidney disease patients undergoing hemodialysis and peritoneal dialysis – Liliana Simões-Silva – Pharmacological Research

Review: Intestinal Microbiome Shifts, Dysbiosis, Inflammation, and Non-alcoholic Fatty Liver Disease – Emma T. Saltzman – Frontiers in Microbiology

Does Low-Protein Diet Influence the Uremic Toxin Serum Levels From the Gut Microbiota in Nondialysis Chronic Kidney Disease Patients? – Ana Paula Black – Journal of Renal Nutrition

The Effect of Oligofructose-Enriched Inulin on Faecal Bacterial Counts and Microbiota-Associated Characteristics in Celiac Disease Children Following a Gluten-Free Diet: Results of a Randomized, Placebo-Controlled Trial – Natalia Drabińska – Nutrients

Preprint: Spatial variation of the native colon microbiota in healthy adults – Kaitlin J Flynn – bioRxiv

Preprint: The intestinal microbiota predisposes to traveller’s diarrhoea and to the carriage of multidrug-resistant Enterobacteriaceae after travelling to tropical regions – Stefano Leo – bioRxiv

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Animal experiments

Influence of Eimeria falciformis Infection on Gut Microbiota and Metabolic Pathways in Mice – Guangping Huang – Infection and Immunity

The Antimicrobial Peptide CRAMP Is Essential for Colon Homeostasis by Maintaining Microbiota Balance – Teizo Yoshimura – The Journal of Immunology

Animal microbiome

*Good Daphnia parents do not control the offspring microbiome – Angela E. Douglas – Journal of Animal Ecology

Effect of antibiotic withdrawal in feed on chicken gut microbial dynamics, immunity, growth performance and prevalence of foodborne pathogens – Sanjay Kumar – PLOSone

Review: The Microbial Zoo in the C. elegans Intestine: Bacteria, Fungi and Viruses – Hongbing Jiang – Viruses

Effects of parental care on resource allocation into immune defense and buccal microbiota in mouthbrooding cichlid fishes – Isabel S. Keller – Evolution

Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats – Guido Bonthond – PeerJ

Effect of ginkgo extract supplementation on in vitro rumen fermentation and bacterial profiles under different dietary conditions – Seongjin Oh – Animal Science Journal

Review: Animal host–microbe interactions – Bethany J. Hoye – Journal of Animal Ecology

Plant, root, and soil microbiome

Oilseed rape cultivation increases the microbial richness and diversity in soils contaminated with cadmium – Xin Wang – Journal of Soils and Sediments

Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters – Emine Gozde Ozbayram – Microorganisms

Bacterial Microbiota of Rice Roots: 16S-Based Taxonomic Profiling of Endophytic and Rhizospheric Diversity, Endophytes Isolation and Simplified Endophytic Community – Felix Moronta-Barrios – Microorganisms

Water and extremophile microbiome

Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria – Catherine Gérikas Ribeiro – The ISME Journal

Distribution Patterns of Microbial Community Structure Along a 7000-Mile Latitudinal Transect from the Mediterranean Sea Across the Atlantic Ocean to the Brazilian Coastal Sea – Jin Zhou – Microbial Ecology

The vertical distribution of prokaryotes in the surface sediment of Jiaolong cold seep at the northern South China Sea – Yuzhi Wu – Extremophiles

A comparative hierarchical analysis of bacterioplankton and biofilm metacommunity structure in an interconnected pond system – Caroline Souffreau – Environmental Microbiology

Chemical and Microbial Quality of Groundwater in Siloam Village, Implications to Human Health and Sources of Contamination – John Ogony Odiyo – International Journal of Environmental Research and Public Health

Microbial Ecology

Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies – Mari Pent – Environmental Microbiology

Fungus-associated bacteriome in charge of their host behavior – Kristin Schulz-Bohm – Fungal Genetics and Biology

Resistome

Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes – Wenguang Xiong – BMC Microbiome

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Probiotics / prebiotics

Effect of VSL#3 Probiotic in a Patient with Glycogen Storage Disease Type Ia and Irritable Bowel Disease-like Disease – Miguel Carnero-Gregorio – Probiotics and Antimicrobial Proteins

New Insight into Biofilm Formation Ability, the Presence of Virulence Genes and Probiotic Potential of Enterococcus sp. Dairy Isolates – Nikola Popović – Frontiers in Microbiology

Effectiveness and Safety of a Probiotic-Mixture for the Treatment of Infantile Colic: A Double-Blind, Randomized, Placebo-Controlled Clinical Trial with Fecal Real-Time PCR and NMR-Based Metabolomics Analysis – Maria Elisabetta Baldassarre – Nutrients

Fecal Microbiome Transplants

Long-term follow-up of the effects of fecal microbiota transplantation in combination with soluble dietary fiber as a therapeutic regimen in slow transit constipation – Xueying Zhang – Science China Life Sciences

Bioinformatics

Identification of fungi in shotgun metagenomics datasets – Paul D. Donovan – PLOSone

MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies – Ahmed A. Metwally – BMC Microbiome

Biotechnology

*Engineered commensal microbes for diet-mediated colorectal-cancer chemoprevention – Chun Loong Ho – Nature Biomedical Engineering

*Unexpected evolutionary benefit to phages imparted by bacterial CRISPR-Cas9 – Pan Tao – Science Advances

Waste and Pollution

*Life on N2O: deciphering the ecophysiology of N2O respiring bacterial communities in a continuous culture – Monica Conthe – The ISME Journal

Metagenomic analysis of microbial community and function involved in cd-contaminated soil – Gang Feng – BMC Microbiology

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Microbes in the news

Humpback microbiome linked to seasonal, environmental changes – Phys.org

 

February 3, 2018

Posted on by

Today’s digest is short, but has exciting reads on how machine learning is improving prediction of antibiotic resistance genes.

General Microbiome

Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation. Puentes-Téllez PE. Microbial Ecology

Review: Role of antimicrobial peptides in controlling symbiotic bacterial populations. Mergaert P. Natural Product Reports

Evaluation of the ability of commercial wine yeasts to form biofilms (mats) and adhere to plastic: implications for the microbiota of the winery environment.Tek EL. FEMS Microbiology Ecology

Gut Microbiome

The mechanistic link between health and gut microbiota diversity.Larsen OFA. Scientific Reports

REVIEW:The Role of Gut Microbiome and Associated Metabolome in the Regulation of Neuroinflammation in Multiple Sclerosis and Its Implications in Attenuating Chronic Inflammation in Other Inflammatory and Autoimmune Disorders.Dopkins N. Immunology

Plant, Soil, and Water Microbiome

Lithobiontic life: “Atacama rocks are well and alive”. Gómez-Silva B.Antonie Van Leeuwenhoek

Contrasting patterns of the bacterial and archaeal communities in a high-elevation river in northwestern China. Hu Y. Journal of Microbiology

Arbuscular Mycorrhizal Fungi and Plant Chemical Defence: Effects of Colonisation on Aboveground and Belowground Metabolomes. Hill EM. Journal of Chemical Ecology

Comparison of plants with C3 and C4 carbon fixation pathways for remediation of polycyclic aromatic hydrocarbon contaminated soils. Sivaram AK. Scientific Reports

Soda pans of the Pannonian steppe harbor unique bacterial communities adapted to multiple extreme conditions. Szabó A. Exremophiles

The effects of glyphosate, glufosinate, paraquat and paraquat-diquat on soil microbial activity and bacterial, archaeal and nematode diversity.Dennis PG. Scientific Reports

Soil commensal rhizobia promote Rhizobium etli nodulation efficiency through CinR-mediated quorum sensing. Miao J. Archives of Microbiology

Distribution of thermophilic endospores in a temperate estuary indicate that dispersal history structures sediment microbial communities.Bell E. Environmental Microbiology

Animal Experiments and Microbiome

Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose. Zhang W. ISME Journal

Increased productivity in poultry birds by sub-lethal dose of antibiotics is arbitrated by selective enrichment of gut microbiota, particularly short-chain fatty acid producers. Banerjee S. Microbiology

Whole metagenome sequencing reveals links between mosquito microbiota and insecticide resistance in malaria vectors. Dada N. Scientific Reports

Virome

The virome of the arbuscular mycorrhizal fungus Gigaspora margarita reveals the first report of DNA fragments corresponding to replicating non-retroviral RNA viruses in Fungi.Turina M. Environmental Microbiology

Techniques/Protocols

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data.Arango-Argoty G. Microbiome