Category Archives: Human gut

October 20, 2017

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A wide variety of studies today from the digestive microbiota of carnivorous pitcher plants, to the skin microbiome of dogs, and the impacts of probiotics on male fertility in a mouse model of obesity. 

Events and jobs

Microbiome World Congress – November 7-8, 2017, Capital Hilton, Washington, DC – registration

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  • General microbiome

The Pelagic Bacterium Paraphotobacterium marinum Has the Smallest Complete Genome Within the Family Vibrionaceae – Zhaobin Huang – Frontiers in Microbiology

Review: Uncultivated microbes in need of their own taxonomy – Konstantinos T Konstantinidis – The ISME Journal

Review: The growing tree of Archaea: new perspectives on their diversity, evolution and ecology – Panagiotis S Adam – The ISME Journal

  • Human respiratory microbiome

Antibiotic exposure and interpersonal variance mask the effect of ivacaftor on respiratory microbiota composition – Anton Y. Peleg – Journal of Cystic Fibrosis

  • Human gut microbiome

Carbapenem-resistant Enterobacteriaceae colonization (CRE) and subsequent risk of infection and 90-day mortality in critically ill patients, an observational study – Thomas Howe McConville – PLOSone

Review: Antibiotics, gut microbiome, and obesity – Karen S. W. Leong – Clinical Endocrinology

Review: Gut microbiota changes in the extreme decades of human life: a focus on centenarians – Aurelia Santoro – Cellular and Molecular Life Sciences

Review: Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation – Christopher J. Anderson – Frontiers in Microbiology

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  • Animal Experiments

Lactobacillus rhamnosus PB01 (DSM 14870) supplementation affects markers of sperm kinematic parameters in a diet-induced obesity mice model – Fereshteh Dardmeh – PLOSone

  • Animal microbiome

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization – Beate M Slaby – The ISME Journal

A polyphenol-enriched diet and Ascaris suum infection modulate mucosal immune responses and gut microbiota composition in pigs – Andrew R. Williams – PLOSone

Individual signatures and environmental factors shape skin microbiota in healthy dogs – Anna Cuscó – Microbiome

Review: Metagenomic investigation of gastrointestinal microbiome in cattle – Minseok Kim – AJAS

  • Plant, root, and soil microbiome

Linking the development and functioning of a carnivorous pitcher plant’s microbial digestive community – David W Armitage – The ISME Journal

Biogeography and organic matter removal shape long-term effects of timber harvesting on forest soil microbial communities – Roland C Wilhelm – The ISME Journal

Differences in soil fungal assemblages associated with native and non-native tree species of varying weediness – David R. Toole – Biological Invasions

Nitric Oxide Accumulation: The Evolutionary Trigger for Phytopathogenesis – Margarida M. Santana – Frontiers in Microbiology

  • Water and extremophile microbiome

Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms – Kevin Anthony Meyer – PLOSone

Mixotrophy drives niche expansion of verrucomicrobial methanotrophs – Carlo R Carere – The ISME Journal

High abundance and expression of transposases in bacteria from the Baltic Sea – Theoden Vigil-Stenman – The ISME Journal

Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms – Kevin Anthony Meyer – PLOSone

High-throughput sequencing revealed novel Dehalococcoidia in dechlorinating microbial enrichments from PCB contaminated marine sediments – B. Matturro – FEMS Microbiology Ecology

Flooding Duration Affects the Structure of Terrestrial and Aquatic Microbial Eukaryotic Communities – Oliver Röhl – Environmental Microbiology

Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept – Christina Pavloudi – PeerJ

The Exometabolome of Two Model Strains of the Roseobacter Group: A Marketplace of Microbial Metabolites – Gerrit Wienhausen – Frontiers in Microbiology

  • Built environment

Indoor microbiota in severely moisture damaged homes and the impact of interventions – Balamuralikrishna Jayaprakash – Microbiome

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  • Probiotics / prebiotics

Review: Probiotics in the Prevention of Gestational Diabetes Mellitus – Luisa F. Gomez Arango – Nutrition and Diet in Maternal Diabetes

  • Phages and viruses

Microencapsulation of Clostridium difficile specific bacteriophages using microfluidic glass capillary devices for colon delivery using pH triggered release – Gurinder K. Vinner – PLOSone

Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology – Rachel L Marine – The ISME Journal

  • Techniques

A simpler and more cost-effective peptide biosynthetic method using the truncated GST as carrier for epitope mapping – Wan-Xiang Xu – PLOSone

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October 19, 2017

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Today, we have a short Digest but with interesting remarks: Alzheimer’s disease associated microbiome, the bacterial tree of Life and more.

 

Human Microbiome

Gut microbiome alterations in Alzheimer’s disease – Nicholas M. Vogt – Scientific Reports

Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease – Veronika B. Dubinkina – Microbiome (BMC)

Male-specific Association Between Fat Free Mass Index and Faecal Microbiota in 2 to 3 Year Old Australian Children – Paula Smith-Brown – Journal of Pediatric Gastroenterology & Nutrition

 

General Microbiome

Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing – Noelle R. Noyes – Microbiome (BMC)

Sulfites inhibit the growth of four species of beneficial gut bacteria at concentrations regarded as safe for food – Sally V. Irwin – PLoS ONE

Research Highlights: Host-microbe interactions: Aiming at GPCRs – Mirella Bucci – Nature Chemical Biology

 

Animal Microbiome

Recombinant Incretin-Secreting Microbe Improves Metabolic Dysfunction in High-Fat Diet Fed Rodents – Paul M. Ryan – Scientific Reports

Microbiota Diversification and Crash Induced by Dietary Oxalate in the Mammalian Herbivore Neotoma albigula – Aaron W. Miller – mSphere

Commentary: Microbes REV up Host Metabolism around the Clock – Geoffrey N. Pronovost – Immunity

Impact of age-related mitochondrial dysfunction and exercise on intestinal microbiota composition – David Houghton – The Journals of Gerontology Series A

Comparative Analysis of Gut Microbiota of Culex restuans (Diptera: Culicidae) Females From Different Parents – Ephantus J Muturi – Journal of Medical Entomology

 

Beneficial Microbes and Molecules

Maternal milk feedings reduce sepsis, necrotizing enterocolitis and improve outcomes of premature infants – J Cortez – Journal of Perinatology

Therapeutic potential of Bifidobacterium breve strain A1 for preventing cognitive impairment in Alzheimer’s disease – Yodai Kobayash – Scientific Reports

Recombinant Incretin-Secreting Microbe Improves Metabolic Dysfunction in High-Fat Diet Fed Rodents – Paul M. Ryan – Scientific Reports

 

Environmental Microbiome

The plant circadian clock influences rhizosphere community structure and function – Charley J Hubbard – The ISME Journal

 

Evolution

Towards a balanced view of the bacterial tree of life – Frederik Schulz – Microbiome (BMC)

 

Extremophiles

Primary and heterotrophic productivity relate to multi-kingdom diversity in a hypersaline mat – Hans C. Bernstein – FEMS Microbiology Ecology

 

Non-Microbiology picks

Sci-Hub provides access to nearly all scholarly literature – Daniel S Himmelstein – PeerJ Preprints

Nature index: On the biotech block – Alexandra Ossola – Nature

 

October 18, 2017

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Today, several reviews, including a trio of reviews about connections between HIV and microbiome.

Gut microbiome

Gut bacterial communities of diarrheic patients with indications of Clostridioides difficile infection – Dominik Schneider – Scientific Data (NPG)

News and Views: Gastric cancer: The gastric microbiota — bacterial diversity and implications – Manish A. Shah – Nature Reviews Gastroenterology & Hepatology

Review: The hygiene hypothesis in autoimmunity: the role of pathogens and commensals – Jean-François Bach – Nature Reviews Immunology

The Bacteroidales produce an N-acylated derivative of glycine with both cholesterol-solubilising and hemolytic activity – Alli Lynch – Scientific Reports

Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus – Cristina Llorente – Nature Communications

High-Fat Diet Changes Fungal Microbiomes and Interkingdom Relationships in the Murine Gut – Timothy Heisel – mSphere

Review: Gut Microbiota and Nonalcoholic Fatty Liver Disease: Insights on Mechanisms and Therapy – Junli Ma – Nutrients (MDPI)

Review article: The gut microbiome in inflammatory bowel disease-avenues for microbial management – J. McIlroy – Alimentary Pharmacology & Therapeutics

Commentary: Regulation of glucagon-like peptide-1 sensitivity by gut microbiota dysbiosis – Shunsuke Yamane – Journal Of Diabetes Investigation

Low-grade small intestinal bacterial overgrowth is common in patients with non-alcoholic steatohepatitis on quantitative jejunal aspirate culture – UC Ghoshal – Indian Journal of Gastroenterology

 

Reproductive tract microbiome

The microbiota continuum along the female reproductive tract and its relation to uterine-related diseases – Chen Chen – Nature Communication

 

Microbiome in general

The microbiome beyond the horizon of ecological and evolutionary theory – Britt Koskella – Nature Ecology & Evolution

Trios—promising in silico biomarkers for differentiating the effect of disease on the human microbiome network – Zhanshan (Sam) Ma – Scientific Reports

 

Beneficial microbes and molecules

Prebiotic and Synbiotic Modifications of Beta Oxidation and Lipogenic Gene Expression after Experimental Hypercholesterolemia in Rat Liver – Claudia C. Alves – Frontiers in Microbiology

Vildagliptin increases butyrate-producing bacteria in the gut of diabetic rats – Qian Zhang – PLoS ONE

Caprylic and Polygalacturonic Acid Combinations for Eradication of Microbial Organisms Embedded in Biofilm – Joel Rosenblatt – Frontiers in Microbiology

PostScript: Faecal microbiota transplantation donor stools need screening for poliovirus – Peter Gerald Speck – Gut (BMJ)

 

Environmental research

Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils – Craig Anderson – PeerJ

Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI – Miranda H. Hengy – PeerJ

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing – Yanying Zhang – Frontiers in Microbiology

 

HIV and microbiome

Review: HIV and aging: role of the microbiome – Seema N. Desai – Current Opinion in HIV & AIDS

Review: The functional consequences of the microbiome in HIV: insights from metabolomic studies – Sergio Serrano-Villar – Current Opinion in HIV & AIDS

Review: Cross-reactivity of HIV vaccine responses and the microbiome – Wilton B Williams – Current Opinion in HIV & AIDS

 

Respiratory tract microbiome

Lung Microbiota is Related to Smoking Status and to Development of ARDS in Critically Ill Trauma Patients – Ariane R Panzer – American Journal of Respiratory and Critical Care Medicine

 

More microbes

Adjacent-possible ecological niche: growth of Lactobacillus species co-cultured with Escherichia coli in a synthetic minimal medium – Kouhei Mizuno – Scientific Reports

 

October 15, 2017

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General microbiome

Metagenome Analyses of Multispecies Microbial Biofilms: First Steps Toward Understanding Diverse Microbial Systems on Surfaces – Christel Schmeisser, Functional Metagenomics: Tools and Applications

Prediction analysis for microbiome sequencing data – Tao Wang, arxiv

Metagenomic Cosmid Libraries Suitable for Functional Screening in Proteobacteria – Jiujun Cheng, Functional Metagenomics: Tools and Applications

Moulds associated with contaminated ocular and injectable drugs: FDA recalls, epidemiology considerations, drug shortages, and aseptic processing – Donald G. Ahearn, Medical Mycology

Human skin microbiome

High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs – Bo Zeng, Frontiers in Microbiology

Human vaginal microbiome

Role of Molecular Biology in Diagnosis and Characterization of Vulvo-Vaginitis in Clinical Practice – Donders G.G.G., Gynecologic and Obstetric Investigation

Human gut microbiome

A Review of the Oesophageal Microbiome in Health and Disease – Dervla Kelly, Methods in Microbiology

Prediction of functional profiles of gut microbiota from 16S rRNA metagenomic data provides a more robust evaluation of gut dysbiosis occurring in Japanese type 2 diabetic patients – Ryo Inoue, Journal of Clinical Biochemistry and Nutrition

Human oral microbiome

The Effect of Supragingival Biofilm Re-development on the Subgingival Microbiota in Chronic Periodontitis – Fátima Aparecida Rocha Resende Hartenbach, Archives of Oral Biology

Animal experiments

Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice – Jessica L. Mark Welch, PNAS

Comparative study of probiotic effects of Lactobacillusand Bifidobacteria strains on cholesterol levels, liver morphology and the gut microbiota in obese mice – Rostyslav V. Bubnov, The EPMA Journal

Study on improving anaerobic co-digestion of cow manure and corn straw by fruit and vegetable waste: methane production and microbial community in CSTR process – Xuemei Wang, Bioresource Technology

Animal microbiome

Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites – Lavanya Reddivari, mSystems

Hymenobacter cavernae sp. nov., isolated from a karst cave – Hai-Zhen Zhu, International Journal of Systematic and Evolutionary Microbiology

Plant, root, and soil microbiome

Ciceribacter thiooxidans sp. nov., a novel nitrate-reducing thiosulfate-oxidizing bacterium isolated from sulfide-rich anoxic sediment – Tongchu Deng, International Journal of Systematic and Evolutionary Microbiology

Deinococcus taklimakanensis sp. nov., isolated from desert soil –  Zuobing Liu, International Journal of Systematic and Evolutionary Microbiology

Improvement of the catalytic characteristics of a salt-tolerant GH10 xylanase from Streptomyce rochei L10904 – Qin Li, International Journal of Biological Macromolecules

Trees harness the power of microbes to survive climate change – Jennifer A. Lau, PNAS

Exploring the earthworm gut as model for soil microbial ecology – Fatima Hussain, MBL

Soil proteomics for exploitation of microbial diversity in Fusarium wilt infected and healthy rhizosphere soils of tomato – R. Manikandan, Physiological and Molecular Plant Pathology

The intimate talk between plants and microorganisms at the leaf surface – Wendy Aragón, Journal of Experimental Botany

Metagenomics of Plant Microbiomes – G. Brader, Functional Metagenomics: Tools and Applications

Effects of different soil remediation methods on inhibition of lead absorption and growth and quality of Dianthus superbus L. – Xiaoyu Yang, Environmental Science and Pollution Research

Interactions of Root-Feeding Insects with Fungal and Oomycete Plant Pathogens – Telsa Willsey, Frontiers in Plant Science

Soil proteomics for exploitation of microbial diversity in Fusarium wilt infected and healthy rhizosphere soils of tomato – R. Manikandan, Physiological and Molecular Plant Pathology

Switchgrass Yield, Nutrient Uptake, And Rhizosphere Microbial Community Composition As Affected By Cultivar And Soil Fertility – Anne Sawyer, University of Minnesota Digital Conservancy

Ecoenzymatic stoichiometry and microbial nutrient limitation in rhizosphere soil in the arid area of the northern Loess Plateau, China – Yongxing Cui, Soil Biology and Biochemistry

Soil microbiota respond to green manure in organic vineyards – Claudia M. O. Longa, Journal of Applied Microbiology

Water and extremophile microbiome

Anoxynatronum buryatiense sp. nov., an anaerobic alkaliphilic bacterium from a low mineralization soda lake in Buryatia, Russia – Yana Ryzhmanova, International Journal of Systematic and Evolutionary Microbiology

100 kGy gamma-affected microbial communities within the ancient Arctic permafrost under simulated Martian conditions – Vladimir S. Cheptsov, Extremophiles

Effect of environmental parameters on biodiversity of the fungal component in lithic Antarctic communities – Laura Selbmann, Extremophiles

Biomineralisation of carbonate and sulphate by the halophilic bacterium Halomonas maura at different manganese concentrations – Almudena Rivadeneyra, Extremophiles

Biosurfactant production by haloalkaliphilic Bacillusstrains isolated from Red Sea, Egypt – Khouloud M.Barakat, The Egyptian Journal of Aquatic Research

Mass Spectrometry for the Study of Microbial Communities in Environmental Waters – Inês C. Santos, Advances in Chemical Pollution, Environmental Management and Protection

Responses of microbial community to pH stress in bioleaching of low grade copper sulfide – Yuguang Wang, Bioresource Technology

Mass Spectrometry for the Study of Microbial Communities in Environmental Waters – Inês C. Santos, Advances in Chemical Pollution, Environmental Management and Protection

Waste microbes

Microbial characteristics analysis and kinetic studies on substrate composition to methane after microbial and nutritional regulation of fruit and vegetable wastes anaerobic digestion – Chunhui Zhao, Bioresource Technology

Antibiotic resistance genes and associated microbial community conditions in aging landfill systems – Dong Wu, Environmental Science and Technology

Bioinformatics

Bioinformatics in Microbiome Analysis – Yuhan Hao, Methods in Microbiology

Techniques

Enhancing Metagenomic Approaches Through Synthetic Biology – Luana de Fátima Alves, Functional Metagenomics: Tools and Applications

Enhancing Functional Metagenomics of Complex Microbial Communities Using Stable Isotopes – Marcela Hernández, Functional Metagenomics: Tools and Applications

The P/N (Positive-to-Negative Links) Ratio in Complex Networks—A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome – Zhanshan (Sam) Ma, Microbial Ecology

Challenges and Opportunities in Discovery of Secondary Metabolites Using a Functional Metagenomic Approach – Alinne L. R. Santana-Pereira, Functional Metagenomics: Tools and Applications

Emerging whole-cell modeling principles and methods – Arthur P. Goldberg, arxiv

Expression Platforms for Functional Metagenomics: Emerging Technology Options Beyond Escherichia coli – Anna Lewin, Functional Metagenomics: Tools and Applications

Microbes in the news

AST: The Linchpin of Antimicrobial Stewardship – James Lewis, ModernMedicine Network

The Black Death Rages In Madagascar –  Julianna LeMieux, American Council on Science and Health

Report: 17 New Species Of Bacteria Found Every Day In World’s Rainforest Cafés – The Onion (Satire)

October 14, 2017

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The marine sponge microbiome, bacterial communication mediated by hydrogen sulfide, a gnotobiotic pig model to study interactions between a defined gut community and antibiotics, probiotics, and rotavirus.

General microbiome

Evolutionary contribution to coexistence of competitors in microbial food webs – Teppo Hiltunen – Proceedings of the Royal Society Biological Sciences

Pregnancy and early life

Effects of Therapeutic Hypothermia on the Gut Microbiota and Metabolome of Infants suffering Hypoxic-Ischemic Encephalopathy at birth – C Watkins – The International Journal of Biochemistry and Cell Biology

Does the maternal vaginal microbiota play a role in seeding the microbiota of neonatal gut and nose? – O Sakwinska – Beneficial Microbes

Ratio of Klebsiella/Bifidobacterium in early life correlates with later development of paediatric allergy – J S Y Low – Beneficial Microbes

Human oral microbiome

Exopolysaccharides regulate calcium flow in cariogenic biofilms – Monika Astasov-Frauenhoffer – PLOS ONE

Human gut microbiome

The Gut Microbiome Feelings of the Brain: A Perspective for Non-Microbiologists – Aaron Lerner – Microorganisms

The composition and metabolism of faecal microbiota is specifically modulated by different dietary polysaccharides and mucin: an isothermal microcalorimetry study – K Adamberg – Beneficial Microbes

Review: Our gut microbiota: a long walk to homeostasis – L M T Dicks – Beneficial Microbes

Animal experiments

Flavanol-Rich Cocoa Powder Interacts with Lactobacillus rhamnossus LGG to Alter the Antibody Response to Infection with the Parasitic Nematode Ascaris suum – Saebyeol Jang – Nutrients

Effect of antibiotic, probiotic, and human rotavirus infection on colonisation dynamics of defined commensal microbiota in a gnotobiotic pig model – H C Huang – Beneficial Microbes

Animal microbiome

Pre-print: An RNA Virome associated to the Golden Orb-weaver Spider Nephila clavipes – Humberto J Debat – bioRxiv

The sponge microbiome project – Lucas Moutinho-Silva – Gigascience

Water and extremophile microbiome

Diversity and Antimicrobial Potential of Predatory Bacteria from the Peruvian Coastline – Luis Linares-Otoya – Marine Drugs

Bioinformatics

Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data – Fanny Berglund – Microbiome

More microbes

Pre-print: Two SecA/SecY Systems with Distinct Roles in the Ecological Adaptations of Bacteria – Xiaowei Jiang – bioRxiv

Pre-print: H2S mediates interbacterial communication through the air reverting intrinsic antibiotic resistance – Daniel Thomas-Lopez – bioRxiv

Pre-print: Interplay between antibiotic efficacy and drug-induced lysis underlies enhanced biofilm formation at subinhibitory drug concentrations – Wen Yu – bioRxiv

Microbes in the news

How switches work in bacteria – EurekAlert

Opinion: Microbiology Needs More Math – Mikhail Tikhonov – The Scientist

Fluctuating environments can help cooperating bacteria – Science Daily

How to study the inside of a humpback whale’s blowhole? Drones, of course – Teresa Welsh – The Sacramento Bee

Scientists Generate 3D Map of Gut Microbiome – Genetic Engineering and Biotechnology News

Microbes on the market

Research Foundation Calls for Canadian Proposals to Study Dietary Interactions with Microbiota – PR Newswire

October 12, 2017

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Interesting papers from every category (especially in “Animal studies, animal microbiome”), and many on molecular mechanisms. Many of the alerts are from books (specifically on yeasts and soil/plant communities) listed below, so be sure to check their table of contents out!

Events and jobs
Biomedical Scientist – microbiology – Edinburgh, Scotland – Matchtech

Technician (Microbiology) – Birmingham, Alabama – LabCorp

Instructor in Microbiology – Corvallis, OR – Oregon State University

Senior Hospital Scientist Microbiology – Tamworth, New South Wales, Australia – NSW Health Pathology

Unlocking the Microbiome – November 15, London, UK – Microbiology Society

General microbiome
The P/N (Positive-to-Negative Links) Ratio in Complex Networks-A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome – Zhanshan (Sam) Ma – Microbial Ecology

Dysbiosis and Its Discontents – Katarzyna B. Hooks – mBio

Book: Yeasts in Natural Ecosystems: Ecology – Andrey Yurkov, María I. Pozo
Contains multiple articles of interest.

Pregnancy and early life
Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment – Heidi Gumpert – Frontiers in Microbiology

Cesarean Section, Formula Feeding, and Infant Antibiotic Exposure: Separate and Combined Impacts on Gut Microbial Changes in Later Infancy – Farzana Yasmin – Frontiers in Pediatrics

Multi-site human microbiome
Oral Lactobacillus Counts Predict Weight Gain Susceptibility: A 6-Year Follow-Up Study – J.A. Rosing – Obesity Facts

Review: Nutritional habits, risk, and progression of Parkinson disease – Roberto Erro – Journal of Neurology

Review: From Osteoimmunology to Osteomicrobiology: How the Microbiota and the Immune System Regulate Bone – Emory Hsu – Calcified Tissue International

Human respiratory microbiome
Review: Role of microbiota on lung homeostasis and diseases – Jian Wang – Science China Life Sciences

Human gut microbiome
Molecular Mechanism by which Prominent Human Gut Bacteroidetes Utilize Mixed-Linkage Beta-Glucans, Major Health-Promoting Cereal Polysaccharides – Kazune Tamura – Cell Reports

Reciprocal Prioritization to Dietary Glycans by Gut Bacteria in a Competitive Environment Promotes Stable Coexistence – Yunus E. Tuncil – mBio

The gut microbiome in atherosclerotic cardiovascular disease – Zhuye Jie – Nature Communications

Cytotoxic and regulatory roles of mucosal-associated invariant T cells in type 1 diabetes – Ophélie Rouxel – Nature Immunology

Review: How diet can impact gut microbiota to promote or endanger health – Benoit Chassaing – Current Opinion in Gastroenterology

Review: Management of inflammatory bowel disease-related anaemia and iron deficiency with specific reference to the role of intravenous iron in current practice – Jürgen Stein – Expert Opinion on Pharmacotherapy

Review: Bile acid-microbiota crosstalk in gastrointestinal inflammation and carcinogenesis – Wei Jia – Nature Reviews Gastroenterology and Hepatology

Review: Environmental triggers in IBD: a review of progress and evidence – Ashwin N. Ananthakrishnan – Nature Reviews Gastroenterology and Hepatology

Animal experiments
Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice – Jessica L. Mark Welch – PNAS

Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine – Leore T. Geller – Science

Increased weight gain by C-section: Functional significance of the primordial microbiome – Keith A. Martinez II – Science Advances

Epicutaneous Tolerance Induction to a Bystander Antigen Abrogates Colitis and Ileitis in Mice – David Dunkin – Inflammatory Bowel Diseases

Dietary fatty acids control the species of N-acyl-phosphatidylethanolamines synthesized by therapeutically modified bacteria in the intestinal tract – Noura S Dosoky – ACS Infectious Diseases

In Vitro Response of Rumen Microbiota to the Antimethanogenic Red Macroalga Asparagopsis taxiformis – Lorenna Machado – Microbial Ecology

Host effects on microbiota community assembly – Kathrin Näpflin – Journal of Animal Ecology
In bumblebees!

Animal microbiome
Comprehensive skin microbiome analysis reveals the uniqueness of human-associated microbial communities among the class Mammalia – Ashley Anne Ross – bioRxiv

Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring – Amy Apprill – mSystems
Drones were involved.

The Microbiome of Seriola lalandi of Wild and Aquaculture Origin Reveals Differences in Composition and Potential Function – Carolina Ramirez – Frontiers in Microbiology

A Novel Lactobacilli-Based Teat Disinfectant for Improving Bacterial Communities in the Milks of Cow Teats with Subclinical Mastitis – Jie Yu – Frontiers in Microbiology

Amplicon sequencing of bacterial microbiota in abortion material from cattle – Sara Vidal – Veterinary Research

Plant, root, and soil microbiome
Book: Soil Biological Communities and Ecosystem Resilience – Editors Martin Lukac, Paola Grenni, Mauro Gamboni
Multiple articles of interest.

Linking nitrogen load to the structure and function of wetland soil and rhizosphere microbial communities – Eric R. Hester – bioRxiv

Template Preparation Affects 16S rRNA High-Throughput Sequencing Analysis of Phyllosphere Microbial Communities – Xiaoyan Tian – Frontiers in Plant Science

Biocontrol of Bacterial Leaf Blight of Rice and Profiling of Secondary Metabolites Produced by Rhizospheric Pseudomonas aeruginosa BRp3 – Sumera Yasmin – Frontiers in Microbiology

Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants – Dominik K Großkinsky – Experimental Botany

Gaining Insight into Plant Responses to Beneficial and Pathogenic Microorganisms Using Metabolomic and Transcriptomic Approaches – Fernando Matías Romero – Metabolic Engineering for Bioactive Compounds

Water and extremophile microbiome
Globally Important Haptophyte Algae Use Exogenous Pyrimidine Compounds More Efficiently than Thiamin – Magdalena A. Gutowskaa – mBio

Fungal community dynamics during a marine dinoflagellate (Noctiluca scintillans) bloom – Jing-YunSun – Marine Environmental Research

Built environment
Biodegradation of tetracycline antibiotics in A/O moving-bed biofilm reactor systems – Han-Yu Chen – Bioprocess and Biosystems Engineering

Food microbiology
Interindividual Variability in Metabolism of [6]-Shogaol by Gut Microbiota – Pei Wang – Journal of Agricultural and Food Chemistry

Microbial technology
Programmed Assembly of Pressure Sensors Using Pattern-Forming Bacteria – Yangxiaolu Cao – Nature Biotechnology
Press: Three words: Synthetic gene circuit. Self-assembling bacteria build pressure sensor – Andrew Silver – The Register

Probiotics / prebiotics / antibiotics
Non-digestible oligosaccharides directly regulate host kinome to modulate host inflammatory responses without alterations in the gut microbiota – Richard Y. Wu – Microbiome

Review: Antibiotics and specialized metabolites from the human microbiota – Walaa K. Mousa – Natural Product Reports

Phages and viruses
Moderate-Throughput Identification and Comparison of Campylobacter-Infecting Bacteriophages – Tylor J. Johnson – bioRxiv

Review: Innate Viral Receptor Signaling Determines Type 1 Diabetes Onset – Zachary J. Morse – Frontiers in Endocrinology

Bioinformatics
A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data – Masanori Kakuta – International Journal of Molecular Sciences

Microbes in the news
Hibernating ribosomes help bacteria survive – Saint Louis University – Science Daily
Paper: The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus – Donna Matzov – Nature Communications

A century-old vaccine vial sheds light on one of medicine’s enduring mysteries – Helen Branswell – STAT News

Predatory bacteria-the quest for a new class of antibiotics – Phys.org

Mind the Gut: Copenhagen Exhibition Explores Bacteria and Feelings – Clara Rodríguez Fernández – Labiotech.eu

Gut Love: Bacteria, Love and Immunology Intersect at Esther Klein Gallery Exhibit – PRWeb

How mouldy mushrooms and frog spawn have been turned into art on Spring Bank – Amgus Young – Hull Daily Mail

Microbes on the market
Kaleido Biosciences and CoreBiome Partner to Accelerate Microbiome Therapeutic Development – Business Wire

Tiffany’s non-microbiology picks
The rise and fall and rise again of 23andMe – Erika Check Hayden – Nature

The future of DNA sequencing – Eric D. Green – Nature

October 11, 2017

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Events and jobs

Microbiology Laboratory Analyst – Cork (Ringaskiddy Road, Monkstown, Co. Cork)

 

Pregnancy and early life

Effect of probiotics on perinatal outcome in patients at high risk of preterm birth. – N Kirihara – The Journal of Obstetrics and Gynaecology Research

 

 

Human oral microbiome

Quantification of carious pathogens in the interdental microbiota of young caries-free adults. – D Bourgeois – PLoS One

 

Human gut microbiome

The gut microbiome in atherosclerotic cardiovascular disease – Z Jie – Nature Communications

Review: The microbiome as a novel paradigm in studying stress and mental health. – RT Liu – The American Psychologist

Review: The mycobiome: Role in health and disease, and as a potential probiotic target in gastrointestinal disease – CL Hager – Digestive and Liver Disease

Review: Selected aspects of the human gut microbiota – M Ventura – Cellular and Molecular Life Sciences

 

Animal experiments 

Modulation of the gut microbiota by the mixture of fish oil and krill oil in high-fat diet-induced obesity mice. – C Ciu – PLoS One

Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets – X Qu – PLoS One

 

Animal microbiome 

Pycnoscelus surinamensis cockroach gut microbiota respond consistently to a fungal diet without mirroring those of fungus-farming termites – C Richards – PLoS One

 

Plant, root, and soil microbiome

The impact of the omics era on the knowledge and use of Lysobacter spp. to control phytopathogenic microorganisms. – G Puopolo – Journal of Applied Microbiology

The effect of pH, electrolytes and temperature on the rhizosphere geochemistry of phytosiderophores. – M Walter – Plant and Soil

Pathogenic potential of environmental resident fungi from ornithogenic soils of Antarctica – JRP Sousa – Fungal Biology

Influences of Different Halophyte Vegetation on Soil Microbial Community at Temperate Salt Marsh – DR Chaudhary – Microbial Ecology

 

Built environment 

Unravelling the core microbiome of biofilms in cooling tower systems. – L Di Gregorio – Biofouling

 

 

Phages and viruses

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics – S Roux – Nature Communications

Nasty Prophages and the Dynamics of Antibiotic-Tolerant Persister Cells – A Harms – bioRxiv

 

Techniques

Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples. – YW Yan – PLoS One

A GLM-based latent variable ordination method for microbiome samples. – MB Sohn – Biometrics

Rapid enteric testing to permit targeted antimicrobial therapy, with and without Lactobacillus reuteri probiotics, for paediatric acute diarrhoeal disease in Botswana: A pilot, randomized, factorial, controlled trial – JM Pernica – PLoS One

A Tomato Spotted Wilt Virus S RNA-based Replicon System in Yeast –  K Ishibashi – Scientific Reports

Analyses Approaches for Bacteria – E Ribeiro – Exposure to Microbiological Agents in Indoor and Occupational Environments

 

Microbes in the news

Bacteria self-organize to build working sensors – EurekAlert

Effects of nutritional factors on the intestinal microbiota – Freie Universität

October 10, 2017

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Effects of amino acid supplements on metabolic health, a discussion of the broader risks and benefits of microbiome research, a book chapter evaluating microbiome statistical analysis tools.

Events and jobs

Assistant Professor in Microbiology, Tenure Track – Department of Microbiology & Immunology, University of British Columbia

General microbiome

Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research – Daria Shamarina – Microbiome

Pregnancy and early life

Review: Early microbiota, antibiotics and health – Alicja M Nogacka – Cellular and Molecular Life Sciences

Human gut microbiome

Amino acid supplements and metabolic health: a potential interplay between intestinal microbiota and systems control – Francesco Bifari – Genes & Nutrition

Microbial dysbiosis in spouses of ulcerative colitis patients: Any clues to disease pathogenesis? – Dario Sorrentino – World Journal of Gastroenterology

Phages and viruses

Pre-print: Nasty Prophages and the Dynamics of Antibiotic-Tolerant Persister Cells – Alexander Harms – bioRxiv

Bioinformatics

Book Chapter: Processing and Analyzing Human Microbiome Data – Xuan Zhu – Statistical Human Genetics

Interpretation of microbiota-based diagnostics by explaining individual classifier decisions – A Eck – BMC Bioinformatics

Techniques

Pre-print: Umbilical cord blood diagnostics for early onset sepsis in premature infants: detection of bacterial DNA and systemic inflammatory response – Leena B Mithal – bioRxiv

Pre-print: Accuracy of microbial community diversity estimated by closed- and open-reference OTUs – Robert C Edgar – PeerJ

Microbes in the news

Bacteria with synthetic gene circuit self-assemble to build working device with gold nanoparticles – Phys Org

New test identifies antibiotic-resistant bacteria in 30 minutes – The Statesman

Microbes on the market

Summit Highlights Microbiome Preservation During Ridinilazole Treatment in Exploratory Phase 2 Clinical Trial at ID Week 2017 – Globe Newswire

October 9, 2017

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Events and jobs
Postdoctoral Researcher (Experimental or Computational) – Cornell University, Ithaca, NY

The Brito Lab at Cornell University in Ithaca, NY works in the area of systems biology of the human microbiome. We are looking for talented postdocs to fill two open positions for postdoctoral researchers interested in investigating mechanistic linkages between microbes and human health outcomes.

Postdoctoral candidates can have an experimental or computational background, or both. One of the positions will be focused on engineering—any experience with synthetic biology or biomaterials is a plus. There are a range of projects in the lab relating to: clinically relevant populations (i.e. inflammatory bowel and neutropenic patients); environmental transmission of organisms and antibiotic resistance; genetic engineering of bacteria; and international research related to the microbiome. The lab strives on the diverse backgrounds of students and postdocs (e.g. microbiology, biomedical engineering, computational biology and genetics).

Start dates are flexible, but could be as early as this Fall. Interested late-stage graduate students or recently-obtained PhDs, should send Ilana Brito (ibrito (at) cornell.edu) a cover letter and CV. Promising candidates will be invited for an interview. We offer a competitive salary and benefits package.

Pregnancy and early life
Diagnosis and management of diaper dermatitis in infants with emphasis on skin microbiota in the diaper area – Maja Šikić Pogačar – International Journal of Dermatology

Human respiratory microbiome
Upregulation of bacterial-specific Th1 and Th17 responses that are enriched in CXCR5+ CD4+ T cells in non-small cell lung cancer – Qin-Yun Ma – International Immunopharmacology

Human gut microbiome
Review: Microbiome-health interactions in older people – Paul W. O’Toole – Cellular and Molecular Life Sciences

Review: Selected aspects of the human gut microbiota – Marco Ventura – Cellular and Molecular Life Sciences

Review: A comprehensive review of non-enterica subspecies of Salmonella enterica – Alexandre Lamas – Microbiological Research

Animal experiments
Effect of dietary supplements in American bullfrogs reared in low and high stocking densities – Jorgina Juliana Gradisse Freitas – Aquaculture Reports

Animal microbiome
Stenotrophomonas-like bacteria are widespread symbionts in cone snail venom ducts – Joshua P. Torres – Applied and Environmental Microbiology

Plant, root, and soil microbiome
Microbial Resistance Mechanisms to the Antibiotic and Phytotoxin Fusaric Acid – Frankie K. Crutcher – Journal of Chemical Ecology

Book: Soil Pollution: From Monitoring to Remediation – Paula Alvarenga, Christian P. Andersen (editors)

Water and extremophile microbiome
Oxic-anoxic regime shifts mediated by feedbacks between biogeochemical processes and microbial community dynamics – Timothy Bush – Nature Communications

Built environment
Impact of carbon monoxide partial pressures on methanogenesis and medium chain fatty acids production during ethanol fermentation – Sofia Esquivel-Elizondo – Biotechnology and Bioengineering

Food microbiology
Volatile Organic Compounds in Feces Associate With Response to Dietary Intervention in Patients With Irritable Bowel Syndrome – Megan Rossi – Clinical Gastroenterology and Hepatology

Tiny but mighty: bacterial membrane vesicles in food biotechnological applications – Yue Liu – Current Opinion in Biotechnology

10 – Microstructure, constituents, and their relationship with quality and functionality of dietary fibers – Naphaporn Chiewchan – Food Science, Technology and Nutrition

Targeting gut microbiota: Lactobacillus alleviated type 2 diabetes via inhibiting LPS secretion and activating GPR43 pathway – Kai-Kai Li – Journal of Functional Foods

Probiotics / prebiotics
Enhancing the viability of Lactobacillus rhamnosus GG after spray drying and during storage – Géraldine Broeckx – International Journal of Pharmaceutics

Review: Challenges and Opportunities of Nontraditional Approaches to Treating Bacterial Infections – Brian N Tse – Clinical Infectious Diseases

Probiotic intervention influences the salivary levels of Matrix Metalloproteinase (MMP)-9 and Tissue Inhibitor of metalloproteinases (TIMP)-1 in healthy adults – Heli Jäsberg – Archives of Oral Biology

Bioinformatics
Detection of complex structural variation from paired-end sequencing data – Joseph G. Arthur – bioRxiv

Codon-Dependent Translational Accuracy Controls Protein Quality in Escherichia coli but not in Saccharomyces cerevisiae – Lyne Jossé – bioRxiv

Techniques
A simple dilute and shoot approach incorporated with pentafluorophenyl (PFP) column based LC-MS/MS assay for the simultaneous determination of trimethylamine N-oxide and trimethylamine in spot urine samples with high throughput – Xiaoguang (Sunny) Li – Journal of Chromatography B

Microbes in the news
Multiple barriers to ending Madagascar’s plague outbreak – Andrew Masterson – Cosmos Magazine

A daughter’s affliction gives mother’s work ‘meaning and purpose’ – Liora Engel-Smith – The Sentinel

Antibiotic apocalypse’: doctors sound alarm over drug resistance – Robin McKie –
The Guardian

Want to cut your risk of urinary tract infection? Drink water, says study – Zee Media Bureau

Statins have power to help elderly fight off killer superbug – Sarah Westcott – Express

October 8, 2017

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General microbiome

Repurposed kinase inhibitors and β-lactams as a novel therapy for antibiotic resistant bacteria – Nathan Wlodarchak, bioRxiv

Isolation and whole genome analysis of endospore-forming bacteria from heroin – Jörn Kalinowski, Forensic Science International: Genetics

Events and jobs

DOCTORAL STUDENT / POSTDOCTORAL RESEARCHER, EARLY INTERACTIONS OF INTESTINAL MICROBIOTA AND THE IMMUNE SYSTEM – University of Helsinki

Director of the Microbiome Research Laboratory – Microbiome Research Laboratory (MRL) at UT Southwestern

Microbiology Faculty Position – University of Chicago

Human gut microbiome

Microbiome, inflammation and colorectal cancer – Ju Chen, Seminars in Immunology

The fecal microbiome of ALS patients – David Brenner, Neurobiology of Aging

Targeting gut microbiota: Lactobacillus alleviated type 2 diabetes via inhibiting LPS secretion and activating GPR43 pathway – Kai-Kai Li, Journal of Functional Foods

Volatile Organic Compounds in Feces Associate With Response to Dietary Intervention in Patients With Irritable Bowel Syndrome – Megan Rossi, Clinical Gastroenterology and Hepatology

Proteomics Dataset: The Colon Mucosa from Inflammatory Bowel Disease Patients, Gastrointestinal Asymptomic Rheumatoid Arthritis Patients, and Controls – Tue Bjerg Bennike, Data in Brief

The mycobiome: Role in health and disease, and as a potential probiotic target in gastrointestinal disease – Christopher L. Hager, Digestive and Liver Disease

Overview of paediatric IBD – David C. Wilson, Seminars in Pediatric Surgery

Improvement of Insulin Sensitivity after Lean Donor Feces in Metabolic Syndrome Is Driven by Baseline Intestinal Microbiota Composition – Ruud S. Kootte, Cell Metabolism

Fasting the Microbiota to Improve Metabolism? – Joel T. Haas, Cell Metabolism

Fecal Transplant in Inflammatory Bowel Disease – Alexander S. Browne, Gastroenterology Clinics of North America

The Brain-Gut Axis and Stress in Inflammatory Bowel Disease  – Charles N. Bernstein, Gastroenterology Clinics of North America

Human oral microbiome

The oral microbiota in colorectal cancer is distinctive and predictive – Burkhardt Flemer, Gut microbiota

Animal experiments

Interhost dispersal alters microbiome assembly and can overwhelm host innate immunity in an experimental zebrafish model – Adam R. Burns, PNAS

Ganoderma lucidum polysaccharides improve insulin sensitivity by regulating inflammatory cytokines and gut microbiota composition in mice – S. Xua, Journal of Functional Foods

Effect of enzymatically hydrolyzed scallop visceral protein powder used as a replacement of fish meal on the growth performance, immune responses, intestinal microbiota and intestinal morphology of broiler chickens – R.E. Xing, Livestock Science

Intestinal microbiota impact sepsis associated encephalopathy via the vagus nerve – Suyan Li, Neuroscience Letters

Animal microbiome

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem – Amanda C. Northrop, Ecosphere

Plant, root, and soil microbiome

Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai –  Katharina Frindte, International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

Ultrastructural observations on prokaryotic associates of benthic foraminifera: Food, mutualistic symbionts, or parasites? – Joan M. Bernhard, Marine Micropaleontology

Food microbiology

Potentially active spoilage bacteria community during the storage of vacuum packaged beefsteaks treated with aqueous ozone and electrolyzed water – Cristian Botta, International Journal of Food Microbiology

Next generation of microbiological risk assessment: Potential of omics data for exposure assessment – Heidy M.W. den Besten, International Journal of Food Microbiology

Characterization of lactic acid bacteria recovered from atole agrio, a traditional Mexican fermented beverage – Kati Väkeväinen, LWT – Food Science and Technology

Probiotics / prebiotics

Prebiotics and Inflammatory Bowel Disease – Heather E. Rasmussen, Gastroenterology Clinics of North America

Probiotics in Inflammatory Bowel Disease – Bincy P. Abraham, Gastroenterology Clinics of North America

Enhancing the viability of Lactobacillus rhamnosus GG after spray drying and during storage – Géraldine Broeckx, International Journal of Pharmaceutics

Microbes in the news

Second grade handwashing experiment leads to big decrease in bacteria, illness – INFECTIOUS DISEASES SOCIETY OF AMERICA, EurekAlert!

UTHealth awarded $3.1 million NIH grant to study how gut bacteria relates to diabetes – UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT HOUSTON, EurekAlert!

Scientists are trying to figure out how to keep bacteria from running rampant on space missions –  Claire Maldarelli, Popular Science

“Good” Gut Bacteria Linked to Melanoma Immunotherapy Response – GEN