Category Archives: Extremophiles

March 9, 2018

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Have a nice Friday! Today we have interesting papers about nasal/oral microbiota, some papers about studies in pathogens (including the use of bacteriophages for selective inhibition of E. coli), DNA extraction studies in meconium, and more!

 

Human/General Microbiome

Review: Microbiota metabolites: Pivotal players of cardiovascular damage in chronic kidney disease – Carmela Cosola – Pharmacological Research

Predictive biomarkers for type 2 of diabetes mellitus: bridging the gap between systems research and personalized medicine – Christina Kraniotou – Journal of Proteomics

The Nasal Microbiome in Asthma – Mina Fazlollahi – Journal of Allergy and Clinical Immunology

Metatranscriptome of the Oral Microbiome in Health and Disease – J. Solbiati – Journal of Dental Research

Nasal Microbiota and Respiratory Tract Infections: The Role of Viral Detection – Insa Korten – American Journal of Respiratory and Critical Care Medicine

Short term dynamics of the sputum microbiome among COPD patients – Rohita Sinha – Plos One

The effect of medical treatments on the bacterial microbiome in patients with chronic rhinosinusitis: a pilot study – Ravi Jain – International Forum of Allergy & Rhinology

The Influence of Cervicovaginal Microbiota on Mucosal Immunity and Prophylaxis in the Battle against HIV – Mara Farcasanu – Current HIV/AIDS Reports

Emerging Mechanisms of Innate Immunity and Their Translational Potential in Inflammatory Bowel Disease – Daniele Corridoni – Frontiers in Medicine

Oropharyngeal Microbiota in Frail Older Patients Unaffected by Time in Hospital – Victoria C. Ewan – Frontiers In Cellular And Infection Microbiology

Influence of Intestinal Indigenous Microbiota on Intrafamilial Infection by Helicobacter pylori in Japan – Takako Osaki – Frontiers in Immunology

Comparison of Meconium DNA Extraction Methods for Use in Microbiome Studies – Lisa F. Stinson – Frontiers in Microbiology

Minireview: Gut Microbiota: An Integral Moderator in Health and Disease – Qingqing Feng –   Frontiers in Microbiology

Activation of Notch-1 in oral epithelial cells by P. gingivalis triggers the expression of the antimicrobial protein PLA2-IIA – Ahmad Al-Attar – Mucosal Immunology

Gut microbial RNA and DNA analysis predicts hospitalizations in cirrhosis – Jasmohan S. Bajaj –  JCI Insight

Physiological Regulation of Drug Metabolism and Transport: Pregnancy, Microbiome, Inflammation, Infection, and Fasting – Edward T. Morgan – Drug Metabolism and Disposition

 

Pathogen Research

A bacteriophage cocktail targeting Escherichia coli reduces E. coli in simulated gut conditions, while preserving a non-targeted representative commensal normal microbiota – Tomasz Cieplak – Gut Microbes

Triclosan Enhances the Clearing of Pathogenic Intracellular Salmonella or Candida albicans but Disturbs the Intestinal Microbiota through mTOR-Independent Autophagy – Chao Wang – Frontiers In Cellular And Infection Microbiology

The Metabolic Sensor GPR43 Receptor Plays a Role in the Control of Klebsiella pneumoniae Infection in the Lung – Izabela Galvão – Frontiers in Immunology

Parasite-Vector Interaction of Chagas Disease: A Mini-Review – Ana Beatriz Bortolozo de Oliveira – The American Journal of Tropical Medicine and Hygiene – Current Issue

Bacillus subtilis spore with surface display of paramyosin from Clonorchis sinensis potentializes a promising oral vaccine candidate – Hengchang Sun – Parasites & Vectors

 

Animal Microbiome

Instar- and host-associated differentiation of bacterial communities in the Mediterranean fruit fly Ceratitis capitata – Antonino Malacrinò – Plos One

Concurrent gut transcriptome and microbiota profiling following chronic ethanol consumption in nonhuman primates – Tasha Barr – Gut Microbes

Integrating molecular and ecological approaches to identify potential polymicrobial pathogens over a shrimp disease progression – Wenfang Dai – Applied Microbiology And Biotechnology

Intestinal bacterial signatures of white feces syndrome in shrimp – Dongwei Hou – Applied Microbiology And Biotechnology

Bile acid metabolism regulated by the gut microbiota promotes non-alcoholic steatohepatitis-associated hepatocellular carcinoma in mice – Shoji Yamada – Oncotarget

Early-life exposure to low-dose oxidants can increase longevity via microbiome remodelling in Drosophila – Fumiaki Obata – Nature Communications

Physiological mechanisms of sustained fumagillin-induced weight loss – Jie An – JCI Insight

Gpr109a Limits Microbiota-Induced IL-23 Production To Constrain ILC3-Mediated Colonic Inflammation – Brinda Bhatt – The Journal in Immunology

Fuzhuan brick tea polysaccharides attenuate metabolic syndrome in high-fat diet induced mice in association with modulation in the gut microbiota – Guijie Chen – Journal Of Agricultural And Food Chemistry

 

Extremophiles

Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain) – Blanca Vera-Gargallo – Genes

 

Plant Microbiome

Disease-induced assemblage of a plant-beneficial bacterial consortium – Roeland L. Berendsen – The ISME Journal

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 7, 2018

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Human Microbiome

The Effect of Lean-Seafood and Non-Seafood Diets on Fecal Metabolites and Gut Microbiome: Results From a Randomized Crossover Intervention Study – Mette Schmedes – Molecular Nutrition & Food Research

Addendum – Invited: Gut Microbiota in Toxicological Risk Assessment of Drugs and Chemicals: The Need of Hour – Ganesan Velmurugan – Gut Microbes

Effects of different thickening agents on infant gut microbiota – C. A. González-Bermúdez – Food & Function

The Impact of Laparoscopic Sleeve Gastrectomy with Duodenojejunal Bypass on Intestinal Microbiota Differs from that of Laparoscopic Sleeve Gastrectomy in Japanese Patients with Obesity – Rieko Kikuchi – Clinical Drug Investigation

Perspective: Precision antimicrobial therapeutics: the path of least resistance? – Caitlin N. Spaulding – npj Biofilms and Microbiomes

Convergent shifts in host-associated microbial communities across environmentally elicited phenotypes – Tyler J. Carrier – Nature Communications

Case report: Successful faecal microbiota transplant for recurrent Clostridium difficile infection delivered by colonoscopy through a diverted ileostomy in a patient with severe perianal Crohn’s disease – Jonathan Digby-Bell – BMJ Case Reports

Outlook: How baby’s first microbes could be crucial to future health – Sarah DeWeerdt – Nature

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

Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples – Roshonda B. Jones – Scientific Reports

Review: Gastrointestinal toxicity of immune checkpoint inhibitors: from mechanisms to management – Mark A. Samaan – Nature Reviews Gastroenterology & Hepatology

Reply: Probiotics, bile acids and gastrointestinal carcinogenesis – Wei Jia – Nature Reviews Gastroenterology & Hepatology

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid – Philipp Kirstahler – Scientific Reports

 

Animal microbiome

Performance, egg quality, nutrient digestibility, and excreta microbiota shedding in laying hens fed corn-soybean-meal-wheat-based diets supplemented with xylanase – X. J. Lei – Poultry Science

Next generation sequencing for gut microbiome characterization in rainbow trout (Oncorhynchus mykiss) fed animal by-product meals as an alternative to fishmeal protein sources – Simona Rimoldi – Plos One

Sugary Kefir Strain Lactobacillus mali APS1 Ameliorated Hepatic Steatosis by Regulation of SIRT-1/Nrf-2 and Gut Microbiota in Rats – Yung-Tsung Chen – Molecular Nutrition & Food Research

Pyrroloquinoline quinone prevents developmental programming of microbial dysbiosis and macrophage polarization to attenuate liver fibrosis in offspring of obese mice – Jacob E. Friedman – Hepatology Communications

Inulin-type fructan improves diabetic phenotype and gut microbiota profiles in rats – Qian Zhang​ – PeerJ

Early-life exposure to low-dose oxidants can increase longevity via microbiome remodelling in Drosophila – Fumiaki Obata – Nature Communications

The influence of caging, bedding, and diet on the composition of the microbiota in different regions of the mouse gut – Aaron C. Ericsson – Scientific Reports

News & Views: The intestinal microbiome influences checkpoint blockade – Cynthia L Sears – Nature Medicine

News Feature: Gut checkpoint: A rising cancer treatment may get a boost from intestinal bacteria – Anna Azvolinsky – Nature Medicine

Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen-recycling gut microbiome – Yi Hu – Nature Communications

Research Highlight: Comparative genomics: Blood, guts and vampire bats – Linda Koch – Nature Reviews Genetics

 

Pathogen research

Serial Clustering of Late Onset Group B Streptococcal Infections in the Neonatal Unit – a Genomic Re-Evaluation of Causality – Elita Jauneikaite – Clinical Infectious Diseases

A multi-omic analysis reveals the role of fumarate in regulating the virulence of enterohemorrhagic Escherichia coli – Cheng-Ju Kuo – Cell Death & Disease

Occurrence of blaNDM Variants Among Enterobacteriaceae From a Neonatal Intensive Care Unit in a Northern India Hospital – Nayeem Ahmad – Frontiers in Microbiology

 

Food Microbes

Lactobacillus rossiae strain isolated from sourdough produces putrescine from arginine – Beatriz del Rio – Scientific Reports

 

Environmental Microbiology

Microbial diversity associated to the anaerobic sediments of a soda lake (Mono Lake, CA) – Patricia Rojas – Canadian Journal of Microbiology

March 6, 2018

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In today’s digest we have many interesting articles, particularly in “General Microbiome” section. Check a review on integrative view of cell cycle control in E. coli by L. Dewachter, an article on the return of cultures in microbiology by V. Marx, an article on microbial altruism and cheating in social amoebas by S. Noh. Don’t miss great articles from other sections, like “Water microbiome” where I would recommend an article deciphering the evolution and metabolism of an anammox bacterium by M. Strous and an article about globally overlooked nanoplanktonic diatoms by K. Leblanc. Happy reading!

Events

The Human Microbiome, EMBL Heidelberg, Germany, 16 – 19 Sep 2018

Jobs

Qc Analyst- Microbiology, Liverpool, UK

General microbiome

Commensal Koch’s postulates: establishing causation in human microbiota research – Anne Neville – Current Opinion in Microbiology

Escherichia coli Lrp regulates one-third of the genome via direct, cooperative, and indirect routes – Grace M. Kroner – bioRxiv

Review: An integrative view of cell cycle control in Escherichia coli – Liselot Dewachter – FEMS Microbiology Reviews

[Section Head] is Ravdin Lecture in the Basic and Surgical Sciences Microbiome Medicine: This Changes Everything  – John C. Alverdy – Journal of the American College of Surgeons

Regulation of Allergic Immune Responses by Microbial Metabolites – Hyun Jung Park – Immune Network

Microbiology: the return of culture – Vivien Marx – Nature Methods

Review: Bacterial microcompartments – Cheryl A. Kerfeld – Nature Reviews Microbiology

Proposal of the suffix –ota to denote phyla. Addendum to ‘Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes’ – William B. Whitman – International Journal of Systematic and Evolutionary Microbiology

Genetic signatures of microbial altruism and cheating in social amoebas in the wild – Suegene Noh – PNAS

The use of SWATH to analyse the dynamic changes of bacterial proteome of carbapanemase-producing Escherichia coli under antibiotic pressure – Hanna E. Sidjabat – Scientific Reports

Pregnancy and early life

Early fecal microbiota composition in children who later develop celiac disease and associated autoimmunity – Anniina Rintala – Scandinavian Journal of Gastroenterology

Human oral microbiome

Eliminating bias and accelerating the clinical translation of oral microbiome research in oral oncology – Rohit Kunnath Menon  – Oral Oncology

Acid-resistant genes of oral plaque microbiome from the functional metagenomics – Meng Zhang – Journal of Oral Microbiology

Oral microbiota in autoimmune polyendocrine syndrome type 1 – Øyvind Bruserud – Journal of Oral Microbiology

Human vaginal microbiome

Impact of contraceptive initiation on vaginal microbiota  – Sharon L. Achilles – American Journal of Obstetrics and Gynecology

Human gut microbiome

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

Review: Flavonoid metabolism: the interaction of metabolites and gut microbiota – Kaeko Murota – Bioscience, Biotechnology, and Biochemistry

Data Descriptor: Gut bacterial communities of diarrheic patients with indications of Clostridioides difficile infection – Dominik Schneider – Scientific Data

Animal experiments 

Dietary Tryptophan Restriction Dose-Dependently Modulates Energy Balance, Gut Hormones, and Microbiota in Obesity-Prone Rats – Rizaldy C. Zapata – Obesity

Prevalence of microorganisms associated with feline gingivostomatitis – Hitoshi Nakanishi – Journal of Feline Medicine and Surgery

Effects of Rubus coreanus byproducts on intestinal microbiota and the immune modulation – Da Yoon Yu – Asian-Australasian Journal of Animal Sciences (AJAS)

Host and Environmental Factors Affecting the Intestinal Microbiota in Chickens – Jannigje G. Kers – Frontiers in Microbiology

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

Animal microbiome 

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

Plant, root, and soil microbiome

Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient – Jackson W Sorensen – bioRxiv

Phyllosphere microbiology: at the interface between microbial individuals and the plant host – Mitja N. P. Remus-Emsermann – New Phtyologist

Plant Rhizosphere Selection of Plasmodiophorid Lineages from Bulk Soil: The Importance of “Hidden” Diversity – David Bass – Frontiers in Microbiology

Microbial community structure with trends in methylation gene diversity and abundance in mercury-contaminated rice paddy soils in Guizhou, China – Tatiana A. Vishnivetskaya – Environmental Science: Processes & Impacts

Drought consistently alters the composition of soil fungal and bacterial communities in grasslands from two continents – Raúl Ochoa-Hueso – Global Change Biology

Temporal succession of soil antibiotic resistance genes following application of swine, cattle and poultry manures spiked with or without antibiotics – Yu-Jing Zhang – Environmental Pollution

Water and extremophile microbiome 

Light-dependent processes on the cathode enhance the electrical outputs of sediment microbial fuel cells – Ivo Bardarov – Bioelectrochemistry

Diversity of culturable filamentous Ascomycetes in the eastern South Pacific Ocean off Chile – Jeanett Vera – World Journal of Microbiology and Biotechnology

Stepwise impact of urban wastewater treatment on the bacterial community structure, antibiotic contents, and prevalence of antimicrobial resistance – Mingyu Wang – Environmental Pollution

Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export – Karine Leblanc – Nature Communications

A novel genus of the class Actinobacteria, Longivirga aurantiaca gen. nov., sp. nov., isolated from lake sediment – Jian-Hang Qu – International Journal of Systematic and Evolutionary Microbiology

Desulfothermobacter acidiphilus gen. nov., sp. nov., a thermoacidophilic sulfate-reducing bacterium isolated from a terrestrial hot spring –  E. N. Frolov – International Journal of Systematic and Evolutionary Microbiology

Deciphering the evolution and metabolism of an anammox bacterium from a community genome – Marc Strous –  Nature

Food microbiology

Dynamics of biofilm formation by Listeria monocytogenes on stainless steel under mono-species and mixed-culture simulated fish processing conditions and chemical disinfection challenges – Eleni Papaioannou – International Journal of Food Microbiology

Probiotics / prebiotics

Novel consortium of Klebsiella variicola and Lactobacillus species enhances the functional potential of fermented dairy products by increasing the availability of branched-chain amino acids and the amount of distinctive volatiles – H. Rosales-Bravo – Journal of Applied Microbiology

Bioinformatics

Updating the 97% identity threshold for 16S‌ ribosomal RNA OTUs – Robert C Edgar – Bioinformatics

Biotechnology

Selection and characterization of an anaerobic microbial consortium with high adaptation to crude glycerol for 1,3-propanediol production – Jin-Jie Zhou – Applied Microbiology and Biotechnology

Microbes in the news

Studying how tiny microbes thrive in harsh environments could lead to better treatments for human diseases

Microbes on the market 

FDA fast-tracks Finch’s microbiome capsule for C. difficile

Science, publishing, and career 

Uniting science and stories: Perspectives on the value of storytelling for communicating science

New round of science journalism projects awarded

 

March 4, 2018

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Events and jobs

Phd position in antimicrobial resistance development in biofilm communities – University of Leuven

Professor in Microbiome/Microbiota-Host Interactions – University of Alabama

Microbiology Lab Scientist – Lyneer Staffing

General microbiome

Impact of Brazilian microbiome for boosting agriculture, animal husbandry and human being: a book review – Arthur Prudêncio de Araujo Pereira, Journal of Cleaner Production

Are animals a source of Stenotrophomonas maltophiliain human infections? Contributions of a nationwide molecular study – Aurélie Jayol, European Journal of Clinical Microbiology & Infectious Diseases

The organization of bacterial genomes: Towards understanding the interplay between structure and function – Daan J.W. Brocken, Current Opinion in Systems Biology

Pregnancy and early life

Selective maternal seeding and environment shape the human gut microbiome – Katri Korpela, Genome Research

Ecological Shifts of Supragingival Microbiota in Association with Pregnancy – Wenzhen Lin, Frontiers in Cellular and Infectious Microbiology

Human respiratory microbiome

Impaired diversity of the lung microbiome predicts progression of idiopathic pulmonary fibrosis – Youhei Takahashi, Respiratory Research

Human gut microbiome

Methanogens in humans: potentially beneficial or harmful for health – Prem Prashant Chaudhary, Applied Microbiology and Biotechnology

Gut microbiota alterations and dietary modulation in childhood malnutrition – The role of short chain fatty acids – Ceyda Tugba Pekmez, Clinical Nutrition

Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia – Bruce A. Rosa, Microbiome

Market Integration Predicts Human Gut Microbiome Attributes across a Gradient of Economic Development – Keaton Stagaman, mSystems

A Review of Microbiota and Irritable Bowel Syndrome: Future in Therapies – Bruno K. Rodiño-Janeiro, Advances in Therapy

Characterizing the metabolic phenotype of intestinal villus blunting in Zambian children with severe acute malnutrition and persistent diarrhea – Marta Farràs, PLOS one

Animal experiments

Differences in gut microbiota composition in finishing Landrace pigs with low and high feed conversion ratios – Zhen Tan, Antonie van Leeuwenhoek

Human milk oligosaccharides protect against the development of autoimmune diabetes in NOD-mice – Ling Xiao, Scientific Reports

TRIM31 Deficiency Is Associated with Impaired Glucose Metabolism and Disrupted Gut Microbiota in Mice – Jing Cheng, Frontiers in Physiology

Animal microbiome

Quantitative prediction of shrimp disease incidence via the profiles of gut eukaryotic microbiota – Jinbo Xiong, Applied Microbiology and Biotechnology

Bioturbation activity of three macrofaunal species and the presence of meiofauna affect the abundance and composition of benthic bacterial communities – Élise Lacoste, Marine Environmental Research

Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese – Sergei V. Drovetski, Scientific Reports

Skin microbiomes of California terrestrial salamanders are influenced by habitat more than host phylogeny – Alicia K. Bird, Frontiers in Microbiology

Plant, root, and soil microbiome

Recent Insights on Biological and Ecological Aspects of Ectomycorrhizal Fungi and Their Interactions – Antonietta Mello, Frontiers in Microbiology

Micro-decomposer communities and decomposition processes in tropical lowlands as affected by land use and litter type – Valentyna Krashevska, Oecologia

One-time phosphate fertilizer application to grassland columns modifies the soil microbiota and limits its role in ecosystem services – Israel Ikoyi, Science of The Total Environment

Size-Controlled Production of Gold Bionanoparticles Using the Extremely Acidophilic Fe(III)-Reducing Bacterium, Acidocella aromatica – Intan Nurul Rizki, Minerals

Nematicidal protease genes screened from a soil metagenomic library to control Radopholus similismediated by Pseudomonas fluorescens pf36 – Deqiang Chen, Applied Microbiology and Biotechnology

The structural and functional contributions of β-glucosidase-producing microbial communities to cellulose degradation in composting – Xiangyun Zang, Biotechnology for Biofuels

Diversity and contributions to nitrogen cycling and carbon fixation of soil salinity shaped microbial communities in Tarim Basin – Min Ren, Frontiers in Microbiology

Decomposer food web in a deciduous forest shows high share of generalist microorganisms and importance of microbial biomass recycling – Ruben López-Mondéjar, The ISME Journal

Soil bacterial community shifts driven by restoration time and steppe types in the degraded steppe of Inner Mongolia – Minjie Yao, CATENA

One-time phosphate fertilizer application to grassland columns modifies the soil microbiota and limits its role in ecosystem services – Israel Ikoyi, Science of The Total Environment

Enumeration of Culturable Endophytic Bacterial Population of Different Lycopersicum esculentum L. Varieties – Monika Singh, International Journal of Current Microbiology and Applied Sciences

Isolation and Characterization of Methanol Utilizing Microorganisms from Leguminous Crops – Umang Ahlawat, International Journal of Current Microbiology and Applied Sciences

Isolation of Mercury-Resistant Fungi from Mercury-Contaminated Agricultural Soil – Reginawanti Hindersah, Agriculture

Root-associated fungi shared between arbuscular mycorrhizal and ectomycorrhizal conifers in a temperate forest – Hirokazu Toju, Frontiers in Microbiology

Antagonistic Potential and Molecular Characterization of Trichoderma spp. against Rhizoctonia solani Infecting Ghost Pepper in Manipur, India – Khedarani Koijam, International Journal of Current Microbiology and Applied Sciences

Isolation of Biocontrol (Bacterial) Agents from Chickpea (Cicer arietinum linnaeus) – S. Vijaya Kumar, International Journal of Current Microbiology and Applied Sciences

Potentiality of Native Pseudomonas spp. in Promoting Sugarcane Seedling Growth and Red Rot (Colletotrichum falcatum went) Management – P. Kishore Varma, International Journal of Current Microbiology and Applied Sciences

Interactions between isolates of the fungus Beauveria bassiana and Zea mays – Aimee McKinnon, Lincoln University (thesis)

Metagenome Sequencing of Prokaryotic Microbiota from Two Hypersaline Soils of the Odiel Salt Marshes in Huelva, Southwestern Spain – Blanca Vera-Gargallo, Genome Anouncements

Degradation shaped bacterial and archaeal communities with predictable taxa and their association patterns in Zoige wetland at Tibet plateau – Yunfu Gu, Scientific Reports

Water and extremophile microbiome

Survival of Listeria monocytogenes and Staphylococcus aureus in Synthetic Brines. Studying the Effects of Salt, Temperature and Sugar through the Approach of the Design of Experiments – Antonio Bevilacqua, Frontiers in Microbiology

Saccharolobus caldissimus gen. nov., sp. nov., a facultatively anaerobic iron-reducing hyperthermophilic archaeon isolated from an acidic terrestrial hot spring, and reclassification of Sulfolobus solfataricus as Saccharolobus solfataricus comb. nov. and Sulfolobus shibatae as Saccharolobus shibatae comb. nov. – Hiroyuki D. Sakai,  International Journal of Systematic and Evolutionary Microbiology

Distinct Osmoadaptation Strategies in the Strict Halophilic and Halotolerant Bacteria Isolated from Lunsu Salt Water Body of North West Himalayas – Shivani Vaidya, Current Microbiology

Archaeal Viruses from High-Temperature Environments – Jacob H. Munson-McGee, Genes

Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations – Nina Gunde-Cimerman, FEMS Microbiology Reviews

Tertiary treatment and dual disinfection to improve microbial quality of reclaimed water for potable and non-potable reuse: A case study of facilities in North Carolina – Emily S. Bailey, Science of The Total Environment

The Early Earth Geochemical and Isotope Record of Serpentinizing Environments from Archean Stichtite (Mg6Cr2(OH)16[CO3] · 4H2O) – Erik B. Melchiorre, Precambrian Research

Process performance and population dynamics of ammonium tolerant microorganisms during co-digestion of fish waste and manure – Linn Solli, Renewable Energy

Toxicity assessment of pharmaceutical compounds on mixed culture from activated sludge using respirometric technique: The role of microbial community structure – I.A. Vasiliadou, Science of The Total Environment

Divergent assemblage patterns of abundant and rare microbial sub-communities in response to inorganic carbon stresses in a simultaneous anammox and denitrification (SAD) system – Duntao Shu, Bioresource Technology

Pretreatment of saline antibiotic wastewater using marine microalga – Xueqing Shi, Bioresource Technology

Bioinformatics

Handling gene and protein names in the age of bioinformatics: the special challenge of secreted multimodular bacterial enzymes such as the cbhA/cbh9Agene of Clostridium thermocellum – Wolfgang H. Schwarz, World Journal of Microbiology and Biotechnology

Techniques

Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench – Wei-Kai Wu, Journal of the Formosan Medical Association

The Application of Omics Data to the Development of AOPs – Mary T. McBride, A Systems Biology Approach to Advancing Adverse Outcome Pathways for Risk Assessment

From correlation to causation: analysis of metabolomics data using systems biology approaches – Antonio Rosato, Metabolomics

Application of ensemble deep neural network to metabolomics studies – Taiga Asakura, Analytica Chimica Acta

Genome-reconstruction for eukaryotes from complex natural microbial communities – Patrick T West, Genome Research

Microbes in the news

Magnetic bacteria cause a stir – Christian Harding, Chemistry World

Federal Panel Passes Antibiotic-Resistant Bacteria Resolutions – Troy Brown, MedScape

Dangerous bacteria found in raw milk from Pennsylvania dairy – Coral Beach, Food Safety Network

 

March 3, 2017

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Antiphage defense systems in microbial genomes, oral pathogen inhibition by wine polyphenols and an oral probiotic, and analysis of E. coli gene expression in simulated spaceflight.

Events and jobs

Call for Expressions of Interest: Microbiology Twitter Teachers for New MOOC – Spanish Society for Microbiology

Endowed Chair in Molecular Genetics Waksman Institute of Microbiology – Rutgers University

General microbiome

Creating a 3D microbial and chemical snapshot of a human habitat – Clifford A Kapono – Scientific Reports

Human oral microbiome

Inhibition of Oral Pathogens Adhesion to Human Gingival Fibroblasts by Wine Polyphenols Alone and in Combination with an Oral Probiotic – Adelaida Esteban-Fernández – Journal of Agricultural and Food Chemistry

Human vaginal microbiome

Metatranscriptome analysis of the vaginal microbiota reveals potential mechanisms for protection against metronidazole in bacterial vaginosis – Zhi-Luo Deng – bioRxiv

Human gut microbiome

Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia – Bruce A Rosa – Microbiome

Animal experiments

Pre-print: Orthogonal dietary niche enables reversible engraftment of a gut bacterial commensal – Sean M Kearney – bioRxiv

Pre-print: Clearing the FoG: Antifungal tolerance is a subpopulation effect that is distinct from resistance and is associated with persistent candidemia – Alexander Rosenberg – bioRxiv

Blueberry Supplementation Influences the Gut Microbiota, Inflammation, and Insulin Resistance in High-Fat-Diet–Fed Rats – Sunhye Lee – Journal of Nutrition

Animal microbiome

Woody forages effect the intestinal bacteria diversity of golden pompano Trachinotus ovatus – Biao Chen – AMB Express

Water and extremophile microbiome

Pre-print: Microzooplankton distribution in the Amundsen Sea Polynya (Antarctica) during an extensive Phaeocystis antarctica bloom – Rasmus Swalethorp – bioRxiv

Microbes in space

Pre-print: Analysis of Escherichia coli Flagellin Gene Expression in Simulated Spaceflight Growth Conditions – Kyle M Hetrick – bioRxiv

Phages and viruses

Systematic discovery of antiphage defense systems in the microbial pangenome – Shany Doron – Science

Bioinformatics

Pre-print: VirTect: a computational method for detecting virus species from RNA-Seq and its application in head and neck squamous cell carcinoma – Atlas Khan – bioRxiv

Techniques

Pre-print: Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets – Edouard A Hay – bioRxiv

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem – Stilianos Louca – Microbiome

Improving saliva shotgun metagenomics by chemical host DNA depletion – Clarisse A Marotz – Microbiome

Microbes in the news

Your skin is crawling with bacteria, and some of them might help fight cancer – Claire Maldarelli – Popular Science

Most Viruses And Bacteria Fall From The Sky – Astrobiology Web

Microbes on the market

Six Leading Pharma Firms to Participate at Pharmaceutical Microbiology Event in San Diego – Technology Networks

Science, career, and publishing

Pre-print: Persistent Underrepresentation of Women’s Science in High Profile Journals – Yiqin Alicia Shen – bioRxiv

Pre-print: Female grant applicants are equally successful when peer reviewers assess the science, but not when they assess the scientist – Holly O Witteman – bioRxiv

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 21, 2018

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Events and jobs

BioData World West 2018 – March 13-14 – Hotel Kabuki, San Francisco, CA

General microbiome

[editorial] Systems biology of the human microbiome – BP Bernabé, L Cralle, JA Gilbert – Current Opinion in Biotechnology, 2018

[pre-print] Growth tradeoffs produce complex microbial communities without direct interactions – Michael Manhart – bioRxiv

Exploring the Multifaceted Role of Microbes in Pharmacology – Mitali Mishra – Microbial Biotechnology

Human reproductive or urinary microbiome

Seminal bacterial composition in patients with obstructive and non-obstructive azoospermia – Houyang Chen – Experimental and Therapeutic Medicine

Human respiratory microbiome

Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015 – Jose A. Romero-Espinoza – PLOS One

Human gut microbiome

[pdf[ Phytochemicals that influence gut microbiota as prophylactics and for the treatment of obesity and inflammatory diseases – Lucrecia Carrera-Quintanar – Hindawi

Dietary Fiber Treatment Corrects the Composition of Gut Microbiota, Promotes SCFA Production, and Suppresses Colon Carcinogenesis – F Bishehsari – Genes

A Cross-Talk Between Microbiota-Derived Short-Chain Fatty Acids and the Host Mucosal Immune System Regulates Intestinal Homeostasis and Inflammatory Bowel Disease – Pedro Gonçalves – Inflammatory Bowel Diseases

Animal microbiome

Differential microbial communities of omnivorous and herbivorous cattle in Southern China – Susanna K.P. Lau – Computational and Structural Biotechnology Journal

The gills of reef fish support a distinct microbiome influenced by host-specific factors – Zoe A. Pratte – Applied and Environmental Microbiology

Metagenomic analysis of orange colored protrusions from the muscle of Queen Conch Lobatus gigas (Linnaeus, 1758) – Jaison H. Cuartas – PeerJ

Plant, root, and soil microbiome

Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization – Birgit Wolters – FEMS Microbiology Ecology

Structural and metabolic diversity of rhizosphere microbial communities of Phragmites karka in a tropical coastal lagoon – Pratiksha Behera – Applied Soil Ecology

Responses of soil microbial communities to a short-term application of seaweed fertilizer revealed by deep amplicon sequencing – Mingpeng Wang – Applied Soil Ecology

[pdf] The Green Roof Microbiome: Improving Plant Survival for Ecosystem Service Delivery – Roberta Fulthorpe – Frontiers in Ecology and Evolution

Microbes and Their Role in Drought Tolerance of Agricultural Food Crops – Rout George Kerry – Microbial Biotechnology

Microscopic and Metagenomic Analyses of Peltigera ponojensis (Peltigerales, Ascomycota) – Linda E. Graham – International Journal of Plant Sciences

Frankia Diversity in Host Plant Root Nodules Is Independent of Abundance or Relative Diversity of Frankia Populations in Corresponding Rhizosphere Soils – Seifeddine Ben Tekaya – Applied and Environmental Microbiology

High frequency cropping of pulses modifies soil nitrogen level and the rhizosphere bacterial microbiome in 4-year rotation systems of the semiarid prairie – Chantal Hamel – Applied Soil Ecology

Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization – Birgit Wolters – FEMS Microbiology Ecology

Water and extremophile microbiome

Variability in metagenomic samples from the Puget Sound: Relationship to temporal and anthropogenic impacts – James C. Wallace – PLOS One

Linking the effect of antibiotics on partial-nitritation biofilters: performance, microbial communities and microbial activities – Alejandro Gonzalez-Martinez – Frontiers in Microbiology

The effect of epiphytic macroinvertebrates on microbial communities in different types of macrophyte-dominated shallow lakes – Tomasz Mieczan –  Knowl. Manag. Aquat. Ecosyst

Watershed-induced limnological and microbial status in two oligotrophic Andean lakes exposed to the same climatic scenario – Alex Echeverría-Vega – Frontiers in Microbiology

** A novel β-glucosidase isolated from the microbial metagenome of Lake Poraquê (Amazon, Brazil) – Danyelle Toyama – Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics

Variations in culturable bacterial communities and biochemical properties in the foreland of the retreating Tianshan No. 1 glacier – Xiukun Wu – Brazilian Journal of Microbiology

Food microbiology

Microbial diversity and component variation in Xiaguan Tuo Tea during pile fermentation – Haizhou Li – PLOS One

Metagenomic Insights into Environmental Microbiome and Their Application in Food/Pharmaceutical Industry – Ramya Sree Boddu – Microbial Biotechnology

Phages and viruses

[pre-print] THEA: A novel approach to gene identification in phage genomes – Katelyn McNair – bioRxiv

Bioinformatics

* [pdf] Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models – Aeriel Belk – Genes

COREMIC: a web-tool to search for a niche associated CORE MICrobiome – Richard R. Rodrigues – PeerJ

Techniques

Isotope fractionation in biogas allows direct microbial community stability monitoring in anaerobic digestion – Jo De Vrieze – Environmental Science & Technology

Statistical assessment of DNA extraction methodology for culture-independent analysis of microbial community associated with diverse environmental samples – Rishi Mahajan – Molecular Biology Reports

Microbes in the news

These Bacteria Eat Toxic Metal, ‘Poop’ Gold Nuggets – Live Science

Ed’s non-microbiology picks (can use your own name of course!) (cool non-microbiology science)

Earthquakes follow wastewater disposal patterns in southern Kansas

Ultra-processed foods ‘linked to cancer’

Promising cancer vaccine would use patient’s own cells to train the immune system

Does GMO corn increase crop yields? 21 years of data confirm it does—and provides substantial health benefits

Poor fitness linked to weaker brain fiber, higher dementia risk

Low cigarette consumption and risk of coronary heart disease and stroke: meta-analysis of 141 cohort studies in 55 study reports

Fewer Infants Died In States That Allowed Affordable Care Act

February 19, 2018

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Events and jobs

Research Technician I – University at Buffalo

General microbiome

Non-antibiotic antimicrobial triclosan induces multiple antibiotic resistance through genetic mutation – Ji Lu, bioRxiv

Oncologists tap the microbiome in bid to improve immunotherapy outcomes – Asher Mullard, Nature Reviews Drug Discovery

Nasal microbiome

Establishment of the Nasal Microbiota in the first 18 Months of Life – Correlation with Early Onset Rhinitis and Wheezing – Le Duc Huy Ta, Journal of Allergy and Clinical Immunology

The nasal microbiome in chronic rhinosinusitis: analyzing the effects of atopy and bacterial functional pathways in 111 patients – Mahboobeh Mahdavinia, Journal of Allergy and Clinical Immunology

Pregnancy and early life

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome – Daniela S. A. Goltsman, bioRxiv

Human vaginal microbiome

Microbiota changes impact on sexually transmitted infections and the development of pelvic inflammatory disease – Nathalie Loeper, Microbes and Infection

Human gut microbiome

Efficacy of Bifidobacterium breve Fermented Milk in Maintaining Remission of Ulcerative Colitis – Katsuyoshi Matsuoka, Digestive Diseases and Sciences

Comparison of Different Strategies for Providing Fecal Microbiota Transplantation to Treat Patients with Recurrent Clostridium difficile Infection in Two English Hospitals: A Review – Simon D. Goldenberg, Infectious Diseases and Therapy

Fecal Microbiota Transplant for Refractory Clostridium difficile Infection Interrupts 25-Year History of Recurrent Urinary Tract Infections – Tiffany Wang, Open Forum Infectious Diseases

Fecal microbiota transplantation for severe complicated C. difficile colitis in a patient with acquired immunodeficiency syndrome – P. Martínez-Ayala, Revista de Gastroenterología de México

Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium difficile Patients With and Without IBD – Robert P Hirten, bioRxiv

The impact of a helminth-modified microbiome on host immunity – Tara P. Brosschot &
Lisa A. Reynolds, Mucosal Immunology

Depression and obesity: evidence of shared biological mechanisms – Yuri Milaneschi, Molecular Psychiatry

Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation – Juliana Durack, Nature Communications

Roux-en-Y Gastric-Bypass and sleeve gastrectomy induces specific shifts of the gut microbiota without altering the metabolism of bile acids in the intestinal lumen – Henri Duboc, International Journal of Obesity

Effects of ewe’s milk yogurt (whole and semi-skimmed) and cow’s milk yogurt on inflammation markers and gut microbiota of subjects with borderline-high plasma cholesterol levels: a crossover study – Noemí Redondo, European Journal of Nutrition

Impact of food additives on the gut-brain axis – Mary K. Holder, Physiology & Behavior

Gut microbiota injury in allogeneic haematopoietic stem cell transplantation – Yusuke Shono, Nature Reviews Cancer

Microbiota: Pathobiont peacekeepers – Kirsty Minton, Nature Reviews Immunology

Gut Microbiomics—A Solution to Unloose the Gordian Knot of Biological Effects of Ionizing Radiation – Amy Zhang, Journal of Heredity

Oral microbiome

Host defense against oral microbiota by bone-damaging T cells – Masayuki Tsukasaki, Nature Communications

Beyond Streptococcus mutans: clinical implications of the evolving dental caries aetiological paradigms and its associated microbiome – N. Philip, BDJ

Animal experiments

The Divergence in Bacterial Components Associated with Bactrocera dorsalis across Developmental Stages – Xiaofeng Zhao, Frontiers in Microbiology

Microbiota in fermented feed and swine gut – Cheng Wang, Applied Microbiology and Biotechnology

Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract – Carl J. Yeoman, Scientific Reports

Animal microbiome

Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure – Kieran A. Bates, Nature Communications

The effect of cadmium exposure on diversity of intestinal microbial community of Rana chensinensis tadpoles – Danyang Mu, Ecotoxicology and Environmental Safety

A new cell extraction method reveals hemolymph microbiome of three aquatic invertebrates – Xinxu Zhang, Applied Microbiology and Biotechnology

The gastrointestinal tract microbiota of northern white-cheeked gibbons (Nomascus leucogenys) varies with age and captive condition – Ting Jia, Scientific Reports

Plant, root, and soil microbiome

Manipulation of the rhizosphere microbial community through application of a new bio-organic fertilizer improves watermelon quality and health – Jia Zhao, PLOS One

Water and extremophile microbiome

Seasonal dynamics of tetracycline resistance gene transport in the Sumas River agricultural watershed of British Columbia, Canada – Patricia L. Keen, Science of The Total Environment

Microbial diversity and toxin risk in tropical freshwater reservoirs of Cape Verde – Ana Paula Semedo-Aguiar, bioRxiv

Common hydraulic fracturing fluid additives alter the structure and function of anaerobic microbial communities – Adam C. Mumford, Applied and Environmental Microbiology

Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in A Bioreduced Uranium Contaminated Site after Reoxidation – Bing Li, Applied and Environmental Microbiology

Properties of bacterial communities attached to artificial substrates in a hypereutrophic urban river – Xianlei Cai, AMB Express

Food microbiology

Nitrogen removal enhancement using lactic acid fermentation products from food waste as external carbon sources: performance and microbial communities – Jialing Tang, Bioresource Technology

Probiotics/Prebiotics

Advances in Probiotic Regulation of Bone and Mineral Metabolism – Laura R. McCabe, Calcified Tissue International

Prebiotics as functional food ingredients preventing diet-related diseases – A. Florowska, Food and Function

A prebiotic mixture improved Lactobacillus acidophilus and Bifidobacterium animalisgastrointestinal in vitro resistance in petit-suisse – Marina Padilha, Food and Function

Bioinformatics

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses – Tomáš Větrovský, Bioinformatics

Techniques

Use of Rectal Swab Samples for Analysis of the Intestinal Microbiome in Children – Nan Zhang, Chinese Medical Journal