Category Archives: Human gut

March 12, 2018

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Today we have  interesting reviews by Thomas S.B. about gut microbiome and by F. Newberry about microbiome and virome contribution to myalgic encephalomyelitis/chronic fatigue syndrome. Another highlight for viruses is a commentary by Y.Z. Zhang on how metagenomics has changed our understanding of RNA viruses. Check these recommendations as well as many other articles in today’s digest.

General microbiome

Analysis: Microbiome Research in a Social World – Diana Crow – Cell

Commentary: The Past and Future Biology of the Human Microbiome in an Age of Extinctions – Martin J. Blaser – Cell

Perspective: Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life – Cindy J. Castelle – Cell

Review: The Biology of CRISPR-Cas: Backward and Forward – Frank Hille – Cell

Human skin microbiome

The Microbiome in Dermatology – Shenara Musthaq – Clinics in Dermatology

Fragile skin microbiomes in megacities are assembled by a predominantly niche-based process – Hye-Jin Kim – Science Advances

Human nearly-sterile sites 

Review: Altered microbiome in chronic kidney disease: systemic effects of gut-derived uremic toxins – Wei Ling Lau – Clinical Science

Human urinary microbiome

Microbial metagenome of urinary tract infection – Ahmed Moustafa – Scientific Reports

Human gut microbiome

Neuroinflammation, Gut Microbiome, and Alzheimer’s Disease – Li Lin – Molecular Neurobiology

Gut microbiota and its implications in small bowel transplantation – Chenyang Wang – Frontiers of Medicine

Festschrift for Ronan O’Connell: pouchitis, ulcerative colitis and the microbiome – Aonghus Lavelle – Irish Journal of Medical Science (1971 -)

Lipid nanoparticles to counteract gastric infection without affecting gut microbiota – Catarina Leal Seabraa – European Journal of Pharmaceutics and Biopharmaceutics

Gut microbiota dysbiosis is associated with Henoch-Schönlein Purpura in children – Xingcui Wanga – International Immunopharmacology

Gut Microbiota Signature in Heart Failure Defined From Profiling of 2 Independent Cohorts – Martin Kummen – Journal of the American College of Cardiology

Toxin profile of fecal Clostridium perfringens strains isolated from children with autism spectrum disorders – Góra Bartłomiej – Anaerobe

Exploration of fecal microbiota transplantation in the treatment of refractory diarrhea after renal transplantation  – Bo Gu – Transplantation Proceedings

Review: The Human Gut Microbiome: From Association to Modulation – Thomas S.B. Schmidt – Cell

Animal experiments

Gut microbiota mediates diurnal variation of acetaminophen induced acute liver injury in mice – Shenhai Gong – Journal of Hepatology

Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches – Ramesh J. Pandit – Systematic and Applied Microbiology

Animal microbiome 

Understanding the Intestinal Microbiome in Health and Disease – Marcio Carvalho Costa – Veterinary Clinics of North America: Equine Practice

The association between gut microbiome, sex, age and body condition scores of horses in Maiduguri and its environs – Esther Solomon Mshelia – Microbial Pathogenesis

Plant, root, and soil microbiome

Phenolic compounds as antioxidants and chemopreventive drugs from Streptomyces cellulosae strain TES17 isolated from rhizosphere of Camellia sinensis – Riveka Rani – Microbiome

A decade of Streptococcus thermophilus phage evolution in an Irish dairy plant – Katherine Lavelle – Applied and Environmental Microbiology

Simultaneous application of two herbicides and green compost in a field experiment: Implications on soil microbial community – C. García-Delgado – Applied Soil Ecology

Distribution of prokaryotic communities throughout the Chernozem profiles under different land uses for over a century – Mikhail V. Semenov – Applied Soil Ecology

Water and extremophile microbiome

Brief Communication: Potential for primary productivity in a globally-distributed bacterial phototroph – E. D. Graham – The ISME Journal

Incubation with macroalgae induces large shifts in water column microbiota, but minor changes to the epibiota of co-occurring macroalgae – Melissa Y Chen – Molecular Ecology

The sponge holobiont in a changing ocean: from microbes to ecosystems – L. Pita – Microbiome

Microbiome dynamics in a large artificial seawater aquarium – Nastassia V. Patin – Applied and Environmental Microbiology

Conserved genomic and amino acid traits of cold adaptation in subzero-growing Arctic permafrost bacteria – Isabelle Raymond-Bouchard – FEMS Microbiology Ecology

Built environment

Phenol removal performance and microbial community shift during pH shock in a moving bed biofilm reactor (MBBR) – Hao Zhou – Journal of Hazardous Materials

Evaluation of process performance, energy consumption and microbiota characterization in a ceramic membrane bioreactor for ex-situ biomethanation of H2 and CO2 – Natalia Alfaro – Bioresource Technology

Food microbiology

Assessing the functionality and genetic diversity of lactococcal prophages – Philip Kelleher – International Journal of Food Microbiology

The bacterial biota of laboratory-reared edible mealworms (Tenebrio molitor L.): From feed to frass – Andrea Osimani – International Journal of Food Microbiology

Phages and viruses

Review: Does the microbiome and virome contribute to myalgic encephalomyelitis/chronic fatigue syndrome? – Fiona Newberry –  Clinical Science

Commentary: Using Metagenomics to Characterize an Expanding Virosphere – Yong-Zhen Zhang – Cell

Techniques

Rapid detection of Klebsiella pneumoniae, Klebsiella oxytoca, Raoultella ornithinolytica and other related bacteria in food by lateral-flow test strip immunoassays – Tatsuya Tominaga

Microbes in the news 

Virus from a pond treats man with antibiotic-resistant infection

Manipulating gut microbes may reduce intestinal parasitic infections

Study Shows Gut Bacteria Can Spread to Other Organs And Trigger Disease

Social stress leads to changes in gut bacteria

Could Our Gut Be the Source of a New Generation of Drugs?

Microbes and art

This watercolour painting was created by artistic bacteria

 

March 11, 2018

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Events and jobs

EVEN seminar: Weakest link in water quality control: Drinking water biofilm in premise plumbing – INSTAAR, CU Boulder

General microbiome

Multiscale Evolutionary Dynamics of Host-Associated Microbiomes – Aura Ferreiro, Cell

Egalitarianism in Biofilms – Dawen Gao, Microbial Ecology

Acclimation of Culturable Bacterial Communities under the Stresses of Different Organic Compounds – Hui Wang, Frontiers in Microbiology

Human multi-site microbiome

The Mycobiome: A Neglected Component in the Microbiota-Gut-Brain Axis – Raphaël Enaud, Microorganisms

Human gut microbiome

Gut Microbiota Alteration After Long-Term Consumption of Probiotics in the Elderly – Renyuan Gao, Probiotics and Antimicrobial Proteins

Sex differences in gut microbiota in patients with major depressive disorder – Chen JJ, Neuropsychiatric Disease and Treatment

Oral microbiome

Influence of periodontal treatment on subgingival and salivary microbiotas – Daniel Belstrøm, Journal of Periodontology

Microbiome at sites of gingival recession in children with Hutchinson–Gilford progeria syndrome – Seyed Hossein Bassir, Journal of Periodontology

Subgingival microbial profile of obese women with periodontal disease – Carina M. Silva-Boghossian, Journal of Periodontology

Animal experiments

The effect of probiotics and polysaccharides on the gut microbiota composition and function of weaned rats – Mengxia Wang, Food and Function

Cecal Versus Fecal Microbiota in Ossabaw Swine and Implications for Obesity – Matthew R Panasevich, Physiological Genomics

Antibiotics-induced modulation of large intestinal microbiota altered aromatic amino acid profile and expression of neurotransmitters in the hypothalamus of piglets – Kan Gao, Journal of Neurochemistry

Animal microbiome

Nutrient factories: Metabolic function of beneficial microorganisms associated with insects – Nana Y. D. Ankrah, Environmental Microbiology

Community composition, diversity, and metabolism of intestinal microbiota in cultivated European eel (Anguilla anguilla) – Wei Huang, Applied Microbiology and Biotechnology

Environmental and Host Effects on Skin Bacterial Community Composition in Panamanian Frogs – Brandon J. Varela, Frontiers in Microbiology

Influence of Novel Highly Pathogenic Avian Influenza A (H5N1) Virus Infection on Migrating Whooper Swans Fecal Microbiota – Na Zhao, Frontiers in Cellular and Infectious Microbiology

Plant, root, and soil microbiome

The Soil-Borne Legacy – Peter A.H.M. Bakker, Cell

Water and extremophile microbiome

Haloarchaea from the Andean Puna: Biological Role in the Energy Metabolism of Arsenic – Omar Federico Ordoñez, Microbial Ecology

Occurrence of Legionella in Nonpotable Reclaimed Water – William J. Johnson, American Water Works Association

Water Bacterial and Fungal Community Compositions Associated with Urban Lakes, Xi’an, China – Haihan Zhang, International Journal of Environmental Research and Public Health

Food microbiome

Microbial community and physicochemical dynamics during the production of ‘Chicha’, a traditional beverage of Indigenous people of Brazil – Ludmila Vilela Resende, World Journal of Microbiology and Biotechnology

Techniques

Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton – Emma K. Wear, Environmental Microbiology

Microbes in the news

Pitting Viruses Against Bacteria To Combat The Antibiotic Crisis – SciFri

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 5, 2018

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General microbiome

Characterization of microbiota in male infertility cases uncovers differences in seminal hyperviscosity and oligoasthenoteratozoospermia possibly correlated with increased prevalence of infectious bacteria – C Monteiro – American Journal of Reproductive Immunology

Taxa-function robustness in microbial communities – A Eng – BMC Microbiome

 

Human vaginal microbiome

Impact of contraceptive initiation on vaginal microbiota  – SL Achilles – American Journal of Obstetrics and Gynecology

Human gut microbiome

Review: The gut microbiome and elevated cardiovascular risk in obesity and autoimmunity – LJ Kasselman – Atherosclerosis

Alteration of the fecal microbiota in Chinese patients with Parkinson’s disease – Y Qian – Brain, Behavior, and Immunity

Comparison of reduced metagenome and 16S rRNA gene sequencing for determination of genetic diversity and mother-child overlap of the gut associated microbiota – A Ravi – Journal of Microbiological Methods

Alterations in Gut Microbial Function Following Liver Transplant – JS Bajaj – Liver Transplantation

Animal microbiome 

Tick microbial communities within enriched extracts of Amblyomma maculatum – AS Varela-Stokes – Ticks and Tick-borne Diseases

Bacterial microbiota of Aedes aegypti mosquito larvae is altered by intoxication with Bacillus thuringiensis israelensis – G Tetreau – BMC Parasites & Vectors

Plant, root and soil microbiome

Enhanced phytoremdiation of Robinia pseudoacacia in heavy metal-contaminated soils with rhizobia and the associated bacterial community structure and function – M Fan – Chemosphere

Endophytic and Epiphytic Phyllosphere Fungal Communities Are Shaped by Different Environmental Factors in a Mediterranean Ecosystem – T Gomes – Microbial Ecology

Plant-associated bacteria mitigate drought stress in soybean – SJ Martins – Environmental Science and Pollution Research

Whole genome analysis of six organophosphate-degrading rhizobacteria reveals putative agrochemical degradation enzymes with broad substrate specificity – R Iyer – Environmental Science and Pollution Research

Co-inoculation of Lolium perenne with Funneliformis mosseae and the dark septate endophyte Cadophora sp. in a trace element-polluted soil – C Berthelot – Mycorrhiza

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

Built environment 

Redundancy of anaerobic digestion microbiomes during disturbances by the antibiotic monensin – CM Spirito – Applied and Environmental Microbiology

Food microbiology

The potential use of Debaryomyces hansenii for the biological control of pathogenic fungi in food – N Medina-Córdova – Biological Control

Selection of starter cultures for the production of sour cassava starch in a pilot-scale fermentation process – FCL Penido – Brazilian Journal of Microbiology

Probiotics / prebiotics

The functionality of prebiotics as immunostimulant: Evidences from trials on terrestrial and aquatic animals – A Nawaz – Fish & Shellfish Immunology

Review: Polyphenol-based prebiotics and synbiotics: Potential for cancer chemoprevention – WPDW Thilakarathna – Current Opinion in Food Science

 

Microbes in the news

Mobile nanotweezers can pick, drop live bacteria – The Hindu

Is Your Diet Destroying Beneficial Gut Bacteria? – Care2

Eureka moment to battle drug resistance: Bacteria in University of Hyderabad lake can power antibiotic – Time of India

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

Posted on by

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 2, 2018

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Events and jobs

Enter our ‘scientist at work’ photo contest – Nature

General microbiome

Review: To respond or not to respond — a personal perspective of intestinal tolerance – AM Mowat – Nature Reviews

“Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the type IX secretion system – AE Naas – BMC Microbiome

Human vaginal microbiome

Fractional CO2 laser for genitourinary syndrome of menopause in breast cancer survivors: clinical, immunological, and microbiological aspects – A Becorpi – Lasers in Medical Science

Human gut microbiome

Environment dominates over host genetics in shaping human gut microbiota – D Rothschild – Nature

The gut microbiota and immune checkpoint inhibitors – A Humphries – Human Vaccines and Immunotherapeutics

Probiotic supplementation increases obesity with no detectable effects on liver fat or gut microbiota in obese Hispanic adolescents: a 16-week, randomized, placebo-controlled trial. – RB Jones – Pediatric Obesity

Adaptation of adherent-invasive E. coli to gut environment: Impact on flagellum expression and bacterial colonization ability. – G Sevrin – Gut Microbes

Editorial: Gut microbiomes and their metabolites shape human and animal health – W Park –  Journal of Microbiology

Review: Current understanding of microbiota- and dietary-therapies for treating inflammatory bowel disease – T Eom – Journal of Microbiology

Review: Targeting friend and foe: Emerging therapeutics in the age of gut microbiome and disease – JA Cho – Journal of Microbiology

Review: Mind-altering with the gut: Modulation of the gut-brain axis with probiotics – N Kim – Journal of Microbiology

Gut microbial composition in patients with psoriasis – FM Codoñer – Scientific Reports

Clostridium scindens is present in the gut microbiota during Clostridium difficile infection. A metagenomic and culturomic analysis. – S Amrane – Journal of Clinical Microbiology

Letter to Editor: Microbiome and Esophageal Adenocarcinoma—Letter – NO Kaakoush – Cancer Research

Animal experiments 

Altered gut microbiome promotes proteinuria in mice induced by Adriamycin – Q Jiang – AMB Express

Functional Anthocyanin-Rich Sausages Diminish Colorectal Cancer in an Animal Model and Reduce Pro-Inflammatory Bacteria in the Intestinal Microbiota. – G Fernández – Genes (Basel)

Animal microbiome 

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen – RD Stewart – Nature Communications

The Ruminococci: key symbionts of the gut ecosystem – AJL Reau – Journal of Microbiology

Plant, root, and soil microbiome

Concepts & Synthesis: Toward more robust plant-soil feedback research – MJ Rinella – Ecology

Draft genome sequences of bacteria isolated from the Deschampsia antarctica phyllosphere. – FP Cid – Extremophiles

Competition–colonization tradeoffs structure fungal diversity – GR Smith – The ISME Journal

Water microbiome and extremophile 

Environmental factors driving fungal distribution in freshwater lake sediments across the Headwater Region of the Yellow River, China – J Tian – Scientific Reports

Community assembly processes underlying phytoplankton and bacterioplankton across a hydrologic change in a human-impacted river. – A Isabwe – The Science of the Total Environment

Modulation of microbial consortia enriched from different polluted environments during petroleum biodegradation – R Omrani – Biodegradation

Built environment 

‘Cyclical Bias’ in Microbiome Research Revealed by A Portable Germ-Free Housing System Using Nested Isolation – A Rodriguez-Palacios – Scientific Reports

Phages and viruses

Host-Associated Bacteriophage Isolation and Preparation for Viral Metagenomics – JA Grasis – Viral Metagenomics

Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere – J Abrahão – Nature Communications

Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages – L Cheng – BMC Microbiology

Techniques

Highly sensitive detection and quantification of the secreted bacterial benevolence factor RoxP using a capacitive biosensor: A possible early detection system for oxidative skin diseases. – G Ertürk – PLoS One

Review: Emerging Technologies for Molecular Diagnosis of Sepsis – M Sinha – Clinical Microbiology Reviews

Microbes in the news

Biofilm Replaces Plastic Packaging in this Dutch Supermarket Aisle – Futurism

For the Microbiome, the Nature vs. Nurture Debate Comes into Focus – GEN

With $36M series B, Finch goes full speed ahead in microbiome therapy – Fierce Biotech

Genetics or lifestyle: What is it that shapes our microbiome? – Science Daily

More than soap scum: Learning about biofilms – Silive

7 Startups Treating Disease Using the Microbiome – Nanalyze

ATM keypads, restaurant menus full of bacteria – News3Channel

Non-microbiology picks

Intellectual Synthesis in Mentorship Determines Success in Academic Careers – JF Lienard – bioRxiv