February 22, 2018

In today’s digest you can read: about advantages of Atomic Force Microscopy in studying of oral microbiota in the paper by S. S. Salavadhi; about gut microbiome association with Type 1 diabetes in the paper by J.A. Mullaney; about influence of steroids on the gut microbiota in the review by M.J Tetel and about the ability of Synechococcus cyanobacteria to dynamically change their pigment content to match the ambient light color, in the paper by T. Grébert. These are of course just a few of many interesting articles today. Enjoy!

Events and jobs

MS graduate position: Amoeba microbiome, Conway, Arkansas, US

Research Fellow in Cell Biology – Microscopy, Warwick, UK

PhD Student, ROYAL NIOZ-TEXEL, Texel, the Netherlands

General microbiome

Review: A new piece in the microbiome puzzle – Lindsay J. Pike – Nature Reviews Microbiology

The importance of resolving biogeographic patterns of microbial microdiversity – Alexander B Chase – Microbiology Australia

Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession – Rüdiger Ortiz-Álvarez – the ISME Journal

Pregnancy and early life

Infant formulae supplemented with prebiotics: Are they better than unsupplemented formulae? An updated systematic review – Agata Skórka – British Journal of Nutrition

Early Dietary Patterns and Microbiota Development: Still a Way to Go from Descriptive Interactions to Health-Relevant Solutions – Patricia Iozzo – Frontiers in Nutrition

Roles of Birth Mode and Infant Gut Microbiota in Intergenerational Transmission of Overweight and Obesity From Mother to Offspring – Hein M. Tun – JAMA Pediatrics

Multi-site human microbiome

A blinded observational cohort study of the microbiological ecology associated with pyuria and overactive bladder symptoms – Kiren Gill – International Urogynecology Journal

Oral microbiome

Atomic force microscopy: A three-dimensional reconstructive tool of oral microbiota in gingivitis and periodontitis – Shyam Sunder Salavadhi – Journal of Indian Society of Periodontology

Human gut microbiome

Review: Steroids, stress and the gut microbiome-brain axis – M. J. Tetel – Journal of Neuroendocrinology

Alterations of the Gut Microbiota in Hashimoto’s Thyroiditis Patients – Zhao Fuya – Thyroid

Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota – Sean Michael Kearney – bioRxiv

Alterations in Intestinal Microbiota Lead to Production of Interleukin 17 by Intrahepatic γδ T-cell Receptor-positive Cells and Pathogenesis of Cholestatic Liver Disease – Dana Tedesco – Gastroenterology

Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota – Jane A. Mullaney – BMC Microbiome

Animal experiments

Effect of Dietary Chestnut or Quebracho Tannin Supplementation on Microbial Community and Fatty Acid Profile in the Rumen of Dairy Ewes – Arianna Buccioni – BioMed Research International

Long-Term Treatment with Green Tea Polyphenols Modifies the Gut Microbiome of Female Sprague-Dawley Rats – Jincheng Wang – The Journal of Nutritional Biochemistry

Microbiota-Derived Indole Metabolites Promote Human and Murine Intestinal Homeostasis through Regulation of Interleukin-10 Receptor – Erica E. Alexeev – The Americn Journal of Pathology

Interrelations between the rumen microbiota and production, behavioral, rumen-fermentation, metabolic, and immunological attributes of dairy cows – M. Schären – Journal of Diary Science

Animal microbiome

Disentangling metabolic functions of bacteria in the honey bee gut – Lucie Kešnerová – PLOS One

Plant, root, and soil microbiome

Soil mixture composition alters Arabidopsis susceptibility to Pseudomonas syringae infection – Jana A. Hassan – Plant Direct

Taxonomic structure and function of seed-inhabiting bacterial microbiota from common reed (Phragmites australis) and narrowleaf cattail (Typha angustifolia L.) – Ting Gao – Archives of Microbiology

The soil microbiome — from metagenomics to metaphenomics – Janet K Jansson – Current Opinion in Microbiology

Exometabolomic profiling of bacterial strains cultivated using Arabidopsis root extract as the sole carbon source – Richard Paul Jacoby – Molecular Plant-Microbiome Interactions

A strain of Streptomyces sp. isolated from rhizospheric soil of Crataegus oxycantha producing Nalidixic acid, a synthetic antibiotic – Nidhi Arora – Journal of Applied Microbiology

High microbial diversity promotes soil ecosystem functioning – Pierre-Alain Maron – Applied and Environmental Microbiology

Water and extremophile microbiome

Apportioning bacterial carbon source utilization in soil using 14C isotope analysis of FISH-targeted bacterial populations sorted by Fluorescence Activated Cell Sorting (FACS): 14C-FISH-FACS – Christos Gougoulias – Environmental Microbiology Reports

Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea – E. J. Fleming – Applied and Environmental Microbiology

Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria – Théophile Grébert – PNAS

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning – Zhili He – mBio

Iron and phosphorus deprivation induce sociality in the marine bloom-forming cyanobacterium Trichodesmium – Yael Tzubari – the ISME Journal

Cryptophyta as major bacterivores in freshwater summer plankton – Vesna Grujcic – the ISME Journal

Phages and viruses

The impact of bacteriophages on phyllosphere bacterial abundance and composition – Norma M. Morella – Molecular Ecology

Microbes in the news

Guts and gory: vampire bats need bacteria to digest blood

Using mutant bacteria to study how changes in membrane proteins affect cell functions

February 19, 2018

Posted on February 19, 2018 by aalexiev

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

February 18, 2018

Posted on February 18, 2018 by Tiff

Quite a few articles with alerts from today and the day before. Many interesting articles on microbe/microbe and microbe-host interactions, enjoy!

Events and jobs
Senior Bioinformatician – Host Microbiota Interactions – Wellcome Trust Sanger Institute

Postdoctoral Fellow – ‘Microbiome of intestinal tract cancers’ – Centre for Molecular and Biomolecular Informatics (CMBI)

Department Chair – Department of Microbiology and Immunology – College of Veterinary Medicine Cornell University, Ithaca, New York

Associate Scientist- Microbiology – Aerotek, Los Angeles, CA

Multi-site human microbiome
Differential contributions of specimen types, culturing, and 16S – Lone Heimann Larsen – Journal Of Clinical Microbiology

Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females – Yu-Feng Huang – BMC Medical Genomics

Human oral microbiome
Bacterial microleakage at the abutment-implant interface, in vitro study. – Carlos Larrucea – Clinical Implant Dentistry And Related Research

Comparison of Oropharyngeal Microbiota from Children with Asthma and Cystic Fibrosis. – Sébastien Boutin – Mediators Of Inflammation

Human vaginal microbiome
Review: Cervicovaginal Microbiota and Reproductive Health: The Virtue of Simplicity. – Melis N Anahtar – Cell Host & Microbe

Human gut microbiome
The effect of Clostridium butyricum on symptoms and fecal microbiota in diarrhea-dominant irritable bowel syndrome: a randomized, double-blind, placebo-controlled trial. – Yi-Yuan Sun – Scientific Reports

Association of gut microbial communities with plasma lipopolysaccharide-binding protein (LBP) in premenopausal women – Jessica S Citronberg – ISME

Microbiota Accessible Carbohydrates Suppress Clostridium difficile in a Murine Model – Andrew J Hryckowian – bioRxiv

Review: Gut Microbiota-Based Therapies for Irritable Bowel Syndrome. – Emily K Stern – Clinical And Translational Gastroenterology

Review: A neuroscience perspective of the gut theory of Parkinson’s disease. – Lisa M Smith – The European Journal Of Neuroscience

Microbial-microbial/host interactions
Interactions between predation and disturbances shape prey communities. – Canan Karakoç – Scientific Reports

Elevated success of multispecies bacterial invasions impacts community composition during ecological succession. – Damian W Rivett – Ecology Letters

Competition in biofilms between cystic fibrosis isolates of Pseudomonas aeruginosa is driven by R-pyocins – Olubukola Oluyombo – bioRxiv

Linking associations of rare low-abundance species to their environments by association networks – Tatiana V. Karpinets – Frontiers in Microbiology

Genetic Ablation of Butyrate Utilization Attenuates Gastrointestinal Salmonella Disease. – Denise N Bronner – Cell Host & Microbe

Goblet cell associated antigen passages are inhibited during Salmonella typhimur/cium infection to prevent pathogen dissemination and limit responses to dietary antigens. – Devesha H Kulkarni – Mucosal Immunology

Animal experiments
Cytosolic and secreted peptidoglycan-degrading enzymes in Drosophila respectively control local and systemic immune responses to microbiota – Bernard Charroux – Cell Host & Microbe

Differences in the intestinal microbiota between uninfected piglets and piglets infected with porcine epidemic diarrhea virus. – Mei-Zhou Huang – Plos One

Rumen-protected methionine during the peripartal period in dairy cows and its effects on abundance of major species of ruminal bacteria. – Mohamed K Abdelmegeid – Journal Of Animal Science And Biotechnology

Impact of Chestnut and Quebracho Tannins on Rumen Microbiota of Bovines. – Juan María Díaz Carrasco – Biomed Research International

Starvation influences the microbiota assembly and expression of immunity-related genes in the intestine of grass carp (Ctenopharyngodon idellus) – Ngoc Tuan Tran – Aquaculture

Animal microbiome
The Dynamic Distribution of Small-Tail Han Sheep Microbiota across Different Intestinal Segments. – Hao Zhang – Frontiers In Microbiology

Microbiome assembly of avian eggshells and their potential as transgenerational carriers of maternal microbiota. – H Pieter J van Veelen – The Isme Journal

Plant, root, and soil microbiome
Photoautotrophic organisms control microbial abundance, diversity, and physiology in different types of biological soil crusts. – Stefanie Maier – The Isme Journal

Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil. – Radomir Schmidt – Plos One

Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions. – Corina Diana Ceapă – Plos One

Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments – Liana T. Burghardt – PNAS

Microbial Flora Associated with the Halophyte- – Fehmida Bibi – Frontiers In Microbiology

Root growth improvement of mesquite seedlings and bacterial rhizosphere and soil community changes are induced by inoculation with plant growth-promoting bacteria and promote restoration of eroded desert soil – Cristina Galaviz – Land Degradation and Development

Diversity of root-associated microbial populations of Tamarix parviflora cultivated under various conditions – Marketa Polivkova – Applied Soil Ecology

Succession of the functional microbial communities and the metabolic functions in maize straw composting process – Huawei Wei – Bioresource Technology

Rhizospheric microbial communities are driven by Panax ginseng at different growth stages and biocontrol bacteria alleviates replanting mortality – Linlin Dong – Acta Pharmaceutica Sinica B

Review: Soil protists: a fertile frontier in soil biology research. – Stefan Geisen – Fems Microbiology Reviews

Water and extremophile microbiome
Composition and Activity of Microbial Communities along the Redox Gradient of an Alkaline, Hypersaline, Lake. – Christian F Edwardson – Frontiers In Microbiology

Phosphorus Solubilizing and Releasing Bacteria Screening from the Rhizosphere in a Natural Wetland – Ying Cao – Water

Effects of water flow on submerged macrophyte-biofilm systems in constructed wetlands – Bing Han – Scientific Reports

Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities – Eric M Bottos – bioRxiv

Metagenomic exploration of soils microbial communities associated to Antarctic vascular plants – Marco A. Molina-Montenegro – PeerJ Preprints

Built environment
Liquid co-substrates repower sewage microbiomes – Justus Hardegen – bioRxiv

Investigating antibiotics, antibiotic resistance genes, and microbial contaminants in groundwater in relation to the proximity of urban areas – Edina Szekeres – Environmental Pollution

Influence of secondary water supply systems on microbial community structure and opportunistic pathogen gene markers – Huan Li – Water Research

Review: A review on the applications of microbial electrolysis cells in anaerobic digestion. – Zhengsheng Yu – Bioresource Technology

Probiotics / prebiotics / antibiotics
Tacrolimus concentration to dose ratio in solid organ transplant patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection. – Michael H Woodworth – Transplant Infectious Disease : An Official Journal Of The Transplantation Society

Techniques
Functional imaging of the interaction between gut microbiota and the human host: A proof-of-concept clinical study evaluating novel use for 18F-FDG PET-CT. – Ben Boursi – Plos One

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

How to isolate, identify and determine antimicrobial susceptibility of anaerobic bacteria in routine laboratories? – Elisabeth Nagy – Clinical Microbiology and Infection

Microbes in the news
A trip to ‘the poopy lab’ in the interest of drug development – Eric Boodman – STAT News

Probe provides rapid lung investigation – Pallab Ghosh – BBC News

February 16, 2018

Posted on February 16, 2018 by xinhuang7

Happy Lunar New Year of the Dog!

Today’s Digest contains many news pieces, and also features a major paper on strain tracking post fecal microbiota transplantation, a review on antibacterial proteins shaping the intestinal microbiota, and a call for action to build communities for bioinformatics programming.

Jobs

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

General microbiology

Book chapter: Agro-industrial Lignocellulosic Waste: An Alternative to Unravel the Future Bioenergy – Nidhi V. Maheshwari – Biofuels: Greenhouse Gas Mitigation and Global Warming

Review: Evolutionary Mechanisms Shaping the Maintenance of Antibiotic Resistance – Paulo Durão et al. – Trends in Microbiology

A single amino acid change in the response regulator PhoP acquired during Yersinia pestis evolution affects PhoP target gene transcription and polymyxin B susceptibility – Fukuto HS et al. – Journal of Bacteriology

Validated measurements of microbial loads on environmental surfaces in intensive care units before and after disinfecting cleaning – H. Frickmann et al. – Journal of Applied Microbiology

Human gut microbiome

Review: Proceedings of the 2017 ASPEN Research Workshop—Gastric Bypass: Role of the Gut – Ajay Kumar Jain et al. – Journal of Parenteral & Enteral Nutrition

A Phase 1 Study in Healthy Subjects to Assess the Safety, Tolerability, Pharmacokinetics, and Pharmacodynamics of Multiple Oral Doses of DS-2969b, a Novel GyrB Inhibitor – Vandell AG et al. – Antimicrobial Agents and Chemotherapy

* Antibacterial Weapons: Targeted Destruction in the Microbiota – Benoit Chassaing and Eric Cascales – Trends in Microbiology

Perspective: How to train your microbiome to eat broccoli – Sam H. Au – Science Translational Medicine

* Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation – Christopher S. Smillie – Cell Host & Microbe

Press: Model of fecal transplantation predicts which bacteria will flourish – Medical Xpress

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

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

Animal experiments

Extracellular cholesterol oxidase production by Streptomyces aegyptia, in vitro anticancer activities against rhabdomyosarcoma, breast cancer cell-lines and in vivo apoptosis – Noura El-Ahmady El-Naggar et al. – Scientific Reports

Molecular analyses of two bacterial sampling methods in ligature-induced periodontitis in rats – Carla Raquel Fontana et al. – Clinical and Experimental Dental Research

Animal microbiome

Preprint: Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria – Ines Silva Pais et al. – bioRxiv

Plant, root and soil microbiome

Removal of metals and their pools in plant in response to plant diversity in microcosms of floating constructed wetlands – Wenjuan Han et al. – Ecological Engineering

The Sesamum indicum rhizosphere associated bacterium: A source of Antifungal compound – Renu Chaudhary et al. – Current Topics in Medicinal Chemistry

Intensifying rotations increases soil carbon, fungi, and aggregation in semi-arid agroecosystems – Steven T. Rosenzweig et al. – Agriculture, Ecosystems & Environment

Impact of oxytetracycline and bacterial bioaugmentation on the efficiency and microbial community structure of a pesticide-degrading biomixture – Víctor Castro-Gutiérrez et al. – Environmental Science and Pollution Research

Indigenous endophytic seed bacteria promote seedling development and defend against fungal disease in browntop millet (Urochloa ramosa L.) – S.K. Verma and J.F. White – Journal of Applied Microbiology

Water and extremophile microbiome

Halophilic starch degrading bacteria isolated from Sambhar Lake, India, as potential anode catalyst in Microbial fuel cell: A promising process for saline water treatment – Ankisha Vijay et al. – Bioresource Technology

Sequestration and utilization of carbon dioxide by chemical and biological methods for biofuels and biomaterials by chemoautotrophs: Opportunities and challenges – Indu Shekhar Thakur et al. – Bioresource Technology

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

Neobodonids are dominant kinetoplastids in the global ocean – Olga Flegontova et al. – Environmental Microbiology

Food microbiology

Review: Whole genome sequencing as a typing tool for foodborne pathogens like Listeria monocytogenes – The way towards global harmonisation and data exchange – StefanieLüth et al. – Trends in Food Science & Technology

Phages and viruses

Book chapter: Tick-Borne Viruses and Host Skin Interface – Mária Kazimírová et al. – Skin and Arthropod Vectors

Preprint: The virome of Drosophila suzukii, an invasive pest of soft fruit – Nathan C Medd et al. – bioRxiv

Technology

Microfluidics-based liquid chromatography/mass spectrometry multiple reaction monitoring approach for the relative quantification of Burkholderia cenocepacia secreted virulence factors – Sofie Depluverez et al. – Rapid Communications in Mass Spectrometry

Microbes in the news

Surgeon sets new frontiers in battle against bacteria! – WBWire

The effect of antibacterials on the skin – Zoe Diana Draelo – Dermatology Times

Donor, Recipient Strain Analyses Offer Fecal Transplant Engraftment Clues – Genome Web

Australian Scientist Gets $1 Million to See if Probiotics Can Help Children with CF – Carolina Henriques – Cystic Fibrosis News Today

Do probiotics work? Answers to this and other gut-wrenching questions – Joanna Clay – USC News

Monitoring bacteria on whale skin – EurekAlert

Bacteria Hidden Under Our Feet May Be a New Weapon Against Superbugs – Kristin Houser – Futurism

Which probiotic is right for you? These are the exact bacteria strains to look for – Emily Laurence – Well and Good

How can we harness the power of bacteria-killing viruses? – Claire O’Connell – Sillcon Republic

Manipulating gut bacteria may cut obesity, diabetes risk – The Peninsula

Microbes on the market

Carbiotix launches world’s lowest cost microbiome test – Nathan Gray – Nutra Ingredients

Scientific Communication and Education

* Preprint: Building a local community of practice in scientific programming for Life Scientists – Sarah L.R. Stevens et al. – bioRxiv

February 15, 2018

Posted on February 15, 2018 by barnettburns

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

Also : A cultured community developed from wastewater that can reduce the greenhouse gas N₂O to N₂and help mitigate global warming; the majority of Daphnia microbiomes are not passed from parent to offspring but absorbed from the surrounding environment; and the impacts of CRISPR-Cas9 selection pressure on phage evolution.

Events and jobs

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

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General microbiome

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

Pregnancy and early life

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

Human skin microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

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Animal experiments

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

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

Animal microbiome

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

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

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

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

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

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

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

Plant, root, and soil microbiome

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

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

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

Water and extremophile microbiome

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

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

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

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

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

Microbial Ecology

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

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

Resistome

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

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Probiotics / prebiotics

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

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

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

Fecal Microbiome Transplants

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

Bioinformatics

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

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

Biotechnology

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

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

Waste and Pollution

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

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

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Microbes in the news

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

February 14, 2018

Posted on February 14, 2018 by anjacobson

The role of saliva in structuring human oral bacterial communities, effects of permafrost thaw on methanogenic communities, and articles on the microbiomes of termites, burying beetles, honey bees, and mosquitoes.

Human oral microbiome

A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow – Diana M Proctor – Nature Communications

Human vaginal microbiome

To ‘douche’ or not to ‘douche’: hygiene habits may have detrimental effects on vaginal microbiota – Erdogan Aslan – Journal of Obstetrics and Gynaecology

Human gut microbiome

Elevated circulating levels of succinate in human obesity are linked to specific gut microbiota – Carolina Serena – The ISME Journal

Infection and Microbiome: Impact of Tuberculosis on Human Gut Microbiome of Indian Cohort – Utkarsh Sood – Indian Journal of Microbiology

Comparative metaproteomics analysis shows altered fecal microbiota signatures in patients with major depressive disorder – Zhi Chen – NeuroReport

Animal experiments

Protective effect of Group B Streptococcus type-III polysaccharide conjugates against maternal colonization, ascending infection and neonatal transmission in rodent models – Emiliano Chiarot – Scientific Reports

Animal microbiome

Pre-print: Axenic Aedes aegypti develop without live bacteria, but exhibit delayed development and reduced oviposition – Maria A Correa – bioRxiv

Two novel strains of Torulaspora delbrueckii isolated from the honey bee gut microbiome and their use in honey fermentation – Joseph P Barry – bioRxiv

Gut microbiota in the burying beetle, Nicrophorus vespilloides, provide colonization resistance against larval bacterial pathogens – Yin Wang – Ecology and Evolution

Rampant Host Switching Shaped the Termite Gut Microbiome – Thomas Bourguignon – Current Biology

Plant, root, and soil microbiome

Melanization of mycorrhizal fungal necromass structures microbial decomposer communities – Christopher W Fernandez – Journal of Ecology

Fungal community shifts underpin declining mycelial production and turnover across a Pinus sylvestris chronosequence – Andreas Hagenbo – Journal of Ecology

Mycorrhizal symbioses influence the trophic structure of the Serengeti – Bo Maxwell Stevens – Journal of Ecology

The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome – M A Cregger – Microbiome

Water and extremophile microbiome

Pre-print: Transgenerational inheritance of shuffled symbiont communities in the coral Montipora digitata – Kate Quigley – bioRxiv

Shifts of methanogenic communities in response to permafrost thaw results in rising methane emissions and soil property changes – Shiping Wei – Extremophiles

Food microbiology

Dynamic correlations between microbiota succession and flavor development involved in the ripening of Kazak artisanal cheese – Xiaoji Zheng – Food Research International

Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area – A pilot study – Daleniece Higgins – Food Research International

Phages and viruses

The analysis of the oral DNA virome reveals which viruses are widespread and rare among healthy young adults in Valencia (Spain) – Vicente Pérez-Brocal – PLOS ONE

More microbes

Lactobacillus plantarum lipoteichoic acid inhibits biofilm formation of Streptococcus mutans – Ki Bum Ahn – PLOS ONE

Microbes in the news

In soil-dwelling bacteria, scientists find a new weapon to fight drug-resistant superbugs – Melissa Healy – Los Angeles Times

Source article: Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens – Bradley M Hover – Nature Microbiology

Interdisciplinary approach yields new insights into human evolution – Liz Entman – Vanderbilt University News

Viruses and Bacteria Travel Along a High-Altitude Superhighway – Dave Roos – Seeker

Science, career, and publishing

Pre-print: The impact on authors and editors of introducing Data Availability Statements at Nature journals – Rebecca Grant – bioRxiv

February 13, 2018

Posted on February 13, 2018 by anjacobson

The gut microbiome of honey bee workers, a review of “Foodomics” approaches to studying digestion and bioactivity, and a new genome sequence for a bacterium isolated from a cell phone screen.

Human gut microbiome

Review: Causal effects of the microbiota on immune-mediated diseases – June L Round – Science Immunology

Possible correlation between gut microbiota and immunity among healthy middle-aged and elderly people in southwest China – Xi Shen – Gut Pathogens

Animal experiments

Pre-print: Clostridium difficile alters the structure and metabolism of distinct cecal microbiomes during initial infection to promote sustained colonization – Matthew L Jenior – bioRxiv

Pre-print: Microbiota metabolic product deoxycholic acid controls chicken necrotic enteritis – Hong Wang – bioRxiv

Effects of Bentonite Bgp35b-p on the Gut Microbiota of Mice Fed a High-Fat Diet – Eun-Sook Lee – Science of Food and Agriculture

Animal microbiome

The role of the gut microbiome in health and disease of adult honey bee workers – Kasie Raymann – Current Opinion in Insect Science

Bacterial density rather than diversity correlates with hatching success across different avian species – Juan Manuel Peralta-Sánchez – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Influence of metal contamination in soil on metabolic profiles of Miscanthus x giganteus belowground parts and associated bacterial communities – Hoang Nam Pham – Applied Soil Ecology

Pre-print: In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana – Claudia Bartoli – bioRxiv

Effects of Using Arbuscular Mycorrhizal Fungi to Alleviate Drought Stress on the Physiological Traits and Essential Oil Yield of Fennel – Sedigheh Gheisari Zardak – Rhizosphere

Water and extremophile microbiome

Pre-print: Environmental determinants of pyoverdine production, exploitation and competition in natural Pseudomonas communities – Elena Butaitė – bioRxiv

Bacteria from Coral Ecosystem of Kiltan Island, Lakshadweep: Resource for Hydrolytic Enzymes – L Ramlath – International Journal of Cell Science and Biotechnology

Built environment

Microbacterium telephonicum sp. nov., isolated from the screen of a cellular phone – Praveen Rahi – International Journal of Systematic and Evolutionary Microbiology

Food microbiology

Review: The role of Foodomics to understand the digestion/bioactivity relationship of food – Grégory Pimentel – Current Opinion in Food Science

Phages and viruses

Virus-mediated transfer of nitrogen from heterotrophic bacteria to phytoplankton – Emma J Shelford – Biogeosciences

Small RNA-omics for virome reconstruction and antiviral defense characterization in mixed infections of cultivated Solanum plants – Silvia Turco – Molecular Plant-Microbe Interactions

Metabolomics

UPLC-QTOF-MS metabolomics analysis revealed the contributions of metabolites to the pathogenesis of Rhizoctonia solani strain AG-1-IA – Wenjin Hu – PLOS ONE

Microbes in the news

New imaging technique reveals how dragonfly wings tear bacteria apart – Alayna Hansen – New Atlas

Exploring the microbiome of an ocean bacteria – Kyle Frischkorn – Phys.Org

Microbes on the market

Rebiotix Develops Microbiome Health Index™ to Identify Indicators for Microbiome Restoration – PR Newswire

Bristol-Myers taps Sirenas for ‘global microbiome’ drug discovery – Amirah Al Idrus – FierceBiotech

Givaudan, Unilever target the microbiome – Marc S Reisch – Chemical & Engineering News

February 12, 2018

Posted on February 12, 2018 by xinhuang7

A rich Digest to start your work week. Highlights include a review in Lancet cautionary about precision nutrition, an NIH metagenome FTP site, and a sampling of songbirds that reveals high prevalence of antibiotic resistant bacteria.

Events

Intellectual Property x The Microbiome – SF Bay Area Microbiome Meetup

General microbiology

Expanding our Understanding of the Role of the Microbiome in Health and Disease – Rob Knight – Archives of Medical Research

* NIH Metagnome FTP site

* The Ecosystem Services of Animal Microbiomes – E.A. McKenney et al. – Molecular Ecology

Preprint: Experimental Evolution of Cell Shape in Bacteria – Paul Richard Yulo et al. – bioRxiv

Human skin microbiome

In vitro: Yeasts from skin colonization are able to cross the acellular dermal matrix – Isabele Carrilho Jarros et al. – Microbial Pathogenesis

Human vaginal microbiome

Review: Immunology of the Uterine and Vaginal Mucosae – Jordan Z. Zhou et al. – Trends in Immunology

Human gut microbiome

The Role of Diet in the Treatment of Irritable Bowel Syndrome : A Systematic Review – Rajdeep Singh et al. – Gastroenterology Clinics of North America

Review: Metabolic Surgery : Weight Loss, Diabetes, and Beyond – Manan Pareek et al. – Journal of the American College of Cardiology

Review: Environmental Noise and the Cardiovascular System – Thomas Münzel et al. – Journal of the American College of Cardiology

The effects of synbiotic supplementation on insulin resistance/sensitivity, lipid profile and total antioxidant capacity in women with gestational diabetes mellitus: a randomized double blind placebo controlled clinical trial – Zohoor Nabhani et al. – Diabetes Research and Clinical Practice

* Precision nutrition for prevention and management of type 2 diabetes – Dong D Wang and Frank B Hu – The Lancet Diabetes & Endocrinology

The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids – Cholsoon Jang et al. – Cell Metabolism

Review: Therapeutic implications of the gastrointestinal microbiome – Purna C Kayshap and Eamonn MM Quigley – Current Opinion in Pharmacology

Risk factors for Clostridium difficile infection in intestinal transplant recipients during the first year post transplant – Luis Guzman et al. – Transplant Infectious Disease

Metabolomics

Review: Advances in computational metabolomics and databases deepen the understanding of metabolisms – Hiroshi Tsugawa – Current Opinion in Biotechnology

Animal experiments

Rat: Onion quercetin monoglycosides alter microbial activity and increase antioxidant capacity – Katarzyna Grzelak-Błaszczyk et al. – The Journal of Nutritional Biochemistry

Preview: Cultivating a Relationship with Gut Bacteria – Catherine E. Schretter and Sarkis K. Mazmanian – Cell Metabolism

Effect of two seaweed polysaccharides on intestinal microbiota in mice evaluated by illumina PE250 sequencing – Zhongshan Zhang et al. – International Journal of Biological Macromolecules

Green Tea Polyphenols Modulate Colonic Microbiota Diversity and Lipid Metabolism in High-Fat Diet Treated HFA Mice – Li Wang et al. – Journal of Food Science

Animal microbiome

* Antibiotic resistant bacteria are widespread in songbirds across rural and urban environments – Diana L. Carter et al. – Science of The Total Environment

Effects of chlorogenic acids-enriched extract from Eucommia ulmoides leaves on growth performance, stress response, antioxidant status and meat quality of lambs subjected or not to transport stress – H.W. Liu et al. – Animal Feed Science and Technology

Characterisation of Bergeyella spp. isolated from the nasal cavities of piglets – M. Lorenzo de Arriba et al. – The Veterinary Journal

Horse: The relationships between faecal egg counts and gut microbial composition in UK Thoroughbreds infected by cyathostomins – L.E. Peachey et al. – International Journal for Parasitology

The effects singular or combined administration of fermentable fiber and probiotic on mucosal immune parameters, digestive enzyme activity, gut microbiota and growth performance of Caspian white fish (Rutilus frisii kutum) fingerlings – Ali Taheri Mirghaed et al. – Fish & Shellfish Immunology

Diagnostics and Treatments in Chronic Diarrhea and Weight Loss in Horses – Olimpo Oliver-Espinosa – Veterinary Clinics: Equine Practice

Plant, root and soil microbiome

Diversifying crop rotation increased metabolic soil diversity and activity of the microbial community – Luciana D’Acunto et al. – Agriculture, Ecosystems & Environment

The impact of reconstructed soils following oil sands exploitation on aspen and its associated belowground microbiome – Franck Stefani et al. – Scientific Reports

Water and extremophile microbiome

Antibiotic resistome in landfill leachate from different cities of China deciphered by metagenomic analysis – Renxin Zhao et al. – Water Research

Microbiomes in extremely acidic environments: functionalities and interactions that allow survival and growth of prokaryotes at low pH – Raquel Quatrini and D Barrie Johnson – Current Opinion in Microbiology

Effect of heat shock on hot water plumbing microbiota and Legionella pneumophila control – Pan Ji et al. – Microbiome

Food microbiology

Variability within the dominant microbiota of sliced cooked poultry products at expiration date in the Belgian retail – Wim Geeraerts et al. – Food Microbiology

Modelling the growth of Listeria monocytogenes in Mediterranean fish species from aquaculture production – Araceli Bolívar et al. – International Journal of Food Microbiology

Prebiotic in fruit juice: processing challenges, advances, and perspectives – Thatyane Vidal Fonteles and Sueli Rodrigues – Current Opinion in Food Science

Technology

Multi-omics approach to elucidate the gut microbiota activity. Metaproteomics and metagenomics connection – Maria Guirro et al. – Electrophoresis

Microbes in the news

Can Your Gut Protect You Against Cancer? – Michelle Schoffro Cook – Care2

Millions of Mosquitoes to Be Released in Florida for Good Cause – Inside Edition

Using Special UV Light in Public Spaces Could Kill Flu Viruses, Bacteria – Jakob Nielson – Apex Tribune

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Microbiome Digest – Bik's Picks

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

Category Archives: Human gut

February 22, 2018

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