Category Archives: Human reproductive or urinary

February 3, 2017

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A review of microbes and cancer, seminal microbiome diversity, personalised microbiome-based approaches to Metabolic Syndrome, Thyrve: a new service offering testing and probiotic delivery, and Johnson & Johnson invests in Caelus.

Jobs

Microbiology Technologist Junior– Leeds

General microbiome

Review: Microbes and Cancer – Amiran Dzutsev- Annual Review of Immunology

Pregnancy and early life

Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling- Francesco Asnicar- mSystems

Associations between changes in the maternal gut microbiome and differentially methylated regions of diabetes-associated genes in fetuses: A pilot study from a birth cohort study-Kaori Tachibana- Journal of Diabetes Investigation

Human respiratory microbiome

Changes in the respiratory microbiome during acute exacerbations of idiopathic pulmonary fibrosis-Philip L. Molyneaux-Respiratory Research

Host genetic variation in mucosal immunity pathways influences the upper airway microbiome-Catherine Igartua- Microbiome

Human seminal microbiome

Seminal microbiome in men with and without prostatitis– Reet M€andar- International Journal of Urology

Blood microbiome

Blood Microbiome Quantity and the Hyperdynamic Circulation in Decompensated Cirrhotic Patients– Daniela Traykova- PLOS one

Human gut microbiome

Fecal Microbiota Transplantation in Inflammatory Bowel Disease– W.Reinisch- Digestive Diseases

Review: Role of gut microbiome in ankylosing spondylitis: an analysis of studies in literature– Yong-Yue Xu- Discovery Medicine

Feedback control of AHR signalling regulates intestinal immunity-Chris Schiering- Nature

Editorial: Commensal microbiota as a potential trigger of autoimmune uveitis-Reiko Horai- Expert Review of Clinical Immunology

Colonization with Helicobacter is concomitant with modified gut microbiota and drastic failure of the immune control of Mycobacterium tuberculosis-L. Majlessi- Mucosal Immunology

Review: Food matters: how the microbiome and gut–brain interaction might impact the development and course of anorexia nervosa– Beate Herpertz-Dahlmann- European Child & Adolescent Psychiatry

Gut microbiota dysbiosis contributes to the development of hypertension-Jing Li-Microbiome

Personalized microbiome-based approaches to metabolic syndrome management and prevention-Hagit Shapiro-Journal of Diabetes

Plant microbiome

Leaf-litter microbial communities in boreal streams linked to forest and wetland sources of dissolved organic carbon– Caroline E. Emilson-Ecosphere

Water microbiome

Sediment Microbial Diversity of Three Deep-Sea Hydrothermal Vents Southwest of the Azores-Teresa Cerqueira- Microbial Ecology

Bioinformatics

Consistent metagenomic biomarker detection via robust PCA-Mustafa Alshawaqfeh- Biology Direct

Microbes in the news

University of Maryland Students Send Bacteria to Space

VA is studying gut bacteria in PTSD, TBI patients following success in mice

Pores found in ‘platypus of microbiology’ bacterium push boundaries of evolution

What’s Your Gut Wellness Score? Thryve Launches With New Microbiome Testing Service for Better Health Through Your Stomach

Microbes on the market 

J&J invests in Caelus, pens pacts to grow microbiome R&D

Profound Improvements in Autistic Symptoms with Microbial Therapy

January 27, 2016

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Reviews on prenatal bacterial microbiota, mycobiome in the lower respiratory tract and interesting articles on association of HPV infection with vaginal microbiota; prebiotic and bioactive milk fraction improving NREM sleep.

General microbiome

Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data – Kelly M. Robinson – Microbiome

Pregnancy and early life

*Review: Does a prenatal bacterial microbiota exist? – M Hornef  -Mucosal Immunology

Human respiratory microbiome

*Review: Mycobiome in the Lower Respiratory Tract – A Clinical Perspective – Robert Krause- Frontiers in microbiology

Human vaginal microbiome

*Association of HPV infection and clearance with cervicovaginal immunology and the vaginal microbiota – B Shannon – Mucosal Immunology

Human gut microbiome

Review: Advances in Gut Microbiome Research, Opening New Strategies to Cope with a Western Lifestyle – Gina P. Rodriguez-Castaño – Frontiers in Genetics

Helicobacter pylori infection is associated with an altered gastric microbiota in children – K M Brawner – Mucosal Immunology

*Colonic Absorption of Low-Molecular-Weight Metabolites Influenced by the Intestinal Microbiome: A Pilot Study – Mitsuharu Matsumoto – PLoS One

Review: Advances in Gut Microbiome Research, Opening New Strategies to Cope with a Western Lifestyle – Gina P. Rodriguez-Castaño – Frontiers in Genetics

Animal experiments 

Effect of Lactobacillus Strains on Intestinal Microflora and Mucosa Immunity in Escherichia coli O157:H7-Induced Diarrhea in Mice – Xin Bian  – Current Microbiology

Modulation of gut microbiota and increase in fecal water content in mice induced by administration of Lactobacillus kefiranofaciens DN1 -Dana Jeong – Food & Function

Plant, root, and soil microbiome

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland – Theresa A. McHugh- Environmental Microbiology

Water and extremophile microbiome

Temporal and Spatial Variations of Bacterial and Faunal Communities Associated with Deep-Sea Wood Falls – Petra Pop Ristova – PLoS One

Probiotics / prebiotics

*Dietary Prebiotics and Bioactive Milk Fractions Improve NREM Sleep, Enhance REM Sleep Rebound and Attenuate the Stress-Induced Decrease in Diurnal Temperature and Gut Microbial Alpha Diversity – Robert S Thompson – Frontiers in Behavioral Neuroscience

Changes in the Gut Microbiota After Early Administration of Oral Synbiotics to Young Infants in India – DS Chandel -Journal of Pediatric Gastroenterology Nutrition

Techniques

Home-made cost effective preservation buffer is a better alternative to commercial preservation methods for microbiome research – Sebastian Menke- Frontiers in microbiology

Furosemide enhances the sensitivity of urinary metabolomics for assessment of kidney function – Isaie Sibomana – Metabolomics

Impact of sample processing on human airways microbial metagenomes – Lutz Wiehlmann – Journal of Biotechnology

Microbes in the news 

Scientists develop new flu vaccines for dogs

New Insight Describes Connection between Salmonella Infection and Appetite Loss

Anitha’s non-microbiology picks

Tiny Satellites to Make Big Contributions to Science

First report of metallic hydrogen on earth – Hydrogen turned into metal in stunning act of alchemy that could revolutionise technology and spaceflight

January 16, 2017

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Environmental pollutants have become an increasingly common health hazard. The possible effects of environmental pollutants on gut microbiota and their subsequent effects on health is discussed in highlighted review.

Pregnancy and early life

Antibiotics in Pregnancy Increase Children’s Risk of Otitis Media and Ventilation Tubes – Tine Marie Pedersen – The journal of Pediatrics

Human skin microbiome

Insights into the mast cell–microbiome connection in the skin – Alon Y. Hershko – Journal of Allergy and Clinical Immunology

Microbiota fingerprints lose individually identifying features over time – David Wilkins – Microbiome

Human vaginal microbiome

Association between preterm labor and genitourinary tract infections caused by Trichomonas vaginalis, Mycoplasma hominis, Gram-negative bacilli, and coryneforms – Alaa El-Dien M.S. Hosny – Journal of the Chinese Medical Association

The Vaginal Microbiota and Urinary Tract Infection – Ann E. Stapleton – Microbiol Spectrum

Human nearly-sterile sites 

Metabolic profiles of exudates from chronic leg ulcerations – Adam Junka – Journal of Pharmaceutical and Biomedical Analysis

Human oral microbiome

Review: Ecology of the Oral Microbiome: Beyond Bacteria – Jonathon L. Baker – Trends in Microbiology

On-going Mechanical Damage from Mastication Drives Homeostatic Th17 Cell Responses at the Oral Barrier – Nicolas Dutzan – Immunity

Salivary Gluten Degradation and Oral Microbial Profiles in Health and Celiac Disease – Na Tian  – Applied and Environmental Microbiology

Human gut microbiome

Expert review: Management of Clostridium difficile Infection in Inflammatory Bowel Disease: Expert Review from the Clinical Practice Updates Committee of the AGA Institute – Sahil Khanna – Clinical Gastroenterology and Hepatology

Review: Effects of environmental pollutants on gut microbiota – Yuanxiang Jin – Environmental Pollution

Impact of dietary pattern of the fecal donor on in vitro fermentation properties of whole grains and brans – Sandrayee Brahma – Journal of Functional Foods

Review: The role of the gut microbiota in sepsis – Bastiaan W Haak – The Lancet Gastroenterology & Hepatology

Gut microbiota interactions with the immunomodulatory role of vitamin D in normal individuals – Renata V. Luthold – Metabolism

“Angelakisella massiliensis” gen. nov., sp. nov., a new bacterial species isolated from human ileum – Morgane Mailhe – New Microbes and New Infections

Helicobacter pylori–related metabolic syndrome as predictor of progression to esophageal carcinoma in a subpopulation-based Barrett’s esophagus cohort – Jannis Kountouras – Gastrointestinal Endoscopy

Impact of dietary pattern of the fecal donor on in vitro fermentation properties of whole grains and brans – Sandrayee Brahma – Journal of Functional Foods

Absence of intestinal microbiota increases ß-cyclodextrin stimulated reverse cholesterol transport – Rima H. Mistry – Molecular Nutrition & Food Research

European consensus conference on faecal microbiota transplantation in clinical practice – Giovanni Cammarota – Gut
Animal experiments

Gd-DTPA-induced dynamic metabonomic changes in rat biofluids – Chuanling Wan – Magnetic Resonance Imaging

Increasing dietary nitrate has no effect on cancellous bone loss or fecal microbiome in ovariectomized rats – Melissa N. Conley – Molecular Nutrition & Food Research

Animal microbiome

Improved growth rate and disease resistance in olive flounder, Paralichthys olivaceus, by probiotic Lactococcus lactis WFLU12 isolated from wild marine fish – Thanh Luan Nguyen – Aquaculture

Plant, root, and soil microbiome

The effects of tree species and substrate on carbon sequestration and chemical and biological properties in reforested post-mining soils – Agnieszka Józefowska – Geoderma

Impacts of inorganic and organic fertilization treatments on bacterial and fungal communities in a paddy soil – Jichen Wang – Applied Soil Ecology

Water and extremophile microbiome

Effects of the halophilic fungi Cladosporium sphaerospermum, Wallemia sebi, Aureobasidium pullulans and Aspergillus nidulans on halite formed on sandstone surface – Maisa M.A. Mansour – International Biodeterioration & Biodegradation

Epiphytic Planctomycetes communities associated with three main groups of macroalgae – Joana Bondoso – FEMS Microbiology Ecology

Floc formation reduces the pH stress experienced by microorganisms living in alkaline environments -C.J. Charles – Applied and Environmental Microbiology

Capturing compositional variation in denitrifying communities: A multiple primer approach that includes autotrophic denitrifying Epsilonproteobacteria – S.A. Murdock  – Applied and Environmental Microbiology

Waste and pollution microbiology

Review: Aerobic and anaerobic fungal metabolism and Omics insights for increasing polycyclic aromatic hydrocarbons biodegradation – Sevcan Aydin – Fungal Biology Reviews

Built environment 

Biological invasion in the indoor environment: the spread of Eurotium halophilicum on library materials – Andrea Polo – International Biodeterioration & Biodegradation

Review: Integrated management of the risks of stored grain spoilage by seedborne fungi and contamination by storage mould mycotoxins – An update – Francis Fleurat-Lessard – Journal of Stored Products Research

Food microbiology

Impact of environmental conditions and process modifications on microbial diversity, fermentation efficiency and chemical profile during the fermentation of mezcal in Oaxaca – Manuel R. Kirchmayr – LWT – Food Science and Technology

Anti-aging and redox state regulation effects of A-type proanthocyanidins-rich cranberry concentrate and its comparison with grape seed extract in mice – Jingjing Jiao – Journal of Functional Foods

Probiotics / prebiotics

Probiotic mixture improves fatty liver disease by virtue of its action on lipid profiles, leptin, and inflammatory biomarkers – Hessah Mohammed Al-muzafar – BMC Complementary and Alternative Medicine

January 15, 2017

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Microbes in Idiopathic Pulmonary Fibrosis, review on the female urinary microbiota, koalas with “wet bottom”, virus metagenomics of the Namib desert, biosignatures in fossils.

Jobs

Microbiome Research Associate Job – Merck Research Laboratories – Cambridge, MA – Science Careers

Human urinary tract microbiome

* Review: The female urinary microbiota, urinary health and common urinary disorders – Linda Brubaker – Annals of Translational Medicine

Human respiratory microbiome

* Host-Microbial Interactions in Idiopathic Pulmonary Fibrosis – Philip L Molyneaux – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

The human gut microbiome as source of innovation for health: which physiological and therapeutic outcomes could we expect?: Human gut mibrobiome [SIC] as source of innovation for health – Joël Doré – Thérapie

In French: Microbiote intestinal : qu’en attendre au plan physiologique et thérapeutique ? Le microbiote intestinal comme source d’innovation pour la santé – Joël Doré – Thérapie

Review: Seafood allergen-induced hypersensitivity at the microbiota-mucosal site: implications for prospective probiotic use in allergic response regulation – Linglin Fu – Critical Reviews in Food Science and Nutrition

Review: Impact Of Human Aging And Modern Lifestyle On Microbiota – Maria Gabriela Valle Gottlieb – Critical Reviews in Food Science and Nutrition

Review: Effects of environmental pollutants on gut microbiota – Yuanxiang Jin – Environmental Pollution

Animal experiments

Replacing corn with sorghum in the diet alters intestinal microbiota without altering chicken performance – N. S. Fagundes – Journal of Animal Physiology and Animal Nutrition

Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome – Francesco Rubino – The ISME Journal

Wolbachia Affects Reproduction and Population Dynamics of the Coffee Berry Borer (Hypothenemus hampei): Implications for Biological Control – Yobana A. Mariño – MDPI Insects

Neoagarotetraose protects mice against intense exercise induced fatigue damage by modulating gut microbial composition and function – Na Zhang – Molecular Nutrition & Food Research

Housing Systems Influence Gut Microbiota Composition of Sows but Not of Their Piglets – Tereza Kubasova – PLOS ONE

Effect of Different Lignocellulosic Diets on Bacterial Microbiota and Hydrolytic Enzyme Activities in the Gut of the Cotton Boll Weevil (Anthonomus grandis) – Emiliano Ben Guerrero – Frontiers in Microbiology

Animal microbiome

* Variation in the microbiome of the urogenital tract of koalas (Phascolarctos cinereus) with and without “wet bottom” – Alistair Raymond Legione – bioRxiv

Plant, root, and soil microbiome

* Fossils: Carbonaceous biosignatures of diverse chemotrophic microbial communities from chert nodules of the Ediacaran Doushantuo Formation – Yuangao Qu – Precambrian Research

Plant, soil and microbial controls on grassland diversity restoration: A long-term, multi-site mesocosm experiment – Ellen L. Fry – Journal of Applied Ecology

Pyrosequencing reveals bacterial communities and enzyme activities differences after application of novel chiral insecticide Paichongding in aerobic soils – Jie Chen – Applied Soil Ecology

Cedar and bamboo plantations alter structure and diversity of the soil bacterial community from a hardwood forest in subtropical mountain – Yu-Te Lin – Applied Soil Ecology

The differentiation of soil bacterial communities along a precipitation and temperature gradient in the eastern Inner Mongolia steppe – Minjie Yao – CATENA

Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands – Julia Kyaschenko – The ISME Journal

Association between Grape Yeast Communities and the Vineyard Ecosystems – João Drumonde-Neves – PLOS ONE

Water microbiome

High growth potential and activity of 0.2 µm filterable bacteria habitually present in coastal seawater – Yumiko Obayashi – Biogeosciences Discuss

Chronic exposure effects of silver nanoparticles on stream microbial decomposer communities and ecosystem functions – Ahmed Tlili – Environmental Science & Technology

Waste and pollution microbiology

Global profiling of metabolite and lipid soluble microbial products in anaerobic wastewater reactor supernatant using UPLC/MSe – Phornpimon Tipthara – Journal of Proteome Research

Food microbiology

Rapid concentration detection and differentiation of bacteria in skimmed milk using surface enhanced Raman scattering mapping on 4-mercaptophenylboronic acid functionalized silver dendrites – Panxue Wang – Analytical and Bioanalytical Chemistry

Metagenomics and bioinformatics / Viruses and phages

Robust inference of genetic exchange communities from microbial genomes using TF-IDF – Yingnan Cong – Frontiers in Microbiology

* Virome assembly and annotation: a surprise in the Namib Desert – Uljana Hesse – Frontiers in Microbiology

* Metaviromes of Extracellular Soil Viruses along a Namib Desert Aridity Gradient – Olivier Zablocki – Genome Announcements

Metagenome Sequencing of Prokaryotic Microbiota Collected from Rivers in the Upper Amazon Basin – Célio Dias Santos-Júnior – Genome Announcements

Restoring the Duality between Principal Components of a Distance Matrix and Linear Combinations of Predictors, with Application to Studies of the Microbiome – Glen A. Satten – PLOS ONE

New approach for studying mobile genes using metagenomic analysis – Kazuyuki Ishihara – Oral Diseases

Archaea

New insights into marine group III Euryarchaeota, from dark to light – Jose M Haro-Moreno – The ISME Journal

Techniques

MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling – Kristin Burnum-Johnson – Analyst

An explanation of the Nagoya Protocol and Access and Benefit Sharing, and its implication for microbiology – David Smith – Microbiology

Microbes in the news

You’re probably showering way too often – Rafi Letzter – Business Insider

Viruses May Be Responsible For Life As We Know It – Ryan F. Mandelbaum – Gizmodo

Boost your intake of resistant starch to help your gut thrive – Leslie Beck – The Globe and Mail

We now know bacteria can communicate electrically, and we should be worried
They’re organised – David Nield – Science Alert

Proceed with caution: Autism Causes Update: The Gut-Brain Connection And How A Common Probiotic May Ease Symptoms – Lizette Borreli – Medical Daily

Study provides fundamental insights into functioning of microbiota and human-gut flora symbiosis – News Medical

Microbes on the market

Bristol-Myers Squibb and Enterome Announce Immuno-Oncology Collaboration Focused on Microbiome-Derived Biomarkers, Drug Targets and Bioactive Molecules – SAT Press Releases

Bik’s non-microbiology picks

The Physics of Everyday Life. Why popcorn pops and ducks don’t freeze when swimming in icy water. John Gribbin reviews “Storm in a Teacup” by Helen Czerski – Wall Street Journal

January 11, 2017

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Vaginal microbial  communities associated with HIV acquisition or protection, evolution and function of the appendix, microbes and bird evolution, soil microbes followed for 17 years, and bone microbiome and cause-of-death of an 18th century child.
Jobs

Faculty Position in Microbiome Research – National University of Singapore – Science Careers

Pregnancy and early life

The Role of Early Life Nutrition in the Establishment of Gastrointestinal Microbial Composition and Function – Erin C. Davis – Gut Microbes

Human vaginal microbiome

* Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased HIV Acquisition in Young South African Women – Christina Gosmann – Immunity

Diagnosis and microecological characteristics of aerobic vaginitis in outpatients based on preformed enzymes – Zhi-liang Wang – Taiwanese Journal of Obstetrics & Gynecology

Human respiratory microbiome

Review: The microbiome in mechanically ventilated patients – Yin, Yudong – Current Opinion in Infectious Diseases

Human gut microbiome

* Morphological evolution of the mammalian cecum and cecal appendix – Heather F. Smith – Comptes Rendus Palevol

Exploring the Efficacy of Pooled Stools in Fecal Microbiota Transplantation for Microbiota-Associated Chronic Diseases – Abbas Kazerouni – PLOS ONE

Review: Role of Vitamin D in the Hygiene Hypothesis: The Interplay between Vitamin D, Vitamin D Receptors, Gut Microbiota, and Immune Response – Allison Clark – Frontiers in Immunology

Review: Bacterial Signaling to the Nervous System via Toxins and Metabolites – Nicole J. Yang – Journal of Molecular Biology

Animal experiments

Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior – Caleb Fischer – eLIFE

Gut Microbiota Mediates Protection Against Enteropathy Induced by Indomethacin – Xue Xiao – Scientific Reports

Faecal parameters as biomarkers of the equine hindgut microbial ecosystem under dietary change – P. Grimm – Animal

Characterisation of Early-Life Fecal Microbiota in Susceptible and Healthy Pigs to Post-Weaning Diarrhoea – Samir Dou – PLOS ONE

Animal microbiome

Metagenomic analysis of microbial community of a parasitoid wasp Megaphragma amalphitanum – A.V. Nedoluzhko – Genomics Data

* Review: Ecoimmunology and microbial ecology: Contributions to avian behavior, physiology, and life history – Jessica K. Evans – Hormones and Behavior

Archaeology microbiome

* The Cause of Death of a Child in the 18th Century Solved by Bone Microbiome Typing Using Laser Microdissection and Next Generation Sequencing – Valeria D’Argenio – International Journal of Molecular Sciences

Plant, root, and soil microbiome

Phyllosphere Methylobacterium bacteria contain UVA-absorbing compounds – Shigenobu Yoshida – Journal of Photochemistry and Photobiology B: Biology

Major Crop Species Show Differential Balance between Root Morphological and Physiological Responses to Variable Phosphorus Supply – Yang Lyu – Frontiers in Plant Science

* Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change – Emma J. Sayer – Ecology and Evolution

Water and extremophile microbiome

Two microcrustaceans affect microbial and macroinvertebrate-driven litter breakdown – Sophie Chambord – Freshwater Biology

Biofilms Confer Resistance to Simulated Extra-terrestrial Geochemical Extremes – Adam H Stevens – bioRxiv Preprint

Bioinformatics, statistics, and metagenomics

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer – Aaron Weimann – mSystems

Structural zeros in high-dimensional data with applications to microbiome studies – Abhishek Kaul – Biostatistics

More microbiology

Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response – Robert Heler – Molecular Cell

Press: Researchers Learn to Enhance Bacteria’s Ability to Form Genetic Memories – SciCasts

Microbes in the news
Meet Canada’s ‘poop lady’: “I got to know people up there very well over the years, said Girard, 28. – EurekAlert

A new year for our journal club! – Fiona Whelan – Human Microbiome Journal Club

Oral bacteria linked to preterm labor in Hawaiʻi – Desiree Uyeda – University of Hawai’i News

Mayo’s microbiome study targets diabetes – Brett Boese – Post Bulletin

MicrobEYEome: Liver Cancer Patients Have a Signature Microbiome – GastroEndo News

Presentation: The role of the microbiome in Porcine Reproductive & Respiratory Syndrome (PRRS) – Megan Niederwerder – YouTube

Based on the title this appears to be a good candidate for the “Overselling The Microbiome Award” by Jonathan Eisen: How Sexual Attraction Is Shaped by Gut Bacteria, Infectious Diseases, and Parasites – Kathleen McAuliffe – BigThink

Latest Dengue Update: Bacteria Strain That Stops Dengue Transmission In Mosquitoes Dies In Hot Environment – Minnow Blythe – Counsel Heal

Microbes on the market

Allergan (AGN) Enters Licensing Agreement with Assembly Biosciences (ASMB) to Obtain Worldwide Rights to GI Programs – StreetInsider

Ferring Partners with Intralytix to Develop Bacteriophage Treatments for Conditions Associated with the Microbiome and Drug-Resistant Bacteria – BusinessWire

La Roche-Posay Introduces Prebiotic Skincare Line – PR NewsWire

Indigo’s Preliminary Commercial Data Demonstrate Significant Yield Gains for Growers with Plant Microbiome Product – PR NewsWire

Bik’s non-microbiology picks

The Association of Hot Red Chili Pepper Consumption and Mortality: A Large Population-Based Cohort Study – Mustafa Chopan – PLOS ONE

January 10, 2017

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A culture-based study of 2000 nasal microbiomes, eye metabolites, cardiorespiratory fitness in breast cancer survivors, Akkermansia from a python, chickpea rhizosphere, tobacco wilt suppression, plant rhizosphere mass spectrometry, phyloSkeleton.

Human nasal microbiome

Epidemiological and ecological modelling reveal diversity in microbial population structures from a cross-sectional community swabbing study – Abigail L Coughtrie – bioRxiv

Human eye microbiome

LC-MS-Based Metabolic Fingerprinting of Aqueous Humor – Karolina Pietrowska – Journal of Analytical Methods in Chemistry

Human vaginal microbiome

MS thesis: Metagenomic characterization of the vaginal microbiome – Keshini Devakandan – University of British Columbia

Human gut microbiome

Gut microbiota composition associated with alterations in cardiorespiratory fitness and psychosocial outcomes among breast cancer survivors – Jesseca A. Paulsen – Supportive Care in Cancer

SYN-004 (ribaxamase), an oral β-lactamase designed to protect the gut microbiome from the deleterious effects of certain intravenously administered β-lactam antibiotics, degrades ceftriaxone excreted into the intestine in Phase 2a clinical studies – John F. Kokai-Kun – Antimicrobial Agents Chemotherapy

Animal experiments

Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis – Franziska Faber – PLOS Pathogens

Animal microbiome

Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut – Janneke P. Ouwerkerk – Genome Announcements

Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and in eggs throughout development – Allison H. Kerwin – Environmental Microbiology

Plant, root, and soil microbiome

Competition between rhizobia under different environmental conditions affects the nodulation of a legume – Zhao Jun Ji – Systematic and Applied Microbiology

Combined pre-seed treatment with microbial inoculants and Mo nanoparticles changes composition of root exudates and rhizosphere microbiome structure of chickpea (Cicer arietinum L.) plants – E. N. Shcherbakova – Symbiosis

Interactions of soil particulate organic matter chemistry and microbial community composition mediating carbon mineralization in karst soils – Wei Xiao – Soil Biology and Biochemistry

Metabolic profiling of root exudates from two ecotypes of Sedum alfredii treated with Pb based on GC-MS – Qing Luo – Scientific Reports

Effects of Wetland Vegetation on Soil Microbial Composition: A Case Study in Tumen River Basin, Northeast China– Qin Lei – Chin. Geogra. Sci

Microbial communities in pyrene amended soil–compost mixture and fertilized soil – Iris K. U. Adam – AMB Express

Competition assays and physiological experiments of soil and phyllosphere yeasts identify Candida subhashii as a novel antagonist of filamentous fungi – Maja Hilber-Bodmer – BMC Microbiology

Tobacco bacterial wilt suppression with biochar soil addition associates to improved soil physiochemical properties and increased rhizosphere bacteria abundance – Chengsheng Zhang – Applied Soil Ecology

Editorial: Microbial community ecology: Function over phylogeny – Sean M. Gibbons – Nature Ecology & Evolution

Review: Elucidating rhizosphere processes by mass spectrometry – A review – Ariana Rugova – Analytica Chimica Acta

Water and extremophile microbiome

Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments – Marc Mußmann – The ISME Journal

Food microbiology

Review: An Integrated View of the Effects of Wine Polyphenols and Their Relevant Metabolites on Gut and Host Health – Carolina Cueva – Molecules

Microbiological quality of Brazilian UHT milk: Identification and spoilage potential of spore-forming bacteria – Claudia L O Pinto – International Journal of Dairy Technology

Metabolomics for empirical delineation of the traditional Korean fermented foods and beverages – Digar Singh – Trends in Food Science & Technology

Source tracking of prokaryotic communities in fermented grain of Chinese strong-flavor liquor – Xueshan Wang – International Journal of Food Microbiology

Bioinformatics

phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics – Lionel Guy – Bioinformatics

Microbes in the news

Hyperthermophiles and Cryophiles: The World’s Most Extreme Organisms – Priya Amin – Harvard Science Review

Bik’s non-microbiology picks

Responses of Human Neonates to Highly Diluted Odorants from Sweat – Helene M. Loos – Journal of Chemical Ecology

January 8, 2017

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Human mouth microbiome

Comparison of sputum microbiome of legionellosis-associated patients and other pneumonia patients: indications for polybacterial infections – Hila Mizrahi – Scientific Reports

Human reproductive tract microbiome

Investigation of the microbiota of the reproductive tract in women undergoing a total hysterectomy and bilateral salpingo-oopherectomy – Shana M. Miles – Fertility and Sterility

Human skin microbiome

Review: Performing Skin Microbiome Research: A Method to the Madness – Heidi H. Kong – Journal of Investigative Dermatology

Human gut microbiome

Sleeve gastrectomy drives persistent shifts in the gut microbiome – Cyrus Jahansouz – Surgery for Obesity and Related Diseases

Review: Gut microbiota in vascular disease: Therapeutic target? – Anbazhagan AN – Current Vascular Pharmacology

Review: Alcohol, microbiome, life style influence alcohol and non-alcoholic organ damage – Manuela G. Neuman – Experimental and Molecular Pathology

Reviews in Gastroenterology Clinics of North America
Diet and the Microbiome – Nida Murtaza
The Gut Microbiota in Inflammatory Bowel Disease – Donal Sheehan
The Microbiome-Gut-Brain Axis in Health and Disease – Timothy G. Dinan
Biology of the Microbiome : Interactions with the Host Immune Response – Sylwia Smolinska
Biology of the Microbiome 2: Metabolic Role – Jia V. Li

Animal experiments

Structural and functional alterations in the colonic microbiome of the rat in a model of stress induced irritable bowel syndrome – Nicolaas H Fourie – Gut Microbes

Animal microbiome

Greater Species Richness of Bacterial Skin Symbionts Better Suppresses the Amphibian Fungal Pathogen Batrachochytrium Dendrobatidis – Jonah Piovia-Scott – Microbial Ecology

Plant, root, and soil microbiome

Namib Desert edaphic bacterial, fungal and archaeal communities assemble through deterministic processes but are influenced by different abiotic parameters – Riegardt M. Johnson – Extremophiles

Plant Community Richness Mediates Inhibitory Interactions and Resource Competition between Streptomyces and Fusarium Populations in the Rhizosphere – Adil Essarioui – Microbial Ecology

Changes in Soil Fungal Community Structure with Increasing Disturbance Frequency – Hyunjun Cho – Microbial Ecology

Water and extremophile microbiome

Effect of salinity on mercury methylating benthic microbes and their activities in Great Salt Lake, Utah – Eric S. Boyd – Science of the Total Environment

Waste and pollution microbiology

Low temperature MBBR nitrification: Microbiome analysis – Bradley Young – Water Research

Microbes in space

MELiSSA the minimal biosphere: Human life, waste and refuge in deep space – Jeremy Walker – Future

Metabolomics

Bacterial Signaling to the Nervous System via Toxins and Metabolites – Nicole J. Yang – Journal of Molecular Biology

Bioinformatics

An Informative Approach on Differential Abundance Analysis for Time-course Metagenomic Sequencing Data – Dan Luo – Bioinformatics

Microbial ecology

Cheating fosters species co-existence in well-mixed bacterial communities – Anne Leinweber – ISME Journal

Microbes in the news

Life after death: the science of human decomposition – Mo Costandi

Japan’s fantastic emerald green algae. These great balls of fuzz, look lovely, are zero maintenance and keep water clean – James Wong

Cavities Are Contagious: Kissing And 3 Other Ways Harmful Bacteria Spreads And Causes Tooth Decay – Lizette Borreli – Medical Daily

Same bacteria found in Indian River Lagoon killed 10 in Florida in 2016 | Map – Tyler Treadway – TC Palm

Wake up, wipe out: How oxygen can help take down antiobiotic-resistant bacteria – Cordis

Your child’s microbiome, and why its health matters – Jennifer Graham – The Washington Times

January 7, 2017

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3D modeling of endometrial interaction with vaginal bacteria, insect symbiont determined by host plants, 2011 tsunami effects on  phytoplankton, virus taxonomy, Microbiome Helper and microRNA sensitivity in intestinal stem cells.

Human vaginal microbiome

* Human three-dimensional endometrial epithelial cell model to study host interactions with vaginal bacteria and Neisseria gonorrhoeae – Paweł Łaniewski – Infection and Immunity

Human gut microbiome

Workshop Proceedings: Nutrition Across the Lifespan for Healthy Aging – Proceedings of a Workshop—in Brief – NAS

Review: Gut–brain axis in 2016: Brain–gut–microbiota axis — mood, metabolism and behaviour – Timothy G. Dinan & John F. Cryan – Nature Reviews Gastroenterology & Hepatology

Animal experiments

Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis – Franziska Faber – PLOS Pathogens

Comparative Analysis of Drosophila melanogaster Gut Microbiota with Respect to Host Strain, Sex, and Age – Gangsik Han – Microbial Ecology

Impact of birth weight and postnatal diet on the gut microbiota of young adult guinea pigs – Kait Al – PeerJ

* Host plant species determines symbiotic bacterial community mediating suppression of plant defenses – Seung Ho Chung – Scientific Reports

Animal microbiome

Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges – Gerald Lackner – PNAS

Plant, root, and soil microbiome

Regulation of root development in Arabidopsis thaliana by phytohormone-secreting epiphytic methylobacteria – Jana Klikno – Protoplasma

Diversity and composition of rhizospheric soil and root endogenous bacteria in Panax notoginseng during continuous cropping practices – Yong Tan – Journal of Basic Microbiology

Subsurface Microbial Ecosystems: A Photon Flux and a Metabolic Cascade – Alexander P. Petroff – Journal of Statistical Physics

Water microbiome

* Retrospective analysis of phytoplankton assemblages on the Iwate coast before and after the 2011 tsunami using cryopreserved DNA samples – Yutaka Okumura

Effects of iron deficiency on the growth and photosynthesis of three bloom-forming cyanobacterial species isolated from Lake Taihu – Kui Xu – Phycological Research

Patterns of bacterial diversity in the marine planktonic particulate matter continuum –
Mireia Mestre – The ISME Journal

Bioreactor, waste, and pollution microbiology

Biofilm composition and threshold concentration for growth of Legionella pneumophila on surfaces exposed to flowing warm tap water without disinfectant – Applied and Environmental Microbiology

Enhanced methane production via repeated batch bioaugmentation pattern of enriched microbial consortia – Zhiman Yang – Bioresource Technology

Accelerated acidification by inoculation with a microbial consortia in a complex open environment – Jiadong Yu – Bioresource Technology

Effects of a bacterial consortium from acid mine drainage on cadmium phytoextraction and indigenous soil microbial community – Jin-tian Li – Plant and Soil

Can DNA sequencing show differences between microbial communities in Polish and Danish wastewater treatment plants? – A. Miłobędzka – Water Science & Technology

Frequency dependent microbial growth during cycles of feast and famine – Jason Merritt – arXiv

Viruses and phages

* Consensus statement: Virus taxonomy in the age of metagenomics – Peter Simmonds – Nature Reviews Microbiology

Genomic evolution of bacterial populations under coselection by antibiotics and phage
– Johannes Cairns – Molecular Ecology

Bioinformatics and metagenomics

* Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research – André M. Comeau – mSystems

Transcriptomics

* Functional transcriptomics in diverse intestinal epithelial cell types reveals robust microRNA sensitivity in intestinal stem cells to microbial status – Bailey C.E. Peck – Journal of Biological Chemistry

Biofilms

Tackling Fungal Resistance by Biofilm Inhibitors – Shanchao Wu – Journal of Medical Chemistry

Microbes in the news

Featuring our research: The Secret Lives of Marine Mammal Microbes – Probing the mystery of what goes on inside the guts of dolphins and whales – Emma Hiolski – Scientific American

That cold you have might actually be the worst Bay Area flu outbreak in a decade – Kristin Hanes – SF Gate

Microbiomes in far-flung places: characterizing the arctic Inuit gut microbiome – Stephen Ornes – ASM

Microbes on the market

MoBio’s Microbiome News is back!

OptiBiotix Release: Microbiome Technology Powers The Healthy Weight Loss Company Expansion – BioSpace

Bik’s Non-Microbiology Picks

The crack in this Antarctic ice shelf just grew by 11 miles. A dramatic break could be imminent – Chris Mooney – Washington Post

Citizen Science: It’s that time of year: the annual bird count – Shawn Price – Los Angeles Times

January 1, 2017

Posted on by

Happy New Year, everyone! May 2017 be good for you and your microbes!

Multiple human site microbiome

Disruption of the microbiota across multiple body sites in critically ill children – Matthew B. Rogers – Microbiome

Pregnancy and early life

Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease – Christopher J. Stewart – Microbiome

Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants – Katherine E. Gregory – Microbiome

The developing hypopharyngeal microbiota in early life – Martin Steen Mortensen – Microbiome

Review: Maternal health and the placental microbiome – Elise Pelzer – Placenta

Human respiratory microbiome

Study of the Lung Microbiome. Have We Reached the End of the Beginning? – Alison Morris – American Journal of the Respiratory and Critical Care Medicine

Human urinary tract microbiome

Review: Impact of polymicrobial biofilms in catheter-associated urinary tract infections – Andreia S. Azevedo – Critical Reviews in Microbiology

Human gut microbiome

The gut microbiota in conventional and serrated precursors of colorectal cancer – Brandilyn A. Peters – Microbiome

Interaction between Atypical Antipsychotics and the Gut Microbiome in a Bipolar Disease Cohort – Stephanie A. Flowers – Pharmacotherapy

Book chapter: The Role of the Gastrointestinal Microbiota in Visceral Pain – Kieran Rea – Handbook of Experimental Pharmacology

Review: Microbial nutrient niches in the gut – Fátima C. Pereira – Environmental Microbiology

Animal and bioreactor experiments

Autochthonous probiotic Lactobacillus sp. in the diet of bullfrog tadpoles Lithobates catesbeianus improves weight gain, feed conversion and gut microbiota – S.A. Pereira – Aquaculture Nutrition

The effect of pullulan on the growth and acidifying activity of selected stool microflora of human – Anna Chlebowska-Śmigiel – Current Pharmaceutical Biotechnology

Animal microbiome

Effects of diet type, developmental stage, and gut compartment in the gut bacterial communities of two Cerambycidae species (Coleoptera) – Jeong Myeong Kim – Journal of Microbiology

Metagenomic approach to study the bacterial community in clinical and subclinical mastitis in buffalo – Reena J. Patel – Meta Gene

Plant, root, and soil microbiome

Analysis of copper tolerant rhizobacteria from the industrial belt of Gujarat, western India for plant growth promotion in metal polluted agriculture soils – Murali Sharaff – Ecotoxicology and Environmental Safety

High-Performing Windowfarm Hydroponic System: Transcriptomes of Fresh Produce and Microbial Communities in Response to Beneficial Bacterial Treatment – Seungjon Lee – Molecular Plant-Microbe Interactions

Using soil microbial inoculations to enhance substrate performance on extensive green roofs – Chloe J. Molineux – Science of the Total Environment

Rhizospheric iron and arsenic bacteria affected by water regime: Implications for metalloid uptake by rice – Sarah Zecchin – Soil Biology and Biochemistry

Metabolomics

Stability of Cross-Feeding Polymorphisms in Microbial Communities
– Ivana Gudelj – PLOS Computational Biology

Microbes in the news

Rochester using ‘pickle juice’ to reduce nitrogen – Liz Markhlevskaya – Seacoast Online

Bacteria in soil has antidepressant effects – Jessica Damiano – News Day

10 New Year resolutions for your vaginal health – Cosmopolitan

Heart surgery patients warned about possible exposure to bacteria – Tammy Palmer – Local Syracuse

December 30, 2016

Posted on by

Vancomycin treatment preceding fecal transplantation, a diet for IBD, dieting and gut microbiome diversity, halotolerant extremophiles for recycling pollutants, mass spectrometry on medical swabs.

Human vaginal microbiome

Genital injury signatures and microbiome alterations associated with depot medroxyprogesterone acetate usage and intravaginal drying practices – Kenzie D. Birse – The Journal of Infectious Diseases

Human gut microbiome

Oral Vancomycin Followed by Fecal Transplantation Versus Tapering Oral Vancomycin Treatment for Recurrent Clostridium difficile Infection: An Open-Label, Randomized Controlled Trial – Susy S. Hota – Clinical Infectious Diseases

Fecal Fixation: Fecal Microbiota Transplantation for Clostridium difficile Infection – Stuart Johnson – Clinical Infectious Diseases

SCD diet: Clinical and Fecal Microbial Changes With Diet Therapy in Active Inflammatory Bowel Disease – David L. Suskind – Journal of Clinical Gastroenterology

Press: Changes With Diet Therapy in Active Inflammatory Bowel Disease – Science Daily

Review: From bugs to brains: The microbiome in neurological health – Kyla A. McKay – Multiple Sclerosis and Related Disorders

Animal experiments

Prior Dietary Practices and Connections to a Human Gut Microbial Metacommunity Alter Responses to Diet Interventions – Nicholas W. Griffin – Cell Host & Microbe

Press: Your Crappy American Diet Might Leave Your Gut Bacteria Stunted – Ryan F. Mandelbaum – Gizmodo
Your microbiota’s previous dining experiences may make new diets less effective – EurekAlert

Intestinal Serotonin Transporter Inhibition by Toll-Like Receptor 2 Activation. A Feedback Modulation – Eva Latorre – PLOS ONE

Press: Gut microorganisms affect our physiology – EurekAlert

Alterations in the gut microbiota can elicit hypertension in rats – Sareema Adnan – Physiological Genomics

Plant, root, and soil microbiome

Impact of plant growth-promoting rhizobacteria on root colonization potential and life cycle of Rhizophagus irregularis following co-entrapment into alginate beads -P. Loján – Journal of Applied Microbiology

Review: Soil Bacteria Alter Plant Physiology to Mitigate Salinity Stress Effects in Glycophytes – Ramalingam Radhakrishnan – Frontiers in Plant Science

Presentation abstract: Soil microbial community structures and activities in relation to nitrogen cycling in two contrasting soils in Malawi – community responses to added carbon – Akane Chiba – International Nitrogen Initiative

Waste and pollution microbiology

Pyrosequencing reveals microbial community dynamics in integrated simultaneous desulfurization and denitrification process at different influent nitrate concentrations
– Chuan Chen – Chemosphere

Microbiological water quality in the medical device industry in Italy – Emilio D’Ugo – Microchemical Journal

Halotolerant extremophile bacteria from the Great Salt Lake for recycling pollutants in microbial fuel cells – Matteo Grattieri – Journal of Power Sciences

Functionality of microbial communities in constructed wetlands used for pesticide remediation: Influence of system design and sampling strategy – Tao Lv – Water Research

Metagenomic Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments as Revealed by Functional Taxonomic Strategies – Arghya Mukherjee – bioRxiv

Food microbiology

Saccharomyces uvarum is Responsible for the Traditional Fermentation of Apple CHICHA in Patagonia – ME Rodríguez – FEMS Yeast Research

Metabolomics

Medical swab analysis using desorption electrospray ionization mass spectrometry (DESI-MS) – a non-invasive approach for mucosal diagnostics – Pamela Pruski – Analytical Chemistry

Coping with inevitable accidents in metabolism – Antoine Danchin – Microbial Biotechnology

Techniques

Examining the potential use and long-term stability of guaiac faecal occult blood test cards for microbial DNA 16S rRNA sequencing – Morag Taylor – Journal of Clinical Pathology

Microbes in the news

Short podcast: Academic Minute – Diversifying Your Microbiome. Jack Gilbert details how the sharing of bacteria from person to person could make us healthier in the long run. – Inside Higher Ed

Ancient ‘Eternal Life’ bacteria leaves Russian scientist ‘Illness-Free’ – Harry Walker – Express

Bacteria evolution offers insights into human protein interactions – Brooks Hays – UPI

High school students discover new phages: Genomics research gives youth a leg up on education – Tonya S. Grace – Kentucky New Era

Fermentation expert Sandor Katz on why we shouldn’t fear bacteria – Andrew Sun – SCMP

Novel diet therapy helps children with crohn’s disease and ulcerative colitis reach remission – Science Daily

Prebiotics for your skin: The La Roche-Posay Toleriane Double Repair Moisturizer Could Be the Secret to Better Skin – Sarah Kinonen – Allure