Tag Archives: necrotizing enterocolitis

January 21, 2016

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Beards and MRSA in hospital workers, dysbiosis in Crohns Disease, non-absorbable antibiotics affect offspring in mice, bacterial sunscreens, and bacteria found in a sick-making building.

Events

2nd Annual Microbiome Symposium – January 25, 2016 – Stanford University, Palo Alto, CA

Pregnancy and birth

A necrotizing enterocolitis-associated gut microbiota is already present in the meconium: results of a prospective study – Fardou H. Heida – Clinical Infectious Diseases

Human oral microbiome

Salivary pathogen and serum antibody to assess the progression of chronic periodontitis: a 24-mo prospective multicenter cohort study – T. Morozumi – Journal of Periodontal Research

Human skin microbiome

Bacterial ecology of hospital workers’ facial hair: a cross-sectional study – E. Wakeam – Journal of hospital infection

Human respiratory microbiome

Correlation of the lung microbiota with metabolic profiles in bronchoalveolar lavage fluid in HIV infection – Sushma K. Cribbs – Microbiome

Human gut microbiome

Changes in Colonic Bile Acid Composition following Fecal Microbiota Transplantation Are Sufficient to Control Clostridium difficile Germination and Growth – Alexa R. Weingarden – PLOS ONE

Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn’s Disease – Takahashi K – Digestion

Detecting Microbial Dysbiosis Associated with Pediatric Crohn Disease Despite the High Variability of the Gut Microbiota – Feng Wang – Cell Reports

DNA fingerprinting approaches to trace Escherichia coli sharing between dogs and owners  – Z. Naziri – Journal of Applied Microbiology

Altered intestinal microbiota as a major driving force in alcoholic steatohepatitis – Herbert Tilg – Gut

Impact of Surotomycin on the Gut Microbiota of Healthy Volunteers in a Phase 1 Clinical Trial – Diane M. Citron – Antimicrobial Agents and Chemotherapy

Microbiome animal and bioreactor models

Administration of Non-Absorbable Antibiotics to Pregnant Mice to Perturb the Maternal Gut Microbiota Is Associated with Alterations in Offspring Behavior – Shiro Tochitani – PLOS ONE

Degradation of chondroitin sulfate by the gut microbiota of Chinese individuals –
Qingsen Shang – International Journal of Biological Macromolecules

Streptococcus pneumoniae colonization disrupts the microbial community within the upper respiratory tract of aging mice – Netusha Thevaranjan – Infection and Immunity

Assessing microbial competition in a hydrogen-based membrane biofilm reactor (MBfR) using multidimensional modeling – Kelly J. Martin – Biotechnology and Bioengineering

Animal microbiome

Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs – Pedro R. Frade – PLOS ONE

Plant, root, and soil microbiome

Bacteria increase arid-land soil surface temperature through the production of sunscreens – Estelle Couradeau – Nature Communications

Historical and current climate drive spatial and temporal patterns in fungal endophyte diversity – Hannah Giauque – Fungal Ecology

Location, location, location: priority effects in wood decay communities may vary between sites – Jennifer Hiscox – Environmental Microbiology

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation – Matthew T. Agler – PLOS Biology

Effect of altitude and season on microbial activity, abundance and community structure in Alpine forest soils – José A. Siles – FEMS Microbiology Ecology

Effects of manure and mineral fertilization strategies on soil antibiotic resistance gene levels and microbial community in a paddy–upland rotation system – Hui Lin – Environmental Pollution

Bacterial community compositions in sediment polluted by perfluoroalkyl acids (PFAAs) using Illumina high-throughput sequencing – Yajun Sun – Environmental Science and Pollution Research

Large amounts of easily decomposable carbon stored in subtropical forest subsoil is associated with r-strategy-dominated soil microbes – Yuping Chen – Soil Biology and Biochemistry

Water, waste, and extremophile microbiome

Effects of anthropogenic heavy metal contamination on litter decomposition in streams – A meta-analysis – Verónica Ferreira – Environmental Pollution

Investigation of the microbial community in the Odisha hot spring cluster based on the cultivation independent approach – Archana Singh – Genomics Data

Analysis of bacterial diversity in two oil blocks from two low-permeability reservoirs with high salinities – Meng Xiao – Scientific Reports

Occurrence of mycotoxins and yeasts and moulds identification in corn silages in tropical climate – B.F. Carvalho – Journal of Applied Microbiology

Food microbiology

Molecular diversity of bacteria in commercially available ‘‘Spirulina’’ food supplements – Elisabeth Vardaka – PeerJ

Ineffective hand washing and the contamination of carrots after using a field latrine – J M Monaghan – Letters in Applied Microbiology

Microbiological characterization using combined culture dependent and independent approaches of Casizolu pasta filata cheese – N.P. Mangia – Journal of Applied Microbiology

Microbial dynamics in mixed culture biofilms of bacteria surviving sanitation of conveyor belts in salmon-processing plants – S. Langsrud – Journal of Applied Microbiology

Built environment microbiology

Bacteria in a water-damaged building: associations of actinomycetes and non-tuberculous mycobacteria with respiratory health in occupants – J.-H. Park – Indoor Air

Bioinformatics and metagenomics

Review: Application of multivariate statistical techniques in microbial ecology – O. Paliy – Molecular Ecology

More microbiology

Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus – Kirsten I Bos – eLIFE

Review: Within-host evolution of bacterial pathogens – Xavier Didelot – Nature Reviews Microbiology

This is NOT novel and methods are missing essential steps: A novel method to assess the biodiversity of parasites using 18S rDNA Illumina sequencing; parasitome analysis method – Akina Hino – Parasitology International

Microbes in the news

Found: Desert Hot Spots Just For Microbes – Sarah Laskow – Atlas Obscura

Beards may be more hygienic and bacteria-resistant than shaven skin, study finds – Kate Ng – Independent
Beards may not be that gross, after all – Rachel Thompson – Mashable
Are beards good for your health? – BBC News Magazine

Bacteria or virus? New diagnostic tool could curb antibiotic overuse – Eric Boodman – STAT news

Getting to know the real you – how seriously should we take the health of our internal aliens? – LabNews UK

Probiotics come with bold health claims, but the science is shaky – Megan Scudellari – STAT news

Weekend binges just as bad for the gut as a regular junk food diet, study suggests – Dan Wheelahan – Medical Xpress

Can our gut microbiota contribute to the effect healthy foods have on us? – Gut Microbiota WorldWatch

Science, publishing, and career

Are results in top journals to be trusted? – SK – Economist

The best academic acknowledgements ever – Glen Wright – Times Higher Education
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Microbiome digest, October 24, 2014

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Microbiome of placentas, infant respiratory microbiome, metabolomics, mutipartite genomes, microbes in the news, and some weekend picks.
Human microbiome general

Microbiome/microbiota and allergies – Yuzaburo Inoue, Naoki Shimojo – Seminars in Immunopathology

“In this review, we summarize the recent findings regarding the importance of the microbiome/microbiota in the development of allergic diseases and also the results of interventional studies using probiotics or prebiotics to prevent allergies.”

Pregnancy and birth

Term and preterm labour are associated with distinct microbial community structures in placental membranes which are independent of mode of delivery – Ronan M. Doyle – Placenta

“In this study, 16S rDNA pyrosequencing was used to identify bacteria in placental membranes. Caesarean sections and vaginal deliveries at term were found to harbour common genera”

Early Respiratory Microbiota Composition Determines Bacterial Succession Patterns and Respiratory Health in Children – Giske Biesbroek – Am J Respir Crit Care Med.

“Upper respiratory microbiota profiles of 60 healthy children at the ages of 1.5, 6, 12 and 24 months were characterized by 16S-based pyrosequencing”

From the “old NEC” to the “new NECs” – Melania Puddu – Journal of Pediatric and Neonatal Individualized Medicine

“This review describes in detail the new NECs especially those which affect preterm infants: contagion or lymphocytosis associated, transfusion associated and cow’s milk allergy associated.”

Metagenomics

The effects of variable sample biomass on comparative metagenomics – Meghan Chafee – Environmental Microbiology

“We investigated the interacting effects of DNA input and library amplification by PCR on comparative metagenomic analysis using dilutions of a single complex template from an Arabidopsis-associated microbial community.”

Metabolomics 

The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey – Takashi Narihiro – Environmental Microbiology

“16S pyrotag analysis revealed core populations of known syntrophs (six clades) and methanogens (nine clades) associated with acid degradation, and evidence for substrate- and/or inoculum-dependent specificity in syntrophic partnerships.”

In Vitro Fermentation of Lactulose by Human Gut Bacteria – Bingyong Mao – Journal of Agricultural and Food Chemistry

“This study aimed to identify lactulose-metabolizing bacteria in the human gut, using in-silico and traditional culture methods. “

Epigenomic regulation of host–microbiota interactions – Theresa Alenghat, David Artis – Trends in Immunology

“We review recent advances in understanding the interplay between the microbiota and mammalian epigenomic pathways, and highlight emerging findings that implicate a central role for histone deacetylases (HDACs) in orchestrating host–microbiota interactions.”

More microbiology

Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction – George C. diCenzo – PLOS Genetics

“To gain insight into the role and evolutionary history of these replicons, we have ‘reversed evolution’ by constructing a S. meliloti strain consisting solely of the chromosome and lacking the pSymB chromid and pSymA megaplasmid.”

Microbes in the news

How An Antibiotic Gene Jumped All Over The Tree of Life – Ed Yong – National Geographic

“Metcalf showed that it has also jumped from bacteria into every other major branch of life. It’s in animals, plants, fungi, archaea, and even some viruses.”

Research investigates bacteria on banknotes – Harper Adams University

“This study investigates how easy it is for bacteria and pathogens to survive on currency and whether the material the notes are made of, has an effect on the transfer.”

How millennials will save us all – Jennifer Block – Quartz

“Millennials get a bad rap for loading up on debt, mooching off their parents, and hiding behind technology. But there’s one problem that they may be particularly suited to tackling: our shrinking microbiome.“

Bik’s Picks

World’s Most Asked Questions: How Much Water Should I Drink a Day? – SciShow – Youtube

“People ask Google everything under the sun. One of the most commonly searched questions in the world is “How much water should I drink a day?” SciShow has the answer!”

Ten Simple Rules for Writing a PLOS Ten Simple Rules Article – Harriet Dashnow – PLOS Computational Biology

“This search left us wanting, until we discovered the PLOS Ten Simple Rules collection. We have found them to be a series of concise articles that capture the professional zeitgeist of being a scientist in an approachable manner.”

Satire: Ambitious New High-Speed Rail Plan Will Fly Americans To Japan To Use Their Trains – The Onion

“The transit system that the U.S. has needed for so long is now just a 7,000-mile plane journey to Tokyo’s Narita International Airport and a brief passage through Japanese customs away,” Obama continued.”

Microbiome Digest, October 20, 2014

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Oral core microbiome, symbionts in crabs, sponges, and Drosophila, metabolites in dolphin’s breath, and retraction of a paper favored by Dr. Oz.

Pregnancy and birth

NEC in Twin Pregnancies: Incidence and Outcomes – Sathyaprasad C Burjonrappa, Brian Shea, Diya Goorah – Journal of Neonatal Surgery

“There is a remarkable higher incidence of NEC amongst twins. Abnormal colonization of the gastrointestinal tract appears to be an immediate postpartum event.”

Human oral microbiome

Intraindividual variation in core microbiota in peri-implantitis and periodontitis – Noriko Maruyama – Scientific Reports

“To improve our knowledge of the different communities of complex oral microbiota, we compared the microbial features between peri-implantitis and periodontitis in 20 patients with both diseases. “

Antimicrobial Effect of Lemongrass Oil against Oral Malodor Microorganisms and the Pilot Study of Safety and Efficacy of Lemongrass Mouthrinse on Oral Malodor – Panitta Satthanakul – Journal of Applied Microbiology

“Antimicrobial activity of LG mouthrinse was examined against common odorigenic microorganisms using broth microdilution assay and the disc diffusion method. A randomized double-blind clinical study was performed in 20 healthy volunteers.”

Animal microbiome

Molecular evidence of digestion and absorption of epibiotic bacterial community by deep-sea crab Shinkaia crosnieri – Tomo-o Watsuji – ISME Journal

“A phylogenetic analysis showed that many of the bacterial 16S ribosomal RNA gene sequences obtained from the intestine were closely related to the sequences of the epibionts, thus they were probably derived from the epibionts.”

* In vivo function and comparative genomic analyses of the Drosophila gut microbiota identify candidate symbiosis factors – Peter D. Newell – Frontiers in Microbiology

“We compared microbiota isolates with con-specific or closely related bacterial species isolated from non-fly environments. “

* Two distinct microbial communities revealed in the sponge Cinachyrella – Marie L. Cuvelier – Frontiers in Microbiology

“Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rDNA tag pyrosequencing.”

* Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality – Fan Zhang – FEMS Microbiology Ecology

“PCR cloning and sequencing of archaeal 16S rRNA and amoA genes showed that the archaeal community composition and structure were different from that in seawater and varied among sponge species. “

Plant microbiome

Reduced dependence of rhizosphere microbiome on plant-derived carbon in 32-year long-term inorganic and organic fertilized soils – Chao Ai – Soil Biology and Biochemistry

“Wheat rhizosphere microbiome was studied by stable isotope probing and pyrosequencing.”

Environmental microbiome

Characterization of bacterial communities associated with seasonal water masses from Tongyoung in South Sea of Korea – Sung-Suk Suh – Ocean Science Journal

“In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with two different water masses from Tongyoung in the South Sea of Korea. “

Bacterial community structure of a lab-scale anammox membrane bioreactor – Alejandro Gonzalez-Martinez – Biotechnology Progress

“In this study, next-generation sequencing techniques have been used for the investigation of the bacterial communities of this MBR Anammox for the first time ever. “

Metagenomics & Bioinformatics

GenomePeek: What exactly is that sequencing data? – Katelyn McNair – MicroBEnet

“I wrote the initial version of GenomePeek, and tested it with various data sets using this student’s data. I quickly found that some genes work better than others, and so currently the four genes analyzed are: 16S, recA, rpoB, and groEL.”

Metabolomics

Metabolite Content Profiling of Bottlenose Dolphin Exhaled Breath – Alexander A. Aksenov – Analytical Chemistry

“We have developed a method to reproducibly sample breath from small cetaceans, specifically Atlantic bottlenose dolphins (Tursiops truncatus). “

Proteomics

Symbiosis, Dysbiosis and Rebiosis – the value of metaproteomics in human microbiome monitoring – Lei Mao and Jacqueline Franke – Proteomics

“After a brief review of the history and state-of-the-art of metaproteomics in the field of environmental health research, focus of this perspective article will be put on the role of cross-species joint efforts in symbiosis, dysbiosis and rebiosis of the human gut during human development, pathogenesis and aging.”

More microbiology

Bridging the gap between viable but non-culturable and antibiotic persistent bacteria – Mesrop Ayrapetyan – Trends in Microbiology

“This discussion is intended to stimulate discourse about these seemingly different but very similar dormant states.”

* Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite
Zhang Wang, Martin Wu – PLOS ONE

“Using a phylogenomic approach and leveraging on the increased taxonomic sampling of alphaproteobacterial and eukaryotic genomes, we reconstructed the metabolisms of both proto-mitochondria and pre-mitochondria.”

Real-time video imaging as a new and rapid tool for antibiotic susceptibility testing by the disk diffusion method: a paradigm for evaluating resistance to imipenem and identifying extended-spectrum β-lactamases – Stéphanie Le Page – International Journal of Antimicrobial Agents

“..we present here for the first time video movies of the appearance of the diameter of inhibition by the disk diffusion in real-time. “

Microbes in the news

Can Microbes Help Feed the World? – Amy Mayer – BioScience

“To help meet the challenge for food, scientists are using new technologies to better understand the role that soil microbes might play in bolstering agricultural production. “

Dentists Want To See Studies On Pot-Cavity Link – CBS Local

“Patients are experiencing tooth decay, expensive dentist bills and the pain of dealing with it all. The biggest side effect is dry mouth.”

Bik’s Picks

Brain surgery, by robot, through the cheek – Science Daily

“Engineers have developed a surgical robot designed to perform brain surgery by entering through the cheek instead of the skull that can operate on a patient in an MRI scanner. Additionally, the engineers have designed the system so that much of it can be made using 3-D printing in order to keep the price low.”

* Hilarious cartoons on Imgur: Real Scientists vs. Movie Scientists 

* Authors retract green coffee bean diet paper touted by Dr. Oz – Ivan Oransky – Retraction Watch

“Two authors of a 2012 paper sponsored by a company that made grand claims about green coffee bean extract’s abilities to help people lose weight have retracted it. The study was cited by The Dr. Oz Show, and last month it cost the company a $3.5 million settlement with the Feds.”

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Human microbiome digest, October 7, 2014

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Treating toxic arsenic levels with yoghurt, colonization patterns in low birthweight infants, evil alliances in breastmilk, and smoking and oral microbiome.

Human microbiome general

Opinion: Conservation and stewardship of the human microbiome – Kieran C. O’Doherty – PNAS USA

“Just as humans have impacted many large animal species in the environment, drastic changes in human lifestyle over the past century may have altered the global pool of human-associated microbes; if so, these shifts may pose substantial threats to individual and public health.”

Friends with Social Benefits: Host-Microbe Interactions as a Driver of Brain Evolution and Development? – Roman M. Stilling – Frontiers in Cellular and Infection Microbiology

“Here in this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. “

Pregnancy and birth

Intestinal Colonization Among Very Low Birth Weight Infants in First Week of Life (PDF) – Sourabh Dutta – Indian Pediatrics

“Very low birth weight infants admitted in neonatal intensive care units have abnormal intestinal colonization patterns”

Is a fetus developing in a sterile environment? – Trudy M. Wassenaar and Pinaki Panigrahi – Letters in Applied Microbiology

Probiotics and Necrotizing Enterocolitis – Josef Neu – Clinics in Perinatology (paywalled even at Stanford)

Potential involvement of Campylobacter curvus and Haemophilus parainfluenzae in preterm birth – George Louis Mendz – BMJ Case Reports

“A woman presented with prelabour premature preterm rupture of membranes and delivered extremely preterm at 26 weeks by caesarean section.”

Network analysis reveals a potentially ‘evil’ alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities – Zhanshan Ma – arXiv

“..we reconstructed a milk bacterial community network with the data from Hunt et al (2011), which is the largest 16S-rRNA sequence data set of human milk microbiome available to date.”

Randomized Open-Label Pilot Study of the Influence of Probiotics and the Gut Microbiome on Toxic Metal Levels in Tanzanian Pregnant Women and School Children – Jordan E. Bisanz – mBio

“Consumption of probiotic yogurt had a protective effect against further increases in mercury (3.2 nmol/liter; P = 0.035) and arsenic (2.3 nmol/liter; P = 0.011) blood levels in the pregnant women, but this trend was not statistically significant in the children.”

Human oral microbiome

* Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms – Andrew Maltez Thomas – BMC Microbiology

“DNA was extracted from swabs and the V1 region of the 16S rRNA gene was PCR amplified and sequenced using the Ion Torrent PGM platform, generating 3.7 million high quality reads. “

* Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients – Ji-Hoi Moon – Molecular Oral Microbiology

“Here, we investigated the composition of subgingival bacterial communities from the pooled plaque samples of smokers and non-smokers, 134 samples each group, in Korean moderate chronic periodontitis patients using 16S rRNA gene-based pyrosequencing.”

Human respiratory microbiome

Sinus culture poorly predicts resident microbiota – Leah J. Hauser – International Forum of Allergy & Rhinology

“The association between 16S relative abundance and detection by culture was determined using logistic regression.”

Localization of Burkholderia cepacia Complex Bacteria in Cystic Fibrosis Lungs and Interactions with Pseudomonas aeruginosa in Hypoxic Mucus – Ute Schwab – Infection and Immunity

“We performed immunohistochemistry for Bcc and P. aeruginosa bacteria on 21 coinfected or singly infected CF lungs obtained at transplantation or autopsy. “

Human gut microbiome

* Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity – Sophie Leclercq – PNAS USA

“In this study, we showed that alcohol-dependent subjects with altered intestinal permeability had also altered gut-microbiota composition and activity and remained with high scores of depression, anxiety, and alcohol craving after a short-term detoxification program.”

Structural modulation of gut microbiota during alleviation of type 2 diabetes with a Chinese herbal formula – Jia Xu – ISME Journal

“Pyrosequencing of the V3 regions of 16S rRNA genes revealed a dose-dependent deviation of gut microbiota in response to GQD treatment.”

Modelling the emergent dynamics and major metabolites of the human colonic microbiota – Helen Kettle – Environmental Microbiology

“To reduce the complexity of the system, we divide the bacterial community into 10 bacterial functional groups (BFGs) each distinguished by its substrate preferences, metabolic pathways and its preferred pH range. “

Animal models of microbiome research

Transcriptome analysis of Escherichia coli O157:H7 grown in vitro in the sterile-filtrated cecal content of human gut microbiota associated rats reveals an adaptive expression of metabolic and virulence genes – Guillaume Le Bihan – Microbes and Infection

“A transcriptomic analysis was performed on the EHEC strain EDL933 incubated in vitro in the sterile-filtrated cecal content of human microbiota-associated rats (HMC) compared with EDL933 incubated in the sterile-filtrated cecal content of germ-free rat (GFC).”

Early Innate Immunity to Bacterial Infection in the Lung Is Regulated Systemically by the Commensal Microbiota via Nod-Like Receptor Ligands – Thomas B. Clarke – Infection and Immunity

“Microbiota depletion caused significant defects in the early innate response to lung infection by the major human pathogen Klebsiella pneumoniae.”

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Human microbiome digest, October 6, 2014

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Preterm birth, multiple sclerosis, aging, and Clostridium difficile infection in animal models.

Pregnancy and Birth

Necrotizing Enterocolitis: A Clinical Review on Diagnostic Biomarkers and the Role of the Intestinal Microbiota – Niemarkt, Hendrik J. – Inflammatory Bowel Diseases

“In this review, we discuss the pathogenesis, diagnosis, and treatment of NEC with a focus on the role of microbiota in the development of NEC.”

* Intestinal microbiota of preterm infants differ over time and between hospitals – Diana H Taft – Microbiome Journal

“DNA extracted from stool was used to sequence the 16S rRNA gene by Illumina MiSeq using universal primers. “

Babies’ Gut Bacteria Are Mostly Fixed By Time Spent In The Womb – Nicholas Ellaby – Science 2.0

“Now, a new study published in the journal Proceedings of the National Academy of Sciences has added a critical piece to the puzzle. “

Human Gut Microbiome

Gut microbiome and the risk factors in central nervous system autoimmunity – Javier Ochoa-Repárazemail, Lloyd H. Kasper – FEBS Letters

“Of interest to this review is the consistency between this range of MS risk factors and the gut microbiome. We postulate that the gut microbiome serves as the niche where different MS risk factors merge, thereby influencing the disease process.”

Compositional dynamics of the human intestinal microbiota with aging: Implications for health – B. Lakshminarayanan – The Journal of Nutrition, Health & Aging

“This review summarizes the age-related changes in the microbiota of the gastrointestinal tract (GIT) and the link between the gut microbiota in health and disease. “

Animal models of microbiome research

A Beneficial Effect of Oral Tigecycline Treatment on Clostridium difficile Infection in Gnotobiotic Piglets – Hyeun Bum Kim – Antimicrobial Agents and Chemotherapy

“The efficacy of oral tigecycline treatment (2mg/kg for 7 days) on Clostridium difficile infection (CDI) was evaluated in the gnotobiotic pig model, and its effect on human gut microflora transplanted into the gnotobiotic pig was determined. “

A novel multi-strain probiotic and synbiotic supplement for prevention of Clostridium difficile infection in a murine model – Kanthi Kiran Kondepudi – Microbiology and Immunology

“Feces and cecal contents were collected for microbial cell viability, quantitative PCR (qPCR), toxin analyses and histopathology.“

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Microbiome digest, September 19, 2014

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An update from the Cochrane Review Journal on probiotics to prevent necrotizing enterocolitis, oral microbiome in apical periodontitis or polycystic ovary syndrome, vaginal and gut microbiome, and bacteria in shrimp, soil, and water.
Pregnancy and birth

Probiotics for prevention of necrotizing enterocolitis in preterm infants – Khalid AlFaleh, and Jasim Anabrees – Evidence-Based Child Health: A Cochrane Review Journal

“For this update, searches were made of MEDLINE (1966 to October 2013), EMBASE (1980 to October 2013), the Cochrane Central Register of Controlled Trials (CENTRAL) in The Cochrane Library (2013, Issue 10), and abstracts of annual meetings of the Society for Pediatric Research (1995 to 2013).”

Anne Geddes Unveils New Image Of A Baby Born Too Soon – March of Dimes

“Mrs. Geddes donated the image of Alfred, who was born 8 weeks too soon, weighing just two pounds, six ounces, to the March of Dimes, which made the photo the center of its 2014 World Prematurity Day campaign.”

Human oral microbiome

Highly Diverse Microbiota in Dental Root Canals in Cases of Apical Periodontitis (Data of Illumina Sequencing) – Veiko Vengerfeldt – Journal of Endodontics

“Samples were collected under strict aseptic conditions from 12 teeth … and characterized by profiling the microbial community on the basis of the V6 hypervariable region of the 16S ribosomal RNA gene by using Illumina HiSeq2000 sequencing combinatorial sequence-tagged polymerase chain reaction products.”

Association between Polycystic Ovary Syndrome, Oral Microbiota and Systemic Antibody Responses – Aliye Akcalı – PLOS ONE

“Salivary levels of seven putative periodontal pathogens were analyzed by quantitative real-time polymerase chain reaction and serum antibody levels were analyzed by ELISA. “

Human genital microbiome

The Changing Landscape of the Vaginal Microbiome – Bernice Huang – Clinics in Laboratory Medicine

“The vaginal microbiome is a dynamic ecosystem in which the microbiota play a major role in regulating parameters such as pH and in limiting the growth of potentially harmful organisms”

Human gut microbiome

Review: Diet, gut microbes, and genetics in immune function: can we leverage our current knowledge to achieve better outcomes in inflammatory bowel diseases? – Vanessa A Leone – Current Opinion in Immunology

“This review summarizes our current understanding of dietary-induced changes in gut microbiota on autoimmunity in the context of IBD.”

The evolving role of the gut microbiome in human disease – Lloyd H. Kasper – FEBS Letters

“We are delighted to introduce this Special Issue, which summarizes the current understanding of the complex relationship between the gut microbiome and the host.”

Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment – Michael B Burns – bioRxiv Preprints

“We characterized the microbiome in 44 primary tumor and 44 patient-matched normal colon tissues. We find that tumors harbor distinct microbial communities compared to nearby healthy tissue.”

Gut Microbiota: A Natural Adjuvant for Vaccination – Oliver Pabst, Mathias Hornef – Immunity

“In this issue of Immunity, Oh et al. (2014) reveal an unappreciated facet of how the microbiota influences immune responses. Immunity to nonadjuvanted vaccines depends on Toll-like-receptor-5-mediated sensing of the microbiota.”

Animal and bioreactor models

TLR5-Mediated Sensing of Gut Microbiota Is Necessary for Antibody Responses to Seasonal Influenza Vaccination – Jason Z. Oh – Immunity

“Vaccination of Trl5−/− mice resulted in reduced antibody titers and lower frequencies of plasma cells, demonstrating a role for TLR5 in immunity to TIV. This was due to a failure to sense host microbiota. “

In vivo degradation of alginate in the presence and in the absence of resistant starch – Melliana Jonathan – Food Chemistry

“This study evaluated the intestinal degradability of alginate during 74 days intake in pigs as models for humans. “

Effect of prebiotics on the fecal microbiota of elderly volunteers after dietary supplementation of Bacillus coagulans GBI-30, 6086 – Edna P. Nyangale – Anaerobe

“Single stage batch culture anaerobic fermenters were used and inoculated with fecal microbiota obtained from volunteers after taking a 28 day treatment of Bacillus coagulans GBI-30, 6086 (GanedenBC30 (BC30)) or a placebo.”

Intestinal anastomotic injury alters spatially defined microbiome composition and function – Benjamin D Shogan – Microbiome journal

“Using 16S rRNA amplicon sequencing of samples collected on the day of surgery … and the 6th day following surgery …, we analyzed the changes in luminal versus tissue-associated microbiota at anastomotic sites created in the colon of rats.”

General human microbiome

Microbiome in Human Immunodeficiency Virus Infection – January T. Salas, Theresa L. Chang – Clinics in Laboratory Medicine

“Individuals infected with the human immunodeficiency virus (HIV) have altered microbiome associated with immune activation that impacts the consquence of disease progression”

Shrimp microbiome

Characterization of the intestinal microbiota in Pacific white shrimp, Litopenaeus vannamei, fed diets with different lipid sources – Meiling Zhang – Aquaculture

“an Illumina-based sequencing method was used to examine the intestinal bacterial composition of L. vannamei following six diets with different lipid sources.”

Soil microbiome

Pyrosequencing reveals the effect of mobilizing agents and lignocellulosic substrate amendment on microbial community composition in a real industrial PAH-polluted soil –
S. Lladó – Journal of Hazardous Materials

“Soil microbial community assessment through classical (MPN) and molecular tools (DGGE and pyrosequencing) is provided”

Water microbiome

High-throughput sequencing reveals neustonic and planktonic microbial eukaryote diversity in coastal waters – Joe D. Taylor and Michael Cunliffe – Journal of Phycology

“Here, we use high-throughput 18S rRNA gene sequencing to characterize protist and fungal diversity in the SML at a coastal time-series station and compare with underlying plankton assemblages. “

Microbes in the news

Sex in the Sink: Gene-Swapping Bacteria Are Making New Superbugs – Maggie Fox – NBC News

“Over the past decade, there has been a steady and alarming increase in antibiotic-resistant bacteria, a trend that poses a serious threat to the U.S. medical system,” Segre and colleagues wrote in their report.

Science, publishing, and career

To Get More Out of Science, Show the Rejected Research – Brendan Nyhan – New York Times

“In a new white paper, I propose that the American Political Science Association offer options for articles in a Registered Reports-style format. “

Pushing Women and People of Color Out of Science Before We Go In – Jennifer Selvidge – Huffington Post

“The misogyny and racism I experienced and saw at MIT became more and more concerning, between professors making “get back in the kitchen jokes” and hearing about what seemed to be legions of male PhD student sexually harassing woman undergraduates.”

Bik’s Picks

I want one! These adorable giant African rats detect land mines and TB for a living – Bec Crew – Scientific American

“So yesterday, I adopted an unborn land-mine-detecting African giant pouched rat (Cricetomys gambianus) from Tanzania. “

No sedative necessary: Scientists discover new ‘sleep node’ in the brain – Science Daily

“A sleep-promoting circuit located deep in the primitive brainstem has revealed how we fall into deep sleep. “

Experts: Science Class Can Dazzle With Less Danger – Dan Elliott – ABC News

“On Sept. 3, 13 people, mostly children, were burned by a methanol-fueled flash fire during a science demonstration at the Terry Lee Wells Nevada Discovery Museum in Reno.”

(Satire) Bono Showcases New Genome Sequencers, The i-LUMINA 6 and i-LUMINA 6 plus – the Allium

“Lead singer with the rock band U2, Bono, revealed the latest in genome sequencing technology at a gala event in the Moscone Center in San Francisco, yesterday.”

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Human microbiome digest, September 15, 2014

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MicrobiomeDigest is back! Lots of new papers came out in my 2-week hiatus, so here we go (more tomorrow):

General (Human) Microbiota

Editorial for Special Issue: Insights into Molecular Mechanisms of Microbiota – Eric C. Martens, Justin L. Sonnenburg, David A. Relman – Journal of Molecular Biology

“Understanding the molecular mechanisms that underlie these processes has been a goal for decades, but while recent technological advances have greatly expanded our descriptive view of these ecosystems, our knowledge of underlying functions and mechanisms has lagged. “

A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics – Mohamed S. Donia – Cell

“we identified 3,118 small-molecule biosynthetic gene clusters (BGCs) in genomes of human-associated bacteria and studied their representation in 752 metagenomic samples from the NIH Human Microbiome Project.”

See also:

Mining for Antibiotics, Right Under Our Noses – Carl Zimmer – New York Times

The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease – iHMP Consortium – Cell Host & Microbe

“Here we describe the three models of microbiome-associated human conditions, on the dynamics of preterm birth, inflammatory bowel disease, and type 2 diabetes”

Microbiome in pregnancy and birth
Review: Diet and host–microbial crosstalk in postnatal intestinal immune homeostasis – Nitya Jain & W. Allan Walker – Nature Reviews Gastroenterology & Hepatology

“In this Review, we discuss the current state of knowledge regarding early-life nutrition, its effects on the microbiota and the consequences of diet-induced perturbation of the structure of the microbial community on mucosal immunity and disease susceptibility.”

The early use of appropriate prophylactic antibiotics in susceptible women for the prevention of preterm birth of infectious etiology – Jan Stener Joergensen – Expert Opinion on Pharmacotherapy

“a focused systematic review/meta-analysis, which targeted the use of clindamycin before 22 weeks gestation, in women with objective evidence of abnormal genital tract flora, demonstrated that clindamycin produced a significant decrease in late miscarriage and preterm birth.”

Mucosa-Associated Bacterial Diversity in Necrotizing Enterocolitis – Rachel Brower-Sinning – PLOS ONE

“26 intestinal samples were resected from 19 infants, including 16 NEC samples and 10 non-NEC samples. Bacterial 16S rRNA gene sequences were amplified and sequenced. “

Oral human microbiome

The presence of cariogenic and periodontal pathogens in the oral cavity of one-year-old
infants delivered pre-term with very low birthweights: a case control study – Vlasta Merglova – BMC Oral Health

“At 12 months of age, both groups of infants were examined, and unstimulated saliva samples from the dorsum of the tongue and dental plaque samples were collected.”

Frequent detection of Streptococcus tigurinus in the human oral microbial flora by a specific 16S rRNA gene real-time TaqMan PCR – Andrea Zbinden – BMC Microbiology

“Although S. tigurinus was a frequently detected species of the human oral microbial flora, it was not associated with periodontal disease. “

Oral Microbiome Link to Neurodegeneration in Glaucoma – Konstantin Astafurov – PLOS ONE

“Mouthwash specimens from patients with glaucoma and control subjects were analyzed for the amount of bacteria”

Bacterial community composition of chronic periodontitis and novel oral sampling sites for detecting disease indicators  – Vaia Galimanas – Microbiome

“Using SubG, SupG, and tongue plaque DNA from 11 healthy and 13 diseased subjects, we sequenced V3 regions (approximately 200 bases) of the 16S rRNA gene using Illumina sequencing.”

Human gut microbiome

TLR5-Mediated Sensing of Gut Microbiota Is Necessary for Antibody Responses to Seasonal Influenza Vaccination – Jason Z. Oh – Immunity

“TLR5-mediated sensing of the microbiota also impacted antibody responses to the inactivated polio vaccine, but not to adjuvanted vaccines or the live-attenuated yellow fever vaccine.”

Review: Nutritional iron turned inside out: intestinal stress from a gut microbial
perspective – Guus A.M. Kortman – FEMS Microbiology Reviews

“This review covers the multifaceted aspects of nutritional iron stress with respect to growth, composition, metabolism and pathogenicity of the gut microbiota in relation to human health.”

Review: Host–microbe interactions shaping the gastrointestinal environment – Gerard E. Kaiko, Thaddeus S. Stappenbeck – Trends in Immunology

“Here we review emerging concepts of how microbial metabolic processes control commensal composition, invading pathogens, immune activation, and intestinal barrier function. “

The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota – Pauline D. Scanlan – FEMS Microbiology Ecology

“Here, we survey the prevalence, genetic diversity and temporal stability of Blastocystis in a group of healthy adults (n = 105) using a sensitive PCR assay.”

Evaluation of bifidobacterial community composition in the human gut by means of a targeted amplicon sequencing (ITS) protocol – Christian Milani – FEMS Microbiology Ecology

“Here, we define the internal transcribed spacer (ITS) sequences of all currently known Bifidobacterium taxa, providing a Bifidobacterium-specific primer pair that targets a hypervariable region within the ITS suitable for precise taxonomic identification of all 48 so far recognized members of the Bifidobacterium genus.”

Alzheimer’s disease and the microbiome – James M. Hill – Alzheimer’s & Dementia

“In these preliminary studies we evaluated the effects of the anti-amyloid, anti-oxidant, anti-inflammatory flavonoid quercetin on growth inhibition of the HM-representative Bacteroides galacturonicus (ATCC 43244).”

Complete Suppression of the Gut Microbiome Prevents Acute Graft-Versus-Host Disease following Allogeneic Bone Marrow Transplantation  – Jaak M. Vossen – PLOS ONE

“All patients received T-cell replete marrow from human leukocyte antigens (HLA) matched sibling donors under identical transplantation conditions.”

Associations of the Fecal Microbiome With Urinary Estrogens and Estrogen Metabolites in Postmenopausal Women – Barbara J. Fuhrman – Journal of Clinical Endocrinology & Metabolism

“Our data suggest that women with a more diverse gut microbiome exhibit an elevated urinary ratio of hydroxylated estrogen metabolites to parent estrogen. “

Alterations of the human gut microbiome in liver cirrhosis – Nan Qin – Nature

“Here we characterize the gut microbiome in liver cirrhosis by comparing 98 patients and 83 healthy control individuals. “

Altered intestinal microbiota and blood T cell phenotype are shared by patients with Crohn’s disease and their unaffected siblings – Charlotte R Hedin – Gut

“Faecal microbiology was analysed by quantitative PCR targeting 16S ribosomal RNA, FC by ELISA, blood T cell phenotype by flow cytometry and IP by differential lactulose-rhamnose absorption in 22 patients with inactive CD, 21 of their healthy siblings and 25 controls.”

Detection of bacterial DNA in lymph nodes of Crohn’s disease patients using high throughput sequencing – Claire L O’Brien – Gut

“Universal primers targeting V1–V3 regions of bacterial 16S rRNA genes were used to amplify bacterial DNA and amplicons sequenced using high throughput sequencing. “

Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria – Elizabeth A. Rettedal – Nature Communications

“Here, we show that carefully designed conditions enable cultivation of a representative proportion of human gut bacteria, enabling rapid multiplex phenotypic profiling. “

Animal models of human microbiome research

Innate lymphoid cells regulate intestinal epithelial cell glycosylation – Yoshiyuki Goto – Science

“Here, we show that type 3 innate lymphoid cells (ILC3) induced intestinal epithelial Fut2 expression and fucosylation in mice. “

Effect of Metformin on Metabolic Improvement and Gut Microbiota – Heetae Lee and GwangPyo Ko – Applied and Environmental Microbiology

“In this study, the composition of the gut microbiota was investigated using a mouse model of high-fat-diet (HFD)-induced obesity with and without metformin treatment. “

Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape – J. Gray Camp – Genome Research

“We profiled transcriptome and accessible chromatin landscapes in intestinal epithelial cells (IECs) from mice reared in the presence or absence of microbiota.”

Host adaptive immunity alters gut microbiota – Husen Zhang – ISME Journal

“Here we investigated the role of adaptive immunity on the mouse distal gut microbial composition by sequencing 16 S rRNA genes from microbiota of immunodeficient Rag1−/− mice, versus wild-type mice, under the same housing environment.”

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