Category Archives: Human oral

Microbiome digest, October 21, 2014

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Human oral microbiome

Abstract 4834: Microbiome in Oral Epithelial Dysplasia and Squamous Cell Carcinoma
Deepak Saxena – Cancer Research

“PCR amplicons targeting V3-V5 region of 16S rRNA gene were sequenced by 454 pyrosequencing. “

Human respiratory microbiome

Microbial Communities in the Upper Respiratory Tract of Patients with Asthma and Chronic Obstructive Pulmonary Disease – HeeKuk Park – PLOS ONE

“To account for the qualitative and quantitative diversity of the 16S rRNA gene in the oropharynx, the microbiomes of 18 asthma patients, 17 COPD patients, and 12 normal individuals were assessed using a high-throughput next-generation sequencing analysis.”

Human gut microbiome

Decreased bacterial diversity characterizes an altered gut microbiota in psoriatic arthritis and resembles dysbiosis of inflammatory bowel disease – Jose U. Scher – Arthritis & Rheumatology

“High-throughput 16S rRNA pyrosequencing was utilized to compare community composition of gut microbiota in PsA patients, subjects with psoriasis of the skin and healthy, matched-controls. “

Pregnancy and birth

The Salivary Scavenger and Agglutinin in Early Life: Diverse Roles in Amniotic Fluid and in the Infant Intestine – Martin Parnov Reichhardt – Journal of Immunology

“The present study revealed that SALSA was present in the amniotic fluid (AF) and exceptionally enriched in both meconium and feces of infants. “

Animal microbiome

* Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts – Kevin D. Kohl – FEMS Microbiology Ecology

“We used 16S rRNA sequencing to document changes in colonic and cecal microbiomes of animals representing five classes of vertebrates at four time points through prolonged fasting: tilapia, toads, geckos, quail, and mice. “

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (HMA, LMA) and seawater – Kristina Bayer – FEMS Microbiology Ecology

“By use of GeoChip, altogether 20,273 probes encoding for 627 functional genes and representing 16 gene categories were identified”

Natural volcanic CO2 seeps reveal future trajectories for host–microbial associations in corals and sponges – Kathleen M Morrow – ISME Journal

“The corals Acropora millepora and Porites cylindrica were less abundant and hosted significantly different microbial communities at the CO2 seep than at nearby control sites <500 m away.”
Plant microbiome

Phylogenetic conservatism in plant-soil feedback and its implications for plant abundance – Brian L. Anacke – Ecology Letters

“We conclude that soil biota influence the abundance of close plant relatives in nature.”

Bioreactor microbiome

Influence of Acidic pH on Hydrogen and Acetate Production by an Electrosynthetic Microbiome – Edward V. LaBelle – PLOS ONE

“Production of hydrogen and organic compounds by an electrosynthetic microbiome using electrodes and carbon dioxide as sole electron donor and carbon source, respectively, was examined after exposure to acidic pH (~5). “

Metagenomics / Transcriptomics / Bioinformatics

Census-based rapid and accurate metagenome taxonomic profiling – Amirhossein Shamsaddini – BMC Genomics

“We have developed a robust subsampling-based algorithm implemented in a tool called CensuScope meant to take a ‘sneak peak’ into the population distribution and estimate taxonomic composition as if a census was taken of the metagenomic landscape. “

Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation – Andrew Toseland – BMC Genomics

“To investigate the effect of such techniques on the annotation of metatranscriptome data we assess two commonly employed methods: clustering and de-novo assembly. To do this, we also developed an approach to simulate 454 and Illumina metatranscriptome data sets with varying degrees of taxonomic diversity. “

Microbial Ecology

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review – Hyun-Seob Song – Processes

“In this article, we provide an overview of mathematical tools that include not only current mainstream approaches, but also less traditional approaches that, in our opinion, can be potentially useful. “

A phylogenetic perspective on species diversity, β-diversity, and biogeography for the microbial world – Albert Barberán† and Emilio O. Casamayor – Molecular Ecology

“We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high altitude lakes district dataset to describe phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition.”

Distance-Decay and Taxa-Area Relationships for Bacteria, Archaea and Methanogenic Archaea in a Tropical Lake Sediment – Davi Pedroni Barreto – PLOS ONE

“The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA.”

More microbiology

From Denise Monack’s lab: Role of disease-associated tolerance in infectious superspreaders – Smita Gopinath – PNAS USA

“Using a mouse model of Salmonella infection, we show that levels of Salmonella are equivalent between antibiotic-treated superspreader and nonsuperspreader hosts; however, superspreader hosts are uniquely able to tolerate antibiotic treatment, unlike nonsuperspreader hosts. “

*Also see:  Antibiotics may help Salmonella spread in infected animals, scientists learn – Stanford Medicine News

Spatial organization of bacterial chromosomes – Xindan Wang, David Z Rudner – Current Opinion in Microbiology

“Here, we summarize these different patterns highlighting similarities and differences and discuss the protein factors that help establish and maintain them.”

Bacterial healers: Microbes can redeem themselves to fight disease – Susan Gaidos – Science News

“It’s just a matter of time before bacterial-based treatments become a routine part of a doctor’s toolkit, says microbiologist Robert Britton of the Baylor College of Medicine in Houston, who is studying the relationship between microbes and human health. “

Techniques

Rapid fingerprinting of methanogenic communities by high-resolution melting analysis – Jaai Kim, Changsoo Lee – Bioresource Technology

“The new method produced robust community clustering and ordination results comparable to the results from the commonly used denaturing gradient gel electrophoresis (DGGE) performed in parallel.”

Microbes in the news

Our unique ‘microbial aura’ travels with us wherever we go – Science Friday – PRI

“Unless you lived exactly the same life as me, you would not have the same microbiome. You are, in essence, microbially unique,” explains Jack Gilbert

We’re making a Microbiome Documentary Series and could use your Help – Jamie – Reddit

“My name’s Jamie and I’m part of a team trying to crowdfund a documentary series on the human microbiome titled: ‘Redefining Human’.”

Building houses with bacteria – Euronews

“Houses of the future could be partially built with bacteria. It sounds like science fiction but researchers involved in an EU-backed project in Madrid are working towards making this a concrete reality.”

Bik’s Picks

The Role of Surface Chemistry in Adhesion and Wetting of Gecko Toe Pads – Ila Badge – Scientific Reports

“As expected, under wet conditions, adhesion on a hydrophilic surface (glass) was lower than that on a hydrophobic surface (alkyl-silane monolayer on glass).”

Scientists prepare for an 8-month mission to Mars – on Earth soil- BetaWired

“There’s a new experiment commencing in Hawaii, and the results will help NASA better prepare its astronauts for a lengthy mission to Mars.”

White rhino subspecies is down to one breeding male – Andrea James – BoingBoing

“Sad news from Kenya: the northern white rhino subspecies is down to one breeding male with the death of Suni this month. Only six remain.”

Scientists restore hearing in noise-deafened mice, pointing way to new therapies – ScienceDirect

“Scientists have restored the hearing of mice partly deafened by noise, using advanced tools to boost the production of a key protein in their ears.”

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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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Microbiome digest, October 17, 2014

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Resistance one year after antibiotic treatment, skin microbiome in atopic dermatitis, bacterial 16S rRNA load in the lungs, the rat oral microbiome, and microbes in cheese. And an exciting new discovery by Stanford scientists. Have a great weekend!

 

Multiple site human microbiome

Development of antimicrobial resistance in the normal anaerobic microbiota during one year after administration of clindamycin or ciprofloxacin – Mamun-Ur Rashid – Anaerobe

“Clindamycin or ciprofloxacin or placebo was given for 10 days in three groups. Skin, nasal, saliva, faeces sampling at day -1 and 11, 1, 2, 4 and 12 months.“

Shared microbiome in gums and the lung in an outpatient population – Patrick R. Schmidlin – Journal of Infection

“PCR to determine four periopathogens and seven less pathogenic species in both the periodontal pocket and bronchial protected specimen brush was used. “

Human skin microbiome

* Review: Role of the skin microbiome in atopic dermatitis – Alexander Salava and Antti Lauerma – Clinical and Translational Allergy

“Molecular genetics have dramatically changed our vision of the micro-organisms colonizing the human skin and recently well-documented changes in the skin microbiome in atopic dermatitis have become evident.”

Human respiratory microbiome

* The effect of long-term macrolide treatment on respiratory microbiota composition in non-cystic fibrosis bronchiectasis: an analysis from the randomised, double-blind, placebo-controlled BLESS trial – Geraint B Rogers – The Lancet Respiratory Medicine

“Microbiota composition was determined by 16S rRNA gene sequencing of sputum samples from participants in the BLESS trial”

A Comparison between Droplet Digital and Quantitative PCR in the Analysis of Bacterial 16S Load in Lung Tissue Samples from Control and COPD GOLD 2 – Marc A. Sze – PLOS ONE

“qPCR and ddPCR were performed on these samples using primers spanning the V2 region on the 16S rRNA gene along with negative controls. Total 16S counts were compared between the two methods.”

Human gut microbiome

* With pictures! Fecal microbiota transplantation: A ‘How-To’ guide for nurses – Sharyn Leis – Collegian

“However, to date, much of the literature addresses the procedure from a physician’s point of view, and can therefore be lacking in practical detail. As nurses are often the ‘unsung heroes’ of the procedure, it is timely to address the subject from a nursing perspective.”

The Intestinal Microbiota and Microenvironment in Liver – Hong-Di Ma- Autoimmunity Reviews

“But the interplay between the intestinal tract and the liver may explain the increased association with autoimmune liver diseases and inflammatory bowel diseases. “

Alterations of gut barrier and gut microbiota in food restriction, food deprivation and protein-energy wasting – L. Genton – Clinical Nutrition

“This review… highlights the complex interactions between the components of gut barrier in depleted states due to food deprivation, food restriction and protein energy wasting and shows that these interactions are multidirectional”

Application of next-generation sequencing to study ascitic microbiome in cirrhotic patients with or without spontaneous bacterial peritonitis – Ye Feng- Journal of Microbiology, Immunology and Infection

“Both the 16S polymerase chain reaction approach and the whole genome shotgun approach were adopted for the next-generation sequencing technology. “

Chronic ethanol consumption alters intestinal microbiota impairing immune function – T. Barr – Alcohol

The gastrointestinal microbiome – functional interference between stomach and intestine – Loris R. Lopetuso – Best Practice & Research Clinical Gastroenterology

“This review focuses and speculates on the possible interactions between gastric microorganisms and intestinal microbiota and on the consequences of this interplay in modulating gut health.”

Animal models of microbiome research

Can Pre-Weaning Modulation of Intestinal Microbiota by Oligosaccharides or Amoxicillin Program Adult One in Rats? – Fanny B. Morel – Nutrition

“As revealed by a targeted qPCR approach, programming of adult intestinal microbiota seems to vary according to the nature of the pre-weaning microbiotal modulator.”

Animal microbiome

* Characterization of the rat oral microbiome and the effects of dietary nitrate – Embriette R. Hyde – Free Radical Biology and Medicine

“Demonstrates the utility of using metagenomics techniques to characterize the healthy rat tongue microbiome and to compare it to the healthy human tongue microbiome.”

Soil microbiome

High-Level Diversity of Tailed Phages, Eukaryote-Associated Viruses, and Virophage-Like Elements in the Metaviromes of Antarctic Soils – Olivier Zablocki – Applied and Environmental Microbiology

“The metaviromes of two distinct Antarctic hyperarid desert soil communities have been characterized.”

Food microbiology

Microbial communities involved in Kashar cheese ripening – Oğuz Aydemir – Food Microbiology

“The molecular classification and identification of 594 LAB isolates during Kashar cheese ripening were performed through (GTG)5–PCR fingerprinting of their genomic DNA followed by verification of the (GTG)5–PCR clusters obtained after numerical analysis through 16S rRNA gene sequencing of representative isolates. “

Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food)
Cristina Riquelme – International Journal of Food Microbiology

“Pyrosequencing of tagged amplicons of the V3–V4 regions of the 16S rDNA and Operational Taxonomic Unit-based (OTU-based) analysis were applied to obtain an overall idea of the microbiota in Pico cheese and to elucidate possible differences between cheese-makers (A, B and C) and maturation times.”

Metagenomics/Bioinformatics

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models – Matthew N. Benedict – PLOS Computational Biology

“Here we develop an approach for applying genomic information to predict alternative functions for genes and estimate their likelihoods from sequence homology. “

Microbes in the news

‘Critical Conversation’ to focus on human microbiome – Sue Wuetcher – UB Reporter, University at Buffalo

“David Relman, the Thomas C. and Joan M. Merigan Professor and professor of microbiology and immunology at the Stanford University School of Medicine, will speak on “Your Inner Self: The Human Microbiome in Health and Disease””

 

Bik’s Weekend Picks

Want to Ace That Test? Get the Right Kind of Sleep – Benedict Carey – New York Times

“Scientists now argue that a primary purpose of sleep is learning consolidation, separating the signal from the noise and flagging what is most valuable.”

‘Human face of science’: Researchers dance to raise funds for cancer study – RT.com

“Biomedicine scientists in Barcelona have released a music clip aimed at raising funds for medical research, as well as promoting their profession’s “human face.” The video’s release comes amid low levels of public interest in science throughout Spain.”

In science, popularity breeds unreliability – Tom Siegfried – Science News

“In recent decades, pressure to publish and seek publicity has distorted the scientific enterprise. Scientists need grants. Getting published raises the likelihood of getting those grants. “

Satire: Scientists Discover Two New Kinds Of Bird Poop – The Allium

“Scientists at Stanford University have revealed that they have discovered two new species of bird poop that defy classification. These are the first new species of poop that have been discovered in thirty five years. The findings have been reported this week in the journal Nature.”

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Human microbiome digest, October 14, 2014

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Preterm birth and pathogens, oral antibiotic changes skin microbiota, dynamics of tongue microbes, and detection of candidate phyla in the human mouth.

Pregnancy and birth

Microbiological Profile of PROM in a Tertiary Care Centre in Mangalore, Karnataka State –
Annie Rajaratnam – International Journal of Health Sciences and Research

“A total of 104 cases of PROM that presented after 37 completed weeks’ of gestation were screened for infections by wet mount, Gram stain & routine culture of high vaginal swabs.“

Epidemiologic Factors and Urogenital Infections Associated With Preterm Birth in a Midwestern U.S. Population – Agger, William A – Obstetrics & Gynecology

“Cervical and urine specimens were analyzed by microscopy, culture, and polymerase chain reaction for potential pathogens.”

Human Milk Glycomics and Gut Microbial Genomics in Infant Feces Shows Correlation between Human Milk Oligosaccharides and Gut Microbiota: A Proof-of-Concept Study – Maria Lorna Arao De Leoz – Journal of Proteome Research

“Serial fecal specimens from two healthy breast-fed infants were analyzed by bacterial DNA sequencing to characterize the microbiota and by mass spectrometry to determine abundances of specific HMOs that passed through the intestinal tract without being consumed by the luminal bacteria. “

Human skin microbiome

* Oral Antibiotic Treatment Induces Skin Microbiota Dysbiosis and Influences Wound Healing – Meiling Zhang – Microbial Ecology

“our data demonstrate that antibiotic treatment decreases the bacterial density and alters the bacterial composition in skin wounds, followed by a decrease in RegIIIγ expression, which may contribute to the delayed wound repair. “

Human oral microbiome

* Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping – Jessica L. Mark Welch – Frontiers in Microbiology

“We employed oligotyping to analyze, with single-nucleotide resolution, oral microbial 16S ribosomal RNA (rRNA) gene sequence data from a time course sampled from the tongue of two individuals, and we interpret our results in the context of oligotypes that we previously identified in the oral data from the Human Microbiome Project. “

Host-associated bacterial taxa from Chlorobi, Chloroflexi, GN02, Synergistetes, SR1, TM7, and WPS-2 Phyla/candidate divisions – Anuj Camanocha, Floyd E. Dewhirst – Journal of Oral Microbiology

“The objectives of this study were to create phyla-selective 16S rDNA PCR primer pairs, create selective 16S rDNA clone libraries, identify novel oral taxa, and update canine and human oral microbiome databases.”

Human gut microbiome

Environmental enteropathy and malnutrition: do we know enough to intervene? – William A Petri – BMC Medicine

“Environmental enteropathy (EE) is a poorly defined state of intestinal inflammation without overt diarrhea that occurs in individuals exposed over time to poor sanitation and hygiene.”

* Meta-analyses of human gut microbes associated with obesity and IBD – William A. Walters, Zech Xu, Rob Knight – FEBS Letters

“Here we test for indicator taxa and general features of the microbiota that are generally consistent across studies of obesity and of IBD, focusing on studies involving high-throughput sequencing of the 16S rRNA gene (which we could process using a common computational pipeline). “

Diversity of Microflora in Colonic Mucus from Severe Ulcerative Colitis Patients Analyzed by Terminal Restriction Fragment Length Polymorphism and Clone Libraries of Bacterial 16S rRNA Gene Sequences – I-Nung Huang – Advances in Microbiology

“Also in the clone library analysis, the number of operational taxonomic units (OTU) and the Shannon diversity index were reduced significantly in UC patients.”

The Influence of Whole Grain Products and Red Meat on Intestinal Microbiota Composition in Normal Weight Adults: A Randomized Crossover Intervention Trial – Jana Foerster – PLOS ONE

“Repeatedly data on microbiota were assessed by 16S rRNA based denaturing gradient gel electrophoresis (DGGE).”

Animal and bioreactor models of microbiome research

Assessing non-digestible compounds in apple cultivars and their potential as modulators of obese faecal microbiota in vitro – Luis Condezo-Hoyos – Food Chemistry

“Results showed that relative abundances of Firmicutes, Bacteroidetes, Enterococcus, Enterobacteriaceae, Escherichia coli, and Bifidobacterium in apple cultured faeces tended to resemble the abundance in faeces from lean mice with increased trend in the production of butyric acid. “

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Microbiome Digest, October 9, 2014

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Human microbiome general

Advancing the Microbiome Research Community – Curtis Huttenhower – Cell

“We outline opportunities in interdisciplinary research, analytical rigor, standardization, and policy development for this relatively new and rapidly developing field. “

Human oral microbiome

Bioinformatic investigation of the cost management strategies of five oral microbes – K.J. Cross – Molecular Oral Microbiology

“The aim of this study was to investigate if five oral bacterial species implement cost management strategies to reduce the energy burden of extracellular unrecyclable proteins.”

Human skin microbiome

Identification of molecular mechanisms used by Finegoldia magna to penetrate and colonize human skin – Elizabeth C. Murphy – Molecular Microbiology

“This study examines the molecular mechanisms F. magna uses when colonizing or establishing an infection in the skin. “

Human gut microbiome

Bacterial ClpB heat-shock protein, an antigen-mimetic of the anorexigenic peptide α-MSH, at the origin of eating disorders – N Tennoune – Translational Psychiatry

“Here, using proteomics, we identified ClpB heat-shock disaggregation chaperone protein of commensal gut bacteria Escherichia coli as a conformational antigen mimetic of α-MSH.”

Animal models of microbiome research

Effects of essential oil supplementation of a low-energy diet on performance, intestinal morphology and microflora, immune properties and antioxidant activities in weaned pigs – Zhikai Zeng – Animal Science Journal

Soil microbiome

Poster presentation: Starting study of microbial genetics diversity in soils of mangrove preserved in sergipe – Karla Cristina Santos Freire – BMC Proceedings

“This paper proposes the characterization and evaluation of structures and diversity of microbial communities in the soil of mangroves in three conservation areas located in Sergipe.“

Community assembly of ectomycorrhizal fungi along a subtropical secondary forest succession – Cheng Gao – New Phytologist

“We examined the communities of ectomycorrhizal (EM) fungi in young, intermediate and old forests in a Chinese subtropical ecosystem, using 454 pyrosequencing”

Metagenomics / Bioinformatics

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam – Juanjuan Chai – BMC Evolutionary Biology

“A total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accurate comparison. “

More Microbiology

Halting harmful helminths – Karl F. Hoffmann, Paul J. Brindley, Matthew Berriman – Science

“More than 300 million people are infected each year with parasitic flatworms such as hydatid tapeworms and blood fluke schistosomes. “

Chromosome position effects on gene expression in Escherichia coli K-12 – Jack A. Bryant – Nucleic Acids Research

“Here, using Escherichia coli K-12, we demonstrate that expression of a reporter gene cassette, comprised of the model E. coli lac promoter driving expression of gfp, varies by ∼300-fold depending on its precise position on the chromosome. “

Microbes in the news

‘Good Poop’ Diet Is the Next Big Thing – Daniela Drake – The Daily Beast

“Now a new book, The Skinny Gut Diet, by nutritionist Brenda Watson, tracks the progress of people who follow a diet specifically designed to alter the gut microbiome. “

Another probiotic advantage: Bacteria protects against heavy metal poisoning – Jim Algar – Tech Times

“Probiotic bacteria found in yogurt can protect people from the effects of exposure to heavy metals, particularly in pregnant women and children, a Canadian study suggests.”

Science, publishing, career

The scientists who get credit for peer review – Richard Van Noorden – Nature

“Publons rewards researchers for putting their peer-review activity online. Nature spoke to the startup’s co-founder and two super-users.”

Meet the New Underclass: People With Ph.D.s in Science – Mark Strauss – iO9

“Once upon a time, newly-minted science Ph.D.s would get research jobs at a senior scientist’s laboratory, to train and hone the ideas they would explore at their own labs. But now the supply of post-doctoral students is outpacing demand, creating a new, hyper-educated underclass.”

Glut of postdoc researchers stirs quiet crisis in science –  Carolyn Y. Johnson – Boston Globe

Japan’s Missing Female Scientists – Jack Grove – Times Higher Education

“Too many female scientists are leaving Japan because they do not feel they can get ahead in its “male-dominated” society, a senior university leader has said.”

Bik’s Picks

Cave paintings change ideas about the origin of art – Pallab Ghosh – BBC

“Researchers tell the journal Nature that the Indonesian discovery transforms ideas about how humans first developed the ability to produce art.”

A timeline of a baby’s first hour – Laura Sanders – Science News

Fired science teacher did not have state license – 9 News

“The teacher fired after his science experiment injured four students, one seriously, did not have a valid Colorado teacher’s license.”

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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 2, 2014

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Catching up after some long days of paper writing. Lots of microbiome papers in the Journal of Clinical Investigation, microbiome and Lupus, and biography of skin microbiome.

General (human) microbiome

The Journal of Clinical Investigation has a microbiome issue this month (all behind a subscription wall). Titles include:

The microbiome revolution – Martin J. Blaser
Bacteroides fragilis subverts mucosal biology: from symbiont to colon carcinogenesis – Cynthia L. Sears, Abby L. Geis, Franck Housseau
Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics – Rachel N. Carmody, Peter J. Turnbaugh
Clostridium difficile and the microbiota – Anna M. Seekatz, Vincent B. Young
The microbial basis of inflammatory bowel diseases – Sushila R. Dalal, Eugene B. Chang
Deciphering the tête-à-tête between the microbiota and the immune system – Neeraj K. Surana, Dennis L. Kasper
The contributory role of gut microbiota in cardiovascular disease – W.H. Wilson Tang, Stanley L. Hazen
Antibiotics and the gut microbiota – Sheetal R. Modi, James J. Collins, David A. Relman

When, where and how does microbial community composition matter? – Diana R. Nemergut*, Ashley Shade and Cyrille Violle – Frontiers in Microbiology

“Several papers in this special issue, “The Causes and Consequences of Microbial Community Structure,” use empirical or modeling approaches as well as literature reviews to enrich our mechanistic understanding of the controls over the relationship between community structure and ecosystem processes. “

The bacteriome-mycobiome interaction and antifungal host defense – Jaap ten Oever and Mihai G. Netea – European Journal of Immunology

“In this review, we describe the role of the bacterial microbiome in antifungal host defense.”

Richness and diversity of mammalian fungal communities shape innate and adaptive immunity in health and disease – Lisa Rizzetto – European Journal of Immunology

“In this review, we describe the ecology and the human niches of our fungal “fellow travelers” in both health and disease, discriminating between passengers, colonizers and pathogens based on the interaction of these fungi with the human immune system.”

Pregnancy and Birth

Second trimester amniotic fluid cytokine concentrations, Ureaplasma sp. colonisation status and sexual activity as predictors of preterm birth in Chinese and Australian women
Matthew S Payne – BMC Pregnancy and Childbirth

“Second trimester amniocentesis for measurement of inflammatory markers and Ureaplasma sp. DNA was not indicative of risk of preterm birth, at least in these populations.”

Human oral microbiome

Tongue images and tongue coating microbiome in patients with Colorectal Cancer -Shuwen Han – Microbial Pathogenesis

“To evaluate the differences of tongue images and tongue coating microbiome between patients with colorectal cancer and healthy people.”

Hydrogen Sulfide Production from subgingival plaque samples – A. Basic, G. Dahlén – Anaerobe

“The Karen population studied in Northern Thailand showed poor oral hygiene, general gingivitis and moderate periodontal destruction and little tooth loss.”

Italian-style gluten-free diet changes the salivary microbiota and metabolome of African (Saharawi) celiac children – Ruggiero Francavilla – Digestive and Liver Disease

Human skin microbiome

* Microbiology: An integrated view of the skin microbiome – Patrick D. Schloss – Nature

Biogeography and individuality shape function in the human skin metagenome – Julia Oh – Nature

“Here metagenomic analyses of diverse body sites in healthy humans demonstrate that local biogeography and strong individuality define the skin microbiome. “

Human respiratory microbiome

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

“Ethmoid samples from 54 CRS patients collected during endoscopic sinus surgery were analyzed by both clinical culture and 16S ribosomal RNA (rRNA) gene sequencing. The association between 16S relative abundance and detection by culture was determined using logistic regression.”

Methicillin-Sensitive and Methicillin-Resistant Staphylococcus aureus Nasal Carriage in a Random Sample of Non-Hospitalized Adult Population in Northern Germany – Jaishri Mehraj – PLOS ONE

“A total of 2026 potential participants were randomly selected through the resident’s registration office and invited by mail. They were requested to collect a nasal swab at home and return it by mail. S. aureus was identified by culture and PCR. “

Severity-related changes of bronchial microbiome in COPD – Marian Garcia-Nunez – Journal of Clinical Microbiology

“Bronchial microbiome of COPD patients was analyzed by 16S rRNA gene amplification and pyrosequencing in sputum samples obtained during stability. “

Human gut microbiome

* Intestinal Dysbiosis Associated with Systemic Lupus Erythematosus – Arancha Hevia – mBio

“A group of 20 SLE patients in remission, for which there was strict inclusion and exclusion criteria, was recruited, and we used an optimized Ion Torrent 16S rRNA gene-based analysis protocol to decipher the fecal microbial profiles of these patients and compare them with those of 20 age- and sex-matched healthy control subjects.”

Systems Biology Analysis of Omeprazole Therapy in Cirrhosis Demonstrates Significant Shifts in Gut Microbiota Composition and Function – Jasmohan Singh Bajaj- American Journal of Physiology – Gastrointestinal and Liver Physiology

“15 compensated cirrhotics and 15 age-matched controls underwent serum gastrin measurement, stool microbiota profiling with multi-tagged pyrosequencing and urinary metabolic profiling with NMR spectroscopy to assess microbial co-metabolites before/after a 14-day course of 40mg/day omeprazole under constant diet conditions’

The Impact of Proton Pump Inhibitors on the Human Gastrointestinal Microbiome
Daniel E. Freedberg – Clinics in Laboratory Medicine

The intestinal microbiota and allergic asthma – Marie-Claire Arrietaa, Brett Finlay- Journal of Infection

“By describing some of the most relevant human and animal studies in this field, we explore the concept that significant perturbations of the intestinal and perhaps the lung microbiota are a cause of allergic asthma.”

Minireview: Linking genetic variation in human Toll-like receptor 5 genes to the gut microbiome’s potential to cause inflammation – Cynthia A. Leifer – Immunology Letters

“Loss of TLR5 has profound effects on the microbiota that include greater temporal instability of major lineages and upregulation of flagellar motility genes that may be linked to the reduced levels of anti-flagellin antibodies in the TLR5-/- host.”

A Little O2 May Go a Long Way in Structuring the GI Microbiome – Thomas M. Schmidt, John Y. Kao – Gastroenterology

Microbiome, Innate Immunity, and Esophageal Adenocarcinoma – Jonathan Baghdadi – Clinics in Laboratory Medicine

Animal models of microbiome research

Immunology: Starve a fever, feed the microbiota – Seth Rakoff-Nahoum & Laurie E. Comstock – Nature – belongs to:

Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness – Joseph M. Pickard – Nature

“We hypothesized that the host might utilize internal resources to support the gut microbiota during the acute phase of the disease.”

Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut – Henning Seedorf – Cell

“Microbiota from diverse habitats colonize and compete in the guts of gnotobiotic mice”

Dynamics of gut microbiota in autoimmune lupus – Husen Zhang – Applied and Environmental Microbiology

“We investigated the effects of host genetics, sex, age, and dietary intervention on the gut microbiome in a murine lupus model.”

Clostridium ramosum Promotes High-Fat Diet-Induced Obesity in Gnotobiotic Mouse Models – Anni Woting – mBio

“To clarify the possible obesogenic potential of this bacterial species and to unravel the underlying mechanism, we investigated the role of C. ramosum in obesity development in gnotobiotic mice.”

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Human microbiome digest, September 29, 2014

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Smoking and the subgingival ecosystem, inflammatory bowel diseases, iron in the gut, and metabolism of acetaminophen.

Pregnancy and birth

External influence of early childhood establishment of gut microbiota and subsequent health implications – Peris M. Munyaka – Frontiers in Pediatrics

“Early exposures impacting the intestinal microbiota are associated with the development of childhood diseases that may persist to adulthood”

Human oral microbiome

* Smoking decreases structural and functional resilience in the subgingival ecosystem – Vinayak Joshi – Journal of Clinical Periodontology

“16S cloning and sequencing was used for bacterial identification and multiplexed bead-based flow cytometry was used to quantify the levels of 27 immune mediators.”

Human gut microbiome

Functional Impacts of the Intestinal Microbiome in the Pathogenesis of Inflammatory Bowel Disease – Jennifer Li – Inflammatory Bowel Diseases

“We highlight functional roles of specific bacterial groups in the development and management of IBD. “

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.”

Animal models of microbiome research

The role of intestinal microbiota in murine models of acetaminophen-induced hepatotoxicity – Lucia A Possamai – Liver International

“A urinary metabolic profile was obtained using 1H-NMR. Baseline hepatic glutathione content and CYP2E1 expression were quantified.”

Dietary Xylo-oligosaccharide stimulates intestinal bifidobacteria and lactobacilli but has limited effect on intestinal integrity in rats – Ellen Gerd Christensen – BMC Research Notes

“Changes in faecal and caecal bacterial composition determined by 16S rRNA gene sequencing and quantitative PCR for selected bacterial groups revealed that the overall bacterial composition did not differ markedly“

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Microbiome digest, September 22, 2014

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Temporal stability of the microbiomes of 85 adults, bacteria in breast milk, vaginal microbiome during pregnancy, water microbiomes, and Bik’s Picks.

Human microbiome general

Temporal variability is a personalized feature of the human microbiome – Gilberto E Flores – PeerJ PrePrints

“Here we address this gap in understanding by profiling the forehead, gut (fecal), palm, and tongue microbial communities in 85 adults, weekly over three months.”

Pregnancy and birth

It’s Alive: Microbes and Cells in Human Milk and Their Potential Benefits to Mother and Infant – Lars Bode – Advances in Nutrition

“This article is a summary of the symposium “It’s Alive: Microbes and Cells in Human Milk and Their Potential Benefits to Mother and Infant” held 29 April 2014 at the ASN Scientific Sessions and Annual Meeting at Experimental Biology 2014 in San Diego, CA.”

Microorganisms in the Female Genital Tract during Pregnancy: Tolerance versus Pathogenesis – Bruna de Andrade Ramos – American Journal of Reproductive Immunology

“We review the state of knowledge of microbe–host interactions in gestational tissues and highlight mechanisms that promote tolerance or pathogenesis.”

Determinants and pattern of care seeking for preterm newborns in a rural Bangladeshi cohort – Rashed Shah – BMC Health Services Research

“Only one-fifth (19.7%) of preterm newborns were taken to seek either preventive or curative health care.”

Human oral microbiome

Microbial signature profiles of periodontally healthy and diseased patients – Talita Gomes Baêta Lourenço – Journal of Clinical Periodontology

“Subgingival biofilm was obtained from patients with periodontal health (27), gingivitis (11), chronic periodontitis (35) and aggressive periodontitis (24), and analysed for the presence of >250 species/phylotypes using HOMIM.”

Human gut microbiome

Review: Modulation of the Gut Microbiota by Nutrients with Prebiotic and Probiotic Properties – Céline Druart – Advances in Nutrition

“In this review, we describe how changes in the composition and/or activity of the gut microbiota by administration of nutrients with probiotic or prebiotic properties can modulate host gene expression and metabolism and thereby positively influence host adipose tissue development and related metabolic disorders.”

Mammal microbiome

Resistance to Antibiotics of Clinical Relevance in the Fecal Microbiota of Mexican Wildlife – Jurgi Cristóbal-Azkarate – PLOS ONE

“Here, we used culture and molecular methods to assess ATBR in bacteria in fecal samples from howler monkeys, spider monkeys, tapirs and felids living freely in two regions of the Mexican state of Veracruz under different degrees of human influence.“

Bird microbiome

Do feather-degrading bacteria actually degrade feather colour? No significant effects of plumage microbiome modifications on feather colouration in wild great tits – Staffan Jacob – Naturwissenschaften

“Here, we tested whether (i) keratinolytic microorganisms can degrade feathers in vivo and thus modify the colour of feathers during the nesting period and (ii) whether feather microorganisms have a long-term effect on the investment in colouration of newly moulted feathers.”

Plant microbiome

Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize – David Johnston-Monje – BMC Plant Biology

“The impact of these soil swaps on founder bacterial endophyte communities was tested using 16S-rDNA profiling, culturing and microbial trait phenotyping.“

Microbiota in Wheat Roots, Rhizosphere and Soil in Crops Grown in Organic and Other Production Systems – Leszek Lenc – Journal of Phytopathology

“The other two systems were intermediate, with microbial communities suggesting that the conventional system produced a slightly more suppressive environment than the integrated system. “

Soil microbiome

Bacterial and Archaeal Communities in Bleached Mottles of Tropical Podzols –
K. J. Silva, P. Vidal-Torrado, M. R. Lambais – Microbial Ecology

“In this study, we examined the bacterial and archaeal communities along three Brazilian coastal podzol profiles, as well as in bleached mottles and their immediate vicinity, using 16S rRNA gene profiling.”

Water microbiome

Microplastic is an abundant and distinct microbial habitat in an urban river – Amanda McCormick – Environmental Science & Technology

“Results from high-throughput sequencing showed that bacterial assemblages colonizing microplastic within the river were less diverse and were significantly different in taxonomic composition compared to those from the water column and suspended organic matter.”

Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity – Masanori Fujimoto – PLOS ONE

“The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry.”

Microbial diversity of the Soldhar hot spring, India, assessed by analyzing 16S rRNA and protein-coding genes – Avinash Sharma – Annals of Microbiology

“Bacterial diversity of the Soldhar hot spring, located in the Chamoli district of Uttarakhand, India, was investigated using a clone library, denaturing gradient gel electrophoresis (DGGE) and functional genes.”

Microbial community composition and in silico predicted metabolic potential reflect biogeochemical gradients between distinct peatland types – Zuzana Urbanová and Jiří Bárta – FEMS Microbial Ecology

“Species richness and microbial diversity increased significantly from bog to fen, with SSF in between, reflecting the variation in pH, nutrient availability and peat decomposability. “

A molecular survey of freshwater microeukaryotes in an Arctic reservoir (Svalbard, 79°N) in summer by using next-generation sequencing – Thangavelu Boopathi – Polar Biology

“In this study, freshwater microeukaryotes in an Arctic reservoir at Ny-Ǻlesund (Svalbard, Norway) were studied using the hypervariable V1–V3 small subunit rRNA and 454 pyrosequencing.”

Built Environment

Urban microbiomes and urban ecology: How do microbes in the built environment affect human sustainability in cities? – Gary M. King – Journal of Microbiology

“I provide here a definition of the urban microbiome, and through examples indicate its centrality to human function and wellbeing in urban systems”

Phages and viruses

Metagenomic Evaluation of the Highly Abundant Human Gut Bacteriophage CrAssphage for Source Tracking of Human Fecal Pollution – Elyse Stachler and Kyle Bibby – Environmental Science & Technology

“Here, 86 publically available metagenomes were surveyed to determine the presence and abundance of crAssphage in various environments, and to identify its utility for source tracking of human fecal pollution.”

Microbes in the news

Understanding the Microbiome and Its Impact on Human Health – Kristine Nally – HCPLive

“Instant polling at an educational session of the 2014 American Academy of Pain Management annual clinical meeting in Phoenix, AZ, revealed that only 40 percent of the approximately 350-person audience was “familiar” with the concept of a microbiome.”

Mining the microbiome for medicines – Set a thief… – The Economist

“Antibiotics are not the only things Dr Donia’s technique might turn up, for the bugs in the human microbiome spit out all sorts of other chemicals that could potentially be put to use as drugs.”

Techniques

Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads – Rogan Carr and Elhanan Borenstein – MicroBEnet

“We therefore set out to develop a set of ‘best practices’ for our lab for metagenomic sequence annotation and to prove (or disprove) quantitatively that such direct functional annotation of short reads provides a valid functional representation of the sample.”

Science and publishing

Anonymous peer-review comments may spark legal battle – Kelly Servick – Science Insider

“The power of anonymous comments—and the liability of those who make them—is at the heart of a possible legal battle embroiling PubPeer, an online forum launched in October 2012 for anonymous, postpublication peer review.”

Time to Raise the Profile of Women and Minorities in Science – Brian Welle and Megan Smith – Scientific American

“Along these lines, over the past few years, we discovered some pretty ugly news about our beloved Google Doodles. “

Bik’s Picks

Immune system of newborn babies stronger than previously thought – Science Daily

“Contrary to what was previously thought, newborn immune T cells may have the ability to trigger an inflammatory response to bacteria, according to a new study.”

The Preservation Of Lonesome George – Sarah Fecht – PopSci.com

“Decades after the last giant tortoise was thought to have disappeared from the island of Pinta in the Galapagos, Lonesome George turned up in 1971 and became a conservation icon.”

 Great white sharks partly to blame for otter recovery stall – Peter Fimrite – SF Gate

“Most scientists agree that the number of animals, which are also known as southern sea otters, should be increasing, but hungry predators and a lack of food may be limiting their growth.”

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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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