Category Archives: Human gut

Human microbiome digest, October 27, 2014

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Development of gut microbiome in infants, understanding oral microbiome through high-throughput sequencing, gut bacteria in deceased alcoholics, and bacteria after stroke.

Microbiome general

The symbiont side of symbiosis: do microbes really benefit? – Justine R. Garcia and Nicole M. Gerardo – Frontiers in Microbiology

“We evaluate these hypotheses based on available evidence, which indicate reduced competition and predation are not universal benefits for symbionts. “

Pregnancy and birth microbiome

Review: Diet and the development of the human intestinal microbiome – Noah Voreades – Frontiers in Microbiology

“This review focuses primarily on diet, as it is one of the most pivotal factors in the development of the human gut microbiome from infancy to the elderly.”

Human oral microbiome

Review: Application of high-throughput sequencing in understanding human oral microbiome related with health and disease – Hui Chen and Wen Jiang – Frontiers in Microbiology

“This review describes the application of high-throughput sequencing for characterization of oral microbiota and analyzing the changes of the microbiome in the states of health or disease.”

Human gut microbiome

Cellular and molecular pathways through which commensal bacteria modulate sensitization to dietary antigens – Taylor Feehley, Cathryn R Nagler – Current Opinion in Immunology

“This review will discuss the cellular and molecular pathways activated by commensal bacteria to protect against allergic sensitization.”

Microbial Therapy in Liver Disease: Probiotics Probe the Microbiome–Gut–Liver–Brain Axis – David W. Victor 3rd, Eamonn M.M. Quigley – Gastroenterology

“It is timely, therefore, that Dhiman et al should embark on an ambitious study, reported in this issue of Gastroenterology, designed to assess the efficacy of the probiotic cocktail, VSL#3, as secondary prophylaxis in patients with OHE.”

Changes in gut bacterial populations and their translocation into liver and ascites in alcoholic liver cirrhotics – Sari Tuomisto – BMC Gastroenterology

“Relative ratios of major commensal bacterial communities (Bacteroides spp., Bifidobacterium spp., Clostridium leptum group, Enterobactericaea and Lactobacillus spp.) were determined in faecal samples from post mortem examinations performed on 42 males”

Animal models of microbiome research

Age-related changes in intestinal permeability and gut microbiota after ischemic stroke – Joshua Crapser – Journal of Neuroimmunology

“This study aimed to elucidate the role of systemic factors, such as intestinal stress, underlying the poor outcomes of aging mice after stroke.”

Spatial and temporal colonization dynamics of segmented filamentous bacteria is influenced by gender, age and experimental infection with Helicobacter hepaticus in Swiss Webster mice – Zhongming Ge – Microbes and Infection

“Hh infection in both genders did not alter SFB levels in the jejunum and ileum, but increased SFB levels in the cecum and colon of males compared to the controls”

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Microbiome digest, October 22, 2014

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Microbes in the mouth of patients with heart disease, bile and gall bladder microbiome of pigs, precisely restoring resistance to Clostridium difficile infection, and networks between fungi and plants. And don’t forget the solar eclipse tomorrow PM for most of the US.

Human oral microbiome

Microbial Diversity Similarities in Periodontal Pockets and Atheromatous Plaques of Cardiovascular Disease Patients – Wagner Serra e Silva Filho – PLOS ONE

“Subgingival biofilm and coronary balloons used in percutaneous transluminal coronary angioplasty were collected from 18 subjects presenting with generalized moderate to severe periodontitis and OCAA. DNA was extracted and the gene 16S was amplified, cloned and sequenced.”

Human gut microbiome

Dietary Patterns Differently Associate with Inflammation and Gut Microbiota in Overweight and Obese Subjects – Ling Chun Kong – PLOS ONE

“We aimed to characterize dietary patterns in overweight and obese subjects and evaluate the different dietary patterns in relation to metabolic and inflammatory variables as well as gut microbiota.”

Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men – Anne Salonen – ISME Journal

“Here we report a comprehensive and deep microbiota analysis of 14 obese males consuming fully controlled diets supplemented with resistant starch (RS) or non-starch polysaccharides (NSPs) and a weight-loss (WL) diet.”

Animal models of microbiome research

* Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile – Charlie G. Buffie – Nature

“..we determine that Clostridium scindens, a bile acid 7α-dehydroxylating intestinal bacterium, is associated with resistance to C. difficile infection and, upon administration, enhances resistance to infection in a secondary bile acid dependent fashion.”

* Changes in the Bacterial Microbiota in Gut, Blood, and Lungs following Acute LPS Instillation into Mice Lungs – Marc A. Sze – PLOS ONE

“Bacterial microbiota of the bronchoalveolar lavage fluid, blood, and cecum were determined using 454 pyrotag sequencing and quantitative polymerase chain reaction (qPCR) at 4 through 168 hours post-instillation.”

Specific Microbiome Changes in a Mouse Model of Parenteral Nutrition Associated Liver Injury and Intestinal Inflammation – J. Kirk Harris – PLOS ONE

“Microbiome analysis in the PNALI mouse identified specific alterations within colonic microbiota associated with PNALI and further association of these communities with the lipid composition of the PN solution. “

Animal microbiome

Characterization of the bile and gall bladder microbiota of healthy pigs – Esther Jiménez – Microbiology Open

“We have studied, by culture-dependent techniques and a 16S rRNA gene-based analysis, the microbiota present in the bile, gall bladder mucus, and biopsies of healthy sows”

Characterization of Egg Laying Hen and Broiler Fecal Microbiota in Poultry Farms in Croatia, Czech Republic, Hungary and Slovenia – Petra Videnska – PLOS ONE

“In this study we were therefore interested in the prevalence of selected antibiotic resistance genes and microbiota composition in feces of egg laying hens and broilers originating from 4 different Central European countries determined by real-time PCR and 16S rRNA gene pyrosequencing, respectively. “

Plant microbiome

* Assembly of complex plant–fungus networks – Hirokazu Toju – Nature Communications

“The examined symbiotic network of a temperate forest in Japan includes 33 plant species and 387 functionally and phylogenetically diverse fungal taxa, and the overall network architecture differs fundamentally from that of other ecological networks. “

Soils and sediments

The long-term adaptation of bacterial communities in metal-contaminated sediments: a metaproteogenomic study – David C. Gillan – Environmental Microbiology

“Two freshwater sites, Férin and MetalEurop, differing by one order of magnitude in metal levels (MetalEurop: 3218 mg Zn kg−1; 913 mg Pb kg−1) were compared by shotgun metaproteogenomics. “

Bioinformatics / metabolomics

* Biogeochemical Typing of Paddy Field by a Data-Driven Approach Revealing Sub-Systems within a Complex Environment – A Pipeline to Filtrate, Organize and Frame Massive Dataset from Multi-Omics Analyses – Diogo M. O. Ogawa – PLOS ONE

“We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. “

Estimating coverage in metagenomic data sets and why it matters – Luis M Rodriguez-R and Konstantinos T Konstantinidis – ISME Journal

“We demonstrate here how available solutions can determine the level of sequencing coverage obtained by metagenomic data sets and thus, guide their robust analysis and comparison.”

Immunology

* Fall issue of Stanford Medicine reports on the immune system’s balancing act

“If you want to understand the human immune system, try studying humans — not mice, urges Mark Davis, PhD, in a special report on the immune system in the new issue of Stanford Medicine magazine.”

Bik’s Picks

Genome sequence of a 45,000-year-old modern human from western Siberia – Qiaomei Fu – Nature

“the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. “

Sky spectacle: Partial solar eclipse coming Thursday – USA Today

“In the afternoon, a partial solar eclipse — where the moon covers a part of the sun — will be visible across much of the USA, barring any pesky clouds that could block the show.”

Go Giants! The Science of Baseball – Exploratorium

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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 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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Microbiome digest, October 16, 2014

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Lung microbiome and pneumonia, bacterial vaginosis, microbiome and jetlag, cardiovascular consequences of gut dysbiosis, bacteria in locust guts and cropland in China, and how to earn some $$$ with your poop.

Human respiratory microbiome

Single-Molecule Long-Read 16S Sequencing To Characterize the Lung Microbiome from Mechanically Ventilated Patients with Suspected Pneumonia – Ian Toma – Journal of Clinical Microbiology

“The present study used NGS of essentially full-length PCR-amplified 16S ribosomal DNA from the bronchial aspirates of intubated patients with suspected pneumonia.”

Human vaginal microbiome

Recent progress in understanding the epidemiology of bacterial vaginosis – Kenyon, Chris R.; Osbak, Kara – Current Opinion in Obstetrics & Gynecology

“Bacterial vaginosis epidemiology has been transformed by new theoretical insights and methodologies, such as molecular sequencing. We summarize the progress made in these domains.”

Human gut microbiome

Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis – Christoph A. Thaiss – Cell

“Consequently, jet-lag-induced dysbiosis in both mice and humans promotes glucose intolerance and obesity that are transferrable to germ-free mice upon fecal transplantation.”

Far from the Eyes, Close to the Heart: Dysbiosis of Gut Microbiota and Cardiovascular Consequences – Matteo Serino – Current Cardiology Reports

“Here, we report evidence from the literature, as well as a few controversial reports, regarding the putative role of gut microbiota dysbiosis-induced cardiovascular diseases”

Insect microbiome

Cellulolytic activity and structure of symbiotic bacteria in locust guts – L-J Su – Genetics and Molecular Research

“The diversity of gut symbiotic bacteria was studied using denaturing gradient gel electrophoresis (DGGE). “

Soil microbiome

* Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China – Zhen Zhen – PLOS ONE

“Denaturing gradient electrophoresis (DGGE) fingerprinting analysis showed that the structure and composition of bacterial and fungi communities in the six fertilizer treatments varied at different levels. “

Water microbiome

Substratum-Associated Microbiota – Furey, Paula C.; Liess, Antonia – Water Environment Research

“In this review of the 2013 literature, advances in laboratory, field, and assessment methods are highlighted as are updates in taxonomy and systematics.”

More microbiology

Commensally sourced antibiotics – Cláudio Nunes-Alves – Nature Reviews Microbiology

“Donia et al. have carried out the first systematic screen of biosynthetic gene clusters (BGCs) in the healthy human microbiota and found that BGCs for the thiopeptide class of antibiotics are widely distributed.”

First aid kit for cholera – Andrea Du Toit – Nature Reviews Microbiology

“In a new study, Gordon and colleagues examined the role of the human gut microbiota in V. cholerae infection and showed that one of its members, Ruminococcus obeum, decreases the expression of V. cholerae virulence factors to limit colonization.”

Microbes in the news

* A Poop Bank in Massachusetts Will Pay You $40 Every Day – Chelsea Rice – Boston.com

“All you have to do is visit OpenBiome, launched in 2012 as the only independent nonprofit stool bank in the country.”

Study reveals rats in NYC carry variety of infectious bacteria – Larry McShane – New York Daily News

“The first-of-its-kind study showed the rodents carrying an average of two bacteria capable of causing gastrointestinal problems for humans and the Seoul hantavirus, which causes a potentially life-threatening fever and kidney failure.”

* New Genes = New Archaea? – Molly Sharlach – The Scientist

“The study, published today (October 15) in Nature, also suggests that genetic transfers from bacteria to archaea are at least five times more common than from archaea to bacteria.”

Bik’s Picks

“Epicenters” of resilience – Mary Lou Zoback – Science

“The 25th anniversary of the magnitude (M) 6.9 Loma Prieta earthquake that struck the San Francisco Bay Area on 17 October 1989 is a fitting time to examine what progress has been made in increasing community resilience to minimize seismic risk. “

Cells’ powerhouses were once energy parasites: Study upends current theories of how mitochondria began – Science Daily

“Parasitic bacteria were the first cousins of the mitochondria that power cells in animals and plants — and first acted as energy parasites in those cells before becoming beneficial, according to a new study”

How Did We Become a Society Suspicious of Science? – Keith M. Parsons – Huffington Post

“But something has been lost. Fifty years ago science was king. Science had respect; it was bigger than ideology. No longer. “

 

Biology Week: Bio-bodies Bake Off Public Vote – Physiological Society

“In the lead up to biology week we set you a challenge! We wanted you to celebrate the science of life by creating your own physiology bakes, and you didn’t let us down! ”

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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 13, 2014

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Preterm infant gut microbiome, fecal transplants, microbes in space, and microbiome of 8 different fish species.

Pregnancy and birth

* Development of the preterm infant gut microbiome: a research priority – Maureen W Groer (Jack Gilbert lab) – Microbiome

“This review provides a synthesis of our understanding of the normal development of the infant gut microbiome and contrasts this with dysbiotic development in the VLBW infant.”

Fluorescence in situ hybridization for identification of microorganisms in acute chorioamnionitis – D. Schmiedel – Clinical Microbiology and Infection

“Using a diagnostic fluorescence in situ hybridization probe panel, we visualized Staphylococcus aureus and Streptococcus mitis group in two cases of acute chorioamnionitis. “

The Role of Mycoplasma and Ureaplasma in Adverse Pregnancy Outcomes – Amy P. Murtha – Obstetrics and Gynecology Clinics of North America

* Impact Of Lifestyle On The Gut Microbiota Of Healthy Infants And Their Mothers – The Aladdin Birth Cohort – Helena Marell Hesla – FEMS Microbiology Ecology

“Samples collected from infants at ages six days, three weeks, two months and six months and from their mothers before and after delivery, respectively, were analyzed using 454-pyrosequencing.”

Human gut microbiome

* Oral, Capsulized, Frozen Fecal Microbiota Transplantation for Relapsing Clostridium difficile Infection – Ilan Youngster – JAMA

“Self-ranked health scores improved significantly on a scale of 1 to 10 from a median of 5  for overall health and 4.5  for gastrointestinal-specific health on the day prior to FMT to 8 after FMT administration for both overall and gastrointestinal health (P = .001).”

* Impact of Experimental Hookworm Infection on the Human Gut Microbiota – Cinzia Cantacessi – Journal of Infectious Diseases

“We used 16S rRNA gene amplification and pyrosequencing to characterize, for the first time to our knowledge, the differences in composition and relative abundance of fecal microbial communities in human subjects prior to and following experimental infection with the blood-feeding intestinal hookworm, Necator americanus. “

Genomics of schizophrenia: time to consider the gut microbiome? – T G Dinan – Molecular Psychiatry

“To date, this vast quantity of DNA has been largely ignored in schizophrenia research.”

Animal microbiome

Comparative study on gastrointestinal microbiota of eight fish species with different feeding habits – Jinjin Li – Journal of Applied Microbiology

“The V1 to V3 regions of 16S rRNA gene were analyzed by highthroughput sequencing (454 platform) to compare the gut microbiota of different fish species. “

Dining local: the microbial diet of a snail that grazes microbial communities is geographically structured – Richard O’Rorke – Environmental Microbiology

“we collected 102 snail fecal samples as a proxy for diet, and 102 matched-leaf samples from four locations. We used Illumina amplicon sequencing to determine bacterial and fungal community composition. “

Bacterial associates of seed-parasitic wasps (Hymenoptera: Megastigmus) – Amber R Paulson – BMC Microbiology

“We characterized the bacterial symbionts of Megastigmus (Hymenoptera: Torymidae), a lineage of seed-parasitic chalcid wasps, with the goal of identifying microbes that might play an important role in aiding development within seeds, including supplementing insect nutrition or manipulating host trees.“

Bioreactor microbiome

Biofouling and Microbial Communities in Membrane Distillation and Reverse Osmosis – Katherine R. Zodrow – Environmental Science & Technology

“Phylogenetic analysis using next-generation sequencing of 16S ribosomal DNA showed significant shifts in the microbial communities. “

Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture – Amy A Boaro – FEMS Microbiology Ecology

“16S rDNA pyrosequencing results revealed increased alpha diversity in the microbial community after the perturbation, and a persistence of the dominant community members over the duration of the experiment.”

Environmental microbiome

Effects of Bioavailable Heavy Metal Species, Arsenic, and Acid Drainage from Mine Tailings on a Microbial Community Sampled Along a Pollution Gradient in a Freshwater Ecosystem – Togwell A. Jackson – Geomicrobiology Journal

“Ribosomal ribonucleic acid, fatty acid, and phospholipid analyses, along with assays of CO2 production, denitrification, and enzyme activities, were performed to characterise the microflora; and environmental conditions were defined by various physicochemical analyses, including determination of bioavailable metal species. “

The role of macrobiota in structuring microbial communities along rocky shores – Catherine A Pfister​, Jack A Gilbert, Sean M Gibbons – PeerJ

“At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton.”

Microbes in (simulated) space

The development and succession of microbial communities in 90-day Bioregenerative Life Support Experiment in the Lunar Palace 1 – Yi Sun – 40th COSPAR Scientific Assembly

“In this study, the development and succession of the microbial communities of air, water system, plant system, and key facilities surfaces in Lunar Palace 1 were continuously monitored and analyzed by using plate counting method and molecular biological method during the 90-day experiment.”

The viability of native microbial communities in martian environment (model) – Vorobyova, Elena – 40th COSPAR Scientific Assembly

“It was shown that in simulated conditions close to the parameters of the Martian regolith, the diversity of natural bacterial communities was not decreased, and in some cases the activation of some bacterial populations occurred in situ.”

Food microbiology

Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine – Joanita Sulaiman – Frontiers in Microbiology

“Whole genome shotgun (WGS) method revealed that the fermentation brine was dominated by the bacterial genus Weissella and later dominated by the fungal genus Candida.”

Transcriptomics/metagenomics

Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities – Leyden Fernandez – BMC Genomics

“We have here characterized and analyzed the metaregulome of three different environments, as well as their impact in the adaptation to particular variable physico-chemical conditions. “

Other microbiology

Inverse Correlation Between Helicobacter pylori Colonization and Obesity in a Cohort of Inner City Children – Hanh D. Vo – Helicobacter

“Our findings in a North American cohort are in agreement with studies from Asia and Europe suggesting that H. pylori infection decreases the prevalence of obesity in children.”

Microbes in the news

* Podcast: Your Home, Your Bacteria – Science Friday

“Jack Gilbert… is trying to develop a better understanding of the way people, bacteria, and the environment around them interact, from the kitchen floor to the greater Chicago area.”

Landmark Crohn’s Microbiome Study Yields Important Findings – David Wild – GastroEndoNews

“The association suggests that there is a potential link between the presence of these microbes and the serologic biomarkers, but that needs to be determined in future studies,” said Dr. Xavier, who presented the study at Digestive Disease Week 2014”

Is that how the capsules will look like? Good news: You can take your fecal transplants orally – Rachel Feltman – Washington Post

“In a study published Saturday in the Journal of the American Medical Association, researchers report that the same success rate can be reached by processing the healthy excrement into capsules and administering the pills by mouth.“

Probiotics on the brain: A growing number of scientists now believe that gut bacteria can influence mental health – Elizabeth Gehrman – Boston Globe

“Whenever someone says there’s an impossibility in medicine,” says Williams, “they end up being corrected in a few years.”

Unravelling the link between gut bacteria and horse health – University of Surrey

“Researchers at the University of Surrey, in collaboration with colleagues from Reading and Liverpool universities, have been awarded £100,000 funding by Petplan Charitable Trust… to create a laboratory model of the horse’s hindgut.”

The Second Brain: Gut Bacteria Control Human Behavior to Get the Best Nutrients – David Gutierrez – Epoch Times

“Bacteria within the gut are manipulative,” researcher Carlo Maley, PhD, said. “There is a diversity of interests represented in the microbiome, some aligned with our own dietary goals, and others not.”

Science, publishing, career

Sometimes My Job Seems Like a Secret – Amy Davidson – Speaking Of Research

“You are going to hell.” “You are a horrible person.” “We cannot be friends anymore.”

Sell yourself: Adding substance to your personal statement – Brian Rybarczyk – Science Careers at Science Magazine

“Obtaining feedback on your personal statement (or any piece of writing) can be intimidating, but feedback is essential for creating a polished and readable document.”

Bik’s Picks

Why Orange Juice Tastes Disgusting After You Brush Your Teeth: Finally, an answer – Sarah Fecht – Popular Science

“In a handy video, the American Chemical Society has explained why orange juice (and food in general) tastes like soap after you brush your teeth. “

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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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Microbiome digest, October 8, 2014

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Blogging from our yearly retreat in Santa Cruz, California: Rethinking Enterotypes, Wolbachia phylogenomics,  hydrothermal vents, and the influence of salamanders on soil microbiome.

Human Microbiome General

Genes & cells: Body microbes make useful molecules: Human microbiome produces thousands of drug candidates – Tina Hesman Saey – Science News

Human Gut Microbiome

Rethinking “Enterotypes” – Dan Knights – Cell Host and Microbe

“However, as discussed here, several different methods of collapsing enterotype variation into a few discrete clusters suggest that enterotype distribution is continuous and can vary widely within an individual.”

Fecal Bacterial Community Changes Associated with Isoflavone Metabolites in Postmenopausal Women after Soy Bar Consumption – Cindy H. Nakatsu – PLOS ONE

“Using DGGE profiles of PCR amplified 16S rRNA genes (V3 region) to compare microbial communities in fecal samples collected one week before and one week during soy supplementation revealed significant differences (ANOSIM p<0.03) before and after soy supplementation in all subjects. “

Insect microbiome

Phylogenomic analyses uncover origin and spread of the Wolbachia pandemic – Michael Gerth  – Nature Communications

“Here we present the first comprehensive phylogenomic analysis of Wolbachia supergroup relationships based on new whole-genome-shotgun data.”

Coral microbiome

Comparing Bacterial Community Composition of Healthy and Dark Spot-Affected Siderastrea siderea in Florida and the Caribbean – Christina A. Kellogg – PLOS ONE

“Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. “

Soil Microbiome

Summer temperature increase has distinct effects on the ectomycorrhizal fungal communities of moist tussock and dry tundra in Arctic Alaska – Luis N. Morgado – Global Change Biology

“We used Ion Torrent sequencing of the rDNA internal transcribed spacer 2 (ITS2) region to compare ECM fungal communities in plots with and without long-term experimental warming in both dry and moist tussock tundra.”

A metagenomics-based approach to the top-down effect on the detritivore food web: a salamanders influence on fungal communities within a deciduous forest – Donald M. Walker – Ecology and Evolution

“From each sample, DNA was extracted, fungal-specific amplification performed, and 454 pyrosequencing was used to sequence the nuclear ribosomal internal transcribed spacer (ITS2) region and partial ribosomal large subunit (LSU).”

Water microbiome

Evolutionary Strategies of Viruses, Bacteria and Archaea in Hydrothermal Vent Ecosystems Revealed through Metagenomics – Rika E Anderson – PLOS ONE

“Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, “

Metabolomics

Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine – Brianna B. Williams – -Cell Host and Microbe

“Using a combination of genetics, biochemistry, and crystallography, we identify and characterize two phylogenetically distinct enzymes found in the human microbiome that decarboxylate tryptophan to form the β-arylamine neurotransmitter

Techniques

Selective Microbial Genomic DNA Isolation Using Restriction Endonucleases – Helen E. Barnes – PLOS ONE

“Using synthetic genome mixtures, we demonstrate 80% recovery of Escherichia coli genomic DNA even when only femtogram quantities are spiked into 10 µg of human DNA background.”

 More Microbiology

Pseudomonas aeruginosa eradicates Staphylococcus aureus by manipulating the host immunity – Erwan Pernet – Nature Communications

“Our results indicate that a bacterium can eradicate another bacterium by manipulating the host immunity.”

Preparation and evaluation of low-calorie functional ice cream containing inulin, lactulose and Bifidobacterium lactis  – Majid Hashemi- International Journal of Dairy Technology

“This study was aimed to investigate the effects of replacing 5% fat and sugar by inulin and lactulose, respectively, on the survival of Bifidobacterium lactis and physicochemical and sensorial characteristics of the ice cream. “

Microbes in the News

Second Genome, Mayo Clinic team up to explore the microbiome – Stephanie M. Lee – SF Gate

“Second Genome will identify up to eight conditions in which the microbiome potentially plays a role, and the Mayo Clinic will provide human clinical samples for patients with those diseases.”

 Oral health affects overall health – PhillyTrib

“The evidence shows that an infection from periodontitis, or gum disease, can put you at risk for other serious conditions like heart disease, stroke and more.”

Safety Bees: Bacteria From Bees Used To Fight Infections – The Ledger

 “A group of 13 lactic-acid bacteria found in fresh honey from the honey stomach of bees could be the key to bringing an old folk remedy into modern science”

Bik’s Picks  

How dinosaurs divided their meals at the Jurassic dinner table – Science Daily

“How the largest animals to have ever walked on Earth fed, and how this allowed them to live alongside one another in prehistoric ecosystems, is the subject of new research.”

Imitation, Genetic Lineages, and Time Influenced the Morphological Evolution of the Violin – Daniel H. Chitwood – PLOS ONE

“Here, I provide an analysis of morphological evolution in the violin family, sampling the body shapes of over 9,000 instruments over 400 years of history.”

Cat Watch 2014: What’s it like being a cat? – BBC

“Cats are at a crucial point in their evolutionary journey as they transform from solitary hunters to domestic pets, a study by the BBC and the Royal Veterinary College has revealed.”
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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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