Category Archives: Human oral

Human microbiome, June 19

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The journal Immunity has a special with several great papers on (gut) microbiome and diet. And even Martha Stewart is writing about the microbiome! In style, of course.

Oral microbiome

Screen Shot 2014-06-19 at 10.50.07 PMMining the Mouth’s Many Microbes – Tracy Vence – The Scientist

““The whole world passes through the oral cavity,” said Purnima Kumar, an assistant professor of periodontology at the Ohio State University College of Dentistry. This makes investigating the microbial communities present in the mouth a challenge.”

Gut microbiome

Screen Shot 2014-06-19 at 10.49.36 PMFinding the Missing Links among Metabolites, Microbes, and the Host – Pieter C. Dorrestein – Immunity

“Here, we provide our perspective on these connections and outline a systematic research program that could turn these individual links into a broader network that allows us to understand how these components interact. “

Screen Shot 2014-06-19 at 10.51.41 PMMining the Human Gut Microbiota for Effector Strains that Shape the Immune System – Philip P. Ahern – Immunity

“Here, we discuss a scalable, less biased approach for identifying effector strains in complex microbial communities that impact immune function. The approach begins by identifying uncultured human fecal microbiota samples that transmit immune phenotypes to germ-free mice.”

Screen Shot 2014-06-19 at 10.51.09 PMDiet, Metabolites, and “Western-Lifestyle” Inflammatory Diseases – Alison N. Thorburn – Immunity

“This review highlights what is currently known about diet, metabolites, and their associated immune pathways in relation to the development of inflammatory disease.”

Screen Shot 2014-06-19 at 10.52.28 PMInflammatory Bowel Disease as a Model for Translating the Microbiome – Curtis Huttenhower – Immunity

“IBD thus represents perhaps the most comprehensive current model for understanding the human microbiome’s role in complex inflammatory disease. Here, we review the influences of the microbiota on IBD and its potential for translational medicine.”

Screen Shot 2014-06-19 at 10.54.48 PMCulturomics and pyrosequencing evidence of the reduction in gut microbiota diversity in patients with broad-spectrum antibiotics – Grégory Dubourg – International Journal of Antimicrobial Agents

“Culturomics was performed on four stool samples from patients treated with large-scale antibiotics to assess the diversity of their gut flora in comparison with other culture-dependent studies. Pyrosequencing of the V6 region was also performed and was compared with a control group.”

Screen Shot 2014-06-19 at 10.55.24 PMLong-term monitoring of the human intestinal microbiota from the 2nd week to 13 years of age – Akihito Endo – Anaerobe

“Few long term follow-up studies have been reported and we therefore characterized the development of intestinal microbiota of ten subjects from the 2nd week of life to 13 years of age. PCR-denaturing gradient gel electrophoresis combined with several bacterial group-specific primer sets demonstrated the colonization steps of defined bacterial groups in the microbiota”

Respiratory microbiome

Time between sputum sample collection and storage significantly influences bacterial sequence composition from Cystic Fibrosis respiratory infections – Leah Cuthbertson – Journal of Clinical Microbiology

“Aliquots were stored at room temperature before freezing at -80°C for increasing intervals up to 72 hour period. Samples were treated with propidium monoazide, to distinguish live from dead cells, prior to DNA extraction, and 16S rRNA gene pyrosequencing was used to characterise the bacterial composition.”

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Human Pharyngeal Microbiome May Play a Protective Role in Respiratory Tract Infections – Zhancheng Gao – Genomics, Proteomics & Bioinformatics

“Recent studies have demonstrated that the pharyngeal microbiome comprises an abundance of bacterial species that interact with the local epithelial and immune cells, and together, they form a unique micro-ecological system.”

Skin and wounds microbiology

Screen Shot 2014-06-19 at 10.57.13 PMMicrobial profiling of combat wound infection through detection microarray and next-generation sequencing – Nicholas A. Be – Journal of Clinical Microbiology

“We employed a microarray capable of detecting all sequenced pathogens for interrogation of 124 wound samples from extremity injuries in combat-injured U.S. service members. A subset of samples was also processed via next-generation sequencing and metagenomic analysis. “

Press coverage:

Screen Shot 2014-06-19 at 11.00.07 PMHealing warriors by making a census of combat wounds’ microbiota – Melissa Healy – LA Times

“New research suggests that physicians treating future U.S. troops (and perhaps those treating some of today’s wounded warriors) may be able to take a fast and thorough census of the microorganisms living in a combat wound and tailor their treatment accordingly.”

Human microbiome in the news

Screen Shot 2014-06-19 at 10.56.06 PM4 habits for a healthy gut – Martha Stewart – CNN

“Studies also suggest that diabetic and obese patients tend to lack a diversity of bacteria, and the Cleveland Clinic found that some bacteria metabolize components of egg and meat to produce a compound that aids in the clogging of arteries.”

Screen Shot 2014-06-19 at 10.44.58 PMWebinar: The Promise of the Microbiome: Function and Dysfunction in Humans and Beyond – Science Magazine, featuring David Relman, Rob Knight, and Jack Gilbert

“During this webinar, the speakers will:

  • Provide a brief introduction to microbiomes and how they may fundamentally impact our study of the natural world
  • Share their research data on human and nonhuman microbiota, including microbe-associated environmental impacts on human health
  • Discuss the role of microbiomes in obesity and malnutrition
  • Answer your questions live during the webinar!”

Bacterial detection in blood and other sites

Screen Shot 2014-06-19 at 10.58.32 PMMassive Parallel Sequencing Provides New Perspectives on Bacterial Brain Abscesses – Øyvind Kommedal – Journal of Clinical Microbiology

“Bacterial 16S rRNA genes were amplified directly from the specimens and sequenced using Ion Torrent technology, with an average of 500,000 reads per sample. The results were compared to those from culture- and Sanger sequencing-based diagnostics.”

Animal models of microbiota

Screen Shot 2014-06-19 at 10.59.25 PMDiet-Induced Alterations in Gut Microflora Contribute to Lethal Pulmonary Damage in TLR2/TLR4-Deficient Mice – Yewei Ji – Cell Reports

“Here, we show that chronic intake of a high-fat diet (HFD), not a low-fat diet, leads to severe pulmonary damage and mortality in mice deficient in Toll-like receptors 2 and 4 (DKO).”

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Human microbiome, June 18

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Today we “Hover or Cover” the toilet seat, compare uBiome and American Gut results, and learn about bacterial diversity and stem cell transplants, breast milk microbiota, and culturomics.

Microbiome in the news

Screen Shot 2014-06-18 at 10.31.46 PMHere’s the poop on getting your gut microbiome analyzed – Tina Hesman Saey – ScienceNews

“When the second set of gut results came in, I was shocked. The results didn’t match at all with µBiome. “

WATCH: Is it OK to sit on a public toilet seat? – ScienceAlert

“It’s a dilemma we’ve all faced at some point: should you ever let your bum touch a public toilet seat? Thankfully Mitch and Greg from AsapSCIENCE have examined the evidence and come up with the (somewhat surprising) answer in their latest episode.”

Gut Reactions – Claudia Wallis – Scientific American

“Intestinal bacteria may help determine whether we are lean or obese”

10 Things You Need To Know About Your Microbiome – Raphael Kellman – MindBodyGreen

Pregnancy and Birth

Gut and Breast Milk Microbiota and Their Role in the Development of the Immune Function – Maria Elisabetta Baldassarre – Current Pediatrics Reports

“In newborns, the maternal gut microbiota may either come across into the amniotic fluid or secrete factors that enter the amniotic fluid and affect the development of oral tolerance in utero.”

Oral microbiome

Acquiring and maintaining a normal oral microbiome: current perspective
Egija Zaura – Frontiers in Cellular and Infection Microbiology

“In this review we present our hypothesis on how a healthy oral microbiome is acquired and maintained.”

Gut microbiome

The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation – Ying Taur – Blood

“Fecal specimens were collected from 80 recipients of allo-HSCT at the time of stem cell engraftment. Bacterial 16S rRNA gene sequences were characterized, and microbial diversity was estimated using the inverse Simpson index. “

Culturomics and pyrosequencing evidence of the reduction in gut microbiota diversity in patients with broad-spectrum antibiotics – Grégory Dubourg – International Journal of Antimicrobial Agents

“Culturomics was performed on four stool samples from patients treated with large-scale antibiotics to assess the diversity of their gut flora in comparison with other culture-dependent studies. Pyrosequencing of the V6 region was also performed and was compared with a control group. “

Screen Shot 2014-06-18 at 10.33.33 PMCharacterization of bacterial community shift in human Ulcerative Colitis
patients revealed by Illumina based 16S rRNA gene amplicon sequencing – Sandeep A Walujkar – Gut Pathogens

“Mucosal microbiota was analyzed by means of 16S rRNA gene-based Illumina high throughput sequencing. Quantitative real-time PCR (qPCR) was performed to determine total bacterial abundances.”

Keeping peace with the microbiome: acetate dampens inflammatory cytokine production in intestinal epithelial cells – Nicholas Arpaia – Immunology & Cell Biology

“In this issue, Ishiguro et al.2 show that the short-chain fatty acid (SCFA), acetate, produced during carbohydrate fermentation by commensal microorganisms in the cecum, is capable of dampening responses within intestinal epithelial cells (IEC), and functions by targeting the downstream signaling proteins that are activated on recognition of bacterial flagellin by TLR5”

Respiratory microbiome

A large genomic island allows Neisseria meningitidis to utilize propionic acid, with implications for colonisation of the human nasopharynx – Maria Chiara E. Catenazzi – Molecular Microbiology

“Here we identify a genomic island (the prp gene cluster) in N. meningitidis that enables this species to utilize propionic acid as a supplementary carbon source during growth, particularly under nutrient poor growth conditions. “

Animal and in vitro models of human microbiome

Observation of Inflammatory Responses in Mice Orally Fed with Bacteriophage T7 – Kwangseo Park – Journal of Applied Microbiology

“This study investigated the inflammatory responses in mice fed orally with bacteriophages. The mice were fed with either murine norovirus (MNV) or bacteriophage T7 for 10 days and then sacrificed. “

Development of an oral mucosa model to study host-microbiome interactions during wound healing – Tine De Ryck – Applied Microbiology and Biotechnology

“Microbiota derived from oral swabs were cultured on an agar/mucin layer and challenged with monolayers of keratinocytes grown on plastic or collagen type I layers embedded with fibroblasts.”

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Human microbiome, June 16

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A guide to your poop and more serious papers about oral, vaginal microbiomes and bacteria detection in joint fluids.

Oral microbiome

Screen Shot 2014-06-16 at 11.19.50 PMBacteria choose to fight and flee (commentary on a recent PNAS paper by Stacy et al. )- Christina Tobin Kåhrström – Nature Reviews Microbiology

“Together, these data suggest an elegant mechanism by which A. actinomycetemcomitans uses catalase to enzymatically ‘fight’ H2O2 and dispersin B to ‘flee’ from the close vicinity of S. gordonii, where H2O2 levels are highest, to a location where access to L-lactate is still possible. “

Oral challengesFornitersChallenges in the culture-independent analysis of oral and respiratory samples from intubated patients – Vladimir Lazarevic – Front. Cell. Infect. Microbiol.

“We explored the bacterial community diversity of the microbiota from oral and respiratory samples of intubated patients hospitalized in the intensive care unit and we discuss the technical challenges that may arise while using culture-independent approaches to study these types of samples.”

Vaginal microbiome

Ashok VagInfluence of the tryptophan-indole-IFNγ axis on human genital Chlamydia trachomatis infection: role of vaginal co-infections – Ashok Aiyar – Front. Cell. Infect. Microbiol.

“In this review, we discuss the natural history of genital chlamydial infections, morphological and molecular changes imposed by IFNγ on Chlamydia, and finally, the microenvironmental conditions associated with vaginal co-infections that can ameliorate the effects of IFNγ on C. trachomatis.”

Gut microbiome

ToiletThe Not-So-Gross Guide to Your Poop – Laura Barcella – Refinery29

“So, what is your excrement trying to tell you? Read on for clues about how to decipher your bowel movements.”

Bacteria detection in otherwise sterile sites

Screen Shot 2014-06-16 at 11.24.38 PMRapid isolation and diagnosis of live bacteria from human joint fluids by using an integrated microfluidic system – Wen-Hsin Chang – Lab on a Chip

 

“…an integrated microfluidic system capable of detecting live bacteria from clinical PJI samples within 55 minutes is developed in this study. This system employs an ethidium monoazide (EMA)-based assay and a PCR with universal bacterial primers and probes to isolate and detect only the live bacteria that commonly cause PJI. “

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Human microbiome, June 13

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Sjögren’s disease, diabetes, and Clostridium difficile infection. And the importance of a good title.

Oral microbiome

ScienceCodexSjögren’s Syndrome significantly increases risk of heart attack – Science Codex

“A new study presented today at the European League Against Rheumatism Annual Congress (EULAR 2014) showed a significantly increased risk of heart attack in patients with Sjögren’s syndrome (SjS), particularly in the first year following diagnosis.”

Gut microbiome

DiabetologiaStudy shows gut microbe composition different in young children with and without type 1 diabetes [zipped PDF]- Marcus de Goffau and Hermie Hansen – Diabetologia

and in the press:

diabetesStudy shows gut microbe composition different in young children with and without type 1 diabetes – Medical Xpress

“New research published in Diabetologia (the journal of the European Association for the Study of Diabetes) shows that children diagnosed with type 1 diabetes have a less balanced composition of gut bacteria compared with children of the same age without diabetes. “

KefirStaggered and tapered antibiotic withdrawal (STAW) with administration of Kefir for recurrent Clostridium difficile infection – Johan S. Bakken – Clinical Infectious Diseases

“Daily administration of the probiotic Kefir given in combination with a staggered and tapered antibiotic withdrawal regimen may resolve recurrent Clostridium difficile infection as effectively as fecal microbiota transplantation (FMT).”

Animal models of human microbiome and disease

I’m trying hard to wrap my brain around this title:
AACGastrointestinal Colonization With a Cephalosporinase-Producing Bacteroides Species Preserves Colonization Resistance Against Vancomycin-Resistant Enterococcus and Clostridium difficile in Cephalosporin-Treated Mice – Usha Stiefel – Antimicrobial Agents and Chemotherapy

“Stool concentrations of VRE and ceftriaxone were measured, cecal levels of C. difficile 24 hours after incubation were quantified, and denaturing gradient gel electrophoresis (DGGE) of microbial 16S rRNA genes was performed to evaluate antibiotic effect on the microbiota. “

In the press, much better title:

Good bacteria armed with antibiotic resistance protect gut microbiome – Science Codex

“The novel aspect of the research is that the enzyme produced by these bacteria, beta-lactamase, is a major cause of antibiotic resistance, says first author, Usha Stiefel. Interestingly, the enzyme is not only protecting the bacteria that produce it but also the rest of the bacteria making up the intestinal microbiome.”

Screen Shot 2014-06-13 at 11.16.23 PMCurative effect of the probiotic strain Lactobacillus fermentum L23 in a murine model of vaginal infection by Gardnerella vaginalis – M. Daniele – Letters in Applied Microbiology

“Bacterial vaginosis is a common vaginal infection characterized by changes in the vaginal microbiota. The objective of this work was to evaluate the colonization ability and curative effect of Lactobacillus fermentum L23 after vaginal administration in female BALB/c mice infected with Gardnerella vaginalis. “

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Human microbiome, June 12

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Today digest features the comparison of the HMP vs MetaHIT extraction protocols, microbiota and food consumption, mites in your skin, and a TIME article with a critical view.

Oral microbiome

Screen Shot 2014-06-12 at 9.59.53 PMGum disease bacteria selectively disarm immune system, study finds – Medical express

“In a new study, University of Pennsylvania researchers show that bacteria responsible for many cases of periodontitis cause this imbalance, known as dysbiosis, with a sophisticated, two-prong manipulation of the human immune system.”

Gut microbiome

yin yangReview: The Yin and Yang of Bacterial Resilience in the Human Gut Microbiota – Molly K. Gibson – Journal of Molecular Biology

“Here we review the mechanisms by which the host modulates the gut community composition during health and disease, and discuss prospects for antibiotic and probiotic therapy for restoration of a healthy intestinal community following disruption.”

obese women fructInulin-type fructans modulate intestinal Bifidobacterium species populations and decrease fecal short-chain fatty acids in obese women – Nuria Salazar – Clinical Nutrition

“ITF consumption selectively modulates Bifidobacterium spp. and decreases fecal SCFA concentration in obese women. ITF could lessen metabolic risk factors associated with higher fecal SCFA concentration in obese individuals.”

Screen Shot 2014-06-12 at 8.36.07 PMGlossary of the Gut Microbiome – Compiled by The American College of Gastroenterology

 

Skin microbiome

Screen Shot 2014-06-12 at 9.44.13 PMThese mites live on your face and come out to have sex at night – Joseph Stromberg – Vox

“Right now, there are thousands of mites on your face. They’re microscopic, but closely related to spiders and ticks. And despite your reaction to hearing this news, there’s absolutely nothing wrong with you.”

Animal models of human microbiome and disease

vitkQuantification of phylloquinone and menaquinones in feces, serum, and food by high-performance liquid chromatography-mass spectrometry – J. Philip Karl – Journal of Chromatography B

“We developed a novel method employing high-performance liquid chromatography-mass spectrometry with atmospheric pressure chemical ionization (LC-APCI-MS) for simultaneous quantification of 11 vitamin K vitamers that can be applied in feces, serum and food.”

Microbial Bioreactors

vegetalBeneficial effects of fermented vegetal beverages on human gastrointestinal microbial ecosystem in a simulator – Fernanda Bianchi – Food Research International

“To monitor the effects on microbial community composition, plate counts on specific growth media and a PCR-DGGE analysis were performed on samples from all colon compartments – ascending, transverse and descending.”

Microbiome conference

Screen Shot 2014-06-12 at 8.42.07 PMKenneth Rainin Foundation’s 2014 Innovations Symposium to Feature Virus Hunters and Gut Explorers – Taming the Microbiome – July 15 – 16, 2014, San Francisco.

“This year’s dynamic keynote speakers each bring a unique perspective on the human microbiome.”

Microbiome in the Press

timeExercise Helps Your Gut Bacteria: Amazing, Overblown, or Plain Incorrect? – Alexandra Sifferlin – Time

“Though he sees great promise in researching the microbiome, Eisen says it irks him when studies are blown out of portion both by scientists and the press.”

Screen Shot 2014-06-12 at 9.56.29 PMHere’s bacteria you ought to be eating – Craig Sailor – The Olympian

“Blake is a big proponent of raw, living fermented foods. The probiotic or friendly bacteria in the food provides nutrients and vitamins. “They also produce digestive enzymes that help us get more out of our food,” she said.”

breadWhite Bread May Encourage Growth Of ‘Good’ Bacteria – Jaleesa Baulkman – University Herald (mentions a study featured here that was recently published in American Chemical Society’s Journal of Agricultural and Food Chemistry.)

“Researchers said their most novel finding was that white bread boosted Lactobacillus, a group of beneficial bacteria. The results were surprising because white bread is a much-maligned food. “

Techniques: DNA extraction from stool

Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis – Agata Wesolowska-Andersen – Microbiome

“We observed significant differences in distribution of bacterial taxa depending on the method. While eukaryotic DNA was most efficiently extracted by the MetaHIT protocol, DNA from bacteria within the Bacteroidetes phylum was most efficiently extracted by the HMP protocol.”

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Human microbiome, June 11

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Bacterial community classes in HMP subjects, oral health in postmenopausal women, and gut epithelial regeneration.

Human microbiome – general

Yanjiao Zhou ExplorationExploration of bacterial community classes in major human habitats – Yanjiao Zhou – Genome Biology

“Here, we present an analysis of the groupings of bacterial communities in stool, nasal, skin, vaginal and oral habitats in a healthy cohort of 236 subjects from the Human Microbiome Project.” “We identified 2 to 6 community classes for each of the 18 habitats from the HMP healthy cohort by clustering augmented by manual inspection.”

ExploringExploring New Horizons in Microbiome Research – Christoph A. Thaiss, Eran Elinav – Cell Host & Microbe

“Leading scientists in microbiome research met at Lake Titisee, Germany, in April 2014 to discuss the current state of the field, the most urgent and unresolved questions, state-of-the-art technological advances, and new avenues of future research. “

Oral microbiome

Screen Shot 2014-06-11 at 9.35.26 PMPorphyromonas gingivalis Manipulates Complement and TLR Signaling to Uncouple Bacterial Clearance from Inflammation and Promote Dysbiosis – Tomoki Maekawa – Cell Host & Microbe

“As previously reported, P. gingivalis remodels the oral microbiota into a dysbiotic state by exploiting complement. Now we show that in neutrophils P. gingivalis disarms a host-protective TLR2-MyD88 pathway via proteasomal degradation of MyD88, whereas it activates an alternate TLR2-Mal-PI3K pathway. “

Screen Shot 2014-06-11 at 10.08.26 PMUB receives $4 million NIH grant to study oral health in postmenopausal women – Pat Donovan – University at Buffalo

“These techniques involve Next Generation Sequencing (NGS) using culture-independent techniques to identify 16S rRNA genes and allow for a more complete and detailed characterization of the microbial composition and diversity of the human oral cavity, Wactawski-Wende says.”

Pregnancy and Birth

Screen Shot 2014-06-11 at 10.09.30 PMPregnant Women With Posttraumatic Stress Disorder and Risk of Preterm Birth – Kimberly Ann Yonkers – JAMA Psychiatry

“Longitudinal, prospective cohort study of 2654 women who were recruited before 17 completed weeks of pregnancy from 137 obstetrical practices in Connecticut and Western Massachusetts.”

Animal models of human microbiota

Screen Shot 2014-06-11 at 10.07.04 PMThe Cytosolic Bacterial Peptidoglycan Sensor Nod2 Affords Stem Cell Protection and Links Microbes to Gut Epithelial Regeneration – Giulia Nigro – Cell Host & Microbe

“We used in vitro cultured organoids of intestinal crypts from mice, reinforced with in vivo experiments, to examine the crypt-microbiota interface.”

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Human microbiome, June 10

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Today we’ll cover the lung microbiome, salivary gland function, NEC, and sequencing of cosmid clones.
Oral microbiome

AutophagyAutophagy Correlates with Maintenance of Salivary Gland Function Following Radiation – Maria Morgan-Bathke – Nature Scientific Reports

“Thus, autophagy appears to play a beneficial role in salivary glands following radiation”

UbiquitousUbiquitous Sialometabolism Present among Oral Fusobacteria – Saori Yoneda – PLOS ONE

“Using microarray analysis, we examined the transcriptional response of F. nucleatum subspecies nucleatum to whole blood in order to identify some of the genetic responses that might occur during the transition from health to disease.”

NYU and UCSF researchers develop a framework for monitoring oral cancer – ScienceCodex

“”We know that other cancers, including gallbladder, colon, lung and prostate, have been associated with particular bacterial infections, so we hypothesized that shifts in the composition of the normal oral cavity microbiome could be promoters or causes of oral cancer,” said Dr. Albertson.”

Respiratory microbiome

Screen Shot 2014-06-10 at 9.32.19 PMBreathing Life into Lung Microbiome Research – Rina Shaikh-Lesko – The Scientist

“Although it’s far less populated than the mouth community that helps feed it, researchers increasingly appreciate the role of the lung microbiome in respiratory health.”

Impact off extImpact of Experimental Human Pneumococcal Carriage on Nasopharyngeal Bacterial Densities in Healthy Adults – Joshua R. Shak – PLOS ONE

“To better understand how these bacteria change in relation to pneumococcal colonization, we used species-specific quantitative PCR to examine bacterial densities in 52 subjects 7 days before, and 2, 7, and 14 days after controlled inoculation of healthy human adults with S. pneumoniae serotype 6B.”

Pregnancy and Birth

BrainModerate and Late Preterm Birth: Effect on Brain Size and Maturation at Term-Equivalent Age – Jennifer M. Walsh – Radiology

“MLPT birth is associated with smaller brain size, less-developed myelination of the posterior limb of the internal capsule, and more immature gyral folding than those associated with full-term birth. “

Preemie Research Highlights Concerns With Human Experimentation – Frederick Reese – Mintpress

“Parents weren’t fully aware of the risks associated with a medical research trial they allowed their babies to participate in.”

Screen Shot 2014-06-10 at 9.30.20 PMSmall Intestinal Intraepithelial TCRγδ+ T Lymphocytes Are Present in the Premature Intestine but Selectively Reduced in Surgical Necrotizing Enterocolitis – Jörn-Hendrik Weitkamp – PLOS ONE

“In human preterm infants, the proportion of IEL was reduced by 66% in 11 NEC ileum resections compared to 30 non-NEC controls (p<0.001). While γδ IEL dominated over conventional αβ IEL early in gestation in mice and in humans, γδ IEL were preferential decreased in the ileum of surgical NEC patients compared to non-NEC controls (50% reduction, p<0.05).”

Antibiotics and microbiome

Synthetic Biologics and Enterome Bioscience Collaborate on Microbiome Research to Support Synthetic Biologics’ C. difficile Program – MarketWatch

“Synthetic Biologics, Inc. (nyse mkt:SYN), a developer of novel anti-infective biologic and drug candidates targeting specific pathogens that cause serious infections and diseases, and Enterome Bioscience SA, a pioneer in the development of innovative disease management solutions based on a deep understanding of the gut microbiome, today announced that they have entered into an agreement to conduct metagenomic research on the effects of beta-lactam antibiotics on the gastrointestinal microflora (microbiome) of human patients”

Animal models of human disease

Screen Shot 2014-06-10 at 9.38.10 PMSaccharomyces boulardii Administration Changes Gut Microbiota and Reduces Hepatic Steatosis, Low-Grade Inflammation, and Fat Mass in Obese and Type 2 Diabetic db/db Mice – Amandine Everard – mBio

“Here we found that type 2 diabetic and obese mice (db/db) treated with Saccharomyces boulardii exhibited reduced body weight, fat mass, hepatic steatosis, and inflammatory tone. “

Metagenomics and sequencing

Evaluation of a pooledEvaluation of a Pooled Strategy for High-Throughput Sequencing of Cosmid Clones from Metagenomic Libraries – Kathy N. Lam – PLOS ONE

“We investigated a hybrid Sanger/Illumina pooled sequencing strategy that omits barcoding altogether, and we evaluated this strategy by comparing the pooled sequencing results to reference sequence data obtained from traditional barcode-based sequencing of the same set of clones. “

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Human Microbiomes, June 9

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Apples and coffee are good for your teeth, exercise good for your microbial diversity, role of microbiota in lung cancer, and lots of metabolomics papers.

Human Oral Microbiome (and some skin too!)

AppleAnticaries effect of an antioxidant-rich apple concentrate on enamel in an experimental biofilm-demineralisation model – Rodrigo A. Giacaman – Journal of Applied Microbiology

“Streptococcus mutans biofilms exposed to ARAC after a cariogenic challenge with sucrose induced lower enamel demineralisation than the positive control. The highest dilution of ARAC at 1: 100,000 (v/v) showed the most marked reduction in demineralisation of about fifty seven percent.”

CRIPSrConservation of streptococcal CRISPRs on human skin and saliva – Refugio Robles-Sikisaka – BMC Microbiology

“We investigated the conservation of CRISPR content from streptococci on skin and saliva of human subjects over 8-weeks to determine whether similarities existed in the CRISPR spacer profiles and whether CRISPR spacers were a stable component of each biogeographic site”

Screen Shot 2014-06-10 at 2.09.54 AMAntibacterial effect of coffee: calcium concentration in a culture containing teeth/biofilm exposed to Coffea Canephora aqueous extract – N. Meckelburg -Letters in Applied Microbiology

“This study revealed an inhibitory action of Coffea canephora against dental biofilm. This coffee species caused bacterial lysis and consequent release of calcium into the medium.”

Human gut microbiome

ClarkeExercise and associated dietary extremes impact on gut microbial diversity – Siobhan F Clarke – Gut

“… athletes had a higher diversity of gut micro-organisms, representing 22 distinct phyla, which in turn positively correlated with protein consumption and creatine kinase.”

BMReview: Molecular ecological tools to decipher the role of our microbial mass in obesity – GDA Hermes – Beneficial Microbes

“ This review aims to describe the different molecular approaches and their contributions to our understanding of the role of the GI microbiota in host energy homeostasis. ”

Screen Shot 2014-06-10 at 1.00.40 AMFecal microbiome analysis as a diagnostic test for diverticulitis – L. Daniels – European Journal of Clinical Microbiology & Infectious Diseases

“Differences in bacterial phylum abundance and diversity (Shannon index) of the resulting profiles were assessed by conventional statistics. Dissimilarity in microbiome composition was analyzed with principal coordinate analysis (PCoA) based on cosine distance measures. “

Impaired Innate Immune Function Associated with Fecal Supernatant from Crohn’s Disease Patients: Insights into Potential Pathogenic Role of the Microbiome – Meelu, Parool – Inflammatory Bowel Diseases

Opinion Article: Gut Microbes and Host Physiology: What Happens when you Host Billions of Guests? – Jennifer L. Pluznick – Frontiers in Endocrinology

“The literature is rife with examples of phenotypes which were not easily replicated by other groups – even when using the “same mice” – and we should consider whether some of these examples may be, in fact, due to the influence of gut microbiota.”

ProalInflammatory Disease and the Human Microbiome – Amy D Proal – Discovery Medicine

“The microbes that contribute to this dysfunction are often inherited from family members. Immunosuppressive therapies for inflammatory disease allow pathogens driving these processes to spread with greater ease.”

BMUnderstanding gut microbiota in elderly’s health will enable intervention through probiotics – G. Pérez Martínez – Beneficial Microbes

“Intervention studies of probiotics and prebiotics in elderly are not very abundant, but most cases showed that Bifidobacterium populations can efficiently be stimulated with a concomitant decrease of Enterobacteria. “

ClarkeGut Microbiota: The Neglected Endocrine Organ – Gerard Clarke – Molecular Endocrinology

“Indirectly and through as yet unknown mechanisms, the gut microbiota exerts control over the hypothalamic-pituitary-adrenal axis (HPA).”

The June issue of Gut this month features the abstracts from the British Society of Gastroenterology Annual General Meeting 16–19 June 2014 in a Supplemental issue

Human respiratory microbiome

Screen shot 2014-06-09 at 04.19PM, Jun 09The potential role of lung microbiota in lung cancer attributed to household coal burning exposures – H. Dean Hosgood III – Environmental and Molecular Mutagenesis

“This study seeks to explore the role of lung microbiota in lung cancer among never smoking Xuanwei women and how coal burning may influence these associations.”

Pregnancy and Birth

StrongholdPregnancy’s Stronghold on the Vaginal Microbiome – Marina R. S. Walther-António – PLOS ONE

“For a majority of the patients (n = 8), the vaginal microbiome was dominated by Lactobacillus crispatus throughout pregnancy.”

Masters Thesis: The Effect of Nutrition on the Microbiome in Pregnant Women and the Use of Micronutrient Supplemented Probiotic Yogurt to Improve Outcomes – Megan Kathleen Enos – University of Western Ontario

“The aims of this study were to characterize the gut, oral, and vaginal microbiotas of pregnant women ….. a clinical study was performed in Mwanza, Tanzania”

WopereisThe first thousand days – intestinal microbiology of early life: establishing a symbiosis – Harm Wopereis – Pediatric Allergy and Immunology

“This review provides an overview of the development of the intestinal microbiota, its bidirectional relationship with the immune system, and its role in impacting health and disease, with emphasis on allergy, in early life.”

Metabolomics

RinehartMetabolomic data streaming for biology-dependent data acquisition – Duane Rinehart – Nature Biotechnology

“Here we describe a solution to the time demands of metabolomic data upload to XCMS Online. In brief, we designed XCMS Online software that enables uploading of metabolomic data files from the instrument computer workstation as they are acquired. “

SulekA combined metabolomic and phylogenetic study reveals putatively prebiotic effects of high molecular weight arabino-oligosaccharides when assessed by in vitro fermentation in bacterial communities derived from humans – Karolina Sulek – Anaerobe

“All tested carbohydrate sources resulted in a significant increase of Bifidobacterium spp. between 1.79 fold (HA) and 1.64 fold (FOS) in the microbial populations after fermentation”

FariaInterplay between anthocyanins and gut microbiota – Ana Faria – J. Agric. Food Chem

“This review aimed to compile information regarding interaction of anthocyanins with microbiota, in two perspectives: i) identification of their colonic metabolites as potential bioactive molecules and ii) their role as prebiotic agents.”

Identification of the metabolites of myricitrin produced by human intestinal bacteria in vitro using ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry – Le-yue Du – Expert Opinion on Drug Metabolism & Toxicology

“To investigate the metabolic routes and metabolites of myricitrin, an important active ingredient of traditional herbal medicine, yielded by the isolated human intestinal bacteria, which have not been reported previously”

CrossA prospective study of serum metabolites and colorectal cancer risk – Amanda J. Cross – Cancer

“No overall associations were observed between serum metabolites and colorectal cancer, but serum glycochenodeoxycholate, a bile acid metabolite, was positively associated with colorectal cancer among women”

Gut microbiota and cardiometabolic outcomes: influence of dietary patterns and their associated components – Julia MW Wong – Am J Clin Nutr

“Examples of dietary components that alter the gut microbial composition include prebiotics and resistant starches.”

GaldzickiThe Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology – Michal Galdzicki – Nature Biotechnology

“Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers.”

Animal models of human disease

Animal models of gastrointestinal and liver diseases. Animal models of necrotizing enterocolitis: pathophysiology, translational relevance, and challenges – Peng Lu – American Journal of Physiology – Gastrointestinal and Liver Physiology

“In an attempt to provide some guidance to the growing community of NEC researchers, we now seek to review the key features of the major NEC models that have been developed in mammalian and nonmammalian species and to assess the advantages, disadvantage, challenges and major scientific discoveries yielded by each. “

Oral infection ecoliOral infection with enteropathogenic Escherichia coli triggers immune response and intestinal histological alterations in mice selected for their minimal acute inflammatory responses – Amanda Bardella Vulcano – Microbiology and Immunology

“In summary, it was found that EPEC triggers immune responses and intestinal histological alterations but does not produce evidence of diarrheal disease in mice infected by the oral route.”

Screen Shot 2014-06-10 at 2.00.38 AMDistinct signatures of host–microbial meta-metabolome and gut microbiome in two C57BL/6 strains under high-fat diet – Alesia Walker – ISME J

“A combinatory approach using metabolomics and gut microbiome analysis techniques was performed to unravel the nature and specificity of metabolic profiles related to gut ecology in obesity. “

General Human Microbiome

Why There is No Single Healthy Microbiome – Erik Garnas – Organic Fitness

“This quest for the perfect microbiome has not only led many people to tweak their diet and lifestyle in an attempt to be the best possible host, but also to the rapid growth of what is now a billion dollar market of probiotics, prebiotics, and other products that are specifically designed to modulate the microbial communities in and on the human body. “

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Human microbiomes, June 6

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Bacteria causing IBD (in an animal model), gut microbiota from Spanish infants, and radiation therapy damaging teeth.

Gut microbiome

GutAn intestinal arsonist: pathobiont ignites IBD and flees the scene – Stefan Jellbauer and Manuela Raffatellu – Gut

“Evidence for Proteobacteria as a potential trigger of IBD has been deduced by cohort studies showing that inflammatory diarrhoea caused by either Salmonella species or Campylobacter species predisposes genetically susceptible individuals to developing IBD”

AIEC pathobiont instigates chronic colitis in susceptible hosts by altering microbiota composition – Benoit Chassaing – Gut

“Transient AIEC colonisation, in WT mice, did not alter inflammatory markers, bacterial loads, microbiota composition, nor its pro-inflammatory potential. By contrast, transient AIEC colonisation of T5KO mice drove chronic inflammation which correlated with microbiota components having higher levels of bioactive LPS and flagellin.”

BBAReview: Rapidly expanding knowledge on the role of the gut microbiome in health and disease -M.C. Cénit – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

“In this review we describe the different approaches used to characterize the human microbiome, review current knowledge about the gut microbiome, and discuss the role of gut microbiota in immune homeostasis and autoimmunity.”

Screen Shot 2014-06-07 at 1.49.49 AMEx-Merck exec’s new microbiome startup has a pill that works like a fecal transplant against C. diff – Ransdell Pierson – MedCityNews

“The Seres oral capsule, called SER 109, in early clinical trials quickly eliminated symptoms in more than 90 percent of patients, Pomerantz said in a telephone interview.”

Malnutrition ‘damages gut bacteria’ – BBC Health News

“A team studied the gut health of malnourished children in Bangladesh. Writing in the journal Nature they said the bacterial make-up was not fully restored to normal after food supplements were given.”

Oral microbiome

ToothRadiation therapy alters microhardness and microstructure of enamel and dentin of permanent human teeth – Ligia Maria Napolitano Gonçalves – Journal of Dentistry

“The effects of gamma irradiation on dental substrate might contribute to increased risk of radiation tooth decay associated with salivary changes, microbiota shift and high soft and carbohydrate-rich food intake.”

Pregnancy and Birth

Screen Shot 2014-06-07 at 1.52.06 AMMicrobial Succession in the Gut: Directional Trends of Taxonomic and Functional Change in a Birth Cohort of Spanish Infants – Yvonne Vallès – PLOS Genetics

“Here, we analyze the patterns of taxonomic and functional change in the gut microbiota during the first year of life for a birth cohort of 13 infants. We detect that individual instances of gut colonization vary in the temporal dynamics of microbiota richness, diversity, and composition at both functional and taxonomic levels. “

Probiotics

Screen Shot 2014-06-07 at 1.53.11 AMProbiotics: Separating the Hype From the Healthy – Nikki Fotheringham – HuffingtonPost

“That’s right baby; we’re all just sacks of seething bacteria! Now before you freak out, remember that the word “bacteria” has been given negative connotations by the Purell-fueled paranoia of the germ police. “

 

Metabolomics

Journal of functional foodsStructural features and feruloylation modulate the fermentability and evolution of antioxidant properties of arabinoxylanoligosaccharides during in vitro fermentation by human gut derived microbiota – Jeroen Snelders – Journal of Functional Foods

“Two AXOS samples with a low average degree of arabinose substitution, specifically differing in average degree of polymerization, and three AXOS samples, specifically differing in ferulic acid (FA) content and appearance (free or bound), were incubated with cultured human colon microbiota.”

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Human microbiomes, June 5

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Today we have some commentaries on recent papers about microbiotas in malnutrition or on placentas, and new papers about oral bacteria in the bloodstream, helminths, and coincidental killers.

Oral microbiome

Screen Shot 2014-06-05 at 7.59.36 PMDissemination of Periodontal Pathogens in the Bloodstream after Periodontal Procedures: A Systematic Review – Anna Carolina Ratto Tempestini Horliana – PLOS ONE

“MEDLINE, EMBASE and LILACS databases were searched in duplicate through August, 2013 without language restriction. Observational studies were included if blood samples were collected before, during or after periodontal procedures of patients with periodontitis”

Screen Shot 2014-06-05 at 7.56.12 PMThe Emerging Landscape of Salivary Diagnostics – Yong Zhang- OHDM – Omics Online

“Here we review recent developments in salivary diagnostics that have been accomplished using salivaomics, the mechanisms of saliva diagnostics, as well as the translational and clinical application of saliva biomarkers”

Gut microbiome

Screen Shot 2014-06-05 at 7.57.14 PMInfection and Co-infection with Helminths and Plasmodium among School Children in Côte d’Ivoire: Results from a National Cross-Sectional Survey – Richard B. Yapi – PLOS Neglected Tropical Diseases

“We carried out the first national survey on parasitic worm and Plasmodium infection among children in 92 schools all over Côte d’Ivoire. Questionnaires were administered to determine the children’s socioeconomic status and infection-related risk factors. We found an overall prevalence of Plasmodium infection of 63.3%.”

ColonSome Antibiotics May Slightly Increase Colon Cancer Risk – Bahar Gholipour – LiveScience

“The researchers compared the amount of antibiotics the patients had taken at least six months before being diagnosed with cancer, to the amount of antibiotics taken by a group of about 86,000 healthy people.”

Screen Shot 2014-06-05 at 10.07.58 AMWhy Can’t Once-Malnourished Children “Catch Up”? Answer May Lie in Gut – Karen Weintraub – National Geographic

“There’s something lacking in our current approach to treatment,” said Gordon, who suspects the children may need to eat therapeutic foods for longer and/or get supplements of probiotics, or beneficial microorganisms, to catch up. “We need to think of food as interacting with this microbial organ.”

Screen Shot 2014-06-05 at 8.03.26 PMSevere hunger can have lasting effects for gut health, study finds – MedicalXPress

“Nutrition therapy has saved the lives of millions of malnourished infants, but may not restore an imbalance in gut bacteria that is key to long-term health and vitality, researchers said Wednesday.”

Pregnancy and birth

Screen Shot 2014-06-05 at 8.05.15 PMGearing up for a closer look at the human placenta – Jocelyn Kaiser – Science

“A placenta sustained you and every person ever born for 9 months, serving as your lungs and kidneys and pumping out hormones while you developed in the womb. Problems with this disk-shaped mass of tissue can contribute to everything from preterm births to diseases of middle age. Yet when a baby is born, hospitals usually throw the placenta away.”

Screen Shot 2014-06-05 at 9.57.32 AMMicrobirth: Why ‘Seeding Baby’s Microbiome’ Needs to Be on Every Birth Plan – Toni Harman – HuffingtonPost

“The latest scientific research is now starting to indicate that if the baby is not properly seeded with the mother’s own bacteria at birth, then the baby’s microbiome, in the words of Rodney R Dietert, Professor of Immunotoxicology at Cornell University, is left “incomplete”.”

General human microbiome

Screen Shot 2014-06-05 at 8.07.51 PMCoincidental killers – We assume that microbes evolved to attack humans when actually we are just civilian casualties in a much older war – Ed Yong – Aeon Magazine

“And some supposedly pathogenic bacteria were often common parts of the environment. ‘These organisms become accidental pathogens,’ says the microbiologist Arturo Casadevall from Yeshiva University in New York. ‘They’ll still be there even if you remove all the animals from the planet. And yet, evolution selected for just the right combination of traits to cause disease in humans.’”

Screen Shot 2014-06-05 at 8.12.08 PMSilicon Valley’s Top Ten Tech Trends – Jacqueline Vanacek – Forbes
Trend #7: Data-driven healthcare (from your gut).

The combination of personal health and fitness data, genomics, and even microbiomics will drive healthcare choices from real outcomes and individual probabilities. And since the bacteria in our digestive tracks has greater influence on our health than previously known, we really are what we eat!

Microbiome and Bioinformatics

Screen Shot 2014-06-05 at 8.11.20 PMBOTUX: Bayesian–like operational taxonomic unit examiner – Vishal N. Koparde – International Journal of Computational Biology and Drug Design

“Bayesian–like operational taxonomic unit examiner (BOTUX) is a new tool for the classification of 16S rRNA gene sequences into operational taxonomic units (OTUs) that addresses the problem of overestimation caused by errors introduced during PCR amplification and DNA sequencing steps”

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