Category Archives: Human gut

Human microbiome, June 26

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Mass spectrometry on Neanderthal poop – how cool is that? Then, nice article about fecal transplants, the Bristol Stool Chart Mug, role of bacteria in colon cancer, and Mycobacterium tuberculosis as a possible human symbiont.

Gut microbiome

Screen Shot 2014-06-26 at 10.22.55 PMThe Neanderthal Meal: A New Perspective Using Faecal Biomarkers – Ainara Sistiaga – PLOS ONE

“Our gas chromatography-mass spectrometry results from El Salt (Spain), a Middle Palaeolithic site dating to ca. 50,000 yr. BP, represents the oldest positive identification of human faecal matter.”

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I enjoyed reading this article. And not just because they mentioned one of our studies.
Getting to the Bottom of Fecal Transplants – Ricki Lewis – PLOS.org

“(…) babies’ bacteria were quite different at the outset, but by the end of the year, their communities resembled those in the adult digestive tract. And it was published right here at PLOS.”

41C8qjeUK2LWhich led me to the awesome The Bristol Stool Chart Mug – Amazon
Which I then ordered.

 

CRCFusobacterium and Enterobacteriaceae: Important players for CRC? – Emma Allen-Vercoea, Christian Jobin – Immunology Letters

“Not surprisingly, microbial dysbiosis is associated with numerous intestinal disorders including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). In this piece, we will review recent evidence that gut microbial dysbiosis can influence intestinal disease, including colitis and CRC.”

Screen Shot 2014-06-26 at 9.45.42 PMPrevalence and Duration of Asymptomatic Clostridium difficile Carriage among Healthy Subjects in Pittsburgh, Pennsylvania – Alison L. Galdys – Journal of Clinical Microbiology

“The prevalence of C. difficile carriage in this healthy cohort is concordant with prior estimates. C. difficile-colonized individuals may be important reservoirs for C. difficile and may falsely test positive for infections due to C. difficile when evaluated for community-acquired diarrhea caused by other enteric pathogens.”

Blood sugar improves with first gastrointestinal microbiome modulator, NM504 – Science Daily

“The not-yet-named therapeutic, NM504, is the first in a new class of therapies known as GI microbiome modulators. “

Role of humanRole of human gut microbiota metabolism in the anti-inflammatory effect of traditionally used ellagitannin-rich plant materials – Jakub P. Piwowarski – Journal of Ethnopharmacology

“The formation of urolithins was determined by ex vivo incubation of human faecal samples with aqueous extracts from selected plant materials.”

Me and my microbiome – New Scientist

“Now there are claims that a truly villainous bacterium – Mycobacterium tuberculosis, which causes TB – is actually symbiotic and helped us evolve our large brains (see “ Eat meat TB brainy”). “

Eat meat TB brainy – Adrian Williams, Robin Dunbar – New Scientist

“The tuberculosis bacterium co-evolved with humans at least 70,000 years ago, and possibly a great deal earlier. Could chronic TB infections have originally been beneficial to human life? Did the pathogen act as a symbiont, supplying nicotinamide at times of meat deficiency?”

Animal models of human microbiota and disease

Screen Shot 2014-06-26 at 9.47.30 PMIncorporation of therapeutically modified bacteria into gut microbiota inhibits obesity – Zhongyi Chen – Journal of Clinical Investigation

“Here, we demonstrated that administration of engineered NAPE-expressing E. coli Nissle 1917 bacteria in drinking water for 8 weeks reduced the levels of obesity in mice fed a high-fat diet. “

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Human and cell phone microbiome, June 24

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The PhoneBiome has finally been characterized. Effect of maltodextrin on gut microbiome, and obesity and risk for preterm birth.

Skin and phone microbiome

Mobile phones carry the personal microbiome of their owners – James F. Meadow – Peer J

“We found that about 22% of the bacterial taxa on participants’ fingers were also present on their own phones, as compared to 17% they shared on average with other people’s phones. “

Gut microbiome

The Metabolizable Energy of Dietary Resistant Maltodextrin Is Variable and Alters Fecal Microbiota Composition in Adult Men – David J. Baer – The Journal of Nutrition

“RM intake was associated with statistically significant increases (P < 0.001) in various operational taxonomic units matching closest to ruminococcus, eubacterium, lachnospiraceae, bacteroides, holdemania, and faecalibacterium, implicating RM in their growth in the gut. “

B cells as a critical node in the microbiota–host immune system network –
Emma Slack – Immunological Reviews

“In this review, we address how B-cell responses to members of the intestinal microbiota form a robust network with mucus, epithelial integrity, follicular helper T cells, innate immunity, and gut-associated lymphoid tissues to maintain host–microbiota mutualism.”

Classification and quantification of bacteriophage taxa in human gut metagenomes – Alison S Waller – ISME Journal 

“Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. “

Cesarean delivery and risk of inflammatory bowel disease: a systematic review and meta-analysis – Yi Li – Scandinavian Journal of Gastroenterology

“Results of this meta-analysis support the hypothesis that cesarean delivery was associated with the risk of CD but not of UC. The total rate of cesarean delivery of IBD patients was similar with that of control subjects.

Intestinal microbiota in pathophysiology and management of irritable bowel syndrome – Lee KN – World Journal of Gastroenterology

“…the role of the intestinal microbiota in the pathophysiology and management of IBS is not clear. This review provides the accumulating evidence on it.”

Pregnancy and Birth

Maternal Prepregnancy Body Mass Index and Risk of Spontaneous Preterm Birth – Gary M. Shaw – Paediatric and Perinatal Epidemiology

“Analyses of mothers without hypertension and diabetes, adjusted for age, education, height, and prenatal care initiation, showed obesity categories I–III to be associated with increased risk of spontaneous preterm birth at 20–23 and 24–27 weeks among those of parity 1 in each race/ethnic group.”

and

Obesity before pregnancy linked to earliest preterm births, Stanford/Packard study finds – Erin Digitale – Stanford Medicine News Center

“Women who are obese before they become pregnant face an increased risk of delivering their babies before 28 weeks of pregnancy, a new study of nearly 1 million California births has found.”

Maturation of the enteric mucosal innate immune system during the postnatal period – Marcus Fulde and Mathias W. Hornef – Immunological Reviews

“Here, we discuss both adaptive and developmental mechanisms of the mucosal innate immune system that prevent inappropriate stimulation and facilitate establishment of a stable homeostatic host–microbial interaction after birth.”

Early Infant Nutrition and Metabolic Programming: What Are the Potential Molecular Mechanisms? – Stephanie-May Ruchat – Current Nutrition Reports

“This review will present potential molecular mechanisms through which early postnatal nutrition may influence health and disease programming, focusing on research that used “-omics” approaches (i.e., epigenomics, transcriptomics, proteomics, and metabolomics).”

Oral presentation: Serum beta defensin concentration in the first trimester is related to genotype, and is higher in women who develop PPROM and deliver before 34 weeks – CP James – Arch Dis Child Fetal Neonatal Ed

“Serum hBD2 expression is higher in women who have PPROM and PTB. Women with PPROM and PTB have a distinct innate immune profile evident in their serum in the first trimester, which may provide the basis for a predictive test.”

Animal models of human microbiota and disease

Modulation of gut microbiota during probiotic-mediated attenuation of metabolic syndrome in high fat diet-fed mice – Jingjing Wang – ISME Journal

“Weighted UniFrac principal coordinate analysis based on 454 pyrosequencing of fecal bacterial 16S rRNA genes showed that the probiotic strains shifted the overall structure of the HFD-disrupted gut microbiota toward that of lean mice fed a normal (chow) diet. “

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission – Michelle G Rooks – ISME Journal

“Here, we surveyed the gut microbiome of the T-bet−/− Rag2−/− mouse model of colitis during active disease and treatment-induced remission. “

Early-Life Environmental Variation Affects Intestinal Microbiota and Immune Development in New-Born Piglets – Dirkjan Schokker – PLOS ONE

” We observed that the applied antibiotic treatment affected the composition and diversity of gut microbiota and reduced the expression of a large number of immune-related processes. The effect of management procedures on top of the use of an antibiotic was limited.”

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Human microbiome, June 23

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Lactobacillus feeding on human milk, Mycoplasma in preterm birth, and Clostridium difficile infection and gut microbiota.

Pregnancy and birth

Screen Shot 2014-06-23 at 10.51.26 PMA unique gene cluster for the utilization of the mucosal and human milk-associated glycans galacto-N-biose and lacto-N-biose in Lactobacillus casei – Gonzalo N. Bidart – Molecular Microbiology

“The data represent the first characterization of novel metabolic pathways for human milk oligosaccharides and glycoconjugate structures in Firmicutes”

Screen Shot 2014-06-23 at 11.01.13 PMReport from AANP 2014, Nashville, Tennessee: Screening for Bacteria May Help Pregnancy Outcomes – Ed Susman, MedpageToday

“In a single-center study, about 70% of symptomatic women who were screened for vaginal infections with either Mycoplasma Genitalium or Mycoplasma Hominis experienced preterm birth compared with 30% of the asymptomatic women who still underwent screening for the infections at a prenatal visit, reported Allison Phillips, DNP, of Robert Morris University in Pittsburgh, and colleagues.”

Oral microbiome

Screen Shot 2014-06-23 at 10.52.34 PMNew analysis reveals previously ‘hidden diversity’ of mouth bacteria – MBL

“Using a novel computational method called oligotyping, developed by MBL Assistant Research Scientist A. Murat Eren, scientists analyzed gene sequence data from nine sites in the oral cavity. ” “The study will be published in PNAS Online Early Edition the week of June 23-27, 2014”, but is not yet on PNAS website

Screen Shot 2014-06-23 at 10.53.35 PMEffects of pH and Lactate on Hydrogen Sulfide Production by Oral Veillonella spp. – Jumpei Washio – Applied and Environmental Microbiology

“Thus, in the present study, the H2S-producing activity of growing cells, resting cells, and cell extracts of oral Veillonella species and the effects of oral environmental factors, including pH and lactate, were investigated.”

Gut microbiome

Screen Shot 2014-06-23 at 10.54.40 PMStructural and functional changes in the gut microbiota associated to Clostridium difficile infection – Ana E. Pérez-Cobas – Frontiers in Microbiology

“Here, we analyze the composition and functional differences in the gut microbiota of C. difficile infected (CDI) versus non-infected patients, both patient groups having been treated with AB therapy. To do so we used 16S rRNA gene and metagenomic 454-based pyrosequencing approaches. “

Screen Shot 2014-06-23 at 10.58.40 PMThe HLA-DQ2 genotype selects for early intestinal microbiota composition in infants at high risk of developing coeliac disease – M Olivares – Gut

“Infants with a high genetic risk had significantly higher proportions of Firmicutes and Proteobacteria and lower proportions of Actinobacteria compared with low-risk infants.”

(Both human and animal)
Screen Shot 2014-06-23 at 10.57.57 PMA single genus in the gut microbiome reflects host preference and specificity – A Murat Eren – The ISME Journal

“In our dataset of 57 M sequence reads of the V6 region of the 16S ribosomal RNA gene in samples collected from seven host species, we identified 200 high-resolution taxonomic units within Blautia using oligotyping.”

Screen Shot 2014-06-23 at 10.57.04 PMMicrobiomes are true to type – Andrew H. Moeller and Howard Ochman – PNAS

“Enter Wang et al. (3), who provide both retrospective and experimental evidence that the maintenance of enterotypes in host populations is driven by dietary variation.”

General human microbiome

Screen Shot 2014-06-23 at 10.56.07 PMMicrobiota and neurodevelopmental windows: implications for brain disorders
– Yuliya E Borre – Trends in Molecular Medicine

“This review compares the parallel early development of the intestinal microbiota and the nervous system.”

Animal models of human microbiome

Screen Shot 2014-06-23 at 11.00.16 PMThe murine appendiceal microbiome is altered in spontaneous colitis and its pathological progression – Sultan Alkadhi – Gut Pathogens

“The appendiceal dysbiosis observed in our Winnie mice is commensurate with, and adds to extant literature data. The presence of Helicobacteraceae (Proteobacteria) only in colitic Winnie mice (but not control mice) is consistent with reports of increased Helicobacter in IBD patients. “

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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 17

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Gut bacteria swapping DNA segments, what happens after a fecal transplant, intestinal archaea, and more.

Gut microbiome

Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut – Michael J. Coyne – mBio

“Using seven coresident Bacteroidales species from one individual and eight from another, we identified five large chromosomal regions, each present in a minimum of three of the coresident strains at near 100% DNA identity.”

Recovery of the Gut Microbiome following Fecal Microbiota Transplantation – Anna M. Seekatz – mBio

“Here we investigated changes in the fecal microbiota structure following FMT in patients with recurrent C. difficile infection, and imputed a hypothetical functional profile based on the 16S rRNA profile using a predictive metagenomic tool.”

The Intestinal Archaea Methanosphaera stadtmanae and Methanobrevibacter smithii Activate Human Dendritic Cells – Corinna Bang – PLOS ONE

“Taken together, our findings strongly argue that the archaeal gut inhabitants M. stadtmanae and M. smithii are specifically recognized by the human innate immune system. “

Microbiota and Metabolome Associated with Immunoglobulin A Nephropathy (IgAN) –
Maria De Angelis – PLOS ONE

“This study aimed at investigating the fecal microbiota, and the fecal and urinary metabolome of non progressor (NP) and progressor (P) patients with immunoglobulin A nephropathy (IgAN). “

Respiratory microbiome

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

“These data on bacterial associations are the first to be reported surrounding experimental human pneumococcal colonization and show that co-colonizing effects are likely subtle rather than absolute.”

Vaginal microbiome

Diversity and stability of cultured vaginal lactobacilli in pregnant women from a multi-ethnic urban UK population – S.M. Husain – Journal of Applied Microbiology

“Self-collected vaginal swabs at 13 and 20 weeks gestation were obtained from women attending for routine antenatal care and cultured for lactobacilli.”

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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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