Human microbiome digest, October 14, 2014

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, August 29, 2014

@MicrobiomDigest will be enjoying vacation for the next two weeks, so I won’t be able to post as much as usual. I might occasionally have some time and internet access at the same time, and post something, but don’t rely on this blog during that time for your daily Microbiome fix. But I will be back! Enjoy this last (short) one for now:
Human oral microbiome

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

Human gut microbiome

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease – Noah W Palm – Cell

Modulation of immune development and function by intestinal microbiota – Agnieszka M. Kabat – Trends in Immunology

 

Worms, bacteria, and micronutrients: an elegant model of our diet – Lutfu Safak Yilmaz, Albertha J.M. Walhout – Trends in Genetics

 

Mammal microbiome

Spatial heterogeneity of gut microbiota reveals multiple bacterial communities with distinct characteristics (in flying squirrels) – Hsiao-Pei Lu – Scientific Reports

Social influences on the gut microbiome of developing monkeys – W.Z. Amaral – Brain, Behavior, and Immunity

 

Do Rumen Bacteroidetes Utilize an Alternative Mechanism for Cellulose Degradation? – AE Naas – mBio

 

Characterization of the Fecal Microbiota of Pigs before and after Inoculation with “Brachyspira hampsonii” – Matheus O. Costa – PLOS ONE

 

Sponges and corals

The versatile nature of coral-associated viruses – Bettarel Yvan – Environmental Microbiology

Onset and establishment of diazotrophs and other bacterial associates in the early life history stages of the coral Acropora millepora – Kimberley A. Lema – Molecular Ecology

Rocks and Water Microbiome

Microbial Colonization of Bare Rocks: Laboratory Biofilm Enhances Mineral Weathering – F. Seiffert – Procedia Earth and Planetary Science

Microbial diversity and biogeochemical cycling in soda lakes – Dimitry Y. Sorokin – Extremophiles

Food microbiome

Switzerland Puts Secret Bacteria In Cheese To Catch Knockoffs – Sarah Zhang – Gizmodo

Bioinformatics

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data – Yuan Zhang – PLOS Computational Biology

Metabolomics

Taking your breath away: metabolomics breathes life in to personalized medicine
Nicholas J.W. Rattray – Trends in Biotechnology

Phages and Viruses

Identifying and analyzing bacteriophages in human fecal samples: what could we discover? – Maite Muniesa1 & Juan Jofre – Future Medicine

Microbes in the news

Hotel rooms aren’t yucky – you colonize them with your own personal bacteria within hours — Rachel Feltman – Washington Post

A touching story: The ancient conversation between plants, fungi and bacteria – David Tenenbaum – News UW Madison

Bik’s Picks

The universal ‘anger face’: Each element makes you look physically stronger and more formidable – Science Daily

Zombie Bacteria Invasion? Nothing To Worry About – Science 2.0

Report: Ice Bucket Challenge Causing Ecological Mayhem in California – The Allium (Satire)

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Microbiome digest, August 4, 2014

Relief in a pressing problem, microbes at high altitude, and microbiome in cystic fibrosis.

Human gut microbiome

So glad this one finally came out!  Structural changes in the gut microbiome of constipated patients – Lixin Zhu – Physiological Genomics

“A cross-sectional pilot study was performed to compare stool microbial composition of 8 constipated patients and 14 non-constipated controls using 16S rRNA gene pyrosequencing.”

Microbiota and diabetes: an evolving relationship – Herbert Tilg, Alexander R Moschen – Gut

“A further hint towards an association between microbiota and T2D has been derived from studies in pregnancy showing that major gut microbial shifts occurring during pregnancy affect host metabolism.”

Harnessing the Intestinal Microbiome for Optimal Therapeutic Immunomodulation – S. Viaud – Cancer Research

“gut commensals, through lipopolysaccharide and other bacterial components, switch the tumor microenvironment, in particular the redox equilibrium and the TNF production of intratumoral myeloid cells during therapies with platinum salts or intratumoral TLR9 agonists combined with systemic anti-IL10R Ab respectively.”

Specific genetic and microbial signature associated with paediatric ileal Crohn’s disease -Isobel Leake – Nature Reviews Gastroenterology & Hepatology

“An increase in DUOX2 expression was associated with an expansion of Proteobacteria across all forms of IBD, whereas downregulation of APOA1 expression in association with depletion of certain Firmicutes and Bacteroidetes taxa was found to be specific for Crohn’s disease.”

Skin and wounds microbiome

Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research – Brendan Hodkinson and Elizabeth Grice – Advances in Wound Care

“The purpose of this review is to outline the current platforms, their applications, and the steps necessary to undertake microbiome studies using next-generation sequencing.”

Human respiratory microbiome

Directly Sampling the Lung of a Young Child with Cystic Fibrosis Reveals Diverse Microbiota – Perry S Brown – Annals ATS

“After pathologic examination verified that this child’s lung tissue reflected CF lung disease, we used bacterial rRNA gene pyrosequencing and computational phylogenetic analysis to identify the microbiota in serial sections of the tissue.”

Respiratory Viruses and Bacteria among Pilgrims during the 2013 Hajj – Samir Benkouiten – Emerging Infectious Diseases

“One third (36.3%) of the participants had acquired S. pneumoniae during their stay. Our results confirm high acquisition rates of rhinovirus and S. pneumoniae in pilgrims and highlight the acquisition of coronavirus E229.”

Fish microbiome

The Colonization Dynamics of the Gut Microbiota in Tilapia Larvae – Christos Giatsis – PLOS ONE

“Our results showed that variation in gut microbiota between replicate tanks was not significantly higher than within tank variation, suggesting that there is no tank effect on water and gut microbiota. “

Soil microbiome

FEMS Microbiology Ecology has a special issue on Polar and Alpine Microbiology with many papers on microbiomes of ice and soil. Here is the Editorial:
Polar and alpine microbiology in a changing world – John C. Priscu – FEMS Microbiology Ecology

“By virtue of their relatively rapid growth rates and metabolic diversity, we can expect microorganisms to be the first responders to fluctuating climatic conditions.”

Altitudinal Distribution Patterns of Soil Bacterial and Archaeal Communities Along Mt. Shegyla on the Tibetan Plateau – Jun-Tao Wang – Microbial Ecology

“Our results found that the ratio of bacterial to archaeal 16S rRNA gene abundance was negatively related with elevation.”

Water microbiome

Satellite remote sensing data can be used to model marine microbial metabolite turnover – Peter E Larsen – ISME Journal

“We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters”

Microbial Ecology

Changes in community assembly may shift the relationship between biodiversity and ecosystem function – Joseph E. Knelman and Diana R. Nemergut – Frontiers Microbiology

“Can differences in community assembly alter the relationship between biodiversity and ecosystem function?”

Probiotics

Lactobacillus rhamnosus GG suspected infection in a newborn with intrauterine growth restriction – I. Sadowska-Krawczenko – Beneficial Microbes

“Genotyping with the rep-PCR and AFLP methods confirmed the 100% genetic similarity for both the strain isolated from patient blood and the probiotic product.”

Can Eating Probiotic Yogurt Help Lower Your High Blood Pressure? – Susmita Baral – Wall St Cheat Sheet

“Now, a new study (published Monday in the journal Hypertension) has found another added benefit of probiotics — it may reduce high blood pressure.”

Microbes in the News

Your garden hose: a potential health risk due to Legionella spp. growth facilitated by free-living amoebae – Jacqueline Marie Thomas – Environmental Science & Technology

“Here we present data on FLA and Legionella spp. detected in water and biofilm of two garden hose types over 18 months. “

Truth about your toothbrush – Anne Agbaje – Bussiness Day Online

“You don’t store your plates and glasses by the toilet, so why would you want to place your toothbrush there?” McCombs says. “It’s just common sense to store your toothbrush as far away from the toilet as possible.”

Metabolomics

Fecal volatile organic compounds: a novel, cheaper method of diagnosing inflammatory bowel disease? – Chris SJ Probert – Expert Review of Clinical Immunology

“…this article will focus specifically on the fecal VOC metabolome and its potential role in identifying a novel diagnostic method for IBD.”

Review: Emerging mass spectrometry techniques for the direct analysis of microbial colonies – Jinshu Fang, Pieter C Dorrestein – Current Opinion in Microbiology

“In this review/perspective, we illustrate the emerging mass spectrometry methodologies that enable the interrogation of specialized metabolites directly from microbial colonies.”

Techniques

Improved performance of the PacBio SMRT technology for 16S rDNA sequencing – Jennifer J. Mosher – Journal of Microbiological Methods

“With accurate read lengths of > 1400 base pairs, the PacBio system opens up the possibility of identifying microorganisms to the species level in environmental samples.”

 

Bik’s Picks

The Secret to a Tattoo’s Permanence: The Immune System – Olga Khazan – The Atlantic

“We rarely stop and think about the science of tattoos. In fact, some people don’t even stop and think before getting tattooed.”

 

Mathematical equation to predict happiness: Doesn’t depend on how well things go, but on whether things are better than expected – Science Daily

The happiness of over 18,000 people worldwide has been predicted by a mathematical equation, with results showing that moment-to-moment happiness reflects not just how well things are going, but whether things are going better than expected.”

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Microbiome and general science digest, July 11

Most recent results from American gut, a metagenomics pipeline, arsenic toxicity, polio and dengue vaccines, and pregnancy urine metabolomics to predict preterm birth.

Human gut microbiome

American GutAmerican Gut releases latest results and pipeline – Jeff Leach – American Gut

“The latest American Gut results are out and we’re very excited to share them with the American Gut community. We now have sequencing and analysis data from 3,238 participants, and as of today, this data equates to 101 million DNA sequences and 27 gigabytes of sequencing information.”

Screen shot 2014-07-11 at 04.27PM, Jul 11Place of upbringing in early childhood as related to inflammatory bowel diseases in adulthood: a population-based cohort study in Northern Europe – Signe Timm – European Journal of Epidemiology

“This study suggests a protective effect from livestock farm living in early childhood on the occurrence of IBD in adulthood, however only among subjects born after 1952. We speculate that lower microbial diversity is an explanation for the findings.”

Pregnancy and birth

Urinary pretermUrinary metabolic profiles in early pregnancy are associated with preterm birth and fetal growth restriction in the Rhea mother–child cohort study – Léa Maitre – BMC Medicine

“Here we used an exploratory metabolic profiling approach (metabolomics) to investigate the association between birth outcomes and metabolites in maternal urine collected early in pregnancy as part of the prospective mother–child cohort Rhea study. “

Metagenomics

MedusaMetagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue – Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen – PLOS Computational Biology

“Here we present the bioinformatics pipeline MEDUSA that facilitates analysis of metagenomic reads at the gene and taxonomic level. We also constructed a global human gut microbial gene catalogue by combining data from 4 studies spanning 3 continents. “

Proteomics

Proteomics Staph aureusGenomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine and Human-associated Staphylococcus epidermidis strains – Kirsi Savijoki – Journal of Proteome Research

“Pilot experimental infection studies indicated that while ATCC12228 was able to infect bovine host, the PM221 strain caused more severe clinical signs. “

Dengue

Demanou DengueEvidence of Dengue Virus Transmission and Factors Associated with the Presence of Anti-Dengue Virus Antibodies in Humans in Three Major Towns in Cameroon – Maurice Demanou – PLOS Neglected Tropical Diseases

“Sera were screened for anti-dengue virus IgG and IgM antibodies. Risk factors of seropositivity were tested using logistic regression methods with random effects.”

Carrasco DenguePredictive Tools for Severe Dengue Conforming to World Health Organization 2009 Criteria – Luis R. Carrasco – PLOS Neglected Tropical Diseases

“Higher risk of severe dengue (SD) was associated with female gender, lower than normal hematocrit level, abdominal distension, vomiting and fever on admission. “

Infection and host response

Screen shot 2014-07-11 at 03.35PM, Jul 11Development of Fatal Intestinal Inflammation in MyD88 Deficient Mice Co-infected with Helminth and Bacterial Enteropathogens – Libo Su – PLOS Neglected Tropical Diseases

“We found that MyD88 knockout mice co-infected with H. polygyrus and C. rodentium developed more severe intestinal inflammation and elevated mortality compared to the wild-type mice.”‘

Screen shot 2014-07-11 at 04.28PM, Jul 11Distinct Lipid A Moieties Contribute to Pathogen-Induced Site-Specific Vascular Inflammation – Connie Slocum – PLOS Pathogens

“our results point to a pivotal role for activation of the non-canonical inflammasome in P. gingivalis infection and demonstrate that P. gingivalis evades immune detection at TLR4 facilitating chronic inflammation in the vasculature. “

Dengue

Dengue vaccine lancetClinical efficacy and safety of a novel tetravalent dengue vaccine in healthy children in Asia: a phase 3, randomised, observer-masked, placebo-controlled trial – Maria Rosario Capeding – The Lancet

“Our findings show that dengue vaccine is efficacious when given as three injections at months 0, 6, and 12 to children aged 2–14 years in endemic areas in Asia, and has a good safety profile. “

Also see comment: Dengue vaccines: dawning at last? – Annelies Wilder-Smith – The Lancet

Poliovirus

Jacob John polioEffect of a single inactivated poliovirus vaccine dose on intestinal immunity against poliovirus in children previously given oral vaccine: an open-label, randomised controlled trial – Jacob John – The Lancet

“The substantial boost in intestinal immunity conferred by a supplementary dose of IPV given to children younger than 5 years who had previously received OPV shows a potential role for this vaccine in immunisation activities to accelerate eradication and prevent outbreaks of poliomyelitis.”

Also see comment: Polio endgame management: focusing on performance with or without inactivated poliovirus vaccine – Kimberly M Thompson – The Lancet

Microbes in the News

Screen shot 2014-07-11 at 04.28PM, Jul 11 1How Gross Is Your Phone? A Motherboard Science Experiment – Jason Koebler – Motherboard

“All I wanted to do was recreate a relatively simple study I had just written about. Instead, I ended up creating something vaguely dangerous, which mortified the director of a local DIY biology lab. Here’s what happens when you perform experiments on your coworkers.”

Arsenic metabolism

Screen shot 2014-07-11 at 04.29PM, Jul 11Lung tumors in mice induced by “whole-life” inorganic arsenic exposure at human-relevant doses – Michael P. Waalkes – Archives of Toxicology

“Breeder male and female CD1 mice were exposed to 0, 50, 500 or 5,000 ppb arsenic (as sodium arsenite) in the drinking water for 3 weeks prior to breeding, during pregnancy and lactation, and after weaning (at week 3) groups of male and female offspring (initial n = 40) were exposed for up to 2 years.”

Dr. Bik’s Picks

Scorpions are master architects, according to new research – Science Daily

“The burrows made by scorpions follow a very sophisticated design, beginning with a short, vertical entrance shaft that flattened out a few centimeters below the surface into a horizontal platform, new research has found.”

Beach Sand Used To Make A Battery That Lasts Three Times Longer – Douglas Main – Popular Science

“Sink your toes into this: Beach sand can be used to make lithium-ion batteries that last three times longer than current models, according to a study published in the journal Scientific Reports.”

World Now “A Safer Place”, thanks to creation of Potential Pandemic Virus – The Allium

“Yes, I get your point that they could potentially kill millions of people and hospitalise millions more, causing untold human suffering and extraordinary economic damage, but think of all the advantages to the creation of these bugs”.

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Human and cell phone microbiome, June 24

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

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

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.”

Screen Shot 2014-06-19 at 10.46.12 PM

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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