Category Archives: Human gut

Human microbiome, July 17

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Protozoa detection in fecal samples from children, airway microbiome, and Staphylococcus transmission between mother and child.

Oral microbiome

Oral Lihong GuoIntercellular communications in multispecies oral microbial communities – Lihong Guo – Frontiers in Microbiology

“This review will summarize the evidence that oral microbes participate in intercellular communications with co-inhabitants through cell contact-dependent physical interactions, metabolic interdependencies, as well as coordinative signaling systems to establish and maintain balanced microbial communities.”

Respiratory microbiome

Screen Shot 2014-07-17 at 4.58.37 PMAirway Microbiome Dynamics in Exacerbations of Chronic Obstructive Pulmonary Disease – Yvonne J. Huang – Journal of Clinical Microbiology

“In this study, temporal changes in the airway microbiome before, at the onset of, and after an acute exacerbation were examined in 60 sputum samples collected from subjects enrolled in a longitudinal study of bacterial infection in COPD.”

Screen Shot 2014-07-17 at 4.59.26 PMTime between Collection and Storage Significantly Influences Bacterial Sequence Composition in Sputum Samples from Cystic Fibrosis Respiratory Infections – Leah Cuthbertson – Journal of Clinical Microbiology

“Samples were treated with propidium monoazide to distinguish live from dead cells prior to DNA extraction, and 16S rRNA gene pyrosequencing was used to characterize their bacterial compositions.”

Gut microbiome

Screen Shot 2014-07-17 at 4.58.09 PMThe devil lies in the details: How variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes – Eric C. Martens – Journal of Molecular Biology

“Here, we review the recent literature on this topic and posit that numerous, subtle variations in polysaccharides diversify the spectrum of available nutrient niches, each of which may be best filled by a subset of microorganisms that possess the corresponding proteins to recognize and degrade different carbohydrates”

Pregnancy and birth

Protozoa pediatricDetection of intestinal protozoa in paediatric patients with gastrointestinal symptoms by multiplex real-time PCR – L. Maas – Clinical Microbiology and Infection

“The performance of a multiplex real-time PCR for the detection of Blastocystis, Dientamoeba fragilis, Giardia lamblia, Cryptosporidium species and Entamoeba species in faecal samples was evaluated in an observational prospective study.”

Staph transmTransmission of Staphylococcus aureus between mothers and infants in an African setting – F. Schaumburg – Clinical Microbiology and Infection

“We aimed to investigate the transmission of S. aureus between mothers and their newborns during the first year after delivery in an African setting. In a longitudinal cohort study, colonization of Gabonese mother–infant pairs was assessed at delivery and after 1, 9 and 12 months.”

Commentary: Travelling within the fetal gut: simple rules for an arduous journey
Qiling Xu – BMC Microbiology

“A recent paper in BMC Biology addresses this issue with live imaging of gut explants from mouse embryos.”

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Human (and fish) microbiome, July 16

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Oral microbiome in children with leukemia, and effects of antibiotics on fish microbiota.

Human oral microbiome

Oral Microbiota Distinguishes Acute Lymphoblastic Leukemia Pediatric Hosts from Healthy Populations – Yan Wang – PLOS ONE

“The oral microbiota of leukemia patients had lower richness and less diversity compared to healthy controls.”

Human gut microbiome

Editorial: New bacteria associated with diarrhoea – Cláudio Nunes-Alves – Nature Reviews Microbiology

“Pop et al. used high throughput 16S rRNA sequencing to compare the faecal microbiota composition in 992 children from Gambia, Mali, Kenya and Bangladesh”

Pregnancy and birth

Yes, this one is not really microbiome-related, but it touched my heart:

Screen Shot 2014-07-16 at 11.49.15 PMStrangers help with photo in midst of tragedy – Dorrine Mendoza, CNN

“”My daughter recently passed away after a long battle in the children’s hospital. She was in the hospital her whole life and we were never able to get a photo without all her tubes. Can someone remove the tubes?””

Fish microbiome

Effects of antibiotic on the bacterial microflora in two commercially
important catfish species, Clarias batrachus and Heteropneustes fossilis in
Bangladesh – Md. Shahdat Hossain – Journal of Coastal Life Medicine

“During the experiment, bacterial loads were estimated as colony forming unit (CFU/g) by every alternate day in the aquarium water, gills, skin and intestine of fish.”

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Human microbiome, July 15

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Not-always-rare taxa in a wide range of ecosystems, microbiome in early life, focus on Lactobacillus and Bacteroides and microbiota and inflammation.

General microbiome

Science Webinar: The promise of the microbiome: Function and dysfunction in humans and beyond – David A. Relman, Jack A. Gilbert, Rob Knight

“Microbiomes–the distinct microbial populations that colonize an array of bodily and environmental niches–are rapidly gaining prominence in numerous fields of research. “

Gut microbiome

Screen shot 2014-07-15 at 05.18PM, Jul 15Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity – Ashley Shade – mBio

“Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure.”

Screen shot 2014-07-15 at 05.20PM, Jul 15Functional genomics of Lactobacillus casei establishment in the gut – Hélène Licandro-Seraut – PNAS

“By determining the relative quantity of each of the 1,110 mutants before and after the in vivo challenge, we identified a core of 47 L. casei genes necessary for its establishment in the gut. “

Screen shot 2014-07-15 at 05.21PM, Jul 15Tuning transcription of nutrient utilization genes to catabolic rate promotes growth in a gut bacterium – Varsha Raghavan – Molecular Microbiology

“We report that the regulator controlling utilization of chondroitin sulfate (CS) in the mammalian gut symbiont Bacteroides thetaiotaomicron is activated by an intermediate in CS breakdown rather than CS itself.”

Pregnancy and Birth

Screen shot 2014-07-15 at 06.38PM, Jul 15 1Review: The Microbiome in Early Life: Self-Completion and Microbiota Protection as Health Priorities – Rodney R. Dietert – Birth Defects Research Part B: Developmental and Reproductive Toxicology

“This minireview considers the benefits of refocusing attention away from treating the patient as a mammalian human to managing the complete patient: a majority microbial superorganism. “

Screen shot 2014-07-15 at 06.38PM, Jul 15Review: Anaerobes and Bacterial Vaginosis in Pregnancy: Virulence Factors Contributing to Vaginal Colonisation – Charlene W. J. Africa – Int. J. Environ. Res. Public Health

“This paper reviewed new available information regarding possible factors contributing to the establishment of the BV vaginal biofilm, examined the proposed role of anaerobic microbial species recently detected by new culture-independent methods and discusses developments related to the effects of BV on human pregnancy. “

Oral microbiome

Review: Acquisition and maturation of oral microbiome throughout childhood: An update – Benedita Sampaio-Maia – Dental Research Journal

“This revision presents an overview of this renewed knowledge on oral microbial community acquisition in the newborn and on the evolution of this microbiome to adulthood. “

 

Animal models of human microbiome and disease

Screen shot 2014-07-15 at 05.17PM, Jul 15Commensal microbes drive intestinal inflammation by IL-17–producing CD4+ T cells through ICOSL and OX40L costimulation in the absence of B7-1 and B7-2 – Lijun Xin – PNAS

“Here we show that B7 deprivation in mice overrides the necessity for Tregs in averting systemic autoimmunity and inflammation in extraintestinal tissues, whereas peripherally induced Tregs retained in the absence of B7 selectively mitigate intestinal inflammation caused by Th17 effector CD4+ T cells. “

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Human microbiome, July 14

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Ethnic variation in vaginal microbiomes, effect of chemotherapy on human milk, response of (murine) microbiota to infection.

Oral microbiome

Screen shot 2014-07-14 at 12.23PM, Jul 14Advancements toward a Systems Level Understanding of the Human Oral Microbiome – Jeffrey S. Mclean – Frontiers in Cellular and Infection Microbiology

“This review will discuss some of the recent insights into the oral microbiome at a fundamental level, existing knowledge gaps, as well as challenges that have surfaced and the approaches to address them.”

Vaginal microbiome

Screen shot 2014-07-14 at 12.24PM, Jul 14Ethnic Variations in Cervical Cytokine Concentrations and Vaginal Flora During Pregnancy – Riana Dutt – American Journal of Reproductive Immunology

“Semi-quantitative vaginal cultures and concentrations of cervical cytokines were compared between Caucasian and non-Caucasian women.”

Gut microbiome

Screen shot 2014-07-14 at 12.25PM, Jul 14A functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe – Almut Heinken – Journal of Bacteriology

“In this study, we present an integrated, iterative approach of computational modeling, in vitro experiments, metabolomics and genomic analysis to accelerate the identification of metabolic capabilities for poorly characterized (anaerobic) microorganisms.”

Pregnancy and birth

Screen shot 2014-07-14 at 12.26PM, Jul 14Effect of chemotherapy on the microbiota and metabolome of human milk, a case report – Camilla Urbaniak – Microbiome

“Mature milk was collected every two weeks over a four month period from a lactating woman undergoing chemotherapy for Hodgkin’s lymphoma. Mature milk was also collected from healthy lactating women for comparison. Microbial profiles were analyzed by 16S sequencing and the metabolome by gas chromatography-mass spectrometry.”

Animal models

Clara Belzer miceDynamics of the Microbiota in Response to Host Infection – Clara Belzer – PLOS ONE

“Employing a murine model of infectious colitis with the pathogen Citrobacter rodentium, we generated a 2-month time-series of 16S rDNA gene profiles, and quantitatively cultured commensals, from multiple intestinal sites in infected and uninfected mice. “

Prune juice animal modelCarbohydrate-Free Peach (Prunus persica) and Plum (Prunus domestica) Juice Affects Fecal Microbial Ecology in an Obese Animal Model – Giuliana D. Noratto – PLOS ONE

“Fecal samples were obtained after 11 weeks of fruit or control juice administration. Real-time PCR and 454-pyrosequencing were used to evaluate changes in fecal microbiota. Over 1,500 different Operational Taxonomic Units at 97% similarity were detected in all rats.”

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Microbiome and general science digest, July 11

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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 microbiome, July 9

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Microbiome in pediatric Crohn’s disease patients, tipping elements in the human intestinal ecosystem, and oral microbes in the respiratory tract of carcinoma patients.

Gut microbiome

Crohn diseasePediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature – Yael Haberman – Journal of Clinical Investigation

“Here, we characterized the global pattern of ileal gene expression and the ileal microbial community in 359 treatment-naive pediatric patients with CD, patients with ulcerative colitis (UC), and control individuals. “

Tipping elementsTipping elements in the human intestinal ecosystem – Leo Lahti – Nature Communications

“Here, based on a deep phylogenetic analysis of the intestinal microbiota in a thousand western adults, we identify groups of bacteria that exhibit robust bistable abundance distributions. These bacteria are either abundant or nearly absent in most individuals, and exhibit decreased temporal stability at the intermediate abundance range. “

Respiratory microbiome

Detection and identification of oral anaerobes in intraoperative bronchial fluids of patients with pulmonary carcinoma – Ayako Hasegawa – Microbiology & Immunology

“This study aimed to quantify and identify bacteria in intraoperative bronchial fluids and to evaluate the relationship between impairment of cough/swallowing reflexes and silent aspiration of oral bacteria in elderly patients. “

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

“This genomic island is absent from the close relative of N. meningitidis, the commensal Neisseria lactamica, which chiefly colonizes infants not adults. “

Animal models of microbiome and disease

Microbiota-Driven Immune Cellular Maturation Is Essential for Antibody-Mediated Adaptive Immunity to Staphylococcus aureus Infection in the Eye – Tanweer Zaidi – Infection and Immunity

“ In germfree mice, there was no protective efficacy of antibody to PNAG due to the lack of LY6G+ inflammatory cell coeffector recruitment to the cornea.”

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Human microbiome, July 8

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Female urinary microbiome, stool microbiome and vaccine responses, and gut microbiome in ulcerative colitis patients.

Urinary tract

The Female Urinary Microbiome: a Comparison of Women with and without Urgency Urinary Incontinence – Meghan M. Pearce – mBio

“In this study, we used 16S rRNA gene sequencing to classify bacterial DNA and expanded quantitative urine culture (EQUC) techniques to isolate live bacteria in urine collected by using a transurethral catheter from women with UUI and, in comparison, a cohort without UUI. “

Gut microbiome

Stool Microbiota and Vaccine Responses of Infants – M. Nazmul Huda – Pediatrics

“Bifidobacterium predominance may enhance thymic development and responses to both oral and parenteral vaccines early in infancy”

Novel Gut-Based Pharmacology of Metformin in Patients with Type 2 Diabetes Mellitus – Antonella Napolitano – PLOS ONE

“Microbiota abundance of the phylum Firmicutes was positively correlated with changes in cholic acid and conjugates, while Bacteroidetes abundance was negatively correlated.”

This one was already published online in September 2013 but it came out in print this week : Commentary: Roseburia hominis: a novel guilty player in ulcerative colitis pathogenesis – Herbert Tilg – Gut

“In recent years evidence was accumulating that the gut microbiota and its manipulation might constitute one of those relevant ‘environmental’ factors. “

A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis – Kathleen Machiels – Gut

“The composition of the fecal microbiota of UC patients differs from that of healthy individuals: we found a reduction in R hominis and F prausnitzii, both well-known butyrate-producing bacteria of the Firmicutes phylum. “

Pregnancy and birth

Direct Evidence for the Presence of Human Milk Oligosaccharides in the Circulation of Breastfed Infants – Karen C. Goehring – PLOS ONE

“At least some ingested HMOs are absorbed intact into the circulation and excreted in the urine and their concentrations in these fluids correlate with levels of the corresponding mother’s milk”

Commentary: More than a gut feeling: predicting surgical necrotising enterocolitis – Jörn-Hendrik Weitkamp – Gut

“The paper by Sylvester et al 8 describes a new non-invasive approach of combining clinical data and selected urine peptide biomarkers to develop an algorithm to predict progression of suspected medical NEC to surgical disease. “

refers to: A novel urine peptide biomarker-based algorithm for the prognosis of necrotising enterocolitis in human infants – Karl G Sylvester – Gut

“Ensemble modelling combining clinical parameters with biomarker analysis dramatically improves our ability to identify the population at risk for developing progressive NEC.”

Animal models

Host Responses to the Pathogen Mycobacterium avium subsp. paratuberculosis and Beneficial Microbes Exhibit Host Sex Specificity – Enusha Karunasena – Applied and Environmental Microbiology

“The differences observed suggest that male and female gut tissues and microbiota respond to newly introduced microorganisms differently and that gut-associated microorganisms with host immune system responses and metabolic activity are supported by biology distinct to the host sex.”

General human microbiome

Phylogenetics and the human microbiome – Frederick A Matsen IV – Submitted to Systematic Biology

“In this paper I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.”

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Human microbiome, July 7

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Phages and CRISPRs in human mouth, new metagenomes from MetaHit, and vaginal microbiota.

General microbiome

Journal Nurse PractionersReview: An Overview of the Microbiome and the Effects of Antibiotics – Hillary Taggart – The Journal for Nurse Practitioners

“This review provides a basic introduction of what the microbiome is and how it plays a role in obesity, gastrointestinal, immune, and mental health, including a brief mention of implications for the pediatric population.”

Oral microbiome

Screen shot 2014-07-07 at 01.54PM, Jul 07Characterization of bacteriophage communities and CRISPR profiles from dental plaque – Mayuri Naidu (with David Pride) – BMC Microbiology

“We sampled the saliva and dental plaque from 4 healthy human subjects to determine whether plaque was populated by viral communities, and whether there were differences in viral communities specific to subject or sample type.”

Gut microbiome

Screen shot 2014-07-07 at 01.45PM, Jul 07 1An integrated catalog of reference genes in the human gut microbiome – Junhua Li – Nature Biotechnology

“Here we combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) project with 1,018 previously sequenced samples to create a cohort from three continents that is at least threefold larger than cohorts used for previous gene catalogs. “

Screen shot 2014-07-07 at 01.45PM, Jul 07Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes – H Bjørn Nielsen (and 142 other authors) – Nature Biotechnology

“Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences.”

Screen shot 2014-07-07 at 01.47PM, Jul 07Commensal microbial regulation of natural killer T cells at the frontiers of the mucosal immune system – Sebastian Zeissig, Richard S. Blumberg – FEBS Letters

“Here, we outline the mechanisms of bidirectional cross-talk between the microbiota and CD1d-restricted NKT cells and discuss how a perturbation of these processes can contribute to the pathogenesis of immune-mediated disorders at mucosal surfaces.”

Screen shot 2014-07-07 at 01.48PM, Jul 07Review/Book chapter Gastrointestinal microbiota – Katherine Stephens – Advanced Nutrition and Dietetics in Gastroenterology

“This chapter summarizes the functions of the human gastrointestinal tract. A main function of the GI microbiota is modulation of the immune system. The chapter focues on the factors influencing composition of the microbiota.”

Pathogens journalPerturbation of the Human Microbiome as a Contributor to Inflammatory Bowel Disease – Bayan Missaghi – Pathogens

“This review presents an outline of the loss of a normal microbiome as an etiology of immune dysregulation and IBD pathogenesis initiation. “

Screen shot 2014-07-07 at 01.49PM, Jul 07 137 People Want to Peer Inside Your Poop…You Know, for Science – Angus Chen – Discover Magazine

“Rob Knight, a microbiologist at the University of Colorado, Boulder, and his colleagues want poop from every person in America.”

Mediterranean Diet and Health: Food Effects on Gut Microbiota and Disease Control
Federica Del Chierico – International Journal of Molecular Sciences

“For this purpose, we present a study proposal relying on the generation of individual gut microbiota maps from MD-aware children/adolescents. “

Respiratory microbiome

Screen shot 2014-07-07 at 02.02PM, Jul 07Evidence that intraspecific trait variation among nasal bacteria shapes the distribution of Staphylococcus aureus – Ben Libberton – Infection and Immunity

“We characterised S. aureus growth inhibition by the culturable bacterial aerobe consortia of 60 nasal microbiomes, revealing intraspecific variation in growth inhibition and that inhibitory isolates clustered within communities that were culture-negative for S. aureus. “

Vaginal microbiome

Screen shot 2014-07-07 at 01.53PM, Jul 07Characterization of the vaginal microbiota of healthy Canadian women through the menstrual cycle – Bonnie Chaban – Microbiome

“Polymerase chain reaction (PCR) was performed to amplify the universal target region of the cpn60 gene and generate amplicons representative of the microbial community. Amplicons were pyrosequenced, assembled into operational taxonomic units, and analyzed. “

Pregnancy

The effects of designation and volume of neonatal care on mortality and morbidity outcomes of very preterm infants in England: retrospective population-based cohort study – SI Watson – BMJ Open

“High-volume neonatal care provided at the hospital of birth may protect against in-hospital mortality in very preterm infants. “

Understanding the Complexity of the Immune System during Pregnancy – Karen Racicot – American Journal of Reproductive Immunology

“In this review, we discuss our present understanding of the ‘immunity of pregnancy’ in the context of the response to cervical and placental infections and how these responses affect both the mother and the fetus.”

 

Animal models of human microbiota or disease

Screen Shot 2014-07-07 at 11.00.33 PMGalacto‐oligosaccharides attenuate renal injury with microbiota modification – Satoshi U. Furuse – Physiological Reports

“The microbiota analysis indicated that GOS significantly increased three bacterial families and decreased five families in the Nx rats. “

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Human microbiome digest, July 3

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Short chain fatty acids and gut microbiota, microbial eukaryotes in the human gut, Pseudomonas in stool, and a smelly Anaerococcus isolated from arm pits.

Gut microbiome

Fernandes ObeseAdiposity, gut microbiota and faecal short chain fatty acids are linked in adult humans – J Fernandes – Nutrition & Diabetes

“Our objectives were to compare dietary intakes, faecal SCFA concentrations and gut microbial profiles in healthy lean (LN, BMIless than or equal to25) and overweight or obese (OWOB, BMI>25) participants.”

Ellagic Acid Metabolism by Human Gut Microbiota: Consistent Observation of Three Urolithin Phenotypes in Intervention Trials, Independent of Food Source, Age, and Health Status – Francisco A. Tomás-Barberán – Journal of Agricultural and Food Chemistry

“Interestingly, a higher percentage of phenotype B was observed in those volunteers with chronic illness (metabolic syndrome or colorectal cancer) associated with gut microbial imbalance (dysbiosis).”

Screen shot 2014-07-03 at 03.04PM, Jul 03Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity – Laura Wegener Parfrey – Frontiers in Microbiology

“We curated the SILVA ribosomal database to reflect current knowledge of eukaryotic taxonomy and employ it as a phylogenetic framework to compare eukaryotic diversity across environment. We show that adults from the non-western population harbor a diverse community of protists, and diversity in the human gut is comparable to that in other mammals.”

Screen shot 2014-07-03 at 03.04PM, Jul 03Faecal carriage of Pseudomonas aeruginosa in healthy humans: antimicrobial susceptibility and global genetic lineages – Vanesa Estepa – FEMS Microbiology Ecology

“The aim of this study was to analyse the Pseudomonas aeruginosa faecal carriage rate in 98 healthy humans and to perform the phenotypic and genotypic characterization of recovered isolates. The genetic relatedness among the isolates was analysed by pulsed-field gel electrophoresis and multilocus sequence typing that was compared with worldwide epidemic clones. “

helminth infectHelminth Infections, Type-2 Immune Response, and Metabolic Syndrome – Aprilianto E. Wiria – PLOS Pathogens

“Are Helminth Infections Associated with Metabolic Syndrome?”

Skin microbiome

Screen shot 2014-07-03 at 03.02PM, Jul 03A newly discovered Anaerococcus strain responsible for axillary odor and a new axillary odor inhibitor, pentagalloyl glucose – Takayoshi Fujii – FEMS Microbiology Ecology

“We aimed to investigate anaerobic bacteria that had not been previously studied for axillary odor formation. A new anaerobic Anaerococcus sp. A20, that releases 3-hydroxy-3-metyl-hexanoic acid (HMHA, main component of axillary odor) from its glutamyl conjugate, was discovered from axillary isolates. “

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Human and other microbiomes, July 2

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Fungi in the mouth, microbiome in celiac disease, viruses in bats, fecal microbiota of penguins, and bacteria in water and concrete.

Human oral microbiome

Screen Shot 2014-07-02 at 10.35.22 PMMolecular Analysis of Fungal Populations in Patients with Oral Candidiasis Using Internal Transcribed Spacer Region – Shinsuke Ieda – PLOS ONE

“In this study we examined the fungal flora in patients with oral candidiasis and investigated changes in the flora after antifungal treatment using length heterogeneity-polymerization chain reaction (LH-PCR) analysis of ITS regions.”

Human respiratory microbiome

Screen Shot 2014-07-02 at 10.35.47 PMLetter: No Clinical Association of Live Attenuated Influenza Virus with Nasal Carriage of Bacteria or Acute Otitis Media – Kathleen L. Coelingh, Robert B. Belshe – mBio

“We write this note to clarify the article “Live Attenuated Influenza Vaccine Enhances Colonization of Streptococcus pneumoniae and Staphylococcus aureus in Mice” by Mina et al. (1) in order that patients or clinicians not misinterpret the study’s clinical relevance.”

Human gut microbiome

Review: Screen Shot 2014-07-02 at 10.16.45 PMIntestinal Microbiota and Probiotics in Celiac Disease – Luís Fernando de Sousa Moraes – Clinical Microbiology Reviews

“This review aims to discuss the characteristics of the microbiota in CD subjects and the use of probiotics as a novel therapy for CD. “

Bat microbiome

Screen Shot 2014-07-02 at 10.36.24 PMBat Distribution Size or Shape as Determinant of Viral Richness in African Bats – Gaël D. Maganga – PLOS ONE

“We investigated the determinants of viral richness in 15 species of African bats (8 Pteropodidae and 7 microchiroptera) in Central and West Africa for which we provide new information on virus infection and bat phylogeny. “

Bird microbiome

Screen Shot 2014-07-02 at 10.36.58 PMInfluence of Fasting during Moult on the Faecal Microbiota of Penguins – Meagan L. Dewar – PLOS ONE

“Therefore, the present study aimed to examine the microbial composition and diversity of the GI microbiota of fasting little (Eudyptula minor) and king penguins (Aptenodytes patagonicus) penguins during early and late moult.”

Invertebrate microbiome

Screen Shot 2014-07-02 at 10.37.27 PMBacterial Community Composition in the Gut Content and Ambient Sediment of Sea Cucumber Apostichopus japonicus Revealed by 16S rRNA Gene Pyrosequencing – Fei Gao – PLOS ONE

“The composition of the bacterial communities in the contents of the foregut and hindgut of the sea cucumber Apostichopus japonicus and in the ambient surface sediment was surveyed by 16S rRNA gene 454-pyrosequencing. “

Plant microbiome

Screen Shot 2014-07-02 at 10.37.55 PMSelecting Microbial Strains from Pine Tree Resin: Biotechnological Applications from a Terpene World – Cristina Vilanova – PLOS ONE

“The taxonomic and functional diversity of the cultivated, resin-tolerant fraction of the whole microbiota were unveiled by high-throughput sequencing, which resulted in the detection of more than 40 bacterial genera among the terpene-degrading microorganisms, and a range of genes involved in the degradation of different terpene families.”

Water and concrete microbiology

Screen Shot 2014-07-02 at 10.38.23 PMCoupling Genetic and Chemical Microbiome Profiling Reveals Heterogeneity of Archaeome and Bacteriome in Subsurface Biofilms That Are Dominated by the Same Archaeal Species – Alexander J. Probst – PLOS ONE

“Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current.”

Screen Shot 2014-07-02 at 10.38.41 PMMicrobial Quality and Phylogenetic Diversity of Fresh Rainwater and Tropical Freshwater Reservoir – Rajni Kaushik – PLOS ONE

“The taxonomic richness and phylogenetic relationship of the freshwater reservoir with those of the fresh rainwater were also assessed using 16 S rRNA gene clone library construction. “

Screen Shot 2014-07-02 at 10.29.38 PMBacteria and concrete-a love-hate relationship – Embriette Hyde

“Sometimes bacteria appear to harm concrete, sometimes they appear to help it.”

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