Human microbiome digest, October 7, 2014

Treating toxic arsenic levels with yoghurt, colonization patterns in low birthweight infants, evil alliances in breastmilk, and smoking and oral microbiome.

Human microbiome general

Opinion: Conservation and stewardship of the human microbiome – Kieran C. O’Doherty – PNAS USA

“Just as humans have impacted many large animal species in the environment, drastic changes in human lifestyle over the past century may have altered the global pool of human-associated microbes; if so, these shifts may pose substantial threats to individual and public health.”

Friends with Social Benefits: Host-Microbe Interactions as a Driver of Brain Evolution and Development? – Roman M. Stilling – Frontiers in Cellular and Infection Microbiology

“Here in this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. “

Pregnancy and birth

Intestinal Colonization Among Very Low Birth Weight Infants in First Week of Life (PDF) – Sourabh Dutta – Indian Pediatrics

“Very low birth weight infants admitted in neonatal intensive care units have abnormal intestinal colonization patterns”

Is a fetus developing in a sterile environment? – Trudy M. Wassenaar and Pinaki Panigrahi – Letters in Applied Microbiology

Probiotics and Necrotizing Enterocolitis – Josef Neu – Clinics in Perinatology (paywalled even at Stanford)

Potential involvement of Campylobacter curvus and Haemophilus parainfluenzae in preterm birth – George Louis Mendz – BMJ Case Reports

“A woman presented with prelabour premature preterm rupture of membranes and delivered extremely preterm at 26 weeks by caesarean section.”

Network analysis reveals a potentially ‘evil’ alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities – Zhanshan Ma – arXiv

“..we reconstructed a milk bacterial community network with the data from Hunt et al (2011), which is the largest 16S-rRNA sequence data set of human milk microbiome available to date.”

Randomized Open-Label Pilot Study of the Influence of Probiotics and the Gut Microbiome on Toxic Metal Levels in Tanzanian Pregnant Women and School Children – Jordan E. Bisanz – mBio

“Consumption of probiotic yogurt had a protective effect against further increases in mercury (3.2 nmol/liter; P = 0.035) and arsenic (2.3 nmol/liter; P = 0.011) blood levels in the pregnant women, but this trend was not statistically significant in the children.”

Human oral microbiome

* Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms – Andrew Maltez Thomas – BMC Microbiology

“DNA was extracted from swabs and the V1 region of the 16S rRNA gene was PCR amplified and sequenced using the Ion Torrent PGM platform, generating 3.7 million high quality reads. “

* Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients – Ji-Hoi Moon – Molecular Oral Microbiology

“Here, we investigated the composition of subgingival bacterial communities from the pooled plaque samples of smokers and non-smokers, 134 samples each group, in Korean moderate chronic periodontitis patients using 16S rRNA gene-based pyrosequencing.”

Human respiratory microbiome

Sinus culture poorly predicts resident microbiota – Leah J. Hauser – International Forum of Allergy & Rhinology

“The association between 16S relative abundance and detection by culture was determined using logistic regression.”

Localization of Burkholderia cepacia Complex Bacteria in Cystic Fibrosis Lungs and Interactions with Pseudomonas aeruginosa in Hypoxic Mucus – Ute Schwab – Infection and Immunity

“We performed immunohistochemistry for Bcc and P. aeruginosa bacteria on 21 coinfected or singly infected CF lungs obtained at transplantation or autopsy. “

Human gut microbiome

* Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity – Sophie Leclercq – PNAS USA

“In this study, we showed that alcohol-dependent subjects with altered intestinal permeability had also altered gut-microbiota composition and activity and remained with high scores of depression, anxiety, and alcohol craving after a short-term detoxification program.”

Structural modulation of gut microbiota during alleviation of type 2 diabetes with a Chinese herbal formula – Jia Xu – ISME Journal

“Pyrosequencing of the V3 regions of 16S rRNA genes revealed a dose-dependent deviation of gut microbiota in response to GQD treatment.”

Modelling the emergent dynamics and major metabolites of the human colonic microbiota – Helen Kettle – Environmental Microbiology

“To reduce the complexity of the system, we divide the bacterial community into 10 bacterial functional groups (BFGs) each distinguished by its substrate preferences, metabolic pathways and its preferred pH range. “

Animal models of microbiome research

Transcriptome analysis of Escherichia coli O157:H7 grown in vitro in the sterile-filtrated cecal content of human gut microbiota associated rats reveals an adaptive expression of metabolic and virulence genes – Guillaume Le Bihan – Microbes and Infection

“A transcriptomic analysis was performed on the EHEC strain EDL933 incubated in vitro in the sterile-filtrated cecal content of human microbiota-associated rats (HMC) compared with EDL933 incubated in the sterile-filtrated cecal content of germ-free rat (GFC).”

Early Innate Immunity to Bacterial Infection in the Lung Is Regulated Systemically by the Commensal Microbiota via Nod-Like Receptor Ligands – Thomas B. Clarke – Infection and Immunity

“Microbiota depletion caused significant defects in the early innate response to lung infection by the major human pathogen Klebsiella pneumoniae.”

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Human microbiome digest, September 16, 2014

Still catching up after my vacation, but almost there!

Some general microbiome reviews, using saliva to track human evolution, probiotics that actually change the microbiome, and several animal model studies.

 

General microbiome reviews

Which is more important for classifying microbial communities: who’s there or what they can do? – Zhenjiang Xu – ISME Journal

“… might we not instead expect that function would be substantially more important for classifying biologically meaningful groups of samples than who is providing those functions? “

Microbiome analysis – from technical advances to biological relevance – Michelle I. Smith – F1000Prime Reports

“Here, we introduce techniques that go beyond identifying the taxa present within a sample and examine the biological function of the microbiome or the host-microbiome interaction.”

From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity – Melania E. Cristescu – Trends in Ecology & Evolution

“DNA-based species identification, known as barcoding, transformed the traditional approach to the study of biodiversity science. “

Human oral microbiome

Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies – Karsten Henne – BMC Evolutionary Biology

“By focussing on the house-keeping gene gdh .., on the virulence gene gtf .. of mitis-streptococci and on the 16S-23S rRNA internal transcribed spacer (ITS) region of the Fusobacterium nucleatum/periodonticum-group we here tested the hypothesis that bacterial genes from human saliva have the potential for distinguishing human populations.’

Microbial community in persistent apical periodontitis: a 16S rRNA gene clone library analysis – M. N. Zakaria – International Endodontic Journal

“Whilst a diverse bacterial species were observed in the persistent apical lesions, some characteristic patterns of bacterial community were found in the symptomatic lesions. “

The Adenoid Microbiome in Recurrent Acute Otitis Media and Obstructive Sleep Apnea – Carolyn P. Ojano-Dirain – Otolaryngology – Head and Neck Surgery

“Microbes are present on all adenoid specimens, however, the microbial profile differs between recurrent AOM and OSA.”

Human gut microbiome

Susceptibility to Campylobacter Infection Is Associated with the Species Composition of the Human Fecal Microbiota – Johan Dicksved – mBio

“Here we address this by prospectively studying the gut microbiota composition before, during, and after natural Campylobacter infection in exposed poultry abattoir workers.”

Eukaryote Culturomics of the Gut Reveals New Species – Nina Gouba, Didier Raoult, Michel Drancourt – PLOS ONE

“We further explored this repertoire using PCR-sequencing and culture in seven individuals living in four tropical countries. A total of 41 microeukaryotes including 38 different fungal species and three protists were detected. “

Review: Decade in review—gut microbiota: The gut microbiota era marches on – Francisco Guarner – Nature Reviews Gastroenterology & Hepatology

“Research on the gut microbial communities harboured in the human gut is progressing rapidly owing to the availability of novel and reliable tools for analysis.”

Modulation of Fecal Clostridiales Bacteria and Butyrate by Probiotic Intervention with Lactobacillus paracasei DG Varies among Healthy Adults – Chiara Ferrario – Journal of Nutrition

“High-throughput 16S ribosomal RNA gene sequencing was used to characterize the fecal microbiota in healthy adults (23–55 y old) of both sexes, before and after 4 wk of daily consumption of a capsule containing at least 24 billion viable Lactobacillus paracasei DG cells”

Review: The gut microbiota, bacterial metabolites and colorectal cancer – Petra Louis, Georgina L. Hold & Harry J. Flint – Nature Reviews Microbiology

“In this Review, we discuss the relationship between diet, microbial metabolism and CRC and argue that the cumulative effects of microbial metabolites should be considered in order to better predict and prevent cancer progression.”

Changes of the human gut microbiome induced by a fermented milk product – Patrick Veiga – Nature Scientific Reports

“Our data challenge the view that microbes ingested with food have little impact on the human GM functioning and rather provide support for beneficial health effects.”

Gut Microbiome and Multiple Sclerosis – Pavan Bhargava, Ellen M. Mowry – Current Neurology and Neuroscience Reports

“We examine the different sources of information linking the gut microbiota to multiple sclerosis and examine the future avenues for utilizing the knowledge of the gut microbiome to potentially treat and prevent multiple sclerosis.”

Microbial Modulation of Insulin Sensitivity – Muhammad Tanweer Khan, Max Nieuwdorp, Fredrik Bäckhed – Cell Metabolism

“The gut microbiota has emerged as an integral factor that impacts host metabolism and has been suggested to play a vital role in metabolic diseases such as obesity, insulin resistance, type 2 diabetes, and cardiovascular disease.”

Gut Microbial Community Structure and Complications After Kidney Transplantation: A Pilot Study – Lee, John R – Transplantation

“We characterized bacterial composition by polymerase chain reaction amplification of the 16S rRNA V4-V5 variable region and deep sequencing using the Illumina MiSeq platform.’

Human genital microbiome

Association between cigarette smoking and the vaginal microbiota: a pilot study – Rebecca M Brotman – BMC Infectious Diseases

“Smokers had a lower proportion of vaginal Lactobacillus spp. compared to non-smokers.”

Pregnancy and birth

Human Breast Milk – The Magic In The Microbiome – Science20

“Ma et al (2014 submitted manuscript) recently postulated that the opportunistic pathogen such as Staphylococcus aureus, which has been confirmed to exist in the human milk microbiome, is normally suppressed by a network of beneficial bacteria coexisted in the breast milk microbiome, but may become source of infectious mastitis when the host environment permits.”

Animal models of human microbiome research

Antibiotic Treatment of Pregnant Non-Obese Diabetic Mice Leads to Altered Gut Microbiota and Intestinal Immunological Changes in the Offspring – N. Tormo-Badia – Scandinavian Journal of Immunology

“we found a differential clustering of gut microbiota in the offspring from NOD mothers treated with antibiotics during gestation compared with offspring from control mothers.”

Shifts in microbiota species and fermentation products in a dietary model enriched in fat and sucrose – U. Etxeberria – Beneficial Microbes

“The aim of the present study was to identify gut microbiota dysbiosis and associated metabolic changes produced in male Wistar rats fed a HFS diet for 6 weeks and compare it with the basal microbial composition.”

The short chain fatty acids, butyrate and propionate, have differential effects on the motility of the guinea pig colon – Norm R. Hurst – Neurogastroenterology & Motility

“We hypothesized that the effect of SCFAs on colonic motility varies with chain length and aimed to determine the effects of SCFAs on propagating and non-propagating contractions of guinea pig proximal and distal colon.”

Small Bowel Resection Induces Long-Term Changes in the Enteric Microbiota of Mice – J. Sommovilla – Journal of Gastrointestinal Surgery

Bowel resection induces long-term changes in the microbial community of the murine ileum, but not at more distal sites of the gastrointestinal tract. “

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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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Human microbiome, July 8

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, June 30

Hypotheses about oral microbiota and disease, effect of rhinovirus infection on nasal microbiome,  the gut microbiome in children with diarrhea in low-income countries, primate vaginal microbiomes, and much more.

Oral microbiome (also see Probiotics and Biofilms in today’s General digest)

Screen Shot 2014-06-30 at 11.18.32 PMHistorical and contemporary hypotheses on the development of oral diseases: are we there yet? – Bob T. Rosier – Frontiers in Cellular and Infection Microbiology

“In this comprehensive review, we describe how these different hypotheses, and the ideas around them, arose and test their current applicability to the understanding of the development of oral disease. Finally, we conclude that an all-encompassing ecological hypothesis explaining the shifts from health to disease is still lacking.”

PeriodontitisThe inflammophilic character of the periodontitis-associated microbiota – George Hajishengallis – Molecular Oral Microbiology

“This Review discusses evidence that periodontitis-associated communities are ‘inflammo-philic’ (= loving or attracted to inflammation) in that they have evolved to not only endure inflammation but also to take advantage of it. “

Respiratory microbiome

Screen Shot 2014-06-30 at 11.19.43 PMCharacterization of the nasopharyngeal microbiota in health and during rhinovirus challenge – Allen EK – Microbiome

“Rhinovirus illnesses were induced by self-inoculation using the finger to nose or eye natural transmission route in ten otherwise healthy young adults.”

Gut microbiome

Screen Shot 2014-06-30 at 11.20.28 PMDiarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition – Mihai Pop – Genome Biology

“We use high throughput 16S rRNA gene sequencing to compare fecal microbiota composition in children under five years of age who have been diagnosed with moderate to severe diarrhea (MSD) with the microbiota from diarrhea-free controls. “

Structure of the gut microbiome following colonization with human feces determines colonic tumor burden – Baxter NT – Microbiome

“We transplanted fecal microbiota from three CRC patients and three healthy individuals into germ-free mice, resulting in six structurally distinct microbial communities. Subjecting these mice to a chemically induced model of CRC resulted in different levels of tumorigenesis between mice. “

Commensal bacteria directly suppress in vitro degranulation of mast cells in a MyD88-independent manner – Kazumi Kasakura – Bioscience, Biotechnology, and Biochemistry

“Here, we show that heat-killed commensal bacteria suppressed degranulation of mast cells in vitro in a MyD88-independent manner.”

Screen Shot 2014-06-30 at 11.21.29 PMCo-occurrence of driver and passenger bacteria in human colorectal cancer
Jiawei Geng – Gut Pathogens

“Building on the driver-passenger model, we used 454 pyrosequencing of bacterial 16S rRNA genes associated with 10 normal, 10 adenoma, and 8 tumor biopsy samples, and found 7 potential driver bacterial genera and 12 potential passenger bacterial genera (7 being pro-inflammatory and 5 anti-inflammatory). “

Review: Intestinal Microbiota and the Efficacy of Fecal Microbiota Transplantation in Gastrointestinal Disease – Olga Aroniadis – Gastroenterology & Hepatology

“The published revelations about the human microbiome are bringing the strength of science to clinical observation and enhancing the understanding of not only disease but also how much of a person’s daily function and health depends on the microorganisms living in intimate relationship with each cell in the body.”

Screen Shot 2014-06-30 at 11.22.43 PMDietary Intervention with Yoghurt, Synbiotic Yogurt or Traditional Fermented Sobya: Bio-Potency among Male Adolescents Using Five Bio-Markers of Relevance to Colonic Metabolic Activities – Laila Hussein – Food and Nutrition Sciences

“The mean fecal total lactobacilli counts increased (P < 0.05) three weeks after daily consumption of the three fermented supplements (P < 0.05), when compared to the pre-intervention levels. Similar trends were observed for genus bifidobacterium. On the contrary, enterobacteraceae counts were reduced in all the three groups consuming fermented supplements.”

Vaginal microbiome (also see pregnancy)

Screen Shot 2014-06-30 at 11.23.32 PMPrimate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance – Suleyman Yildirim – ISME J (uncorrected proof, link to Chapman Research)

“Our results indicated that all primates exhibited host-specific vaginal microbiota and that humans were distinct from other primates in both microbiome composition and extent of diversity”

Skin microbiome

New Molecular Techniques to Study the Skin Microbiota of Diabetic Foot Ulcers
Jean-Philippe Lavigne – Advances in Wound Care

“Molecular tools have better documented the composition and organization of the skin flora. Further advances are required to elucidate which among the many bacteria in the DFU flora are likely to be pathogens, rather than colonizers.”

General human microbiome 

Shrinkage of the human core microbiome and a proposal for launching microbiome biobanks – Abolfazl Barzegari – Future Microbiology

“This article suggests launching microbiome biobanks for archiving native microbiomes, supervising antibiotic use, probiotic design and native starter production, as well as advertising a revisit to native lifestyles.”

Review: Blowing on Embers: Commensal Microbiota and our Immune System
Darina S. Spasova and Charles D. Surh – Frontiers in Immunology

“This review discusses the recent advances in this field, focusing on the close relationship between the adaptive immune system and commensal microbiota, a constant and abundant source of foreign antigens.”

Microbiome: Second Genome Is Finding Disease Mechanisms, Biomarkers, And Therapeutics – Wayne Koberstein – Life Science Leader

“We now understand that biological processes such as inflammation, barrier function, metabolism, and energy homeostasis are directly linked to our microbiome,” says Peter DiLaura, president and CEO of Second Genome.

Mayo Clinic and Whole Biome Announce Collaboration to Research the Role of the Human Microbiome in Women’s Diseases Using Unique Medical Laboratory Tests – DarkDaily

“This joint research effort will initiate a new field of clinical laboratory diagnostic tests that target the human microbiome”

Prokaryotes versus Eukaryotes: Who is hosting whom? – Guillermo Tellez – Frontiers in Veterinary Science

“Our aim here is to encourage empirical inquiry into the relationship between mutualism and evolutionary diversification between prokaryotes and eukaryotes which encourage us to postulate: Who is hosting whom?”

Animal models of microbiome and disease

Combination of Metagenomics and Culture Based Methods to Study the Interaction Between Ochratoxin A and Gut Microbiota – Mingzhang Guo

“Changes in functional genes of gut microbiota including signal transduction, carbohydrate transport, transposase, amino acid transport system and mismatch repair were observed.”

Functional divergence in gastrointestinal microbiota in physically-separated genetically identical mice – G. B. Rogers – Scientific Reports

“We report significant divergence in both the composition and metabolism of gut microbiota in genetically-identical adult C57BL/6 mice housed in separate controlled units within a single commercial production facility.”

Alteration of Gut Bacteria and Metabolomes After Glucaro-1,4-Lactone Treatment Contributes to the Prevention of Hypercholesterolemia – Baogang Xie – J. Agric. Food Chem

“Colonic flora test results reveal that the quantity of Bifidobacterium and Lactobacillus in the intestines respectively increase by about 1.7- and 4.2-fold in rats treated with 1,4-GL compared with those in the control group. “

Pregnancy and birth

Oral presentation: The evolution of the vaginal microbiome throughout uncomplicated pregnancy in a UK population – M Chandiramani – Arch Dis Child Fetal Neonatal Ed

“Vaginal swabs were collected at time points across gestation (8–12, 20–22, 28–30 and 34–36 weeks) and the postpartum period (6 weeks) from 43 women delivered at term. Resident bacterial communities were determined using the Illumina MiSeq platform generated from bar-coded amplicons of 16S rRNA gene fragments.”

Screen Shot 2014-06-30 at 11.26.14 PMGroup B Streptococcus β-hemolysin/Cytolysin Breaches Maternal-Fetal Barriers to Cause Preterm Birth and Intrauterine Fetal Demise in Vivo – Tara M. Randis – Journal of Infectious Diseases

“We used a new murine model to evaluate the contribution of the pore-forming GBS β-hemolysin/cytolysin (βH/C) to vaginal colonization, ascension, and fetal infection.”

Zinc and copper levels in low birth weight deliveries in Medani Hospital, Sudan –
Abass RM – BMC Research Notes

“Maternal zinc and copper levels, as well as cord copper levels, are lower in LBW newborns than in those with normal weight.”

Effective Biomarkers for Diagnosis of Neonatal Sepsis – Vineet Bhandari – Journal of Pediatric Infectious Diseases

“The diagnostic utility of the following biomarkers seems to be most practical in the early (interleukin [IL]-6, IL-8, tumor necrosis factor-alpha, neutrophil CD64), mid (procalcitonin) and late (C-reactive protein) phases of neonatal sepsis.”

Review: Association of Periodontal Disease and Pre-term Low Birth Weight Infants
Manjusha Varadan, Jaiganesh Ramamurthy – The Journal of Obstetrics and Gynecology of India

“The association of periodontitis as risk factor for pre-term birth has been in extensive research in the past two decades when a number of studies investigated this relationship.”

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Human microbiome, June 27

How to grow the “Most Wanted” gut bacteria in microfluidic chips, effect of Vitamin D on gut microbiota, and probiotics for your skin.

Human gut microbiome

Screen Shot 2014-06-27 at 10.10.29 PMGene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project’s Most Wanted taxa – Liang Ma – PNAS

“We developed a microfluidics-based, genetically targeted approach to address these challenges. This approach corrects sampling bias from differential bacterial growth kinetics, enables the use of growth stimulants available only in small quantities, and allows targeted isolation and cultivation of a previously uncultured microbe from the human cecum that belongs to the high-priority group of the Human Microbiome Project’s “Most Wanted” list.”

From the ICE/ENDO meeting: Vitamin D May Improve Metabolic Health of African American Men – Lara C. Pullen – Medscape.com

“Vitamin-D supplementation not only improved insulin sensitivity but also shifted the microbiome from a prediabetes spectrum to a healthy signature. “

Exploring the Microbiome – Chris Anderson – Genetic Engineering & Biotechnology News

““These cover a broad range of options including complex approaches like fecal transplants that could include early uncharacterized strains of bacteria and other microorganisms, all the way to reductionist approaches,” noted Bernat Olle, a partner in the venture capital firm Puretech Ventures, who moderated a panel “Microbiome modulators: Opportunities and Challenges to Creating a New Drug Class” Thursday at BIO 2014.”

Human skin microbiome

LiveScienceProbiotics Hold Promise for 4 Skin Conditions – Cari Nierenberg – Live Science

“Bowe said probiotics — whether they are eaten as foods, taken as supplements or spread topically — are not a stand-alone treatment for skin problems, but could be used by patients in combination with their current treatment.”

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Human microbiome, June 26

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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