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 –

“(…) 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. “



Human Microbiomes, June 9

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

Human Oral Microbiome (and some skin too!)

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

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

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

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

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

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

Human gut microbiome

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Human respiratory microbiome

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

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

Pregnancy and Birth

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

Animal models of human disease

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

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

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

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

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

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

General Human Microbiome

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

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