Human microbiomes, June 5

Today we have some commentaries on recent papers about microbiotas in malnutrition or on placentas, and new papers about oral bacteria in the bloodstream, helminths, and coincidental killers.

Oral microbiome

Screen Shot 2014-06-05 at 7.59.36 PMDissemination of Periodontal Pathogens in the Bloodstream after Periodontal Procedures: A Systematic Review – Anna Carolina Ratto Tempestini Horliana – PLOS ONE

“MEDLINE, EMBASE and LILACS databases were searched in duplicate through August, 2013 without language restriction. Observational studies were included if blood samples were collected before, during or after periodontal procedures of patients with periodontitis”

Screen Shot 2014-06-05 at 7.56.12 PMThe Emerging Landscape of Salivary Diagnostics – Yong Zhang- OHDM – Omics Online

“Here we review recent developments in salivary diagnostics that have been accomplished using salivaomics, the mechanisms of saliva diagnostics, as well as the translational and clinical application of saliva biomarkers”

Gut microbiome

Screen Shot 2014-06-05 at 7.57.14 PMInfection and Co-infection with Helminths and Plasmodium among School Children in Côte d’Ivoire: Results from a National Cross-Sectional Survey – Richard B. Yapi – PLOS Neglected Tropical Diseases

“We carried out the first national survey on parasitic worm and Plasmodium infection among children in 92 schools all over Côte d’Ivoire. Questionnaires were administered to determine the children’s socioeconomic status and infection-related risk factors. We found an overall prevalence of Plasmodium infection of 63.3%.”

ColonSome Antibiotics May Slightly Increase Colon Cancer Risk – Bahar Gholipour – LiveScience

“The researchers compared the amount of antibiotics the patients had taken at least six months before being diagnosed with cancer, to the amount of antibiotics taken by a group of about 86,000 healthy people.”

Screen Shot 2014-06-05 at 10.07.58 AMWhy Can’t Once-Malnourished Children “Catch Up”? Answer May Lie in Gut – Karen Weintraub – National Geographic

“There’s something lacking in our current approach to treatment,” said Gordon, who suspects the children may need to eat therapeutic foods for longer and/or get supplements of probiotics, or beneficial microorganisms, to catch up. “We need to think of food as interacting with this microbial organ.”

Screen Shot 2014-06-05 at 8.03.26 PMSevere hunger can have lasting effects for gut health, study finds – MedicalXPress

“Nutrition therapy has saved the lives of millions of malnourished infants, but may not restore an imbalance in gut bacteria that is key to long-term health and vitality, researchers said Wednesday.”

Pregnancy and birth

Screen Shot 2014-06-05 at 8.05.15 PMGearing up for a closer look at the human placenta – Jocelyn Kaiser – Science

“A placenta sustained you and every person ever born for 9 months, serving as your lungs and kidneys and pumping out hormones while you developed in the womb. Problems with this disk-shaped mass of tissue can contribute to everything from preterm births to diseases of middle age. Yet when a baby is born, hospitals usually throw the placenta away.”

Screen Shot 2014-06-05 at 9.57.32 AMMicrobirth: Why ‘Seeding Baby’s Microbiome’ Needs to Be on Every Birth Plan – Toni Harman – HuffingtonPost

“The latest scientific research is now starting to indicate that if the baby is not properly seeded with the mother’s own bacteria at birth, then the baby’s microbiome, in the words of Rodney R Dietert, Professor of Immunotoxicology at Cornell University, is left “incomplete”.”

General human microbiome

Screen Shot 2014-06-05 at 8.07.51 PMCoincidental killers – We assume that microbes evolved to attack humans when actually we are just civilian casualties in a much older war – Ed Yong – Aeon Magazine

“And some supposedly pathogenic bacteria were often common parts of the environment. ‘These organisms become accidental pathogens,’ says the microbiologist Arturo Casadevall from Yeshiva University in New York. ‘They’ll still be there even if you remove all the animals from the planet. And yet, evolution selected for just the right combination of traits to cause disease in humans.’”

Screen Shot 2014-06-05 at 8.12.08 PMSilicon Valley’s Top Ten Tech Trends – Jacqueline Vanacek – Forbes
Trend #7: Data-driven healthcare (from your gut).

The combination of personal health and fitness data, genomics, and even microbiomics will drive healthcare choices from real outcomes and individual probabilities. And since the bacteria in our digestive tracks has greater influence on our health than previously known, we really are what we eat!

Microbiome and Bioinformatics

Screen Shot 2014-06-05 at 8.11.20 PMBOTUX: Bayesian–like operational taxonomic unit examiner – Vishal N. Koparde – International Journal of Computational Biology and Drug Design

“Bayesian–like operational taxonomic unit examiner (BOTUX) is a new tool for the classification of 16S rRNA gene sequences into operational taxonomic units (OTUs) that addresses the problem of overestimation caused by errors introduced during PCR amplification and DNA sequencing steps”

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Human microbiome digest, June 4, 2014

Today’s featured paper describes the gut microbiota of malnourished Bangladeshi children and was published in Nature. But we also cover oral cancer and babies’ dummies (pacifiers).

Gut microbiome

Screen Shot 2014-06-05 at 12.35.59 AMPersistent gut microbiota immaturity in malnourished Bangladeshi children – Sathish Subramanian – Nature

“ In the current study, bacterial species whose proportional representation define a healthy gut microbiota as it assembles during the first two postnatal years were identified by applying a machine-learning-based approach to 16S ribosomal RNA data sets generated from monthly faecal samples obtained from birth onwards in a cohort of children living in an urban slum of Dhaka, Bangladesh, who exhibited consistently healthy growth. “

Screen Shot 2014-06-05 at 12.37.44 AMAnd an accompanying News And Views: Population health: Immaturity in the gut microbial community – Elizabeth K. Costello- Nature

“Undernourished children fall behind not only on growth, but also on maturation of their intestinal bacterial communities, according to a study comparing acutely malnourished and healthy Bangladeshi children.”

Screen Shot 2014-06-05 at 12.36.53 AMThe Scientist also writes about the Subramanian paper: How Malnutrition Affects the Microbiome – Rina Shaikh-Lesko – The Scientist

“The gut bacterial communities of severely malnourished children appear to be less developed than those of healthy children, a study on Bangladeshi infants and toddlers finds.”

Oral microbiome

Screen Shot 2014-06-05 at 12.34.59 AMChanges in Abundance of Oral Microbiota Associated with Oral Cancer – Brian L. Schmidt – PLOS ONE

“To investigate changes in the microbiome associated with oral cancers, we profiled cancers and anatomically matched contralateral normal tissue from the same patient by sequencing 16S rDNA hypervariable region amplicons. “

The strange micro-biome that is your mouth – Paul Kulpinski – Mountain Waves Healing Arts

“In this post I will report on my most recent self-experiment. Some of this experiment was intentional, and some of it was non-intentional – with regards to my oral hygiene at least.”

Pregnancy and birth

Screen Shot 2014-06-05 at 12.43.20 AMMothers should suck their babies’ dummies, scientists say – Sarah Knapton – The Telegraph

“Children whose mother’s sucked their dummies to clean them were a third less likely to develop asthma and eczema, Prof Graham Rook, told the Cheltenham Science Festival. “If the parents pick up the dummy right away and sterilises it or replace it with a new clean one, that child has a considerably greater chance of having eczema and asthma,” he said.”

Influence of interpregnancy interval on birth timing – EA DeFranco – BJOG: An International Journal of Obstetrics & Gynaecology

“While short IPI is a known risk factor for preterm birth, our data show that inadequate birth spacing is associated with decreased gestational age for all births.”

Health of Hispanic Moms and Babies a Growing Concern, New Report Says – Hola Arkansas

“March of Dimes Global Ambassador Thalia Urges Hispanic Women To Be Informed About Pregnancy and Baby Health”

 

General microbiome
Pharmacomicrobiomics: The Impact of Human Microbiome Variations on Systems Pharmacology and Personalized Therapeutics – A summary of key findings and applications from the Human Microbiome Project. – Marwa ElRakaiby – Omics Journal

In this review article, we summarize the key findings and applications of the HMP that may impact pharmacology and personalized therapeutics.

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Human microbiome digest, June 3, 2014

Antimicrobial proteins in saliva, Lactobacillus spp and preterm birth, and probiotics. It’s been a long day, so no pictures today.

Oral microbiome

Salivary antimicrobial proteins associate with age related changes in streptococcal composition in dental plaque – Jennifer Malcolm – Molecular Oral Microbiology

“Dental plaque and saliva were collected from 57 children aged 12-24 months at baseline, of whom 23 children were followed-up at three-years of age. At each time, saliva was assessed for LL37, HNPs 1-3, calprotectin, lactoferrin, salivary IgA, total plaque bacteria and Streptococcus mutans.”

Pregnancy and birth

Characterisation of the vaginal Lactobacillus microbiota associated with preterm delivery – Ljubomir Petricevic – Nature Scientific Reports

“This study suggests that dominating L. iners alone detected in vaginal smears of healthy women in early pregnancy might be associated with preterm delivery”

Development of the preterm gut microbiota in infants at risk of necrotising enterocolitis and sepsis – Christopher Stewart – Doctoral thesis, Northumbria University

Intestinal Microbial Community Profiles of a Newborn Preterm Infant Using Pyrosequencing Analysis: Pilot Study (in Korean)- Jong-Geol Kim – Neonatal Medicine

“The bacterial community in the newborn’s meconium was quite similar to that in the AF, which was dominated by Sphingomonas (45.2%). “

Gut microbiome

Relating the metatranscriptome and metagenome of the human gut – Eric A. Franzosa with Curtis Huttenhower – PNAS

“Measurements of microbial species, gene, and gene transcript composition within self-collected samples were consistent across sampling methods.”

Defining the diversity of microbial eukaryotic communities in the mammalian gut within the context of environmental eukaryotic diversity – Laura W. Parfrey – Frontiers in Microbiology

“We show that adults from non-western populations harbor a diverse community of protists, and diversity in the human gut is comparable to that in other mammals. “

General human microbiome

Culturing For Cures – UCSF Scientists Explore the Bacterial Communities that Live In and On Our Bodies to Find Treatments for Disease – Claire Conway – UCSF News

“Scientists are hard at work trying to leverage the extraordinary healing powers of the microbiome, mining it for treatments of a variety of conditions, including asthma, irritable bowel syndrome and obesity.”

Probiotics

Autoinducer-2 Plays a Crucial Role in Gut Colonization and Probiotic Functionality of Bifidobacterium breve UCC2003 – Steven E. A. Christiaen – PLOS ONE

“we conclude that bifidobacteria operate a LuxS-mediated system for gut colonization and pathogen protection that is correlated with iron acquisition”

Urinary metabolomic fingerprinting after consumption of a probiotic strain in women with mastitis – Rosa Vázquez-Fresno – Pharmacological Research

“The application of NMR-based metabolomics enabled the identification of the overall effects of probiotic consumption among women suffering from mastitis and highlighted the potential of this approach in evaluating the outcomes of probiotics consumption.”

Animal models of gut microbiota

Effects of subchronic exposure of silver nanoparticles on intestinal microbiota and gut-associated immune responses in the ileum of Sprague-Dawley rats – Katherine Williams – Nanotoxicology

“This study evaluated changes in the populations of intestinal-microbiota and intestinal-mucosal gene expression in Sprague-Dawley rats (both male and female) that were gavaged orally with discrete sizes of AgNP (10, 75 and 110 nm) and silver acetate.”

Metabolomics

Oral Abstract: The high colon cancer risk in African Americans can be reduced by dietary modification – Stephen O’Keefe – Cancer & Metabolism

“dietary switch between these two populations produces reciprocal changes in the microbiome, metabolome, and mucosal biomarkers of risk within 2 weeks”

Strategies in Discovery Metabolomics – Kate Marusina – GenEngNews

Microbiome conferences

2nd World Congress on Targeting Microbiota – Institut Pasteur, Paris, France – October 16-17, 2014

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Human microbiome digest, June 2, 2014

Roberto Romero and Jacques Ravel report on the vaginal microbiome in the setting of term and preterm deliveries, red wine might be good for your teeth, and secretory IgA and gut microbiota influence each other.

Pregnancy and birth

Gut microbiome

Respiratory microbiome

Oral microbiome

Skin microbiome

  • Screen Shot 2014-06-02 at 2.35.33 PMNot sure if I would pay $36 for this review, but here it is: Cutaneous microbiome studies in the times of affordable sequencing – Marjana Tomic-Canic – Journal of Dermatological Science –  “We now know that four phyla, Actinobacteria, Firmicytes, Proteobacteria and Bacteroidetes, constitute preponderance of skin bacteria, while Malassezia dominates the fungal microbiome. “

More human microbiome

Metabolomics

Animal models of gut microbiome

Microbiome in the news

  • Screen Shot 2014-06-02 at 3.08.55 PMOur bodies, our bugs, and learning to love the bacteria that live inside us – Jane Macdougall – National Post – “Eating yogurt instead of taking a pill might sound crazy, but it’s worth considering why that is”
  • Blaser QA TK TK – Carl Zimmer – Wired.com – “Microbiologist Martin Blaser of New York University School of Medicine says that many species of germs are disappearing from our bodies—and that’s a problem.”
  • This appear to be a highly biased study: Experts warn over bad bacteria count – Taiwanese children compare poorly with their Asian peers in good and bad bacteria count, which could make them more susceptible to diseases – Wei Yi-chia and Jason Pan – Taipei Times – “The study, released on Thursday by the Association for Lactic Acid Bacteria (TALAB), found that Taiwanese schoolchildren have up to 30 times more Escherichia coli and 15 times more Clostridium perfringens — two of the “bad” bacteria — than kids of the same age in Japan.”
  • Shampoo and Soap Wreak Havoc on the Skin’s Microbiome Say Researchers – Donna Westlund – Guardian Libery Voice

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Human microbiome digest, May 29 2014

Today we observe World Digestive Health Day, but we will also learn more about the human reproductive organs – of both genders!

Gut microbiome

Genital microbiome

Pregnancy and Birth

Animal models of gut microbiota

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Digest May 27, 2014

Today’s Picks feature thousand cultured GI tract species, host-microbiome interactions during pregnancy, metagenome assemblies using Hi-C, and the microbiomes of snow leopards and possums.

Human microbiome general

Human Gut Microbiome

Pregnancy and birth microbiome

Respiratory tract microbiome

Mammalian microbiome

Amphibian microbiome

Insect microbiome

Fish microbiome

Animal and bioreactor models of gut microbiome

Environmental microbiome

Microbiome and Metabolomics

Phages and viruses

  • Beyond Antibiotics – “Today there is renewed interest in phages as warnings intensify that a “post-antibiotic” era looms” – Roger Highfield – Newsweek

Infection, sepsis, and host response

Microbial Ecology papers

Arsenic metabolism

Chromosome organization

General lab techniques papers

Dr. Bik’s Picks

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Digest May 23, 2014

Today’s digest features showering with bacteria instead of soap, bacteria on the Mars rover, phages and bacteria reading through stop-codons, and a meteor shower tonight. What do meteor showers have to do with microbiome papers, you ask? Well, nothing. They are just cool to watch. So put on that fleece, get yourself to a dark place outside, and look North. Or stay inside and read today’s new digest.

General microbiome papers

Human oral microbiome papers

Human gut microbiome papers

Human genital microbiome papers

Pregnancy and birth papers

Metagenomics

Chromosomal organization

Antibiotics and resistance papers

Pathogenicity papers

Phages and viruses

Microbes in space

More Microbes

Bacteria in the news

Dr. Bik’s Picks

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Digest May 22, 2014

Today’s digest features armpits, helminths and fish probiotics.

Skin microbiome papers

Gut microbiome papers

Pregnancy and birth microbiome papers

Animal microbiome papers

General microbiome papers

Dengue papers

Arsenic metabolism papers

Science, Ethics and Misconduct

Dr. Bik’s Picks

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Digest May 21, 2014

The first digest on this website features the microbiomes of saliva, placenta, and planes. Enjoy!

Oral microbiome papers

Gut microbiome papers

Pregnancy and birth microbiome papers

Respiratory microbiome  papers

Environmental microbiome papers

Dr. Bik’s Picks