Animal, plant, and environmental microbiome digest, June 2, 2014

Microbiomes of rumen, salamanders, insects, corals, sponges and soil.

Mammalian microbiome

Amphibian microbiome

Insect microbiome

  • Screen Shot 2014-06-02 at 3.19.02 PMReview: Towards an integrated understanding of gut microbiota using insects as model systems – Mathieu Pernice – Journal of Insect Physiology – we give a brief overview of the characteristics of the gut microbiota in insects in terms of low diversity but high variability at intra- and interspecific levels and we investigate some of the ecological and methodological factors that might explain such variability. “

Coral and sponge microbiome

Algae and Plant microbiome

Environmental microbiome

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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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More Microbiology and Science, May 29 2014

In tonight’s digest, antimicrobial tolerance in biofilms, oil spills and dolphins, and dog people vs. cat people.

Biofilms

More microbiology

Marine mammals

Scientific publishing

  • Screen Shot 2014-05-29 at 10.53.15 PMNature’s publisher launches a new peer-reviewed, online-only journal that will accept descriptions of data sets: Publishing Data – Jef Akst – The Scientist

Dr. Bik’s Picks

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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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Environmental microbiome digest, May 29 2014

Today, we will learn about microbial communities in Petroleum “muck” and blue jeans.

Environmental microbiomes

  • Metagenomic Approach for Understanding Microbial Population from Petroleum Muck – M. N. Joshi – Genome Announcements –  “the first report which describes a next generation sequencing based study of microbial diversity from petroleum pipelines”
  • Opening session ASM 2014 (2h video): Microbes in Symbiosis, Signaling and at Sea – Michael Laub, Lora Hooper, Ove Hoegh-Guldberg
  • Screen Shot 2014-05-29 at 4.53.06 PMCan You Really Clean Your Jeans By Freezing Them? – Sam Brock and Kinsey Kiriakos – NBC Bay Area – “We traveled to an environment that is filled with bacteria, the zoo, and showcased a brand new pair of Levi’s jeans while we fed the lemurs, handled worms, grazed with the goats and transplanted saliva from the local zebu (a species of cattle) onto the pants. Next, we took the jeans to the Stanford lab for analysis. Perez swabbed the jeans for bacteria, both inside and out, before we froze them overnight and after.”

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More microbiology and science, May 28, 2014

In this digest we’ll focus on general microbiology papers that I thought were interesting. And we’ll learn that swim diapers are leaky,  that both urine as well as kid’s pools are not sterile, and that Gemmatimonadetes are photosynthetic.

Bacteria are Everywhere

More Microbes

General Science

Scientific writing and publishing

Dr. Bik’s Picks

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Environmental Microbiome digest – May 28, 2014

In this post, I collected papers about microbial communities in the hospital, soil and rocks.

Microbiome of the built environment

Soil and water microbiome

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Human microbiome digest – May 28, 2014

Today I will have four separate posts, to see if that would work better. This post is all about the human microbiome, with articles about arthritis, childhood wheezing, and pregnancy.

Human Gut Microbiome

Screen shot 2014-05-28 at 06.03PM, May 28Human Respiratory Microbiome

Screen shot 2014-05-28 at 06.08PM, May 28Pregnancy and Birth

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Infection and host response digest – May 28, 2014

Hi all,

Today I’m just playing with different layouts for my digests, by splitting them up into smaller groups of topics. In this post, you will find dengue, phages, and infection/host response papers.

Dengue

Phages and viruses

Infection and Host ReponseScreen Shot 2014-05-28 at 7.32.41 PM

Staphylococcus aureus

Arsenic metabolism

 

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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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