Author Archives: eliesbik

Human microbiome digest, July 21

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Today we have articles on two microbiome pioneers: Rob Knight and Jeffrey Gordon, as well as papers on periodontitis, eczema, Crohn’s disease, and Helicobacter.

General microbiome

The effects of the microbiota on the host immune system – Jacek Karczewski – Autoimmunity

“This review is focused on host–microbiota interactions, specifically on influence of bacterial-derived signals on immune cell function and the mechanisms by which these signals modulate the development and progression of inflammatory and autoimmune diseases.”

Imposition of encapsulated non-indigenous probiotics into intestine may disturbs human core microbiome – Abolfazl Barzegari – Frontiers in Microbiology

“We envision that the lack of survivability of some of the probiotic candidates within such hostile milieu of GIT may negatively affect the coevolving process of bacteria in human host and hence impact the endpoint health promotion goals.”

40 under 40: Rob Knight – Cell

“Some dead scientists who I would have loved to have had the opportunity to work with include Carl Woese, Richard Feynman, Francis Crick, Erwin Chargaff, Sewall Wright, Benjamin Franklin, Antonie van Leeuwenhoek, Robert Boyle, Eratosthenes, and Lucretius. These lists are intended to be illustrative rather than exhaustive; according to my NSF Conflict of Interest form I have written grants or papers with about 750 people, all of whom I admire.”

Jeffrey I. Gordon, M.D., Will Receive Pitt’s Dickson Prize at Science 2014—Sustain It! – University of Pittsburgh

“A scientist who has explored how the tens of trillions of microbes that live in the gastrointestinal tract and their genes influence human physiology, metabolism and nutritional status will receive the University of Pittsburgh’s 2014 Dickson Prize in Medicine.”

Oral microbiome

Quantitative analysis of classical and new putative periodontal pathogens in subgingival biofilm: a case–control study – N. N. Al-hebshi – Journal of Periodontal Research

“Pooled subgingival biofilm samples were obtained from 40 patients with chronic periodontitis and 40 healthy controls. Taqman q-PCR assays were used to determine the absolute and relative counts of Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Parvimonas micra, Filifactor alocis, oral Synergistetes and oral TM7s. “

Skin microbiome

Review: Microbiota in Healthy Skin and in Atopic Eczema – Giuseppe Baviera – BioMed Research International

“This review also highlights recent observations on the importance of innate immune systems and the relationship with normal skin microflora for the maintenance of healthy skin.”

Gastric microbiome

Microbial Profile of the Stomach: Comparison between Normal Mucosa and Cancer Tissue in the Same Patient – Incheol Seo – Journal of Bacteriology and Virology

“In this study, we identified differences in the microbial communities between gastric cancer and normal gastric mucosa by comparing the microbiomes of tissues from the same patients. The clustering analysis results showed different bacterial communities between normal gastric mucosa and gastric cancer.”

Motility and Chemotaxis Mediate the Preferential Colonization of Gastric Injury Sites by Helicobacter pylori – Eitaro Aihara – PLOS Pathogens

“Using anesthetized mice in which we have induced microscopic damage to the stomach surface, we find that H. pylori is able to rapidly detect and navigate towards this damage site. Within minutes, bacterial accumulation slows repair of the damage.”

Gut microbiome

Metabolic Modeling of Common Escherichia coli Strains in Human Gut Microbiome
Yue-Dong Gao – BioMed Research International

“we investigated the E. coli strains in human gut microbiome using deep sequencing data and reconstructed genome-wide metabolic networks for the three most common E. coli strains, including E. coli HS, UTI89, and CFT073. “

Analysis of Gut Microbiome and Diet Modification in Patients with Crohn’s Disease [PDF] – Sumathi Sankaran Walters – Symbiosis

“Fecal samples were obtained from patients with Crohn’s disease in a pilot diet crossover trial comparing the effects of a specific carbohydrate diet (SCD) versus a low residue diet (LRD) on the composition and complexity of the gut microbiota and resolution of IBD symptoms. The gut microbiota composition was assessed using a high-density DNA microarray PhyloChip “

Review: Managing the manager: Gut microbes, stem cells and metabolism –
M. Serino – Diabetes & Metabolism

“The LPS-sensitive cell types can be seen within bone marrow-derived cells (BMC), which are involved in the development of inflammation in the adipose tissue of obese and type 2 diabetic mice. “

 

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General microbiology and science, July 18

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Talking to bacteria to make them feel more comfortable (Bacteria whisperers!), probiotics, viruses vs. helminths, and women in Science.

Phages, viruses, helminths

Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation – Lisa C. Osborne – Science

“Helminth coinfection resulted in impaired antiviral immunity and was associated with changes in the microbiota and STAT6-dependent helminth-induced alternative activation of macrophages.”

Probiotics

Lactobacillus rhamnosus L34 and Lactobacillus casei L39 suppress Clostridium difficile-induced IL-8 production by colonic epithelial cells – Prapaporn Boonma – BMC Microbiology

“We screened Lactobacillus conditioned media from 34 infant fecal isolates for the ability to suppress C. difficile-induced IL-8 production from HT-29 cells. Factors produced by two vancomycin-resistant lactobacilli, L. rhamnosus L34 (LR-L34) and L.casei L39 (LC-L39), suppressed the secretion and transcription of IL-8 without inhibiting C. difficile viability or toxin production. “

Cross-talk between probiotic lactobacilli and host immune system – T.S. Kemgang – Journal of Applied Microbiology

“This review summarizes the interplay existing between the host immune system and probiotic lactobacilli, that is, with emphasis on lactobacilli as a prototype probiotic genus.”

General microbiology

Talking to bacteria? Towards light-mediated sensing of bacterial comfort – G. Zafrilla – Letters in Applied Microbiology

“The framework is to convert the human voice into electric pulses, these into light pulses exciting bacterial fluorescent proteins, and convert light-emission back into electric pulses, which will be finally transformed into synthetic voice messages.”

Bacteria in the news

More Forgotten Virus, Bacteria Vials Found at Federal Lab – Newsplex.com

“Food and Drug Administration officials said Wednesday the undocumented collection contained 327 carefully packaged vials, listing pathogens like dengue, influenza and rickettsia.”

1 weird tip to not die of smallpox – Beth Skwarecki – PLOS Blogs

“Jenner then attempted to infect the child with smallpox twenty more times in his life. Fortunately for the kid, the vaccine had worked.”

Women in Science

Science Has a Gender Problem. Science Just Made It Worse – Katy Waldman – Slate

“Transgender sex workers should not be expected to thank Science for “raising awareness” of them as erotic objects, jokes, or disease vectors. “

Survey of Academic Field Experiences (SAFE): Trainees Report Harassment and Assault – Kathryn B. H. Clancy – PLOS ONE

“Little is known about the climate of the scientific fieldwork setting as it relates to gendered experiences, sexual harassment, and sexual assault. We conducted an internet-based survey of field scientists (N = 666) to characterize these experiences. “

Dr. Bik’s Picks

Long read: One of a kind: What do you do if your child has a condition that is new to science? – Seth Mnookin – The New Yorker

“At first, they said, he seemed to represent a challenging problem for each new specialist to solve. But, as one conjecture after another was proved wrong, the specialists lost interest; many then insisted that the cause of Bertrand’s illness lay in someone else’s area of expertise. “

Introduction to special issue: Slicing the wheat genome – Kellye Eversole – Science

“Together, these Research Articles explore multiple dimensions of the 17-gigabase wheat genome and pave the way toward achieving a full reference sequence to underpin wheat research and breeding”

 

Earth-like soils on Mars? Ancient fossilized soils potentially found deep inside impact crater suggest microbial life – Science Daily

“Soil deep in a crater dating to some 3.7 billion years ago contains evidence that Mars was once much warmer and wetter, says a geologist based on images and data captured by the rover Curiosity.”

How Colors Smell – Julie Beck – The Atlantic

“But what color is the smell of, say, soap? A new study published in PLOS One finds that some people say white, some say yellow, some say blue. “

Suspects in science museum’s dinosaur heist turn themselves in – Andrew Kenney – Charlotte Observer

“A man and woman, both 21, turned themselves over to N.C. State Capitol Police on Thursday in the case of the missing model dinosaur.”

 

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Human and bioreactor microbiome, July 18

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An upcoming radio show on the human microbiome that looks interesting, dental calculus from prehistoric skeletons (without bacterial analysis unfortunately), and animals models of microbiome research.

General microbiome

City Visions: Exploring the Human Microbiome – KALW public radio – Monday July 21 at 7 pm at 91.7 FM in San Francisco

“Join host David Onek as we explore these questions and more with Bay Area researchers who are leading the new field of microbiome exploration and discovery.”

Oral microbiome

Dental Calculus Reveals Unique Insights into Food Items, Cooking and Plant Processing in Prehistoric Central Sudan – Stephen Buckley – PLOS ONE

“Here we present a suite of results from the multi-period Central Sudanese site of Al Khiday. We demonstrate the ingestion in both pre-agricultural and agricultural periods of Cyperus rotundus tubers. “

Animal models of gut microbiota and disease

Gut Microbial Metabolism Drives Transformation of Msh2-Deficient Colon Epithelial Cells – Antoaneta Belcheva – Cell

“We report that altering the microbiota composition reduces CRC in APCMin/+MSH2−/− mice, and that a diet reduced in carbohydrates phenocopies this effect. “

Exposure to a social stressor disrupts the community structure of the colonic mucosa-associated microbiota – Jeffrey D Galley – BMC Microbiology

“..we used high throughput pyrosequencing to assess the effects of a single 2-hour exposure to a social stressor, called social disruption (SDR), on colonic mucosa-associated microbial profiles of C57BL/6 mice.”

Bioreactor microbiome

Ethyl tert-Butyl Ether (ETBE)-degrading microbial communities in enrichments from polluted environments – Yoann Le Digabel – Journal of Hazardous Materials

“Clone libraries of the 16S rRNA gene were prepared from each enrichment. The analyses of the DNA sequences obtained showed different taxonomic compositions with a majority of Proteobacteria in three cases.”

Microbial community structure of wastewater treatment subjected to high mortality rate due to ozonation of return activated sludge – S. Isazadeh – Journal of Applied Microbiology

“The bacterial community structures were investigated by 16S rRNA gene amplicon high-throughput pyrosequencing and fluorescence in situ hybridization (FISH). The structures remained highly similar throughout the experiment despite the ozone treatment.”

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Playing with post frequency and format

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UPDATE:

OK, this is embarrassing – the instructions below are not enough to stop the immediate notifications of new posts. You will also need to unsubscribe from the direct email. But this is getting very complicated. Apparently, it not currently possible for me in WordPress to set up a daily digest for my subscribers. I apologize to all my readers and I will switch back to 1-3 updates a day.

Still, I would appreciate any suggestions on improvements for this blog. Thanks!

Elisabeth Bik

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Dear readers,

If you have subscribed to receive MicrobiomeDigest updates per email, you will have noticed that I have been playing with the post format. One of my readers suggested to post each interesting paper separately, which might allow for an easier way to search and find older posts. The search function in WordPress, and also some other plug-ins that I played with do a good job finding posts, but it does not really show you where the search terms show up in the posts.

So, for today, I will post each paper that I find separately. This would work best in combination with a “daily digest” that will send out an email once a day that will lists all the recent posts.  Unfortunately, I have not found a way to send out daily compilations – any suggestions would be appreciated. I am currently working with the Jetpack plugin of WordPress, and it does not have that option.

But there is a work-around: You can set up to receive a daily (or weekly) digest by creating (or updating) a WordPress account. You can do that here.

Fill out the email adress on which you want to have the updates, create username/password. An email will be sent to your email address, and you will need to activate the account by clicking a button in the email.

Then, you will need to go back to the WordPress account page, and on the right, click the Edit button next to “Blogs I Follow”. Here is a direct link to that page. The name of my blog is “Microbiomedigest.com”. Click “delivery settings” to change the email frequency to “daily” or “weekly”.

We will see if this works better. If you absolutely hate this, or have any suggestions to make this blog format work, please let me know. My email is eliesbik [at] stanford [dot] edu   without spaces and brackets. I’d be happy to switch to any format, but with only one suggestion so far, I am not sure what the majority of my readers would like.

Also, I would love to have a bigger audience! So please spread the word about this blog.

Thanks you all, and have a great weekend,

Elisabeth Bik

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Foxp3+ T Cells Regulate Immunoglobulin A Selection and Facilitate Diversification of Bacterial Species Responsible for Immune Homeostasis

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Screen Shot 2014-07-18 at 2.08.20 PMFoxp3+ T Cells Regulate Immunoglobulin A Selection and Facilitate Diversification of Bacterial Species Responsible for Immune Homeostasis – Shimpei Kawamoto – Immunity

“Here we show that in mice, Foxp3+ T cells contributed to diversification of gut microbiota, particularly of species belonging to Firmicutes”

 

Long-Term and Seasonal Dynamics of Dengue in Iquitos, Peru

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Screen Shot 2014-07-18 at 2.09.19 PMLong-Term and Seasonal Dynamics of Dengue in Iquitos, Peru – Steven T. Stoddard – PLOS Neglected Tropical Diseases

“We studied 10 years (2000–2010) of laboratory-confirmed, clinic-based surveillance data collected in Iquitos, Peru. We characterized inter and intra-annual patterns of dengue dynamics on a weekly time scale using wavelet analysis. “

Bifidobacterium longum and Bifidobacterium breve isolates from preterm and full term neonates: Comparison of cell surface properties

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Screen Shot 2014-07-18 at 2.31.12 PMBifidobacterium longum and Bifidobacterium breve isolates from preterm and full term neonates: Comparison of cell surface properties
Valérie Andriantsoanirina – Anaerobe

“Our results suggest the existence of variations in bifidobacteria membrane structure and/or composition that may reflect adaptation of these bacteria to the intestinal environment of either preterm or full term neonates. “

Gut microbiota and obesity

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Review: Gut microbiota and obesity: role in aetiology and potential therapeutic target
Carthage P. Moran – Best Practice & Research Clinical Gastroenterology

Mechanisms behind the link between obesity and gastrointestinal cancers – Herbert Tilg – Best Practice & Research Clinical Gastroenterology

“Whereas underlying pathomechanisms remain unclear, chronic inflammation accompanying obesity has evolved in the last years as a crucial contributing factor.”

Review: Autoimmune diseases, gastrointestinal disorders and the microbiome in schizophrenia

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Review: Autoimmune diseases, gastrointestinal disorders and the microbiome in schizophrenia: more than a gut feeling – Emily G. Severance – Schizophrenia Research

“this review surveys associative and experimental data linking autoimmunity, GI activity and schizophrenia, and proposes that understanding of disrupted biological pathways outside of the brain can lend valuable information regarding pathogeneses of complex, polygenic brain disorders.”