Category Archives: General Microbiome

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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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. “

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.”

 

General microbiology and science, July 17

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Detection of microbes in clinical samples, phages living in viruses, and archaea in biofilms.

Microbial detection in clinical samples

Metagenomic analysis of a sample from a patient with respiratory tract infection reveals the presence of a γ-papillomavirus – Marta Canuti – Frontiers in Microbiology

“We therefore concluded that the detected γ-papillomavirus is unlikely to be the causative agent of the respiratory complaints and its presence in the nose of the patient is not related to the disease.”

Detection of intestinal protozoa in paediatric patients with gastrointestinal symptoms by multiplex real-time PCR – L. Maas – Clinical Microbiology and Infection

“The performance of a multiplex real-time PCR for the detection of Blastocystis, Dientamoeba fragilis, Giardia lamblia, Cryptosporidium species and Entamoeba species in faecal samples was evaluated in an observational prospective study.”

Are Quantitative Bacterial Wound Cultures Useful? – George Kallstrom – Journal of Clinical Microbiology

“This minireview briefly summarizes the clinical microbiology of wound cultures, with an emphasis on the history and utility (or lack thereof) of the quantitative wound culture.”

Phages and viruses

The origins of giant viruses, virophages and their relatives in host genomes – Aris Katzourakis and Amr Aswad – BMC Biology

“These viruses, together with the transposon-related virophages that infect them, pose a number of questions about their evolutionary origins that need to be considered in the light of the complex entanglement between host, virus and virophage genomes.”

Antibiotics

Antibiotics promote aggregation within aquatic bacterial communities – Gianluca Corno – Frontiers in Microbiology

“In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses.”

Biofilms and Archaea

Biofilm formation of mucosa-associated methanoarchaeal strains – Corinna Bang – Frontiers in Microbiology

“Here, the ability of three methanoarchaeal strains, Methanobrevibacter smithii and Methanosphaera stadtmanae, which form part of the human gut microbiota, and the Methanosarcina mazei strain Gö1 to grow on different surfaces and form biofilms was investigated. “

Microbial ecology

Persistence in the shadow of killers – Robert M. Sinclair – Frontiers in Microbiology

“What we show is that coexistence is not only possible, but that it is possible even if the absolute fitness advantage of the sensitive strain over the killer strain is arbitrarily small. We do this by performing a specifically targeted mathematical analysis on our model, rather than via simulations.”

General microbiology

Editorial: Bioterrorism: myth or reality? – G. Greub and M. P. Grobusch – Clinical Microbiology and Infection

Dr. Bik’s Picks

Today I can only cry for the people onboard flight MH17.

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Non-human microbiome, July 17

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Microbiomes of sparrows, stinkbugs, corals, grapevine, and archeological stones.

Bird microbiome

Screen Shot 2014-07-17 at 5.14.56 PMGut Bacterial Diversity of the House Sparrow (Passer domesticus) Inferred by 16S rRNA Sequence Analysis – Leticia Mirón – Metagenomics

“This study is the first description of the diversity of bacteria along the whole intestine of a wild bird (Passer domesticus). Pyrosequencing of the 16S rRNA gene unveiled a high bacterial diversity, distributed in 11 bacterial phyla. “

Insect microbiome

StinkybugsSymbiont polyphyly, co-evolution, and necessity in pentatomid stinkbugs from Costa Rica – Kalia S. I. Bistolas – Frontiers in Microbiology

“The gut microbiota of 13 micro-allopatric tropical pentatomid species, from a Costa Rican lowland rainforest, was characterized and compared with insect and host plant phylogenies.”

Coral microbiome

CoralsReview: A genomic approach to coral-dinoflagellate symbiosis: studies of Acropora digitifera and Symbiodinium minutum – Chuya Shinzato – Frontiers in Microbiology

“Here we review recent genomic data derived from the scleractinian coral, Acropora digitifera, and the endosymbiotic dinoflagellate, Symbiodinium minutum. “

Plant microbiome

Screen Shot 2014-07-17 at 5.15.23 PMPyrosequencing detects human and animal pathogenic taxa in the grapevine endosphere – Sohail Yousaf – Frontiers in Microbiology

“We used pyrosequencing and phylogenetic analyses of the 16S rDNA gene. We identified several HAPT, and focused on four genera (Propionibacterium, Staphylococcus, Clostridium, and Burkholderia). “

Built Environment microbiome

Screen Shot 2014-07-17 at 5.15.49 PM 1Biological nanosilver particles for the protection of archaeological stones against microbial colonization – Ashraf M M Essa – International Biodeterioration & Biodegradation

“The stones treated with silicon polymer loaded with AgNPs showed an elevated antimicrobial potentiality against A. niger and S. parvullus.”

Water microbiome

Screen Shot 2014-07-17 at 5.16.30 PM16S rDNA-based analysis reveals cosmopolitan occurrence but limited diversity of two cyanobacterial lineages with contrasted patterns of intracellular carbonate mineralization – Marie Ragon – Frontiers in Microbiology

“To explore the diversity of these two distant cyanobacterial lineages representing two different patterns of intracellular calcification, we designed specific primers against their 16S rRNA genes and looked for their occurrence in a wide variety of samples. “

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