Category Archives: Fun

December 16, 2015 #2

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Role of Lactobacillus in early pregnancy, skin microbiome of psoriasis patients before and after a spa treatment, retroviruses in coprolites, colonization of germ-free cockroach guts, more decomposing pigs, kitty poop, and de novo clustering methods are just better. So many papers, I had to do a second installment today.

General human microbiome

Review: Human Microbiome and Its Association With Health and Diseases – Asmaa Althani – Journal of Cellular Physiology

Review: Microbiota, Parasites and Immunity – Judith Allen – Parasite Immunology

Pregnancy and birth (and vaginal microbiome)

Role of Lactobacillus Species in the Intermediate Vaginal Flora in Early Pregnancy: A Retrospective Cohort Study – Alex Farr – PLOS ONE

Human Breast Milk miRNA, Maternal Probiotic Supplementation and Atopic Dermatitis in Offspring – Melanie Rae Simpson – PLOS ONE

Review: The Infant Microbiome: Implications for Infant Health and Neurocognitive Development – Yang, Irene – Nursing Research

Human oral microbiome

Association between Herpesviruses and Chronic Periodontitis: A Meta-Analysis Based on Case-Control Studies – Ce Zhu – PLOS ONE

Short-term Effects of Povidone Iodine and Sodium Fluoride Therapy on Plaque Levels and Microbiome Diversity – Cavan Reilly – Oral Diseases

Review: Saliva and viral infections – Paul L. A. M. Corstjens – Periodontology 2000

Review: The physiology of salivary secretion – Gordon B. Proctor – Periodontology 2000

Human skin microbiome

Skin Microbiome in Patients With Psoriasis Before and After Balneotherapy at the Thermal Care Center of La Roche-Posay – Richard Martin – Journal of Drugs in Dermatology

Importance of Lid Hygiene Before Ocular Surgery: Qualitative and Quantitative Analysis of Eyelid and Conjunctiva Microbiota – Peral, Assumpta – Eye & Contact Lens

Human gut microbiome

Coprolites: Retroviral DNA Sequences as a Means for Determining Ancient Diets – Jessica I. Rivera-Perez – PLOS ONE

Model microbiome

The deterministic assembly of complex bacterial communities in germ-free cockroach guts – Aram Mikaelyan – Applied and Environmental Microbiology

The piglet as a model for studying dietary components in infant diets: effects of galacto-oligosaccharides on intestinal functions – A. Alizadeh – British Journal of Nutrition

Lactobacillus crispatus inhibits growth of Gardnerella vaginalis and Neisseria gonorrhoeae on a porcine vaginal mucosa model – Laura M. Breshears – BMC Microbiology

Vancomycin treatment and butyrate supplementation modulate gut microbe composition and severity of neointimal hyperplasia after arterial injury – Karen J. Ho – Physiological Reports

Necrobiome: the microbiome of death

Shifts in soil biodiversity—A forensic comparison between Sus scrofa domesticus and vegetation decomposition – Ayodeji O. Olakanye – Science & Justice

Animal microbiome

A Longitudinal Study of the Feline Faecal Microbiome Identifies Changes into Early Adulthood Irrespective of Sexual Development – Oliver Deusch – PLOS ONE

Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata – Dustin W. Kemp – PLOS ONE

Salmonella enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks – Khin K. Z. Mon – Frontiers in Veterinary Science

Niche Limits of Symbiotic Gut Microbiota Constrain the Salinity Tolerance of Brine Shrimp – Odrade Nougué – The American Naturalist

Opinion: Blurred lines: pathogens, commensals, and the healthy gut – Paul Wigley – Frontiers in Veterinary Science

Review: The gut microbiome and its potential role in the development and function of newborn calf gastrointestinal tract – Nilusha Malmuthuge – Frontiers in Veterinary Science

Review: An introduction to the avian gut microbiota and the effects of yeast-based prebiotic-type compounds as potential feed additives – Stephanie M. Roto – Frontiers in Veterinary Science

Plant, root, and soil microbiome

Biological attributes of rehabilitated soils contaminated with heavy metals – Jessé Valentim dos Santos – Environmental Science and Pollution Research

Comparison between cultivated and total bacterial communities associated with Cucurbita pepo using cultivation-dependent techniques and 454 pyrosequencing – N. Eevers – Systematic and Applied Microbiology

Euphorbia plant latex is inhabited by diverse microbial communities – Manjula Gunawardana – American Journal of Botany

Bioreactor and waste microbiology

Systematic investigation and microbial community profile of indole degradation processes in two aerobic activated sludge systems – Qiao Ma – Scientific Reports

Pretreatment of piggery wastewater by a stable constructed microbial consortium for improving the methane production – Jian Cai – Water Science & Technology

Bioinformatics and metagenomics

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units – Sarah L. Westcott – PeerJ

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database – Jarmo Ritari – BMC Genomics

RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis – Elisabeth Navarro – BioTechniques

Review: Metagenomics: Retrospect and Prospects in High Throughput Age – Satish Kumar – Biotechnology Research International

Microbes in the news

Human-gut-on-a-chip model offers hope for IBD sufferers – Kat J McAlpine – Harvard

Metagenomics Explainer, with Emory geneticist Tim Read – Lab Land, Emory Health Sciences Research blog

Your Face Is Covered in Mites, and It’s Your Parents’ Fault – Matt Simon – Wired

Science, publishing, and career

Plenty of moustaches but not enough women: cross sectional study of medical leaders – Mackenzie R Wehner – BMJ
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October 30, 2015

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Cave microbiome, vaginal bacteria in cute minipigs, and “disordered” home dust microbiome, and an update on the Beard Microbiome.

Human gut microbiome

Oatmeal porridge: impact on microflora-associated characteristics in healthy subjects – Jørgen Valeur – British Journal of Nutrition

Animal models

The vaginal microbiome is stable in prepubertal and sexually mature Ellegaard Göttingen Minipigs throughout an estrous cycle – Emma Lorenzen – Veterinary Research

Biofilm-associated bacterial amyloids dampen inflammation in the gut: oral treatment with curli fibres reduces the severity of hapten-induced colitis in mice – Gertrude O Oppong – NPJ Biofilms and Microbiomes

Disease tolerance mediated by microbiome E. coli involves inflammasome and IGF-1 signaling – Alexandria M. Palaferri Schieber – Science

Cave microbiome

Microbial mediation of complex subterranean mineral structures – Nicola Tisato – Scientific Reports

Built environment microbiome

Home dust microbiota is disordered in homes of low-income asthmatic children – Christina E. Ciaccio – Journal of Asthma

Food microbiology

A Large Set of Newly Created Interspecific Saccharomyces Hybrids Increases Aromatic Diversity in Lager Beers – Stijn Mertens – Applied and Environmental Microbiology

T-RFLP: Bacterial community and proteome analysis of fresh-cut lettuce as affected by packaging – Mariasole Di Carli – FEMS Microbiology Letters

Viruses and phages

Virus Satellites Drive Viral Evolution and Ecology – Belén Frígols – PLOS Genetics

Bioinformatics and metagenomics

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning – Brian Cleary – Nature Biotechnology

Multi-view Clustering of Microbiome Samples by Robust Similarity Network Fusion and Spectral Clustering – Y. Zhang – Computational Biology and Bioinformatics, IEEE/ACM Transactions

Bacteria in the news

The strain in metagenomics: Two computational tools extract strain-level information from reams of microbial sequence data. – Tal Nawy – Nature Methods

Bacteria found to play role in cow’s milk intolerance – SunCoast news

‘Superhero’ microbiome bacteria protect against deadly symptoms during infection – Salk Institute – EurekAlert

Can changes in the brain affect your microbiome? UB researchers are investigating – Ellen Goldbaum – University at Buffalo

BacteriaHysteria

Not news at all: I-Team: Everyday items we touch are loaded with bacteria – Ryan Walsh – WWLP

Beard microbiome

This was actually funny:  Will Forte (actor from “The Last Man on Earth”) has beard swabbed for bacteria test, fails, at Jimmy Fallon show – Yahoo Video

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Microbiome and [random thing]

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There have been a lot of reviews published recently with titles such as “Gut microbiome and Asthma”, “Microbiome and Smoking”, and “Microbiome and Brain Disorders”. And in order to keep y’all updated here with the latest microbiome literature, I have been dutifully copy/pasting them into the Microbiome Digest. But today, I could not help feeling a tiny bit tired with all these reviews. Here was another one. And another.

It seems that by now every other scientist has written a Microbiome Review. Even I did a long time ago. When it was still in the early days. But now. There. Are. Too. Many.

So this led me to the following tweet:

Screen Shot 2015-07-01 at 10.50.02 PM To kick things off, I suggested a couple of titles:

Screen Shot 2015-07-01 at 10.52.13 PM

And that resulted in a great list of responses. Here is a selection.

Screen Shot 2015-07-01 at 10.53.31 PMScreen Shot 2015-07-01 at 10.54.07 PMScreen Shot 2015-07-01 at 10.55.13 PM

Screen Shot 2015-07-01 at 10.56.05 PMScreen Shot 2015-07-01 at 10.56.30 PM

Screen Shot 2015-07-01 at 10.56.55 PM

You can see all of them here. And now you know what to do this weekend: choose one of these topics, and write a review about it. Just don’t count on it to appear in the Digest. Thank you all!

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The Sound of Microbes

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Apparently, microbes like music. This week, I learned that bacteria and yeasts grow better when Raag Kirwani (Indian classical music) is played in their incubator. Except Serratia, although it was not asked which music it would have preferred.

Effect of audible sound in form of music on microbial growth and production of certain important metabolites – Niral Sarvaiya, Vijay Kothari – Microbiology

But do microbes make sounds? They might do in this post….

It all started with a quote from Jack Gilbert in a Wall Street Journal article about the Hospital Microbiome called Designing a Hospital to Better Fight Infection.

“Overnight, the building became alive with all these human bacteria,” said environmental microbiologist Jack Gilbert at the U.S. Department of Energy’s Argonne National Laboratory in Lemont, Ill., who is directing the project.

I used this quote on Twitter, after which Luke Meister @lukedones replied that “The Hills Are Alive with the Sound of Music” was a better song.

Michele Banks @artologica then replied with this funny picture inspired by The Sound Of Music:

The Hills Are Alive With the Smell of Miiiicrobes - Michele Banks

The Hills Are Alive With the Smell of Miiiicrobes – Michele Banks

And that led to a witty Twitter exchange, some of which with the hashtag #SoundOfMicrobes

@artologica: “Beware of E. coli on schnitzel with noodles…”

@lukedones: “When the dog bites//Pasteurella incites//A microbiological disaster …”

@MicrobiomDigest: “The wards are alive, with the stench of microbes”

@artologica: “These are a few of my faaaaavorite bugs”

@MicrobiomDigest: “Bugs on petridishes, with colonization wishes”

After which I got a bit carried away, and came up with some more #SoundOfMicrobes lyrics:

Inspired by “Maria“:
“How do you solve a problem like MRSA?”

Inspired by “Favorite Things“:
“When the bugs bites, when the phage stings, when I’m feeling sick
I simply remember my favorite bugs, featured by Dr. Bik”

Inspired by “Edelweiss“:
“Gut microbes, gut microbes, Every morning you greet me
Small and brown, dirty and down, You look happy to leave me”

Inspired by “Climb Ev’ry Mountain“:
“Isolate every sample, Sequence every bug
Follow microbiome startups, Till you find a new drug”

Inspired by “Sixteen Going On Seventeen”
“You are sixteen S rRNA gene, Present in soil and poo
Eager young students, postdocs, PI’s, Will want to sequence you”

Copyright Elisabeth Bik!

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