A review on microbial connections to depression and anxiety, effects of anthocyanins and flavanoids on the gut, and a Nature Communications paper on  Gut microbiota associations with common diseases and prescription medications! Also included are some articles on Oliver Sacks who would have turned 85 yesterday.

General microbiome

Mechanisms of action of vitamin D in colon cancer – Ferrer-Mayorga G – Journal of  Steroid Biochemistry and Molecular Biology

A review of dietary and microbial connections to depression, anxiety, and stress. – Taylor AM – Nutritional Neuroscience

The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants-but not always. – Bengtsson-Palme J – Microbiome

Human respiratory microbiome

Aerodigestive dysbiosis in children with chronic cough. – Kazachkov M – Pediatric Pulmonology

Human gut microbiome

Shifts of Faecal Microbiota During Sporadic Colorectal Carcinogenesis. – Mori G – Scientific Reports

Gut microbiota associations with common diseases and prescription medications in a population-based cohort. -Jackson MA – Nature Communications

Disruption of maternal gut microbiota during gestation alters offspring microbiota and immunity. – Nyangahu DD – Microbiome

Animal experiments 

Delayed differentiation of vaginal and uterine microbiomes in dairy cows developing postpartum endometritis – Raúl Miranda-CasoLuengo – bioRxiv

Dietary fiber increases the butyrate-producing bacteria and improves growth performance of weaned piglets. – Zhao J – J Agric Food Chem

Early intervention with faecal microbiota transplantation: an effective means to improve growth performance and the intestinal development of suckling piglets. – Cheng CS – Animal

Plant, root, and soil microbiome

A common garden experiment with Porphyra umbilicalis (Rhodophyta) evaluates methods to study spatial differences in the macroalgal microbiome – Quigley CTC -Journal of Applied Phycology

Food Microbiology

Consumption of Black Legumes Glycine soja and Glycine max Lowers Serum Lipids and Alters the Gut Microbiome Profile in Mice Fed a High-Fat Diet. – Jing C – Journal of Agricultural Food Chemistry

A systematic literature review of the effect of anthocyanins on gut microbiota populations. – Igwe EO – Journal of Human Nutrition and Dietetics

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Probiotics / prebiotics

The Mechanisms behind the Biological Activity of Flavonoids. – Gonzalez-Paramas AM – Current Medicinal Chemistry

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Swathi’s non-microbiology picks

In honor of Oliver Sacks who would have been 85 yesterday:

• Autobiography: In search of self and science – Tim Radford
• Oliver Sacks on the Three Essential Elements of Creativity – Maria Popova – Brain Pickings

Some interesting papers on redox dynamics , diabetes and the microbiome and new bioinformatics methods for microbiome analysis! Also included is an editorial on the under-representation of women in Nature. 

General microbiome

Review: The Gut Microbiome as a Target for the Treatment of Type 2 Diabetes – Aydin Ö – Current Diabetes Reports

Human respiratory microbiome

Altered intestinal microbiota composition, antibiotic therapy and intestinal inflammation in children and adolescents with cystic fibrosis. – deFreitas MB – PLoS One

Bronchiolitis obliterans syndrome susceptibility and the pulmonary microbiome – Schott C – The Journal of Heart and Lung Transplantation

Human skin microbiome

Review: Atopic Dermatitis – Weidinger S – Nature Reviews Disease Primers

Human gut microbiome

The delayed effects of antibiotics in type 2 diabetes, friend or foe?  – Fu L – Journal of Endocrinology

Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut – Aspen T Reese – eLife

Alterations in the gut bacterial microbiome in fungal Keratitis patients. – Kalayana Chakravarthy – PLoS One

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Animal experiments 

Impact of nutrition and rotavirus infection on the infant gut microbiota in a humanized pig model. – Kumar A – BMC Gastroenterology

Metabolomic signatures distinguish the impact of formula carbohydrates on disease outcome in a preterm piglet model of NEC – Lee Call – Microbiome

Plant, root, and soil microbiome

HCH phytoremediation potential of native plant species from a contaminated urban site in Turda, Romania. – Helga BE – Journal of Environmental Management

Water and extremophile microbiome

Conventional wastewater treatment and reuse site practices modify bacterial community structure but do not eliminate some opportunistic pathogens in reclaimed water. – Kulkarni P  – The Science of Total Environment

Food Microbiology

Biochemical Components Associated with Microbial Community Shift During the Pile-fermentation of Primary Dark Tea – Qin Li – Frontiers in Microbiology

Viral community predicts the geographical origin of fermented vegetable foods more precisely than bacterial community – Mi-Ja Jung – Food Microbiology

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Probiotics / prebiotics

New lactic acid bacteria for skin health via oral intake of heat-killed or live cells. – Kimota Nira H – Animal Science Journal

Bioinformatics

Deciphering microbial interactions in synthetic human gut microbiome communities  – Ophelia S. Venturelli – bioRxiv

PERFect: PERmutation Filtering test for microbiome data – Ekaterina Smirnova – Biostatistics

Determination of intracellular metabolites concentrations in Escherichia coli under nutrition stress using Liquid Chromatography-Tandem Mass Spectrometry – Fenfen Ji – ScienceDirect

Techniques

Generating Germ-Free Drosophila to Study Gut-Microbe Interactions: Protocol to Rear Drosophila Under Axenic Conditions. – Kietz C – Curr Protoc Toxicol

Visualization of Microbiota in Tick Guts by Whole-mount In Situ Hybridization. – Moss CE – JoVE

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Swathi’s non-microbiology picks

Editorial – Nature’s under-representation of women

Analysis of shared heritability in common disorders of the brain – The Brainstorm Consortium – Science

Today and tomorrow, the Biotweeps conference is happening!

@Biotweeps is a Twitter account that features a different biologist each week. Last year, they organized the first Biotweeps conference, where 60 scientists were tweeting about their work. You can read their tweets by looking for #BTCon17 on Twitter.

Today and tomorrow, the second installment of this conference is taking place, with – you guessed right! – the hashtag #BTCon18. I could not find how many presenters there were this year, but I was one of the invited “speakers”. Each speaker gave their talk entirely through tweets, and we all were given a time slot, just like at a regular conference. Regular speakers had a 15-min timeslot in which they could tweet 4-5 slides. Invited speakers could tweet as many tweets as they liked in a 30-min timeslot. You can read all the abstracts here.

My talk was about the vaginal microbiome. Here is my abstract:

2100 Invited presenter – Elisabeth Bik (@MicrobiomDigest)- uBiome San Francisco

The vaginal microbiome: Women and their microbial BFFs

The human body is home to complex communities of microbes: the human microbiome. Most of these microbes are bacteria, and most of these live in our gut. But vaginas contain microbes as well. Which microbes “down there” are our friends, and which are the ones that cause bacterial vaginosis, yeast infections, infertility, or cervical cancer? How can we keep vaginas healthy and happy, and what do we need to do in case of a microbial imbalance? If you are interested in science, have a vagina, or love vaginas owned by others, you do not want to miss this #BTCon18 thread.

If you want to read my “talk” (“tweepinar”?), you can start here.