April 25, 2019

Good morning everyone! (and apologies for the delay, a technical issue regarding the system time difference between Israel and US Pacific time :)).

Due to yesterday extremely rich digest, today’s post will be short- but diverse! Spreading from gut microbiome in infants and beetles, to the effect of microbial communities on sweet wine quality. As a bonus for the upcoming weekend, at the end of the post you’ll find a link to an article listing 10 recommended biotech podcasts.

Happy holidays for all!

General Science and Microbiology

Failure to vaccinate and vaccine failure– Editorial- Nature Microbiology

The problem with unadjusted multiple and sequential statistical testing– Casper Albers- Nature Communications

Human microbiome

**Review – What did we learn from multiple omics studies in asthma?– Olga Ivanova- Allergy

Fecal microbiota transplant for Crohn disease: A study evaluating safety, efficacy, and microbiome profile– Liat Gutin- ueg

Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study– Modupe O. Coker- BJOG

The Gut Microbiome on a Periodized Low-Protein Diet Is Associated With Improved Metabolic Health– Zhencheng Li- Frontiers in Microbiology

Plant microbiome

Characterization of Rhodopseudomonas palustris population dynamics on tobacco phyllosphere and induction of plant resistance to Tobacco mosaic virus infection– Pin Su- bioRxiv

The plant host induces antibiotic production to select the most beneficial colonizers– Ariel Ogran- AEM

Microbial network and soil properties are changed in bacterial wilt susceptible soil– Gaufo Qi- AEM

Water Microbiomes

Fates of antibiotic resistance genes in a distributed swine wastewater treatment plant– Qing-Bin Yuan- Water Environment Research

** Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments– Xiyang Dong- Nature Communications

Animal microbiome

Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle– Ceja Navarro- Nature Microbiology

Gut microbiome-derived phenyl sulfate contributes to albuminuria in diabetic kidney disease– Koichi kikuchi- Nature Communications

Honeybee-specific lactic acid bacterial supplements have no effect on American foulbrood infected honeybee colonies– Jorg G. Stephan- AEM

Food microbiome

Influence of microbial communities on the chemical and sensory features of Falanghina sweet passito wines– F De Fillips- Europe PMC

Microbiome in the News

The Asia Pacific human microbiome market is expected to reach US$ 207.81 Mn in 2025 -Cision

**UPDATED- Critical Reading required– Antibiotics: beneficial side effects are starting to come to light– Claire Bourke- The Conversation. I’m bringing about this post in order to encourage a discussion regarding the issues and claims that were written in this non-scientific article. You’re welcome to share your thoughts about it at the comments section below.

Podcasts

Top 10 Biotech Podcasts to Listen to this Spring– Clara Rodriguez Fernandez- Labiotech.eu

**Personal recommendation- This Week in Microbiolgy (TwiM)

Microbiome digest, November 3, 2014

Human oral and vaginal microbiomes, rumen microbiome of impalas, sample handling and sponges, and two remarkable pieces in the New York Times.

Human oral microbiome

The association between the upper digestive tract microbiota by HOMIM and oral health in a population-based study in Linxian, China – Guoqin Yu – BMC Public Health

“Human Oral Microbe Identification Microarrays were used to test for the presence of 272 human oral bacterial species (97 genera) in upper digestive tract (UDT) samples collected from 659 participants. “

Pregnancy and birth microbiome

Poster: Comparison of the Vaginal Microbiomes of Pregnant Women of Four Ethnicities
and Identification of Taxa Associated with Urogenital Disease – Mendz GL – ECCMID Poster

“Principal component analysis suggested differences in the bacterial populations of healthy women and those with genital infections, with clustering of the latter along the Protobacteria axis “

Animal microbiome

Examination of the Rumen Bacteria and Methanogenic Archaea of Wild Impalas (Aepyceros melampus melampus) from Pongola, South Africa – Laura M. Cersosimo – Microbial Ecology

“In the present study, next-generation sequencing and real-time polymerase chain reaction were used to investigate the diversity and density of the bacteria and methanogenic archaea residing in the rumen of five adult male impalas”

Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges – Cristiane C. Hardoim – Frontiers in Microbiology

Bacterial community profiling of the sympatric keratose species Sarcotragus spinosulus and Ircinia variabilis (Dictyoceratida, Irciniidae) was performed by polymerase chain reaction-denaturing gradient gel electrophoresis and 454-pyrosequecing of 16S rRNA gene fragments. “

Plant microbiome

Soil type-dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce – Susanne Schreiter – FEMS Microbiology Ecology

“16S rRNA gene fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. “

Are heterotrophic and silica-rich eukaryotic microbes an important part of the lichen symbiosis? – David M Wilkinson – Mycology: An International Journal on Fungal Biology

“In this necessarily speculative paper we highlight areas for future research and how newer technologies may be useful for understanding the full suite of organisms involved in the lichen symbiosis.”

Soil microbiome

Selection on soil microbiomes reveals reproducible impacts on plant function – Kevin Panke-Buisse – ISME Journal

“Analysis of the soil microbial community using 16 S rRNA gene sequencing showed distinct microbiota profiles assembling by flowering time treatment.”

Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA – Magdalena R. Osburn – Frontiers in Microbiology

“Geochemical data, energetic modeling, and DNA sequencing were combined with principle component analysis to describe this deep (down to 8100 ft below surface), terrestrial environment.”

Bioinformatic tools

* Seeing the forest for the genes: Using metagenomics to infer the aggregated traits of microbial communities – Noah Fierer – Frontiers in Microbiology

“Microbial ecologists could benefit by borrowing the concept of community-aggregated traits (CATs) from plant ecologists to glean more insight from the ever-increasing amount of metagenomic data being generated.”

Metabolomics

Fructan supplementation of senior cats affects stool metabolite concentrations and fecal microbiota concentrations, but not nitrogen partitioning in excreta – K.A. Barry – Journal of Animal Science

“Fructan supplementation may benefit senior cats as it modulates stool odor-forming compounds and decreases some protein catabolites and pathogenic gut microbiota concentrations without affecting N retention.”

Proteomics

From the Banfield lab: Development of an enhanced metaproteomic approach for deepening the microbiome characterization in the human infant gut – Weili Xiong – Journal of Proteome Research

“….we have designed a novel metaproteomic strategy based on double filtering (DF) the raw samples, a method that fractionates microbial from human cells to enhance microbial protein identification and characterization in complex fecal samples from healthy premature infants. “

More microbiology

Complementarity between targeted real-time specific PCR and conventional broad-range 16S rDNA PCR in the syndrome-driven diagnosis of infectious diseases – A.-S. Morel – European Journal of Clinical Microbiology & Infectious Diseases

“Herein, we report our experience in the diagnosis of infectious diseases over two years, during which 32,948 clinical samples from 18,056 patients were received from France and abroad.”

Microbes in the news

There Is No ‘Healthy’ Microbiome – Ed Yong – New York Times

“The microbiome is complex, varied, ever changing and context-dependent — qualities that are the enemies of easy categorization.”

Study: Ice Man has traces of bacteria that undermined his health – BetaWired

“…they found evidence of the presence of Treponema denticola, an opportunistic pathogen implicated in the development of periodontal diseases. “

Science, publishing, and career

How Do Small Things Make a Big Difference? Activities to Teach about Human–Microbe Interactions – Chandana Jasti – The American Biology Teacher

“In these guided inquiry activities, students investigate human–microbe interactions as they work together to interpret and analyze authentic data from published articles and develop scientific models.”

2014 Life Sciences Salary Survey – Jyoti Madhusoodanan – The Scientist

“This year’s data reveal notable variation in compensation for life scientists working in different fields, sectors, and regions of the world.”

Academic Science Isn’t Sexist – Wendy M. Williams and Stephen J. Ceci – New York Times

Our analyses show that women can and do prosper in math-based fields of science, if they choose to enter these fields in the first place.”

and two rebuttals:
Academic science is sexist: We do have a problem here – Emily Willingham
The flawed and offensive logic of “Academic Science Isn’t Sexist” in the @nytimes – Jonathan Eisen – The Tree of Life

Bik’s Picks

Standing time and all-cause mortality in a large cohort of Australian adults – Hidde P. van der Ploeg – Preventive Medicine

“Increasing standing may hold promise for alleviating the health risks of prolonged sitting.”

A Face to Remember – Kerry Grens – The Scientist

“Once dominated by correlational studies, face-perception research is moving into the realm of experimentation—and gaining tremendous insight.”

* With a very cute picture: Rovers Disguised as Baby Penguins Can Quietly Infiltrate Penguin Colonies – Rachel Nuwer – Smithsonian

“Pursuing this hunch, they outfitted the rover with a big ball of fluff and a little penguin head and arms. ”

[hr]

Human microbiome digest, October 27, 2014

Development of gut microbiome in infants, understanding oral microbiome through high-throughput sequencing, gut bacteria in deceased alcoholics, and bacteria after stroke.

Microbiome general

The symbiont side of symbiosis: do microbes really benefit? – Justine R. Garcia and Nicole M. Gerardo – Frontiers in Microbiology

“We evaluate these hypotheses based on available evidence, which indicate reduced competition and predation are not universal benefits for symbionts. “

Pregnancy and birth microbiome

Review: Diet and the development of the human intestinal microbiome – Noah Voreades – Frontiers in Microbiology

“This review focuses primarily on diet, as it is one of the most pivotal factors in the development of the human gut microbiome from infancy to the elderly.”

Human oral microbiome

Review: Application of high-throughput sequencing in understanding human oral microbiome related with health and disease – Hui Chen and Wen Jiang – Frontiers in Microbiology

“This review describes the application of high-throughput sequencing for characterization of oral microbiota and analyzing the changes of the microbiome in the states of health or disease.”

Human gut microbiome

Cellular and molecular pathways through which commensal bacteria modulate sensitization to dietary antigens – Taylor Feehley, Cathryn R Nagler – Current Opinion in Immunology

“This review will discuss the cellular and molecular pathways activated by commensal bacteria to protect against allergic sensitization.”

Microbial Therapy in Liver Disease: Probiotics Probe the Microbiome–Gut–Liver–Brain Axis – David W. Victor 3rd, Eamonn M.M. Quigley – Gastroenterology

“It is timely, therefore, that Dhiman et al should embark on an ambitious study, reported in this issue of Gastroenterology, designed to assess the efficacy of the probiotic cocktail, VSL#3, as secondary prophylaxis in patients with OHE.”

Changes in gut bacterial populations and their translocation into liver and ascites in alcoholic liver cirrhotics – Sari Tuomisto – BMC Gastroenterology

“Relative ratios of major commensal bacterial communities (Bacteroides spp., Bifidobacterium spp., Clostridium leptum group, Enterobactericaea and Lactobacillus spp.) were determined in faecal samples from post mortem examinations performed on 42 males”

Animal models of microbiome research

Age-related changes in intestinal permeability and gut microbiota after ischemic stroke – Joshua Crapser – Journal of Neuroimmunology

“This study aimed to elucidate the role of systemic factors, such as intestinal stress, underlying the poor outcomes of aging mice after stroke.”

Spatial and temporal colonization dynamics of segmented filamentous bacteria is influenced by gender, age and experimental infection with Helicobacter hepaticus in Swiss Webster mice – Zhongming Ge – Microbes and Infection

“Hh infection in both genders did not alter SFB levels in the jejunum and ileum, but increased SFB levels in the cecum and colon of males compared to the controls”

[hr]