April 20, 2020

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God morgon!

Good morning from Sweden. To all my friends who have lost the track of time during the quarantine, it is Monday and the beginning of a new week. Today’s digest is a very light one. However, it carries a super interesting preprint that studies the impact of the pandemic on publication speed of different medical journals. The study reports that, on average, the COVID-19 related papers were expedited through the peer-review process at a 49% (up to 80% in case of certain journals) higher pace than the mean pre-pandemic publishing speed (Yes, there is a pre-pandemic and, possibly, a post-pandemic era now). Although this is a controversial topic, I guess the preprint did a very good job of discussing the reasons behind and impact of accelerated publishing.

In my personal opinion, it is great to be able to get valuable scientific information as soon as it is produced. However, as the paper points out, there has to be some sort of trade-off between the quality of a publication and the time taken by the peer-review process. It could be argued that the quarantine measures might have made it easier for some reviewers to focus their attention on the peer-review, making it faster, but there is no information on ‘who’ reviewed these papers. Also, the article highlights what a lot of scholars have been warning about – the amount of post-publishing corrections that these papers would require (more work for Ms Bik!).

What do you think could be the reasons behind this unprecedented celerity of publishing? Could it be the availability of more spare time to review papers? or could this be an instance of politicization of science (as someone pointed out in the comments section of the article)? What could be the impact of this swiftness, both positive and negative, on the scientific realm? Would it be possible, or advisable, to keep up this trend of swift publishing in the post-pandemic era? Let’s discuss in the comments section.

Apart from this highly thought-provoking article, there is another interesting article on the identification of bacterial strains that may promote maize (corn, for my American friends) growth in chilling conditions.

There is another interesting article that tries to establish a link between the gut microbiome and memory. The study focused on microbiome-specific genetic and metabolomic changes that may impact memory. The study was performed in mice.

Enjoy the articles, have a great week, and stay safe!

COVID 19

Preprint: Pandemic Publishing: Medical journals drastically speed up their publication process for Covid-19 – Serge P.J.M. Horbach

Preprint: Coronavirus Infection and PARP Expression Dysregulate the NAD Metabolome: A Potentially Actionable Component of Innate Immunity – Collin D Heer, et al.

Animal microbiome

Genetic and metabolic links between the murine microbiome and memory – Jian-Hua Mao, et al. – Microbiome

Plant root-soil microbiome

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions – Stien Beirinckx, et al. – Microbiome

Microbial interactions

Preprint: Expanding the diversity of bacterioplankton isolates and modeling isolation efficacy with large scale dilution-to-extinction cultivation – Michael W. Henson, et al.

 

April 19, 2020

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Hello from the Sonoran Desert! It is a lovely morning here in Tucson, Az. I am excited to send my first contribution to Microbiome Digest! There is a lot of diversity in today’s digest, but if microbes thriving in all kinds of strange, extreme conditions are your area of interest, you’ll be interested in the book compiling the latest studies on extremophiles. Each chapter focuses on a particular environment, ranging from deserts to deep-sea hydrothermal vents, and explores the mechanisms allowing microbes to survive these incredible conditions.

If like me, you are a computational biology enthusiast and a machine learning addict, you should enjoy reading the last entry, a short perspective paper examining how machine learning algorithms can help predict antibiotic resistance!

Have a great Sunday!

General microbiology

Preprint: Interspecies interactions in bacterial colonies are determined by physiological traits and the environment – Booth – BioRxiv

Human gut and mouth microbiome

Bacterial colonization reprograms the neonatal gut metabolome – Bittinger – Nature microbiology

Salivary Factors that Maintain the Normal Oral Commensal Microflora – Carpenter – Journal of dental research

Preprint: Metagenomic Next-Generation Sequencing of Rectal Swabs for the Surveillance of Antimicrobial Resistant Organisms on the Illumina Miseq and Oxford MinION Platforms – Yee – bioRxiv

Animal microbiome

Preprint: Mortality of native and invasive ladybirds co-infected by ectoparasitic and entomopathogenic fungi – Haelewaters – bioRxiv

Built environment

Preprint: The Microbes Found in the Honey of New York City Beehives – Weiss – BioRxiv

Correlation between autochthonous microbial communities and key odorants during the fermentation of red pepper (Capsicum annuum L.) – Xu – Food Microbiology

Water and extremophile microbiome

Book: Microbial Versatility in Varied Environments: Microbes in Sensitive Environments – collective – Springer Nature

The seasonal variation of microbial communities in drinking water sources in Shanghai – Guo – Journal of Cleaner Production

Plant, root and soil microbiome

LDPE microplastics significantly alter the temporal turnover of soil microbial communities –  Wang – Science of the total environment

High abundance of Ralstonia solanacearum changed tomato rhizosphere microbiome and metabolome – Wen – BMC Plant Biology

Phages and viruses

Preprint : First evidence of virus-like particles in the bacterial symbionts of Bryozoa – Vishnyakov – BioRxiv

Microbial community development on model particles in the deep sulfidic waters of the Black Sea – Suominen – Environmental microbiology

The stepwise assembly of the neonatal virome is modulated by breastfeeding – Liang – Nature

Bioinformatics

Preprint: Bayesian classification, anomaly detection, and survival analysis using network inputs with application to the microbiome – Josephs – arXiv

Techniques

Preprint: Expanding the diversity of bacterioplankton isolates and modeling isolation efficacy with large scale dilution-to-extinction cultivation – Henson – bioRxiv

Catalyzing rapid discovery of gold-precipitating bacterial lineages with university students – Riley – PeerJ

COVID-19 and career

Science-ing from home – Powell – Nature

My non-microbiology pick

Perspective: Lean, mean, learning machines – Wheeler – Nature review microbiology

COVID-19 and Staying Sane

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We are living in an insane time. Within the past month, a lot of the world has been put on lockdown, toilet paper is a rare commodity for some reason, and a new virus is sweeping across the world. For many researchers such as myself, this pandemic has shut down a huge portion of our lives since labs are no longer open. Terrifyingly enough, we now have to get used to doing all our work cooped up in our homes. 

When working at home, it’s extremely easy to beat yourself up for not being as driven or productive as you would like, but here is the most important thing for you to remember: NO ONE IS EXPECTING YOU TO BE AS PRODUCTIVE AS YOU WERE BEFORE. This pandemic is unprecedented, and it is causing everyone’s lives to go haywire. Adjusting to such big changes is hard, and it’s unreasonable for anyone to expect you to maintain the same level of productivity during these crazy times. 

For many researchers, lab work is a huge portion of time that is suddenly gone. At least for me, filling the hole that the lack of research has left has been challenging. However, there are still plenty of opportunities to keep working and building research skills while social distancing. Here are a couple of things: 

  1. Learn a new programming language. Codeacademy is giving away Pro memberships to the first 10,000 people to sign up with a .edu email address because of the COVID-19 pandemic. Although Codeacademy is meant for absolute beginners, it does provide a good jumping-off point into further work with programming. Aside from Codeacademy, Datacamp has courses in data analysis languages as well, covering Python, R, Command-Line, and more. 
  2. Brush up on your bioinformatics. There are some really great resources available online tutorials and example datasets to practice on. Bioconductor, for instance, has a huge list of online resources and example data sets to practice using R as a biologist. There are also many tutorials online for using the command-line in bioinformatics, one of which can be found here. 
  3. Use your social media as a scientist. Now more than ever, Twitter is the perfect place to read about the newest advances in science and jump in on the discussion as well. Even on topics unrelated to COVID-19, scientific discussion is thriving now more than ever. 
  4. Work on your writing skills. While this is probably obvious to any researcher, I still feel like I should mention this. Take this time to write a new review, finally write that Materials and Methods section, or just finish up anything that might be waiting on your to-do list. 
  5. Find out more about something random that interests you by reading a bunch of literature. Whether this is just catching up on a huge backlog of papers you need to get around to reading, or diving headfirst into a completely new field, 

But what can you do outside of work to stay sane? One great thing you can do to fill this new time is to find a new hobby! Baking bread is weirdly popular now, with my coworkers sharing recipes and pictures of the masterpieces they made (if you’re looking for a neat recipe, check out this one). If you’re also looking to contribute to stopping the spread of COVID-19, you could do something simple like sewing face masks as well.

One of the most important things you have to do during this time is to take mental health days. This could be as simple as just taking one day a week to not think about work and focus on relaxing. These breaks can go a long way in reminding you that work doesn’t control your life, even though it might seem like that now more than ever. 

This is a difficult time for everyone, and learning how to adapt to a life without physical work is extremely challenging. By taking small steps, we can all learn to adapt and come out of this pandemic as stronger researchers.

April 16, 2020

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Greetings from Pittsburgh, PA! I’ve been following Microbiome Digest for several years, but this is my first contribution. Although my research is in a different subject area now, my PhD work focused on host-associated microbiota. That topic still has a special place in my heart, so below you’ll find research articles focused on the microbiota of calves, honey bees, dogs, giant clams, mosquitos, and bats! If host-associated microbiota isn’t your topic of interest, I’ve also included other articles so you can learn “WhatsGNU” in microbiology!

General microbiome

Review: A benchmark of algorithms for the analysis of pooled CRISPR screens – Bodapati et al. – Genome Biology

Animal experiments

Comparison of the ruminal and fecal microbiotas in beef calves supplemented or not with concentrate – Lourenco et al. – PLOS One

The trisaccharide melezitose impacts honey bees and their intestinal microbiota – Seeburger – PLOS One

Fecal shedding of Salmonella spp., Clostridium perfringens, and Clostridioides difficile in dogs fed raw meat-based diets in Brazil and their owners’ motivation – Viegas et al. – PLOS One

Mechanistic molecular responses of the giant clam Tridacna crocea to Vibrio coralliilyticus challenge – Xu et al. – PLOS One

Animal microbiome

Metagenomic analysis of Aedes aegypti and Culex quinquefasciatus mosquitoes from Grenada, West Indies – Ramos-Nino et al. – PLOS One

Detection of novel coronaviruses in bats in Myanmar – Valitutto et al. – PLOS One

Plant, root, and soil microbiome

Plant microbiome analysis after Metarhizium amendment reveals increases in abundance of plant growth-promoting organisms and maintenance of disease-suppressive soil – Barelli et al. – PLOS One

The genome evolution and domestication of tropical fruit mango – Wang et al. – Genome Biology

Water and extremophile microbiome

Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica – Dillion et al. – PLOS One

Preprint: Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy – Metcalfe et al. – bioRxiv

Built environment

A comparative analysis of drinking water employing metagenomics -Brumfield et al. – PLOS One

Prevalence and pollution characteristics of antibiotic resistant genes in one high anthropogenically-impacted river – Li and Zhang – PLOS One

Longitudinal survey of microbiome associated with particulate matter in a megacity – Qin et al. – Genome Biology

Phages and viruses

Ozone efficacy for the control of airborne viruses: Bacteriophage and norovirus models – Dubuis et al. – PLOS One

Bioinformatics

Decode-seq: a practical approach to improve differential gene expression analysis – Li et al. – Genome Biology

WhatsGNU: a tool for identifying proteomic novelty – Moustafa and Planet – Genome Biology

A Zipf-plot based normalization method for high-throughput RNA-seq data – Wang – PLOS One

April 15, 2020

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Hi folks! Another new volunteer poster here up from the ranks of the recently recruited. Today’s post is pre-print and plant/soil heavy. If up until now you’ve focused your reading on animal microbiomes, now’s a great time to check in on our photosynthesizing friends. Lots of great work today on the affect of management strategies on plant-associated and soil microbes. If the transition into the world of the leafy green is too jarring, perhaps try easing yourself in with Marchese et al.’s work on the mycobiome of sea cucumbers – a critter which is plant in common name only.

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Pregnancy and early life

Review: Breast Milk, a Source of Beneficial Microbes and Associated Benefits for Infant Health – Lyons et al. – Nutrients

Human respiratory microbiome

Comment: Microbiota and chronic lung disease in preterm infants. Where is the truth? – Nandakumar and Aly – Journal of Perinatology

Human skin microbiome

The cutaneous microbiome in hospitalized patients with pressure ulcers – de Wert Luuk et al. – Scientific Reports

Human vaginal microbiome

Inflammatory and antimicrobial properties differ between vaginal Lactobacillus isolates from South African women with non-optimal versus optimal microbiota – Manhanzva et al. – Scientific Reports

A meta-analysis of mannose-binding lectin gene polymorphisms with the risk of recurrent vulvovaginal infections – Kalia et al. – Scientific Reports

Human gut microbiome

Review: Gut Microbial Metabolites of Aromatic Amino Acids as Signals in Host–Microbe Interplay – Liu et al. – Trends in Endocrinology & Metabolism

Preprint: Computational Modeling of the Gut Microbiota Predicts Metabolic Mechanisms of Recurrent Clostridioides difficile Infection – Henson – bioRxiv

Preprint: Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica – Liao et al. – bioRxiv

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Animal experiments

Preprint: Validating the use of bovine buccal sampling as a proxy for the rumen microbiota using a time course and random forest classification approach – Young et al. – bioRxiv

Animal microbiome

Gut microbial diversity across a contact zone for California voles: implications for lineage divergence of hosts and mito‐nuclear mismatch in the assembly of the mammalian gut microbiome – Lin et al. – Molecular Ecology

Diversity and bioactivity of fungi associated with the marine sea cucumber Holothuria poli: disclosing the strains potential for biomedical applications – Marchese et al. – Journal of Applied Microbiology

Perspective: Microbiome maturation during a unique developmental window – Videvall – Molecular Ecology

Preprint: Microbial interactions in the mosquito gut determine Serratia colonization and blood feeding propensity – Kozlova et al. – bioRxiv

Plant, root, and soil microbiome

Reduced microbial diversity induces larger volatile organic compound emissions from soils – Abis et al. – Scientific Reports

Increased temperatures alter viable microbial biomass, ammonia oxidizing bacteria and extracellular enzymatic activities in Antarctic soils – Barnard et al. – FEMS Microbiology Ecology

One ring to rule them all: an ecosystem engineer fungus fosters plant and microbial diversity in a Mediterranean grassland – Zotti et al. – New Phytologist

Changes in soil fungal communities following anthropogenic disturbance are linked to decreased lodgepole pine seedling performance – Beck et al. – Journal of Applied Ecology

Long-term effects of stump removal and tree species composition on the diversity and structure of soil fungal communities – Modi et al. – FEMS Microbiology Ecology

Effect of treated sewage characteristics on duckweed biomass production and microbial communities – Iwano et al. – Water Science and Technology

Review: Functional roles of microbial symbionts in plant cold tolerance – Acuña‐Rodríguez et al. – Ecology Letters

Preprint: Dryland cropping system, weed communities, and disease status modulate the effect of climate conditions on wheat soil bacterial communities – Ishaq et al. – bioRxiv

Preprint: Cropping systems that improve richness convey greater resistance and resilience to soil fungal, relative to prokaryote, communities – Finn et al. – bioRxiv

Water and extremophile microbiome

Diverse groups of fungi are associated with plastics in the surface waters of the Western South Atlantic and the Antarctic Peninsula – Lacerda et al. – Molecular Ecology

Nitrification kinetics and microbial community dynamics of attached biofilm in wastewater treatment – Skoyles et al. – Water Science and Technology

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Techniques

Data normalization strategies in metabolomics: Current challenges, approaches, and tools – Misra – European Journal of Mass Spectrometry

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Microbes on the market

Blog: COVID-19: Impact of Coronavirus Pandemic on Human Microbiome Market 2020. Top Leaders are Dohme Corp, Seres Therapeutics, Synthetic Biologics Inc, Synlogic – Publicist 360

 

 

April 14, 2020

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Hello,

Hope this finds you all well. This is my first post, and hopefully not the last. Here are some interesting articles for you to enjoy today. You may notice that I will end up posting a lot about stress, sleep, and mental illness. I’m pretty diverse and also have a soft spot for nature.

Happy reading.

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  • Pregnancy and early life

Review: Maternal Vertical Transmission Affecting Early-life Microbiota Development S. Wang, et al.

  • Human skin microbiome

Bacteriophage of the Skin Microbiome in Patients with Psoriasis and Healthy Family Controls H. Wang, et al.

  • Human vaginal microbiome

Clinical Research: A 28 Day Clinical Assessment of a Lactic Acid-containing Antimicrobial Intimate Gel Wash Formulation on Skin Tolerance and Impact on the Vulvar Microbiome E. Bruning, et al.

  • Human gut microbiome

Altered Fecal Microbiome Years after Traumatic Brain Injury R. J. Urban, et al.

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  • Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

A Uniquely Altered Oral Microbiome Composition Was Observed in Pregnant Rats With Porphyromonas gingivalis Induced Periodontal Disease M.S. Walkenhorst, et al.

  • Animal microbiome (for animals in the wild)

Preprint: Gut microbiome modulates behaviour and life history in two wild rodents J. W. Jameson, et al.

  • Plant, root, and soil microbiome

Review: Recent advances in the role of plant metabolites in shaping the root microbiome R.P. Jacoby, et al.

April 13, 2020

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Hi everyone!

In today’s digest there is a range of exciting papers. The first paper looks into using a COVID-19 RBD vaccine on rodents. You will also find a great study on utilising Myxobacterium to fight cucumber wilt – even as an avid cucumber hater I appreciated this one! A third highlight is an exciting clinical study of heat-inactivated Bifidobacterium in reducing patient IBD symptoms.

COVID-19

Preprint: The SARS-CoV-2 receptor-binding domain elicits a potent neutralizing response without antibody-dependent enhancement – Quinlan et al.

Preprint: Comparison of SARS-CoV-2 infections among 3 species of non-human primates – Lu et al.

Preprint: Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence – Leary et al.

Human gut microbiome

Preprint: Short-chain fatty acid production by gut microbiota from children with obesity is linked to bacterial community composition and prebiotic choice – Holmes et al.

Short Review: In sickness and health: Effects of gut microbial metabolites on human physiology – Glowacki & Martens. PLOS Pathogens.

Animal experiments

Evaluation of microbiome-host relationships in the zebrafish
gastrointestinal system reveals adaptive immunity is a target of bis(2-ethylhexyl) phthalate (DEHP) exposure – Adamovsky et al. Environmental Science & Technology.

Abnormal gut microbiota composition is associated with experimental autoimmune prostatitis‐induced depressive‐like behaviors in mice – Du et al. The Prostate.

Plant, root and soil microbiome

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios – P. Braga et al. Microbiome.

Predatory myxobacterium controls cucumber fusarium wilt by regulating soil microbial community – Ye et al. Microbiome.

Food Microbiology

Green tea polyphenols boost gut-microbiota-dependent mitochondrial TCA and urea cycles in Sprague–Dawley rats – Zhou et al. The Journal of Nutritional Biochemistry.

Probiotics

Heat-inactivated Bifidobacterium bifidum MIMBb75 (SYN-HI-001) in the treatment of irritable bowel syndrome: amulticentre, randomised, double-blind, placebo-controlled clinical trial – Andresen et al. The Lancet Gastroentrology & Hepatology.

April 12, 2020

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¡Buenos dias!

Greetings from Spain as I write my first blog post, I am very excited to have been given this opportunity and I hope I can send a little bit of this enthusiasm to all of you in this sunday morning. In today’s menu we have a really interesting review of Microbiome-Neuronal Signaling along with another of human breast milk with a curius subsection of It’s miRNA composition. All this with many other publications from biorreactors to soil microbiome . I hope you enjoy and forgive my little mistakes.

Hope to see you soon. Adios!

COVID-19

Preprint: A virus that has gone viral: Amino acid mutation in S protein of Indian isolate of Coronavirus COVID-19 might impact receptor binding and thus infectivity Priyanka Saha in bioRxiv

Preprint: Potential host range of multiple SARS-like coronaviruses and an improved ACE2-Fc variant that is potent against both SARS-CoV-2 and SARS-CoV-1 Yujun Li et al. in bioRxiv

Preprint: A Highly Scalable and Rapidly Deployable RNA Extraction-Free COVID-19 Assay by Quantitative Sanger Sequencing Devon Chandler-Brown in bioRxiv

Preprint: Nonmedical Masks in Public for Respiratory Pandemics: Droplet Retention by two-layer Textile Barrier Fully Protects Germ-free Mice from Bacteria in Droplets Alexander Rodriguez-Palacios et al. in bioRxiv

General Microbiome

Linoleic acid induces metabolic stress in the intestinal microorganism Bifidobacterium breve DSM 20213 Alice Senizza et al. in Scientific Reports

Human Gut Microbiome

Preprint: Not just ‘immunity’: how the microbiota can reshape our approach to cancer immunotherapy Federico Boem et al. in Immunotherapy

Review: Toward Understanding Microbiome-Neuronal Signaling K. G. Jameson et al. in Molecullar Cell.

Gut microbiota in children with juvenile idiopathic arthritis: characteristics, biomarker identification, and usefulness in clinical prediction Xubo Qian et al. in BMC Genomics

Fecal-associated microbiome differences between traditional Chinese medicine qi-deficiency and balanced constitutions Jianhua Zhen et al. in Journal of Traditional Chinese Medical Sciences

Gut Microbiota Modulate CD8 T Cell Responses to Influence Colitis-Associated Tumorigenesis Amy I.Yu et al. in Cell Reports

Human Vaginal Microbiome

Review: Recommendations on Screening for Asymptomatic Bacterial Vaginosis in Pregnancy Amanda L. et al. in JAMA

Human nearly-sterile sites

Preprint: Changes to the resistome of Pseudomonas aeruginosa clone ST308 associated with corneal infection over time Mahjabeen Khan et al. in bioRxiv

Pregnancy and early life

Review: Components of human breast milk: from macronutrient to microbiome and microRNA. Su Yeong Kim et al. in Clinical and experimental pediatrics

Animal experiments

The impact of short-term acute heat stress on the rumen microbiome of Hanwoo steers Youl Chang Baek et al. in Journal of Animal Science and Technology (JAST)

Effects of Dietary Microencapsulated Tannic Acid (extracted from Chinese gallnut) Supplementation on the Growth Performance, Intestinal Morphology, and Intestinal Microbiota in Weaning Piglets Meiwei Wang et al. in Journal of Animal Science

Association between oropharyngeal microbiome and weight gain in piglets during pre and post weaning life Andrew Wange Bugenyi et al. in Journal of Animal Science and Technology (JAST)

An early fecal microbiota transfer improves the intestinal conditions on microflora and immunoglobulin and antimicrobial peptides in piglets Teng Teng et al. in Journal of Agricultural and Food Chemistry

Microbial communities and food safety aspects of crickets (Acheta domesticus) reared under controlled conditions X. Fernandez-Cassi et al. in Journal of Insects as Food and Feed

Difference of gut microbiota composition based on the body condition scores in dogs Ju Lan Chun et al. in Journal of Animal Science and Technology (JAST)

Preprint: A Systematic Analysis of Mosquito-Microbiome Biosynthetic Gene Clusters Reveals Antimalarial Siderophores that Reduce Mosquito Reproduction Capacity Jack G Ganley et el. in bioRxiv

Plant, root, and soil microbiome

Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla Yakshi Ortiz et al. in PLOS ONE

Impact of Atrazine Exposure on the Microbial Community Structure in a Brazilian Tropical Latosol Soil Ana Flavia Tonelli Fernandes et al. in Microbes and Environments

Prepint: An intensive multilocation temporal dataset of fungal communities in the root and rhizosphere of Brassica napus NavidBazghaleh in Data et al. in Brief

Comammox bacterial abundance, activity, and contribution in agricultural rhizosphere soils XiaominWang et al. in Science of The Total Environment

Diversity and potential biogeochemical impacts of viruses in bulk and rhizosphere soils Li Bi et al. in Environ Microbiology

Rhizosphere microbiome assemble and its impact on plant growth Qian Qu et al. in Journal of Agricultural and Food Chemistry

Water and extremophile microbiome

Patterns in extracellular enzyme activity and microbial diversity in deep-sea Mediterranean sediments NagissaMahmoudi et al. in Deep Sea Research

Preprint: Towards a probiotic approach for building plumbing – Nutrient-based selection during biofilm formation on flexible polymeric materials Lisa Neu in bioRxiv

Built environment

The biogeography and assembly of microbial communities in wastewater treatment plants in China Bing Zhang et al. in Environmental Science & Technology

Aerobic biodegradation of p-nitrophenol in a nitrifying sludge bioreactor: System performance, sludge property and microbial community shift MingrunLi et al. in Journal of Environmental Management

Microbes on the market

Blog: Microbiome Therapeutics Market 2020 Latest Trends, Technology Studies, Substantial Growth, Key Developments and Future Analysis till 2025 Anita in Science In Me

Blog: Microbiome Sequencing Services Market: Opportunities and Forecast Assessment, 2019-2025 supriya in Curius Desk

Techniques

preprint: Combining light sheet microscopy and expansion microscopy for fast 3D imaging of virus-infected cells with super-resolution Luca Mascheroni et al. in bioRxiv

April 11, 2020

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Happy Saturday morning, y’all! I’m excited for my first contribution to the digest, and hope you enjoy my picks over a luxurious weekend meal. Today’s digest starts with some preprints about COVID including research on a drug that may inhibit viral replication. Other research highlights include an examination of the relationship between the vaginal microbiome and pre-term birth, a preprint on the oral microbiome in space, and a potential new technique for low cost, high-throughput metagenome profiling. Scroll all the way to the end for information about a fun project by a University of Wyoming student called The Microbestiary.

COVID-19
Preprint: Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. Auslander, N. et al.

Preprint: Nelfinavir inhibits replication of severe acute respiratory syndrome coronavirus 2 in vitro. Yamamoto, N. et al.

Preprint: Understanding the B and T cells epitopes of spike protein of severe respiratory syndrome coronavirus-2: A computational way to predict the immunogens. Vashi, Y. et al.

General Microbiome
Preprint: From iron to antibiotics: Identification of conserved bacterial-fungal interactions across diverse partners. Pierce, EC. et al.

Human Gut Microbiome
Review: Unraveling Host-Gut Microbiota Dialogue and Its Impact on Cholesterol Levels. Villette R. et al. Frontiers in Pharmacology.

Metagenomics analysis reveals features unique to Indian distal gut microbiota. Kaur, K. et al. PLOS ONE.

Gut Microbiota Modulate CD8 T Cell Responses to Influence Colitis-Associated Tumorigenesis. Yu, A.I. et al. Cell Reports.

Human Oral Microbiome
Preprint: Characterization of the oral microbiome of medically controlled type-2 diabetes patients. Santos, A. et al.

Human Vaginal Microbiome
Cervicovaginal microbiome and natural history of HPV in a longitudinal study. Usyk, M. et al. PLOS Pathogens.

Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth. Kosti, I. et al. Frontiers in Microbiology.

Water and Extremophile Microbiome
Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef. Hartman, L.M. et al. Animal Microbiome.

Microbial Diversity and Metabolic Potential in the Stratified Sansha Yongle Blue Hole in the South China Sea. He, P. et al. Scientific Reports.

Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources. Compte-Port, S. et al. PLOS ONE.

Animal Experiments and Animal Microbiome
The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts. Vaelli, P.M. et al. eLife.

Metatranscriptomic virome assessment of Rhipicephalus microplus from Colombia. Gomez, G.F. et al. Ticks and Tick-borne Diseases.

Preprint: Metabolic differences between symbiont subpopulations in the deep-sea tubeworm Riftia pachyptila. Hinzke, T. et al.

Preprint: Similar gut bacterial microbiota in two fruit-feeding moth pests collected from different host species and locations. Gong, Q et al.

Plant, Root, and Soil Microbiome
The preceding root system drives the composition and function of the rhizosphere microbiome. Zhou, Y. et al. Genome Biology.

Microbial Co-Occurrence in Floral Nectar Affects Metabolites and Attractiveness to a Generalist Pollinator. Rering, C.C. et al. Journal of Chemical Ecology.

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios. Braga, L.P.P. et al. Microbiome.

A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community. Ye, X. et al. Microbiome.

A plant genetic network for preventing dysbiosis in the phyllosphere. Chen, T. et al. Nature.

Fungal communities differentially respond to warming and drought in tropical grassland soil. de Oliveira, T.B. et al. Molecular Ecology.

Built Environment
An in-depth survey of the microbial landscape of the walls of a neonatal operating room. Derilus, D. et al. PLOS ONE.

Microbes in Space
Preprint: Defining the resilience of the human salivary microbiota by a 520 days longitudinal study in confined environment: the Mars500 mission. Bacci, G. et al.

Phages and Viruses
Phage cocktail containing Podoviridae and Myoviridae bacteriophages inhibits the growth of Pectobacterium spp. under in vitro and in vivo conditions. Zaczek-Moczydłowska, M.A. et al. PLOS ONE.

Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses. Moniruzzaman M., et al. Nature Communications.

Preprint: Infection with novel Bacteroides phage BV01 alters host transcriptome and bile acid metabolism in a common human gut microbe. Campbell, D.E. et al.

Bioinformatics
Preprint: Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera. Kaufman, J. et al.

Techniques
A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling. Hess, M.K. et al. PLOS ONE.

Industrial Microbiome
Open microbiome dominated by Clostridium and Eubacterium converts methanol into i-butyrate and n-butyrate. Huang, S. et al. Applied Microbiology and Biotechnology.

Fun with Microbes
University of Wyoming masters student Erin Bentley was selected for an Arctic Circle Expedition in 2021 where she will characterize microbes and share her discoveries on The Microbestiary.
“The Microbestiary strives to show the public, in welcoming and memorable ways, that the microbial world is populated by strange and beautiful characters,” says Bentley in an article published on the UW website.

April 9, 2020

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Good morning! There’s a diverse set of microbiome papers to share today, ranging from the human microbiome in Lynch Syndrome to the microbes that flavor wine and degrade paintings in art galleries. You may also want to check out the recent news that popular video game Borderlands 3 is introducing a new mini-game that prompts players to help “map” the human gut microbiome—technical details are hard to come by, but it appears to be alignment related. There is also a study that found more than 20 percent of recently published metagenomes are not accessible.

In addition, Microbiome Data Congress 2020 will be held online on May 6 and is offering free registration through tomorrow (Friday, April 10). Speakers include human microbiome researcher Dr. Nikos Kyrpides of the (U.S.) DOE Joint Genome Institute and soil microbiologist Dr. Kari Dunfield of the University of Guelph.

Human gut microbiome

Structure of the Mucosal and Stool Microbiome in Lynch Syndrome, Yan Yan et al., Cell Host & Microbe

Effects of sex and chronic cigarette smoke exposure on the mouse cecal microbiome, Tam and Filho et al., PLOS ONE

The gut microbiome but not the resistome is associated with urogenital schistosomiasis in preschool-aged children, Derick N. M. Osakunor et al., Communications Biology

Perspective: Developing a new class of engineered live bacterial therapeutics to treat human diseases, Mark R. Charbonneau et al., Nature Communications

Review: The gut mycobiome: The overlooked constituent of clinical outcomes and treatment complications in patients with cancer and other immunosuppressive conditions, Galloway-Peña and Kontoyiannis, PLOS Pathogens

Intestinal enteroids recapitulate the effects of short-chain fatty acids on the intestinal epithelium, Sarah C. Pearce et al., PLOS ONE

Animal experiments

A combination of monosodium glutamate and high-fat and high-fructose diets increases the risk of kidney injury, gut dysbiosis and host-microbial co-metabolism, Thatsanapong Pongking et al., PLOS ONE

Plant, root, and soil microbiome

Preprint: Vineyard ecosystems are structured and distinguished by fungal communities impacting the flavour and quality of wine, Di Liu et al., bioRxiv

Bacterial community composition of vermicompost-treated tomato rhizospheres, Juana Munoz-Ucros et al., PLOS ONE

Field Performance of Mixtures of Pseudomonas and Bacillus spp. in Managing Papaya Ringspot Virus Disease and their Effect on Plant Defense Enzyme Activity, Ranasinghe and De Costa, Tropical Agricultural Research

Built environment

Detection of potential biodeterioration risks for tempera painting in 16th century exhibits from State Tretyakov Gallery, Alexander Zhgun et al., PLOS ONE

Microbiome and antibiotic resistome in household dust from Beijing, China, Long-Jun Ding et al., Environment International

Preprint: Microbial dark matter driven degradation of carbon fiber polymer composites, Adam M. Breister et al., bioRxiv

Phages and viruses

Preprint: Primate phageomes are structured by superhost phylogeny and environment, Jan-Frederik Gogarten et al., bioRxiv

Bioinformatics

PIA: More Accurate Taxonomic Assignment of Metagenomic Data Demonstrated on sedaDNA From the North Sea, Becky Cribdon et al., Frontiers in Ecology and Evolution

Techniques

A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling, Melanie K. Hess et al., PLOS ONE

Science, publishing, and career

Every fifth published metagenome is not available to science, Eckert, Di Cesare and Fontaneto et al., PLOS Biology