Category Archives: Techniques

June 3, 2020

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Today’s post covers articles on role of microbiome in sepsis, early life microbiota related to cystic fibrosis and respiratory syncitial virus disease, promise and challenge with cancer microbiome, effect of probiotics on intestinal homeostasis after chemotherapy and many more!

General microbiome

Predictive biology: modelling, understanding and harnessing microbial complexity – Allison J. Lopatkin – Nature Reviews Microbiology

The Gut Microbiome’s Role in the Development, Maintenance, and Outcomes of Sepsis – Max W Adelman – Critical Care

The Promise and Challenge of Cancer Microbiome Research – Sumeed Syed Manzoor – Genome Biology

Antidiabetic Effects of Flavan-3-ols and Their Microbial Metabolites – Estefanía Márquez Campos – Nutrients

Human microbiome

Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome – Roie Levy – PNAS

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale – Soumaya Zlitni – Genome Medicine

Comparative Assessment of Faecal Microbial Composition and Metabonome of Swine, Farmers and Human Control – Shiang Chiet Tan – Scientific Reports

Matching Between Donors and Ulcerative Colitis Patients Is Important for Long-Term Maintenance After Fecal Microbiota Transplantation – Koki Okahara – Journal of Clinical Medicine

Preganancy and early life

Alterations in Vaginal Microbiota and Associated Metabolome in Women With Recurrent Implantation Failure – Min Fu – mBio

Development of the Gut Microbiota in Early Life: The Impact of Cystic Fibrosis and Antibiotic Treatment – Maartje Kristensen – Journal of Cystic Fibrosis

Altered Gut Microbiota in Infants Is Associated With Respiratory Syncytial Virus Disease Severity – Jeffrey N Harding – BMC Microbiology

Ecological Succession in the Vaginal Microbiota During Pregnancy and Birth – M A Rasmussen – Isme Journal

Animal experiments

Host genotype and exercise exhibit species-level selection for members of the gut bacterial communities in the mouse digestive system – R. A. Dowden – Scientific Reports

Repetitive, Mild Traumatic Brain Injury Results in a Progressive White Matter Pathology, Cognitive Deterioration, and a Transient Gut Microbiota Dysbiosis – Mariana Angoa-Pérez – Scientific Reports

Association of Gut Microbiota Composition and Function With an Aged Rat Model of Senile Osteoporosis Using 16S rRNA and Metagenomic Sequencing Analysis – Sicong Ma – Aging

Increasing the Hindgut Carbohydrate/Protein Ratio by Cecal Infusion of Corn Starch or Casein Hydrolysate Drives Gut Microbiota-Related Bile Acid Metabolism To Stimulate Colonic Barrier Function – Yu Pi – mSystems

Plant, root and soil microbiome

Using Soil Bacterial Communities to Predict Physico-Chemical Variables and Soil Quality – Syrie M Hermans – Microbiome

Analysis of bacterial and archaeal communities associated with Fogo volcanic soils of different ages – Corinne Biderre-Petit – Fems Microbial Ecology

Water microbiome

Functional potential and assembly of microbes from sediments in a lake bay and adjoining river ecosystem for polycyclic aromatic hydrocarbon biodegradation – Zaisheng Yan – Environmental Microbiology

Functional foods

Effect of Probiotics on the Maintenance of Intestinal Homeostasis After Chemotherapy: Systematic Review and Meta-Analysis of Pre-Clinical Studies – W G Lima – Beneficial Microbes

Non microbiology picks

Racial Disparities in Knowledge, Attitudes and Practices Related to COVID-19 in the USA– Wilson M Alobuia – Journal of Public Health

Ozone Treatment for Elimination of Bacteria and SARS-CoV-2 for Medical Environments – Craig Westover – BioRxiv

June 2, 2020

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Happy Month of June to all,
June serves as the national month for Alzheimer’s and brain awareness. So I will start today’s digest with some news articles about the same.
Further the digest covers some very fascinating research articles about how the microbiome influences transcriptional profile in Drosophila melanogaster to peripheral blood microbial signatures in COPD. Digest also features some awesome microbe related science communication articles.
Enjoy reading!!!
Have a Safe, Healthy, Happy, and Productive month ahead.

Alzheimer’s and brain awareness news posts

Alzheimer’s & Brain Awareness Month 2020 – Bankston – ASBMB Today

Could the gut microbiome be linked to autism? – Svoboda – Nature Outlook

General microbiome
*Interactions between the microbiome and mating influence the female’s transcriptional profile in Drosophila melanogaster – Delbare et al – bioRxiv

Phenotypic changes of bacteria through opportunity and global methylation leads to antibiotic resistance – Neerathilingam et al – bioRxiv

Human nearly-sterile sites
Peripheral blood microbial signatures in COPD – Morrow et al – bioRxiv

Human gut microbiome
Prebiotics and community composition influence gas production of the human gut microbiota – Yu et al – bioRxiv

Short-term High Intensity Interval Training (HIIT) Exercise Does Not Affect Gut Bacterial Community Diversity or Composition of Lean and Overweight Men -Rettedal et al – Experimental Physiology

Animal experiments
Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes – Clusinska et al – Communications Biology

Water and extremophile microbiome
Phylum-level Diversity of the Microbiome of the Extremophilic Basidiomycete Fungus Pisolithus Arhizus (Scop.) Rauschert: An Island of Biodiversity in a Thermal Soil Desert – Culling et al – MicrobiologyOpen

Food microbiology
Lactobacillus Rhamnosus 2016SWU.05.0601 Regulates Immune Balance in Ovalbumin-Sensitized Mice by Modulating the Immune-Related Transcription Factors Expression and Gut Microbiota – Song et al – Journal of the Science of Food and Agriculture

Techniques
Harnessing Ultrasound-Stimulated Phase Change Contrast Agents to Improve Antibiotic Efficacy Against Methicillin-Resistant Staphylococcus aureus Biofilms – Durham et al – bioRxiv

Microbiome Science communication articles
The hunt for a healthy microbiome – Eisenstein – Nature Outlook

The complex relationship between drugs and the microbiome – Savage -Nature Outlook

The Infant Gut Microbiome and Probiotics that Work – Smilowitz and Taft – The Scientist

June 1, 2020

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God morgon!

Good morning from Sweden. It’s a new week and a new month! I hope everyone is doing good and staying healthy during these tough times. Like the tradition, today’s digest opens with COVID 19 related articles. There is an interesting Q&A article that provides a lot of important information. There is an article that focused on the disease progression and recovery from COVID in children and found out that Computerized Tomography (CT) may not be the best tool when it comes to analyzing COVID in children. Apart form COVID 19, there is also some new interesting information from the structure of Type-IV pilus. Elsewhere in the digest is an article on an easy to use toolkit for microbiome analysis and development of a new path-breaking point-of-care system for rapid detection of mycobacteria.

Hope you’ll enjoy and learn something new from today’s digest!

COVID 19

Q&A: The novel coronavirus outbreak causing COVID-19 – Dale Fisher and David Heymann – BMC Medicine

Preprint: Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes – Ching-Lin Hsieh, et al.

A single-center, retrospective study of COVID-19 features in children: a descriptive investigation – Huijing Ma, et al. – BMC Medicine

Quantifying the impact of physical distance measures on the transmission of COVID-19 in the UK – Christopher I. Jarvis, et al. – BMC Medicine

General Microbiome

Preprint: Microbial strategies for survival in the glass sponge Vazella pourtalesii – Kristina Bayer, et al.

Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria – Xingxing Jian, et al. – Microbiome

Viruses

Preprint: Oropouche virus glycoprotein topology and cellular requirements for virus-like particle assembly – Natalia da silva barbosa, et al.

Bacteria

Preprint: Competition and Caries on Enamel of a Dual-species Biofilm Model of Streptococcus mutans and Streptococcus sanguinis – Natalia Díaz-Garrido, et al.

Preprint: Investigations of dimethylglycine (DMG), glycine betaine and ectoine uptake by a BCCT family transporter with broad substrate specificity in Vibrio species – Gwen Gregory, et al.

Preprint: TsaP binds PilQ and is involved in cyclic di-GMP signaling – Matthew McCallum, et al.

Preprint: SoxS represses flagellar gene expression through RflP in Salmonella enterica Serovar Typhimurium – Srinivas S Thota, et al.

Preprint: Towards Mycobacterium tuberculosis detection at the point-of-care: a brighter solvatochromic probe permits the detection of mycobacteria within minutes – Mireille Kamariza, et al.

Techniques

Preprint: animalcules: Interactive Microbiome Analytics 1 and Visualization in R – W. Evan Johnson, et al.

May 28, 2020

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Hello and welcome to today’s microbiome digest! It’s a compact digest, but quite diverse. You will find a study investigating the effect of high-fat diet in Drosophila found a microbiota-dependent activation of stem-cells; electronic cigarettes were found to negatively influence the oral microbiome, and glycan epitopes present on enveloped viruses (as COVID-19) can be targeted and neutralized by human antibodies against these foreign glycan structures.
Finally, a helpful article during Corona-times, when more and more courses and meetings are held online, features the use of FAIR training material: Ten simple rules for making training materials FAIR. Enjoy!

COVID-19

Is social connectedness a risk factor for the spreading of COVID-19 among older adults? The Italian paradox – Giuseppe Liotta – PLOS ONE

General microbiome

Review: Enhancing bacterial survival through phenotypic heterogeneity – Leila M. Reyes Ruiz – PLOS PATHOGENS

Human respiratory microbiome

Adverse effects of electronic cigarettes on the disease-naive oral microbiome – Sukirth M. Ganesan – Science Advances

Human gut microbiome

Preprint: Shotgun Metagenomics of 361 elderly women reveals gut microbiome change in bone mass loss – Qi Wang – BioRxiv

Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma – Sean P. Polster – Nature Communications

Persistent Diarrhea in Patients With Crohn’s Disease After Mucosal Healing Is Associated With Lower Diversity of the Intestinal Microbiome and Increased Dysbiosis – Karen Boland – Clinical Gastroenterology and Hepatology

Fecal microbiota transplantation in systemic sclerosis: A double-blind, placebo-controlled randomized pilot trial – Havard Fretheim – PLOS ONE

Animal experiments

A high-fat diet induces a microbiota-dependent increase in stem cell activity in the Drosophila intestine – Jakob con Frieling – PLOS GENETICS

The cecal and fecal microbiomes and metabolomes of horses before and after metronidazole administration – Carolyn E. Arnold – PLOS ONE

Plant, root, and soil microbiome

Functional diversity of rhizosphere soil microbial communities in response to different tillage and crop residue retention in a double-cropping rice field – Haiming Tang – PLOS ONE

Water and extremophile microbiome

Microbiome analysis of healthy and diseased sponges Lubomirskia baicalensis by using cell cultures of primmorphs – Lubov Chernogor – PeerJ

Built environment

The use of ozone gas for the inactivation of Bacillus anthracis and Bacillus subtilis spores on building materials – Joseph P. Wood – PLOS ONE

Phages and viruses

* Harnessing the natural anti-glycan immune response to limit the transmission of enveloped viruses such as SARS-CoV-2 – Adrien Breiman – PLOS PATHOGENS

Review: A viral journey to the brain: Current considerations and future developments – Nilda Vanesa Ayala-Nunez – PLOS PATHOGENS

Bioinformatics

Preprint: A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence – Elisa Venturini – BioRxiv

Techniques

Preprint: Fluorescent secreted bacterial effectors reveal an intravacuolar replication compartment for Listeria monocytogenes – Caroline Peron Cane – BioRxiv

Science, publishing, and career

2 Art Gallery Shows to Explore From Home – The New York Times – Check out the art by Anika Yi

Judith’s non-microbiology picks

* Ten simple rules for making training materials FAIR – Leyla Garcia – PLOS COMPUTATIONAL BIOLOGY

May 22, 2020

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We’ve got a decently sized digest today with a lot of environmental microbe papers, including descriptions of novel species. There is also the Cell paper (highlighted) from Peter Turnbaugh’s group on ketogenic diets and the gut microbiome, which has been getting a lot of press. For new bioinformatic and other techniques, we have a new R package to predict functional profiles in Tax4Fun2, an assessment of phylogenetic rooting methods for bacteria, and a description of fiber intervention used in undergraduate classes for active learning.

 Have a great weekend!

Events

Today is the last day of the Virtual Microbiome Summit.

Pregnancy and early life

Women’s multisite microbial modulation during pregnancy – Luiz G. Sparvoli – Microbial Pathogenesis

Multi-site human microbiome

Review: Bi-Directional Interactions Between Microbiota and Ionizing Radiation in Head and Neck and Pelvic Radiotherapy-Clinical Relevance – Nidhya Teresa Joseph – International Journal of Radiation Biology

Human oral microbiome

Defining the oral microbiome by whole-genome sequencing and resistome analysis: the complexity of the healthy picture – Elisabetta Caselli – BMC Microbiology

Human gut microbiome

Ketogenic diets alter the gut microbiome resulting in decreased intestinal Th17 cells – Qi Yan Ang – Cell

Preprint: Host genetic and environmental factors shape the human gut resistome – Caroline I. Le Roy – bioRxiv

MinION Sequencing of colorectal cancer tumour microbiomes—A comparison with amplicon-based and RNA-Sequencing – William S. Taylor – PLOS One (Originally posted to the Digest as a pre-print, now published)

Animal experiments

Broilers divergently selected for digestibility differ for their digestive microbial ecosystems – Marion Borey – PLOS One

Dietary Isomalto/Malto‐Polysaccharides Increase Fecal Bulk and Microbial Fermentation in Mice – Rima H. Mistry – Molecular Nutrition and Food Research

Longitudinal Effects of Dietary Oxidized Lipids on the Gut Microbiome and Mycobiome in Pigs – Folagbayi Arowolo – FASEB Journal

Animal microbiome

Single-cell amplicon sequencing reveals community structures and transmission trends of protist-associated bacteria in a termite host – Michael E. Stephens – PLOS One

Plant, root, and soil microbiome

Xylella fastidiosa subsp. pauca and olive produced lipids moderate the switch adhesive versus non-adhesive state and viceversa – Valeria Scala – PLOS One

Mitochondrial genome sequence of Phytophthora sansomeana and comparative analysis of Phytophthora mitochondrial genomes – Guohong Cai – PLOS One

nirS-type denitrifying bacterial communities in relation to soil physicochemical conditions and soil depths of two montane riparian meadows in North China. – Xiaoli Han – Environmental Science and Pollution Research

Tissue-Specific Dynamics in the Endophytic Bacterial Communities in Arctic Pioneer Plant Oxyria digyna – Cindy Given – Frontiers in Plant Science

Effects of Cultured Root and Soil Microbial Communities on the Disease of Nicotiana tabacum Caused by Phytophthora nicotianae – Tianbo Liu – Frontiers in Microbiology

Novel putative rhizobial species with different symbiovars nodulate Lotus creticus and their differential preference to distinctive soil properties – M Rejili – FEMS Microbiology Letters

Water, air, and extremophile microbiome

The microbiome of alpine snow algae shows a specific inter-kingdom connectivity and algae-bacteria interactions with supportive capacities – Lisa Krug – ISME Journal

Variation of near surface atmosphere microbial communities at an urban and a suburban site in Philadelphia, PA, USA – JD Stewart – Science of the Total Environment

Pilot-scale petroleum refinery wastewaters treatment systems: performance and microbial communities’ analysis – Fatma Karray – Process Safety and Environmental Protection

Adverse effects of levofloxacin and oxytetracycline on aquatic microbial communities – Zhigao Zhou – Science of the Total Environment

Application of microbial network analysis to discriminate environmental heterogeneity in Fildes Peninsula, Antarctica – Qian Liu – Marine Pollution Bulletin

Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium – HS Tee – ISME Journal

Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site – Christen L. Grettenberger – BMC Microbiology

Halocatena pleomorpha gen. nov. sp. nov., an extremely halophilic archaeon of family Halobacteriaceae isolated from saltpan soil – Ashish Verma – IJSEM

Unveiling Cultivable and Uncultivable Halophilic Bacteria Inhabiting Marakkanam Saltpan, India and Their Potential for Biotechnological Applications – Jojy John – Geomicrobiology Journal

Flavobacterium profundi sp. nov., isolated from a deep-sea seamount – Qian Wang – IJSEM

Food microbiology

Molecular epidemiology, genetic diversity and antimicrobial resistance of Staphylococcus aureus isolated from chicken and pig carcasses, and carcass handlers – Onyinye J. Okorie-Kanu – PLOS One

Traditional milk transformation schemes in Côte d’Ivoire and their impact on the prevalence of Streptococcus bovis complex bacteria in dairy products – Aimé R Sanhoun – PLOS One

Comparison of Microbial Communities and Amino Acid Metabolites in Different Traditional Fermentation Starters Used during the Fermentation of Hong Qu Glutinous Rice Wine – Zhang-Cheng Liang – Food Research International

Preprint: Monitoring the microbiome for food safety and quality using deep shotgun sequencing – Kristen L. Beck – bioRxiv

Viruses

Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)? – Ping Liu – PLOS Pathogens

Vector competence of Aedes aegypti from New Caledonia for the four recent circulating dengue virus serotypes – Olivia O’Connor – PLOS Neglected Tropical Diseases

Bioinformatics

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences – Franziska Wemheuer – Environmental Microbiome

Techniques

Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families – Taylor Wade – PLOS One

Science education techniques: Fiber Force: A Fiber Diet Intervention in an Advanced Course-Based Undergraduate Research Experience (CURE) Course – Julia Massimelli Sewall – Journal of Microbiology & Biology Education

Science and art

This photographer creates prints with algae.

Non-microbiology picks:

Herd of fuzzy green “glacier mice” baffles scientists.

May 20, 2020

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Greetings from Pittsburgh, PA!

Television and movies are a welcome distraction from the current global pandemic. For this digest, I’d like to highlight two articles. The article by Sajjad et al. investigates the possibility of resurrection of ancient microbes present in the natural frozen world and is a perfect pair for the monster-of-the-week X-Files episode “Ice.” The second highlighted article focuses on the microbiome present on two ancient Slavonic parchment codices and how this data can be used to provide additional historical context. Maybe Harrison Ford can team up with Piñar et al. to create a fourth movie in the Indiana Jones Franchise based on their work?

Happy reading, everyone!

General microbiome

Effect of a novel synbiotic on Streptococcus mutans – Bijle et al. – Nature Scientific Reports

Culturomics‐based genomics sheds light on the ecology of the new haloarchaeal genus Halosegnis – Durán‐Viseras et al. – Environmental Microbiology

Review: Ecological features of the persistence of Vibrio cholerae: retrospective analysis and actual state of the problem – Menshikova et al. – Jounral of microbiology, epidemiology, and immunobiology

Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage – Reji and Francis – ISME Journal

Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis – Tantivitayakul et al. – Nature Scientific Reports

Plant, root, and soil microbiome

Impacts of forest conversion to plantations on the soil carbon and nitrogen dynamics, and microbial communities – Wang et al. – Soil Biology and Biochemistry

Water and extremophile microbiome

Novel yeast taxa from the cold: description of Cryolevonia giraudoae sp. nov. and Camptobasidium gelus sp. nov. – de Garcia et al. – International Journal of Systematic and Evolutionary Microbiology

Remote sensing reveals Antarctic green snow algae as important terrestrial carbon sink – Gray et al. – Nature Communications

Review: Resurrection of inactive microbes and resistome present in the natural frozen world: Reality or myth? – Sajjad et al. – Science of the Total Environment

Built environment

Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value – Piñar et al. – Environmental Microbiology

Bioinformatics

Preprint: Efficiently processing amplicon sequencing data for microbial ecology with dadasnake, a DADA2 implementation in Snakemake – Weißbecker et al. – bioRxiv

Techniques

Editorial: Visualizing the invisible: class excursions to ignite children’s enthusiasm for microbes – McGenity et al. – Microbial Biotechnology

Discovery of thermophilic Bacillales using reduced-representation genotyping for identification – Talamantes-Becerra et al. – BMC Microbiology

May 18, 2020

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God morgon!

Good morning from Sweden. It’s Monday and the beginning of another week. I am quite excited to write today’s digest because there is a super impressive paper that concerns my area of research. Research efforts in Shigella infections have always suffered from the lack of a mouse model of infection. This notorious bacterium causes enteric infections only in humans and all the infection models, that have been in use so far,  are not physiologically that relevant. It was extremely thrilling to read the development of a mouse model that replicates the typical features of human infections. Talking about infection models, there is another interesting development. A group of researchers has reported an African green monkey model for CoViD-19. This is an important development for clinical assessment of potential vaccine and drug candidates against nCoV-19.

Speaking of vaccines, another group has reported a Neisseria meningitidis outer membrane vesicle (OMV) based vaccine that provides cross-species protection against Neisseria gonorrhoeae. This report assumes great importance when you consider the fact that no Neisseria gonorrhoeae vaccine has entered clinical testing for the past 30 years! In addition to this, there is a structural study of budding in Cryptococcus neoformans that has some really beautiful pictures like this one:

Screenshot 2020-05-18 at 14.57.43

Elsewhere in the digest are some interesting reports on the virulence of a root pathogen, Fusarium; metagenomic identification of diverse viruses; a potent mycobacteriophage; and commentary on Coronaviruses as pathogens responsible for pandemics.

Hope you enjoy today’s selection and have a great week!

COVID-19

Preprint: Establishment of an African green monkey model for COVID-19 – Courtney B. Woolsey, et al.

Preprint: Coronavirus, as a source of pandemic pathogens – Tomokazu Konishi

Bacteria Hysteria

Preprint: NAIP-NLRC4-deficient mice are susceptible to shigellosis – Patrick S Mitchell, et al.

Preprint: The serogroup B meningococcal outer membrane vesicle-based vaccine 4CMenB induces cross-species protection against Neisseria gonorrhoeae – Isabelle Leduc, et al.

Preprint: Antimycobacterial potential of Mycobacteriophage under pathophysiological conditions – Yeswanth C Kalapala, et al.

Preprint: A Division of Labor in the Recruitment and Topological Organization of a Bacterial Morphogenic Complex – Paul D Caccamo, et al.

Preprint: Comparative genomics of ocular Pseudomonas aeruginosa strains from keratitis patients with different clinical outcomes – Kathirvel Kandasamy, et al.

Human gut

Preprint: Higher prevalence of Bacteroides fragilis in Crohn’s disease exacerbations and strain-dependent increase of epithelial resistance – Heike E.F. Becker, et al.

Fungi

Preprint: Let it bud: an ultrastructural study of Cryptococcus neoformans surface during budding events – Glauber R. de S. Araujo, et al.

Methods

Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets – Isabel F. Escapa, et al. – Microbiome

A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals – Hyunwook Koh and Ni Zhao – Microbiome

Metagenomics

Preprint: Metagenomic identification of diverse animal hepaciviruses and pegiviruses– Ashleigh F. Porter, et al.

Transcriptomics

Preprint: Transcriptome analysis reveals infection strategies employed by Fusarium graminearum as a root pathogen – Yi Ding, et al.

Microbes in the News

Living on The Space Station Leaves a Microbial ‘Fingerprint’ on Astronauts – Science Alert

What are the best foods to increase happiness? – Eastern Daily Press

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

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 6, 2020

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God morgon!

Good morning from Sweden. This is my first post and following the current trend, it starts with some articles on the COVID19 pandemic. Today’s digest is headlined by some interesting preprints reporting inhibitors of SARS-CoV2 virus, followed by another interesting read suggesting the link between the gut microbiome and ADHD, some articles on our struggle against pathogenic bacteria, virus and fungi, and capped off with a small but informative news article on things one should not do during the COVID19 lockdown.

You might notice that today’s post is dominated by preprints. These preprints, while being an excellent way to disperse information as rapidly as it emerges, aren’t peer-reviewed. Hence, always read them with a pinch of salt!

COVID19

Preprint: In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication – Franck Touret, et al.

Preprint: LY6E Restricts the Entry of Human Coronaviruses, including the currently pandemic SARS-CoV-2 – Xuesen Zhao, et al.

Preprint: Indomethacin has a potent antiviral activity against SARS CoV-2 in vitro and canine coronavirus in vivo – Tianhong Xu, et al.

Preprint: Potent Antiviral Activities of Type I Interferons to SARS-CoV-2 Infection – Emily K. Mantlo, et al.

Microbial interactions

Preprint: Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria – Ryan K Fritts, et al.

Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics – Weipeng Zhang, et al. – Microbiome

Preprint: Accumulation of dead cells from contact killing facilitates coexistence in bacterial biofilms – Gabi Steinbach, et al.

Human microbiome

Preprint: Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice – Anouk C. Tengeler, et al.

Lung function and microbiota diversity in cystic fibrosis – Leah Cuthbertson, et al. – Microbiome

Animal microbiome

Preprint: Functional maturation of the gut microbiota at weaning is influenced by maternal environment in piglets – Martin Beaumont, et al.

Bacteria Hysteria

Preprint: The adaptive transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress – Crispin Zavala-Alvarado, et al.

Preprint: Cytotoxicity of the effector protein BteA was attenuated in Bordetella pertussis by insertion of an alanine residue – Jan Bayram, et al.

Preprint: Antimicrobial peptide induced-stress renders Staphylococcus aureus susceptible to toxic nucleoside analogues – Alexandro Rodriguez-Rojas, et al.

Preprint: (p)ppGpp and malonyl-CoA set the pace for Staphylococcus aureus adaptation to FASII antibiotics and provide a basis for bi-therapy inhibition – Amit Pathania, et al.

Phages and viruses

Preprint: Viral RNA is a target for Wolbachia-mediated pathogen blocking – Tamanash Bhattacharya, et al.

Preprint: Synchronized infection identifies early rate-limiting steps in the hepatitis B virus life cycle – Anindita Chakraborty, et al.

Techniques

Preprint: Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota – Takeo Shibata, et al.

Preprint: Biotinylated surfome profiling identifies potential biomarkers for diagnosis and therapy of Aspergillus fumigatus infection – Lei-Jie Jia, et al.

Bioinformatics

Preprint: Interpretable machine learning framework reveals novel gut microbiome features in predicting type 2 diabetes – Wanglong Gou, et al.

Preprint: Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis – Jenna N Kelly, et al.

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics – Eli Levy Karin, et al. – Microbiome

Preprint: Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes – Jacob Stanley Iramiot, et al.

Microbes in news

News article: Experts study banana disease in Tanzania – The Guardian

News article: What not to do while on COVID-19 lockdown – Jamaica Observer

I know a lot of my fellow researchers are unable to continue their experiments and are yearning to get back to their respective labs. It is a testing time and I believe that patience and perseverance are the biggest strengths of a researcher. So, let’s bank on our strength and hope to see each other on the other side of this global pandemic soon!

With new information emerging every day about COVID19, there is a plethora of misinformation and myths surrounding the virus and the disease. As science enthusiasts, it is pertinent for us to dispel these myths. Here is a small list that I complied a few days back. Check it out!