September 13, 2020

Hello from the Sonoran Desert! In today’s digest, you’ll find quite a few exciting reads! In particular, Stepanauskas and collaborators looked at horizontal gene transfer in marine bacterial genomes in a fascinating preprint. They show that marine microorganisms form “gene exchange networks” within which organisms are able to exchange both flexible and core genes, including genes from the rRNA operon! The authors suggest a new definition of microbial species, broader than the current accepted delineation.

Today’s digest also includes few new papers and proceedings presenting novel bioinformatic tools and methods. Among them, Podlevsky and collaborators presents CasCollect, a novel computational tool allowing the assembly and annotation of Cas genes and CRISPR arrays from metagenomic datasets.

Finally, today’s non-biology piece is a very interesting review on the challenge of Big Data in biology: how modern computational frameworks can enable the storage, transfer, access, and analysis of both unstructured and structured massive biological datasets?

Have a great Sunday!


Human vaginal microbiome

Altered vaginal microbiome and relative co-abundance network in pregnant women with penicillin allergy – Li et al. – Allergy , Asthma & Clinical Immunology

Human gut microbiome

Review: Mechanisms underpinning the efficacy of faecal microbiota transplantation in treating gastrointestinal disease – Segal et al. – Therapeutic Advances in Gastroenterology


Animal microbiome

Preprint: Deep-sea mussels from a hybrid zone on the Mid-Atlantic Ridge host genetically indistinguishable symbionts – Uecker et al. – BioRxiV

Metagenomic analysis of viral communities in Baikal sponges – Butina and Bukin – Limnology and Freshwater Biology

Microbial community associated with Baicalian crustacea near gas-oil deepwater discharges – Khalzov et al. – Limnology and freshwater biology

Plant, root, and soil microbiome

Preprint: Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana root microbiome – Worsley et al. – BioRxiV

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Preprint: Gene exchange networks define species-like units in marine prokaryotes – Stepanauskas et al. – BioRxiV

Preprint: The effects of seasonal anoxia on the microbial community structure in demosponges in a marine lake (Lough Hyne, Ireland) – Schuster et al. – BioRxiV

Food microbiology

Preprint: Diversity and dynamics of fungi during spontaneous fermentations and association with unique aroma profiles in wine – Liu et al. – BioRxiV


Phages and viruses

Depicting the RNA Virome of Hematophagous Arthropods from Belgrade, Serbia – Stanojevic et al. – Viruses

Preprint: An Unconventional Flavivirus and other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome – Hewson et al. – preprints

Bioinformatics

Review: Challenges in gene-oriented approaches for pangenome content discovery – Bonnici et al. – Briefings in Bioinformatics

Conference proceedings: A Data Driven Binning Method to Recover More Nucleotide Sequences of Species in a Metagenome – Vimukti et al. – IEEE

CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data – Podlevsky et al – NAR Genomics and bioinformatics

Techniques

book: Metagenomics: Techniques, Applications, Challenges and Opportunities – Singh et al – Springer Nature Singapore Pte Ltd.


My non-microbiology pick

Review: Big data in biology: The hope and present-day challenges in it Pal et al. – Gene reports

September 11, 2020

Greetings, friends!

This summer I’ve spent a lot of time outside, going on hikes and enjoying nature. Pennsylvania has a high rate of lyme disease so I’m always careful to check myself for ticks after I spend time outdoors. With that in mind, I want to highlight the review article included in today’s digest that focuses on the interactions between Borrelia burgdorgei and ticks. If you’re looking for a book recommendation, Bitten: The Secret History of Lyme Disease and Biological Weapons by Kris Newby is an excellent pairing!

The summer is also a time where many undergraduates gain important research experience. For those of you thinking ahead to next year, today’s digest also includes an article which provides 10 simple rules for an inclusive summer coding program for non-computer-science undergrads.

Finally, I am very excited to promote Black in Microbiology week, which will be held on Twitter and Instagram during the week of September 28th. I’m looking forward to “meeting” lots of new microbiologists and learning about their research! Each day has unique programming and hashtags, so check out the website for more information.

Happy reading!


Events

Black in Micro Week is September 28 – October 4th, 2020 on your favorite social media platforms! Check out the Black in Microbiology website for additional information, including a full programming schedule, and follow @BlackinMicro and #BlackinMicro on Twitter and Instagram.

COVID-19

Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight – Khan et al. – PLOS One

In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age – Lieberman et al. – PLOS Biology

Factors contributing to healthcare professional burnout during the COVID-19 pandemic: A rapid turnaround global survey – Morgantini et al. – PLOS ONE

General microbiome

Review: Ecology and genomics of Actinobacteria: new concepts for natural product discovery – Bergeijk et al. – Nature Reviews Microbiology

Review: Biofilm dispersion – Rumbaugh & Sauer – Nature Reviews Microbiology

Human respiratory microbiome

Whole-genome sequence of multi-drug resistant Pseudomonas aeruginosa strains UY1PSABAL and UY1PSABAL2 isolated from human broncho-alveolar lavage, Yaoundé, Cameroon – Madaha et al. – PLOS ONE

Human gut microbiome

Regional variations in Helicobacter pylori infection, gastric atrophy and gastric cancer risk: The ENIGMA study in Chile – Herrero et al. – PLOS ONE

A comparative study of the gut microbiome in Egyptian patients with Type I and Type II diabetes – Radwan et al. – PLOS ONE

Animal experiments

Review: Interactions between Borrelia burgdorferi and ticks – Kurokawa et al. – Nature Reviews Microbiology

Antimicrobial resistance in ovine bacteria: A sheep in wolf’s clothing? – Silva et al. – PLOS ONE

Water and extremophile microbiome

Characterization of Vibrio cholerae isolates from freshwater sources in northwest Ohio – Daboul et al. – PLOS ONE

Food microbiology

Characterization of β-lactam resistance in K. pneumoniae associated with ready-to-eat processed meat in Egypt – Abdel-Rhman – PLOS ONE

Techniques

Ten simple rules for an inclusive summer coding program for non-computer-science undergraduates – Pennings et al. – PLOS Computational Biology

September 8, 2020

Greetings, friends!

Today’s digest is a very heavy grab bag of articles! Included are many reviews on everything from the microbiome in forensic science to the gut-lung axis. Also included are original research articles focused on a variety of subjects including microplastics, extremophiles, and the bicycle microbiome! Finally, for those of you looking for practical advice, I’ve highlighted an article focused on best practices for writing genome announcements.

Happy reading!

General microbiome

Manipulating denitrifying sulfide removal of Pseudomonas sp. C27 with nitrite as sole nitrogen source: Shotgun proteomics analysis – Guo et al. – Bioresource Technology

Pseudomonas aeruginosa – Candida interplay: Effect on in vitro antibiotic susceptibility of Pseudomonas aeruginosa when grown in the presence Candida culture – Mcllroy et al. – British Journal of Biomedical Science

Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates – Nouws et al. – Scientific Reports

Evolution of diversity explains the impact of pre-adaptation of a focal species on the structure of a natural microbial community – Padfield et al. – The ISME Journal

Biomass-degrading glycoside hydrolases of archaeal origin – Suleiman et al. – Biotechnology for Biofuels

Mining for novel antibiotics in the age of antimicrobial resistance – Udaondo and Matilla – Microbial Biotechology

Multi-site human microbiome

Association between the microbiomes of tonsil and saliva samples isolated from pediatric patients subjected to tonsillectomy for the treatment of tonsillar hyperplasia – Choi et al. – Experimental & Molecular Medicine

Review: The impact of the human microbiome in forensic sciences: A systematic review – García et al. – Applied and Enviornmental Microbiology

Human respiratory microbiome

Review: The evolving role of the lung microbiome in pulmonary fibrosis – Lipinski et al. – Lung Cellular and Molecular Physiology

Review: Recent advances in understanding the ecology of the lung microbiota and deciphering the gut-lung axis – Willis et al. – Lung Cellcular and Molecular Physiology

Human gut microbiome

Altered gut microbiota correlated with systemic inflammation in children with Kawasaki disease – Chen et al. – Scientific Reports

Review: Gut microbiota in human metabolic health and disease – Fan and Pedersen – Nature Reviews Microbiology

Lactose-reduced infant formula with added corn syrup solids is associated with a distinct gut microbiota in Hispanic infants – Jones et al. – Gut Microbes

Animal experiments

Gut bacterial communities and their contribution to performance of specialist Altica flea beetles – Wei et al. – Microbial Ecology

Dynamic changes of gut microbiota of discus fish (Symphysodon haraldi) at different feeding stages – Zhang et al. – Aquaculture

Plant, root, and soil microbiome

Diversity of cultivable microbes from soil of the Fildes Peninsula, Antarctica, and their potential application – Cong et al. – Frontiers in Microbiology

Structural and functional microbial diversity of sandy soil under cropland and grassland – Frąc et al. – PeerJ

Microbiome–environment interactions in antimony-contaminated rice paddies and the correlation of core microbiome with arsenic and antimony contamination – Li et al. – Chemosphere

Review: Implications of endophytic microbiota in Camellia Sinensis: A review on current understanding and future insights – Xie et al. – Bioengineered

Characterizing the nectar microbiome of the non-native tropical milkweed, Asclepias curassavica, in an urban environment – Warren et al. – PLOS ONE

Water and extremophile microbiome

Prokaryotic diversity in stream sediments affected by acid mine drainage – Carlier et al. – Extremophiles

Combination of genetic tools to discern Bacillus species isolated from hot springs in South Africa – Jardine and Ubomba-Jaswa – African Journal of Mirobiology Research

Bioleaching of pyritic coal wastes: bioprospecting and efficiency of selected consortia – Joulian et al. – Research in Microbiology

Genotypic and phylogenetic diversity of new isolates of terrestrial Xanthophyceae (Stramenopiles) from maritime sandy habitats – Rybalka et al. – Phycologia

Paucihalobacter ruber gen. nov., sp. nov., isolated from a haloalkaline lake sediment sample – Wu et al. – Microbiology Society

Comparative analysis of bacterial diversity and community structure in the rhizosphere and root endosphere of two halophytes, Salicornia europaea and Glaux maritima, collected from two brackish lakes in Japan – Yamamoto et al. – Microbes and Environments

Fungal diversity in deep-sea sediments from Magellan seamounts environment of the western Pacific revealed by high-throughput Illumina sequencing – Yang et al. – Journal of Microbiology

Effect of Ferrous Iron Addition on Ammonium Nitrogen Removal and Microbial Communities in Horizontal Subsurface Flow Constructed Wetlands – Zhang et al. – Wetlands

Built environment

Microplastics negatively affect soil fauna but stimulate microbial activity: insights from a field-based microplastic addition experiment – Lin et al. – Proceedings of the Royal Society B

Shared bicycle microbial community: a potential antibiotic-resistant bacteria warehouse – Wu et al. – Folia Microbiologica

Microbial carrying capacity and carbon biomass of plastic marine debris – Zhao et al. – The ISME Journal

Food microbiology

Proteolysis, lipolysis, texture and sensory properties of cheese ripened by Monascus fumeus – Xia et al. – Food Research International

Bioinformatics

Announcement: Best practices for successfully writing and publishing a genome announcement in microbiology resource announcements – Hotopp et al. – Microbiology Resource Announcements

Techniques

Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities – Mooshammer et al. – The ISME Journal

September 4, 2020

Good morning and get ready to enjoy a small, but diverse microbiome digest. Enjoy!

COVID-19
Commentary: Misconceptions about weather and seasonality must not misguide COVID-19 response – Colin J Carlson et al. – Nature Communications


Multi-site human microbiome
Relationship between the composition of the intestinal microbiota and the tracheal and intestinal colonization by opportunistic pathogens in intensive care patients – Candice Fontaine et al. – PLOS One

Human gut microbiome
Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C – Alyssa G. Kent et al. – Nature Communications


Animal experiments
Review: Modulation of gut microbiota in healthy rats after exposure to nutritional supplements – Mirna Cool et al. – Gut Microbes

Animal microbiome
Anthrax toxin component, Protective Antigen, protects insects from bacterial infection – Saleem Alarme – PLOS Pathogens

Environmental gut bacteria in European honey bees (Apis mellifera) from Australia and their relationship to the chalkbrood disease – Sheba Khan et al. – PLOS One

Gut Microbiome Composition is Associated with Age and Memory Performance in Pet Dogs – Eniko Kubinyi et al. – Animals

Plant, root, and soil microbiome
Characterizing the nectar microbiome of the non-native tropical milkweed, Asclepias curassavica, in an urban environment – Magdalena L. Warren et al. – PLOS One

Water and extremophile microbiome
Book chapter:
Analyzing the Diversity of Microbial Communities Residing in Marine Ecosystems – Piyush Chandna et al. – In: Marine Biotechnology


Bioinformatics
Ten simple rules to power drug discovery with data science – Enrico Ferrero et al. – PLOS Computational Biology

Techniques
Review: Sample pre-treatment procedures for the omics analysis of human gut microbiota: turning points, tips and tricks for gene sequencing and metabolomics – Elisa Zubeldia-Varela et al. – Journal of Pharmaceutical and Biomedical Analysis


Publishing
Research Topic: Beyond Conventional Models: Expanding Experimental Systems for Animal-Microbiome Interaction Research

September 2, 2020

Greetings for the month of September: the Haervest-monath (Harvest Month). Today’s microbiome digest consists of a cool editorial article on hidden theatre of microbes. The digest also features two interesting reviews; first one detailing the role of skin microbiota in forensic sciences and the second one with focus on association of sponges and their microbiome.

Let’s celebrate the month of September with some fascinating microbiome studies.

There are flowers enough in the summertime,
More flowers than I can remember—
But none with the purple, gold, and red
That dye the flowers of September!

—Mary Howitt (1799-1888)

General microbiome
*Editorial: Unveiling the Hidden Theatre of Microbes – Böttcher T – ChemBioChem

Chitosan-chelated zinc modulates cecal microbiota and attenuates inflammatory response in weaned rats challenged with Escherichia coli – Feng et al – Journal of Microbiology

Multi-site human microbiome
Potential Associations Among Alteration of Salivary miRNAs, Saliva Microbiome Structure, and Cognitive Impairments in Autistic Children – Ragusa et al – Int. J. Mol. Sci.

Human respiratory microbiome
Review: The importance of airway and lung microbiome in the critically ill – Martin-Loeches et al – Critical Care

Human skin microbiome
A Novel Mycovirus Evokes Transcriptional Rewiring in the Fungus Malassezia and Stimulates Beta Interferon Production in Macrophages – Clancey et al – mBio

A Novel Virus Alters Gene Expression and Vacuolar Morphology in Malassezia Cells and Induces a TLR3-Mediated Inflammatory Immune Response – Park et al – mBio

*Review: Challenges in Human Skin Microbial Profiling for Forensic Science: A Review – Neckovic et al – Genes

Human gut microbiome
Context-aware dimensionality reduction deconvolutes gut microbial community dynamics – Martino et al – Nat Biotechnol

Animal microbiome
*The relationship between microbiomes and selective regimes in the sponge genus Ircinia – Kelly et al – bioRxiv

Techniques
Flow cytometry with cell sorting and sequencing as a tool for the study of the Humboldt Current krill stomach microbiota – Henriquez-Castillo et al – bioRxiv

Microbes in the news
EurekAlert News: Researchers receive $3 million NSF grant to ‘understand the rules of life – Zhou J

September 1, 2020

Today’s post consists of review article on short chain fatty acids, research articles on efficacy of fecal microbiota transplant in patients with C. difficle infection and comorbities, identification of potential microbial biomarkers for preterm birth and a new technique to perform ultrafast microbial community analysis. Happy reading!

General microbiome

A systematic review of the effect of dietary pulses on microbial populations inhabiting the human gut – C.P.F. Marinangeli – Beneficial Microbes

Short chain fatty acids in human gut and metabolic health – E E Blaak – Beneficial Microbes

Human microbiome

The gut microbiome–derived metabolite trimethylamine N-oxide modulates neuroinflammation and cognitive function with aging – Vienna E. Brunt – Geroscience

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial – Suryang Kwak – Microbiome

Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in Patients With Multiple Comorbidities: Long-Term Safety and Efficacy Results From a Tertiary Care Community Hospital – Charumathi Raghu Subramanian – Gastroenterology Research

Gut commensal microbiota and decreased risk for Enterobacteriaceae bacteriuria and urinary tract infection – Matthew Magruder – Gut Microbes

Leveraging sequence‐based faecal microbial community survey data to identify alterations in gut microbiota among patients with Parkinson’s disease – Tianyi Ji – European Journal of Neuroscience

Plasma enterobacterial ClpB levels and ClpB- and α-MSH–reactive immunoglobulins in lung cancer patients with and without anorexia – Alessio Molfino – Nutrition

Identification of Potential Biomarkers in the Cervicovaginal Fluid by Metabolic Profiling for Preterm Birth – AbuZar Ansari – Metabolites

Plant microbiome

Suppression of rice planthopper populations without affecting the rice microbiota by the entomopathogenic fungus Metarhizium anisopliae – Yifan Peng – Applied and Environmental Microbiology

Cold Plasma Treatment of Sunflower Seeds Modulates Plant-Associated Microbiome and Stimulates Root and Lateral Organ Growth – Inga Tamošiūnė – Frontiers in Plant Science

Water microbiome

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments – Da-Shuai Mu – Microbiome

Techniques

Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2 – Jennifer Lu – Microbiome

Non-microbiology picks

Clinical characteristics of children and young people hospitalised with covid-19 in the United Kingdom: prospective multicentre observational cohort study – Olivia V Swann – BMJ

August 23, 2020

Hello from the Sonoran Desert! In today’s digest, you’ll find quite a few exciting papers! For those interested in soil microbiology, you’ll find in today’s digest a very interesting piece on the the biodiversity and ecology of protists in the soils of the McMurdo Dry Valleys (Antarctica). This piece is particularly exciting given that the role and impact of protists in polar regions is largely unknown and understudied.

Curious readers should also take a look at the amazing study by Dunaj and collaborators focusing on spider’s associated microbiome. This piece examines the host-microbe co-evolution of different widow spider species showing a strong congruence of the microbiome beta-diversity and the host phylogeny.

Finally, in today’s non-microbiology pick, I recommend a preprint, that explored the relationship between the use of jargon and citations in cave research articles. Interestingly the authors suggest that the juse of jargon in title and abstract significantly reduces the number of citations a paper recieves!

Have a great Sunday!


Human vaginal microbiome

Review: The vaginal microbiome of sub-Saharan African women: revealing important gaps in the era of next-generation sequencing – Martina Odogwy et al. – PeerJ

Human gut microbiome

Review: Association or Causation? Exploring the Oral Microbiome and Cancer Links – Teles et al. – Journal of Dental research


Animal microbiome

Learning machine approach reveals microbial signatures of diet and sex in dog – Scarsella et al.- Plos One

Spider phylosymbiosis: divergence of widow spider species and their tissues’ microbiomes – Dunaj et al. – BMC Evolutionary Biology

Plant, root, and soil microbiome

Review: The rhizosphere microbiome: functions, dynamics, and role in plant protection – Rabelo de Faria et al. – Tropical Plant Pathology

Review: The Floral Microbiome: Plant, Pollinator, and Microbial Perspectives – Vannette – Annual review of Ecology, Evolution and systematics

Response of soil microbial communities to natural and managed vegetation restoration in a subtropical karst region – Hu et al. – CATENA

Water and extremophile microbiome

Shotgun metagenomics reveal a diverse assemblage of protists in a model Antarctic soil ecosystem – Thompson et al.- Envirmental Microbiology


Phages and viruses

Evolution of a major virion protein of the giant pandoraviruses from an inactivated bacterial glycoside hydrolase – Krupovic et al. – Virus Evolution

Bioinformatics

Predicting Host Phenotype Based on Gut Microbiome Using a Convolutional Neural Network Approach – Reiman et al.- Methods in Molecular Biology, vol 2190. Humana, New York, NY.

Database limitations for studying the human gut microbiome – Dias et al. – PeerJ

Techniques

Review: Microbial High Throughput Phenomics: The Potential of an Irreplaceable Omics – Acin-Albiac et al. – Computational and Structural Biotechnolgy Journal


My non-microbiology pick

Preprint: Specialized terminology limits the reach of new scientific knowledge – Martinez et al. – BioRxiv

August 16, 2020

Today’s quite diverse digest features: a study on antimicrobial resistance in the drinking water microbiome in disinfected and disinfection-free drinking water systems, how Antarctic soil microorganisms stay energised and hydrated, and several awesome webinars and podcasts. Happy reading/listening!

General microbiome

Development of Microbiome Biobanks – Challenges and Opportunities – M.J. Ryan – Trends in Microbiology

Review: STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies – Tehmina Bharucha – The Lancet Infectious Diseases

Theme issue: The role of the microbiome in host evolution – compiled and edited by Oren Kolodny, Benjamin J. Callahan and Angela E. Douglas – Philosophical Transactions of the Royal Society B: Biological Sciences

Selected papers:
Review: Microbiota–host interactions shape ageing dynamics – Miriam Popkes and Dario Riccardo Valenzano – Philosophical Transactions of the Royal Society B: Biological Sciences

Opinion: Pathogen resistance may be the principal evolutionary advantage provided by the microbiome – Michael R. McLaren and Benjamin J. Callahan – Philosophical Transactions of the Royal Society B: Biological Sciences

Gut microbiome

A Randomized Clinical Trial of Fecal Microbiota Transplant for Alcohol Use Disorder – Jasmohan S Bajaj – Hepatology

Urogenital microbiome

Comparative Genomic Study of Lactobacillus jensenii and the Newly Defined Lactobacillus mulieris Species Identifies Species-Specific Functionality – Catherine Putonti – mSphere

Vaginal Estrogen Therapy Is Associated with Increased Lactobacillus in the Urine of Post-Menopausal Women with OAB Symptoms – Dr. Krystal Thomas-White – American Journal of Obstetrics and Gynecology

Vaginal microbiome

Vaginal microbiota, genital inflammation, and neoplasia impact immune checkpoint protein profiles in the cervicovaginal microenvironment – Paweł Łaniewski –npj Precision Oncology

Lateral Gene Transfer Shapes Diversity of Gardnerella spp. – Lindsey L. Bohr – Frontiers in Cellular and Infection Microbiology

Variation of the vaginal microbiome during and after pregnancy in Chinese women – Xiaoai Zhang – medRxiv

Review: Diversity of Vaginal Microbiome in Pregnancy: Deciphering the Obscurity – Parakriti Gupta – Frontiers in Public Health

Pregnancy and early life

Evidence for contamination as the origin for bacteria found in human placenta rather than a microbiota – Rémi Gschwind – PlosOne

Respiratory microbiome

A Novel Description of the Human Sinus Archaeome During Health and Chronic Rhinosinusitis – Brett Wagner Mackenzie – Frontiers in Cellular and Infection Microbiology

Animal microbiome

Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae – Ciara Keating – bioRxiv

Broiler Chickens and Early Life Programming: Microbiome transplant-induced cecal bacteriome dynamics and phenotypic effects – Gustavo A. Ramírez – bioRxiv

Rumen metaproteomics: Closer to linking rumen microbial function to animal productivity traits – Thea Os Andersen – Methods

Fast and Slow-Growing Management Systems: Characterisation of Broiler Caecal Microbiota Development throughout the Growing Period – Laura Montoro-Dasi – animals

Animal experiment

Mucosal or systemic microbiota exposures shape the B cell repertoire – Hai Li – Nature

The immune system fails to mount a protective response to Gram-positive or Gram-negative bacterial prostatitis – Federico Lupo – bioRxiv

Oncogenic Gene Fusions in Non-Neoplastic Precursors as Evidence that Bacterial Infection Initiates Prostate Cancer – Eva Shrestha – bioRxiv

Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy – Lukas F. Mager – Science

Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury in mice – Shanna L. Ashley – Science Translational Medicine

Plant/root/soil microbiome

*A genome compendium reveals diverse metabolic adaptations of Antarctic soil microorganisms – Maximiliano Ortiz – bioRxiv

Healthy soils for healthy plants for healthy humans – Heribert Hirt – EMBO reports

The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer – James P. J. Hall – Frontiers in Microbiology

Review: Plant–microbiome interactions: from community assembly to plant health – Pankaj Trivedi – Nature Reviews Microbiology

Water microbiome

*Differential prevalence and host-association of antimicrobial resistance traits in disinfected and non-disinfected drinking water systems – Maria Sevillano – Science of The Total Environment

MiDAS 3: An ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level microbiome composition of activated sludge – Marta Nierychlo – Water Research

Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in two sequential rapid sand filters – Lianna Poghosyan – Water Research

Shotgun metagenomics of indigenous bacteria collected from the banks of the San Jacinto River for biodegradation of aromatic waste – Rupa Iyer and Ashish Damania – FEMS Microbiology Letters

Viruses and phages

Viruses in wastewater: occurrence, abundance and detection methods – Mary Vermi Aizza Corpuz – Science of The Total Environment

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities – Christian Santos-Medellin – bioRxiv

Techniques

Correlative Light Electron Ion Microscopy reveal in vivo localisation of bedaquiline in Mycobacterium tuberculosis infected lungs – Antony Fearns – bioRxiv

Label-free smartphone quantitation of bacteria by darkfield imaging of light scattering in fluoropolymer micro capillary film allows portable detection of bacteriophage lysis – Sultan İlayda Dönmez – Sensors and Actuators B: Chemical

Bioinformatics

Raven: a de novo genome assembler for long reads – Robert Vaser and Mile Sikic – bioRxiv

SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis – Stevenn Volant – BMC Bioinformatics

Rapid discovery of novel prophages using biological feature engineering and machine learning – Kimmo Sirén – bioRxiv

Critical Relevance of Stochastic Effects on Low-Bacterial Biomass 16S rRNA Gene Analysis – John R. Erb-Downward – mBio

On the complexity of haplotyping a microbial community – Samuel M Nicholls – bioRxiv

Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome‐assembled genomes from a complex aquifer system – Will A. Overholt – Environmental Microbiology

Webinar

Microbiome, machine learning and network models – Amy Willis and Ben Bloem-Reddy – Northwest Data Science Seminar Series

The Gut Brain Axis across the Life Span – John Cryan – iScience webinar

Pushing the Envelope: Remodeling the Gram-negative Outer Membrane – M. Stephen Trent – SG BUG (Singapore Bacterial Ultra Group) seminar series

Podcast

Getting to Know Your Friendly Neighbourhood Microbiologist – Lucie Semenec and Amy Cain – The Joint Academic Microbiology Seminars podcast

Does not compute – Sanjay Srivastava, Alexa Tullett, and Simine Vazire – The Black Goat podcast

August 14, 2020

Good morning from Massachusetts! Dr. Elisabeth Bik will be giving a Zoom talk today on research misconduct in biomedical research. You can register at the link under events. Fittingly, today’s digest includes a preprint on the effects of retraction after misconduct on citations. Other highlights today include an entire theme issue on the microbiome and host evolution and a paper on phylogenomic analyses of archaea attempting to elucidate the DPANN lineage. In early life, the placental microbiome debate rages on with a paper demonstrating evidence for contamination rather than an actual placental microbiome. Finally, I have highlighted a paper studying whether soil archives can give us a glimpse into soil microbial communities of the past.

Have a great weekend!

Events

Dr. Bik is discussing “The Dark Side of Science: Misconduct in Biomedical Research” today at 12PM EDT! Register here.

General microbiome

Theme Issue: The role of the microbiome in host evolution – Philosophical Transactions of the Royal Society B

Pregnancy and early life

Evidence for contamination as the origin for bacteria found in human placenta rather than a microbiota – Rémi Gschwind – PloS One

Human milk microbiome

SARS-CoV-2 in human milk is inactivated by Holder pasteurization but not cold storage – Gregory J. Walker – Journal of Paediatrics and Child Health

Human oral microbiome

Review: Oral microbiome geography: Micron-scale habitat and niche – Jessica L. Mark Welch – Cell Host & Microbe

Human gut microbiome

Epidemiology and associated microbiota changes in deployed military personnel at high risk of traveler’s diarrhea – William A. Walters – PloS One

Animal experiments

Differential alteration in gut microbiome profiles during acquisition, extinction, and reinstatement of morphine-induced CPP – Jianbo Zhang – Progress in Neuro-Psychopharmacology and Biological Psychiatry

Modulation of the intestinal microbiota of broilers supplemented with monensin or functional oils in response to challenge by Eimeria spp. – Alexandre Maciel Vieira – PloS One

Herpes simplex virus infection, Acyclovir and IVIG treatment all independently cause gut dysbiosis – Chandran Ramakrishna – PloS One

Animal microbiome

Raw milk and fecal microbiota of commercial Alpine dairy cows varies with herd, fat content and diet – Francesca Albonico – PloS One

Hydrolytic bacteria associated with natural helminth infection in the midgut of Red Sea marbled spinefoot rabbit fish Siganus rivulatus – Ghada Abd-Elmonsef Mahmoud – Microbial Pathogenesis

Plant, root, and soil microbiome

Book: Agriculturally Important Fungi for Sustainable Agriculture Vol 2: Functional Annotation for Crop Protection – Eds. Ajar Nath Yadav et al. – Springer

Patient propagules: Do soil archives preserve the legacy of fungal and prokaryotic communities? – Gian Maria Niccolò Benucci – PloS One

Labile carbon limits late winter microbial activity near Arctic treeline – Patrick F. Sullivan – Nature Communications

Enhanced biodegradation of crude oil by constructed bacterial consortium comprising salt-tolerant petroleum degraders and biosurfactant producers – Weiwei Chen – International Biodeterioration & Biodegradation

Plant–archaea relationships: a potential means to improve crop production in arid and semi-arid regions – Elizabeth Temitope Alori – World Journal of Microbiology and Biotechnology

First report of Fusarium equiseti causing crown rot and damping-off on durum wheat in Algeria – Amor Bencheikh – Archives of Phytopathology and Plant Protection

Soil microbial diversity and composition: Links to soil texture and associated properties – Qing Xia – Soil Biology and Biochemistry

Water, air, and extremophile microbiome

Effects of different habitats on the bacterial community composition in the water and sediments of Lake Taihu, China – Wenjie Chang – Environmental Science and Pollution Research

Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea – Shanshan Yang – Nature Communications

Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution – Nina Dombrowski – Nature Communications

Preprint: Occurrence, identification and antibiogram signatures of selected Enterobacteriaceae from Tsomo and Tyhume rivers in the Eastern Cape Province, Republic of South Africa – Fadare Temitope Folake — BioRxiv

Built environment

The microbiome of drinking water biofilters is influenced by environmental factors and engineering decisions but has little influence on the microbiome of the filtrate – Ben Ma – Environmental Science & Technology

In-situ remediation of acid mine drainage from abandoned coal mine by filed pilot-scale passive treatment system: Performance and response of microbial communities to low pH and elevated Fe – Haiyan Chen – Bioresource Technology

Bioinformatics and other techniques

De novo sequence assembly requires bioinformatic checking of chimeric sequences – Laila Sara Arroyo – PloS One

Review on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the rapid screening of microbial species: A promising bioanalytical tool – Suresh Kumar Kailasa – Microchemical Journal

Microbes in the News

Using the infant stool microbiome to predict NEC: New machine learning tool predicts devastating intestinal disease in premature infants – Science Daily

Science Publishing and Career

Preprint: Does retraction after misconduct have an impact on citations? A pre-post study – Cristina Candal-Pedreira – bioRxiv

August 13, 2020

Today’s updates – microbiome connections in various disease cohorts such as gastric cancer, IBD, anorexia nervosa, obesity and diabetes; information on gut bacterial polyphosphates and o-glycanases and their role in host immunity and mucin breakdown; and new sequencing strategies to identify antibiotic-resistant genes. Happy reading!

General microbiome

Gut microbiota and COVID-19: A superfluous diagnostic biomarker or therapeutic target? – Emily Klann – Clinical Infectious Diseases

Engineered Live Biotherapeutics: Progress and Challenges – Yang Tan – Biotechnology Journal

Human microbiome

Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity – Lianmin Chen – Nature Communications

Multi-omics data integration in anorexia nervosa patients before and after weight regain: A microbiome-metabolomics investigation – Alessio Maria Monteleone – Clinical Nutrition

Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci – Bruno Cavadas – Microorganisms

Faecal microbiota signatures of IBD and their relation to diagnosis, disease phenotype, inflammation, treatment escalation and anti-TNF response in a European Multicentre Study (IBD-Character) – S. Vatn – Scandinavian Journal of Gastroenterology

A randomized crossover trial on the effect of plant-based compared with animal-based meat on trimethylamine-N-oxide and cardiovascular disease risk factors in generally healthy adults: Study With Appetizing Plantfood—Meat Eating Alternative Trial (SWAP-MEAT) – Anthony Crimarco – Americal Journal of Clinical Nutrition

Whole-blood transcriptome profiling reveals signatures of metformin and its therapeutic response – Monta Ustinova – PlosOne

Microbial Profile During Pericoronitis and Microbiota Shift After Treatment – Xiuling Huang – Frontiers in Microbiology

Animal experiments

Unraveling the camel rumen microbiome through metaculturomics approach for agriculture waste hydrolytic potential – Shweta Srivastava – Archives of Microbiology

Bacterial polyphosphates interfere with the innate host defense to infection – Julian Roewe – Nature Communications

Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown – Lucy I. Crouch – Nature Communications

Nostoc sphaeroids Kütz polysaccharide and powder enrich a core bacterial community on C57BL/6j mice – Meixia Li – International Journal of Biological Macromolecules

Maternal dietary omega-3 deficiency worsens the deleterious effects of prenatal inflammation on the gut-brain axis in the offspring across lifetime – Q. Leyrolle – Neuropsychopharmacology

Water microbiome

Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community – Pratibha Panwar – Microbiome

Techniques

Light into the darkness: Unifying the known and unknown coding sequence space in microbiome analyses – Chiara Vanni – BioRxiv

Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms – Rebecca Yee – European Journal of Clinical Microbiology & Infectious Diseases