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

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

April 23, 2020

The wave of new microbe enthausiasts keeps coming and with it a light digest for today.  I am writing to you from Bremen, Germany, with a selection including a wheat fungi that changes the wheat leaf microbiome and antimicrobial resistance genes identified by whole metagenome shotgun study of nasopharyngal colonization in South Africa.

There is also an interesting article about species identification errors occurring in context of large sequence collection platforms.
And to mix things up a little bit, at the end of a list you find a paper with amazing microscopy featuring the beautiful parasite Trypanosoma brucei and answering the endless question to how this parasite colonizes its insect host, the tsetse fly.


Human respiratory microbiome

Longitudinal changes in the nasopharyngeal resistome of South African infants using shotgun metagenomic sequencing – Rendani I. Manenzhe – PLOS ONE

Human gut microbiome

Resident microbial communities inhibit growth and antibiotic-resistance evolution of Escherichia coli in human gut microbiome samples – Michael Baumgartner – PLOS BIOLOGY


Animal experiments

Preprint: Comparative analysis of beneficial effects of Vancomycin treatment on Th1- and Th2-biased mice and role of gut microbiota – Pratikshya Ray – bioRxiv

Assessment of dietary supplementation with galactomannan oligosaccharides and phytogenics on gut microbiota of European sea bass (Dicentrarchus Labrax) fed low fishmeal and fish oil based diet – Simona Rimoldi – PLOS ONE

Lactobacillus reuteri attenuated allergic inflammation induced by HDM in the mouse and modulated gut microbes – Lingzhi Li – PLOS ONE

Animal microbiome

Occurrence of Mycoplasma gallisepticum in wild birds: A systematic review and meta-analysis – Anna Sawicka – PLOS ONE

Plant, root, and soil microbiome

A fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition – Heike Seybold – Nature Communications


Phages and viruses

SMOOT libraries and phage-induced directed evolution of Cas9 to engineer reduced off-target activity – Derek Cerchione – PLOS ONE

Bioinformatics

BOLD and GenBank revisited – Do identification errors arise in the lab or in the sequence libraries? – Mikko Pentisaari – PLOS ONE


Science, publishing, and career

A pedagogical approach to science outreach – Marni B. McClure – PLOS BIOLOGY

Judith’s non-microbiology picks

Trypanosoma brucei colonizes the tsetse gut via an immature peritrophic matrix in the proventriculus – Clair Rose – Nature Microbiology

April 22, 2020

Welcome to another post from a new volunteer! I’m a Ph.D student studying the infant gut microbiome and I’m excited to be volunteering with Microbiome Digest.

There are several preprints today, including another great study from the CHILD cohort. This one is on maternal consumption of artificially sweetened beverages and the infant gut microbiota. There is also a preprint calling for improvement in scientific conferences. Both are highlighted in green.

Pregnancy and early life

Preprint: Consumption of artificially sweetened beverages during pregnancy impacts infant gut microbiota and body mass index – Isabelle Laforest-Lapointe — bioRxiv

Oral microbiome

Preprint: Genotypic and phenotypic characterization of Streptococcus mutans isolated from dental caries – Mohammad Shahnoor Hossain – bioRxiv

Pyruvate secretion by oral streptococci modulates hydrogen peroxide dependent antagonism – Sylvio Redanz – ISME Journal

Synergism between Corynebacterium and Streptococcus sanguinis reveals new interactions between oral commensals – Puthayalai Treerat – ISME Journal

Animal experiments

The gut microbiota response to helminth infection depends on host sex and genotype – Fei Ling – ISME Journal

Animal microbiome

Lipids and small metabolites provisioned by ambrosia fungi to symbiotic beetles are phylogeny-dependent, not convergent – Yin-Tse Huang – ISME Journal

Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP) – Kshitij Tandon – ISME Journal

Plant, root, and soil microbiome

Active sulfur cycling in the terrestrial deep subsurface – Emma Bell – ISME Journal

Preprint: An antagonistic driver of the microbial phyllosphere suppresses infection of Arabidopsis thaliana by the oomycete pathogen Albugo laibachii via a secreted hydrolase – Katharina Eitzen – bioRxiv

Preprint: Grapevine pruning time affects natural wound colonization by wood-invading fungi – Maria del Pilar Martinez-Diz – bioRxiv

Water and extremophile microbiome

Mixotrophy in marine picocyanobacteria: use of organic compounds by Prochlorococcus and Synechococcus – M.C. Muñoz-Marín – ISME Journal

Food microbiology

Preprint: Antibiotic-resistant Salmonella species and Escherichia coli in broiler chickens from farms, abattoirs and open markets in selected districts of Zambia – Nelson Phiri – bioRxiv

Microbes in the news

Breastfeeding may lead to fewer human viruses in infants
https://www.sciencedaily.com/releases/2020/04/200415110452.htm

Science, publishing, and career

Preprint: Evaluating features of scientific conferences: A call for improvements – Sarvenaz Sarabipour – bioRxiv

April 19, 2020

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

September 13, 2019

In today’s edition, you’ll find a whole new textbook about microbes affecting ecosystem sustainability, reviews about phages and plant viruses, New York Times coverage of clinical trials of FMT for obesity, how to banish “manels” from scientific meetings, and microbiota-related metabolites as biomarkers of aging. Enjoy!

General microbiome
Review: Microbial invasions in terrestrial ecosystems – Madhav P. Thakur – Nature Reviews Microbiology

Preprint: Therapeutically exploring persister metabolism in bacteria – Sayed G. Mohiuddin – bioRxiv

Preprint: Delayed antibiotic exposure induces population collapse in enterococcal communities with drug-resistant subpopulations – Kelsey M Hallinen – bioRxiv

Human gut microbiome
Review: Pairing phages with their hosts in the human gut – Ursula Hofer – Nature Reviews Microbiology

Book chapter: Gut Microbiota and Microbiota-Related Metabolites as Possible Biomarkers of Cognitive Aging – Andrea Ticinesi – Reviews on Biomarker Studies in Aging and Anti-Aging Research

Animal microbiome
Habitat disturbance and the organization of bacterial communities in Neotropical hematophagous arthropods – Kelly L. Bennett – PLOS One

Plant, root, soil microbiome
Book chapter: Rhizospheric Microbiome Engineering as a Sustainable Tool in Agriculture: Approaches and Challenges – Shubham Dubey – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

Book chapter: Dynamics of Plant Microbiome and Its Effect on the Plant Traits – Shivali Sharma – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

Book chapter: Microbial Diversity of the Sundarbans, the World’s Largest Tidal Mangrove Forest, and Its Bioprospects – Kaushik Biswas – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

Water and extremophile microbiome
Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages – Robert E. Danczak – PLOS One

Food microbiology
Book chapter: Microbial Diversity on Grapes and Other Fruits: Role and Significance in Fermentation – M. V. Deshpande – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

The Dynamics Analysis of Fungal Community Diversity During the Fermentation Process of Chinese Traditional Soybean Paste – Jingping Ge – Waste and Biomass Valorization

Phages and viruses
Review: Evolution and ecology of plant viruses – Pierre Lefeuvre – Nature Reviews Microbiology

Bioinformatics
An Integrated Approach for Efficient Multi-Omics Joint Analysis – Massimiliano S. Tagliamonte – Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

Techniques
Polysaccharide-based liquid storage and transport media for non-refrigerated preservation of bacterial pathogens – Janine R. Hutchison – PLOS One

Microbes in the news
Seeking an Obesity Cure, Researchers Turn to the Gut Microbiome -Anahad O’Connor – NY Times

Exclusive: Behind the front lines of the Ebola wars – Amy Maxmen – Nature

Science, publishing, and career
How to banish manels and manferences from scientific meetings – Holly Else – Nature

June 4, 2019

General microbiome
Rigorous Statistical Methods for Rigorous Microbiome Science – Amy D. Willis – mSystems

Understanding microbial community dynamics to improve optimal microbiome selection – Robyn J. Wright – Microbiome

Toward a Better Understanding of Species Interactions through Network Biology – Ryan S. McClure – mSystems

Human respiratory microbiome
Nasal commensal Staphylococcus epidermidis enhances interferon-λ-dependent immunity against influenza virus – Hyun Jik Kim – Microbiome

Human gut microbiome
A Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight Humans – Alfonso Benítez-Páez – mSystems

Gut microbiome identifies risk for colorectal polyps – Ezzat Dadkhah – BMJ Open Gastroenterology

Yogurt improves insulin resistance and liver fat in obese women with nonalcoholic fatty liver disease and metabolic syndrome: a randomized controlled trial – Yang Chen – American Journal of Clinical Nutrition

Preprint: Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids – Robert A Quinn – bioRxiv

Animal models
Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model – Limei Lin – Microbiome

Missing Links: the Role of Primates in Understanding the Human Microbiome – Katherine R. Amato – mSystems

Plant, root, and soil microbiome
Collaborative involvement of woody plant roots and rhizosphere microorganisms in the formation of pedogenetic clays – Frank Reith – Annals of Botany

Water and extremophile microbiome
Effects of sulfamethoxazole and sulfamethoxazole-degrading bacteria on water quality and microbial communities in milkfish ponds – Bea-Ven Chang – Environmental Pollution

Preprint: Temporal dynamics of Bacteria, Archaea and protists in equatorial coastal waters – Caroline Chénard – bioRxiv

Built environment
Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area – Miles Richardson – Microbiome

Phages and viruses
Preprint: The human gut virome is highly diverse, stable and individual-specific – Andrey Shkoporov – bioRxiv

Bioinformatics
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language – Luis Pedro Coelho – Microbiome

Science, publishing, and career
Preprint: The Mastery Rubric for Bioinformatics: supporting design and evaluation of career-spanning education and training – Rochelle E. Tractenberg – bioRxiv

Alyson’s non-microbiology picks
Why Your Metro Commute Is So Insanely Windy – Julie Bogen – The Atlantic

The 2019 Wellcome photography prize: close focus on the human condition – Sean O’Hagan – The Guardian

May 29, 2019

Changes to the pig gut microbiome based on age, gut bacteria community composition in aquatic invertebrates, fungal diversity on limestone cathedral walls, chalk-talk vs PowerPoint in large microbiology lectures.

Human oral microbiome

Applications of the oral microbiome in personalized dentistry – Georgios N Belibasakis – Archives of Oral Biology

Human vaginal microbiome

Detection of Methanobrevibacter smithii in vaginal samples collected from women diagnosed with bacterial vaginosis – Ghiles Grine – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Gut Microbial Dataset of a foraging tribe from rural West Bengal – insights into unadulterated and transitional microbial abundance – Sayak Ganguli – Data in Brief

Gut microbiome of pre-adolescent children of two ethnicities residing in three distant cities – Wei Wei Thwe Khine – Scientific Reports

The eradication of Helicobacter pylori restores rather than disturbs the gastrointestinal microbiota in asymptomatic young adults – Cong He – Helicobacter

Pre-print: Cytometric fingerprints of gut microbiota predict Crohn’s disease state – Peter Rubbens – bioRxiv

Animal experiments

Rapamycin modulates tissue aging and lifespan independently of the gut microbiota in Drosophila – Joseph M Schinaman – Scientific Reports

Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition – Shanlin Ke – BMC Veterinary Research

Pre-print: Effects of Five Products on Gut Microbiota and Short-Chain Fatty Acids of Obese Rats – Simin Tan – bioRxiv

Animal microbiome

Effect of different forage-to-concentrate ratios on ruminal bacterial structure and real-time methane production in sheep – Runhang Li – PLOS ONE

Pre-print: Microbiomes from feces vs. gut in aquatic vertebrates: distinct community compositions between substrates and preservation methods – Sten Anslan – bioRxiv

Plant, root, and soil microbiome

Glycoside Hydrolase Genes Are Required for Virulence of Agrobacterium tumefaciens on Bryophyllum daigremontiana and Tomato – Stephanie L Mathews – Applied and Environmental Microbiology

Effect of water-driven changes in rice rhizosphere on Cd lability in three soils with different pH – Jinjin Wang – Journal of Environmental Sciences

Impact of AMF Claroideoglomus etunicatum on the structure of fungal communities in the tomato rhizosphere – Agnieszka Jamiołkowska – Acta Mycologica

Effect of land use and carbonates on organic matter stabilization and microbial communities in Mediterranean soils – Mireia Martí-Roura – Geoderma

Pre-print: Close-Range Interactions Favor Growth in Random-Paired Extracted Soil Bacteria – Manupriyam Dubey – bioRxiv

Water and extremophile microbiome

New microbial lineages capable of carbon fixation and nutrient cycling in deep-sea sediments of the northern South China Sea – Jiao-Mei Huang – Applied and Environmental Microbiology

Pre-print: Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep – Guojie Cui – PeerJ

Taxonomic structure and potential nitrogen metabolism of microbial assemblage in a large hypereutrophic steppe lake – Xiaodong Qu – Environmental Science and Pollution Research

Built environment

Fungal diversity and distribution across distinct biodeterioration phenomena in limestone walls of the old cathedral of Coimbra, UNESCO World Heritage Site – João Trovão – International Biodeterioration & Biodegradation

Probiotics/prebiotics

Dietary probiotics have different effects on the composition of fecal microbiota in farmed raccoon dog (Nyctereutes procyonoides) and silver fox (Vulpes vulpes fulva) – Yongjia Peng – BMC Microbiology

Microbes in the news

Microbiome therapies could be the next frontier in medicine. But how exactly do you make them? – Kate Sheridan – STAT

Possible link between infant gut microbiome and development of allergies – Bob Yirka – Medical Xpress

Science, career, and publishing

Pre-print: Rock the Chalk: A five-year comparative analysis of a large microbiology lecture course reveals improved outcomes of chalk-talk compared to PowerPoint – Christopher M Waters – bioRxiv

May 23, 2019

Composition of the human mucosa-associated microbiota, changes in gut microbial diversity with social rank in cichlid fish, microbes supporting sustainable rice production, the effects of tweeting on article engagement in medical education.

General microbiome

Global change microbiology — big questions about small life for our future – Antje Boetius – Nature Reviews Microbiology

Human oral microbiome

Review: The Structure of Dental Plaque Microbial Communities in the Transition from Health to Dental Caries and Periodontal Disease – Alex M Valm – Journal of Molecular Biology

Human gut microbiome

Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps – Florent Ailloud – Nature Communications

Pre-print: Complete genome assembly of clinical multidrug resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial resistance genes and plasmids – Thomas V Syndenham – bioRxiv

Composition of the mucosa-associated microbiota along the entire gastrointestinal tract of human individuals – FER Vuik – United European Gastroenterology Journal

Animal experiments

Loss of function dysbiosis associated with antibiotics and high fat, high sugar diet – Aaron W Miller – The ISME Journal

Saccharomyces boulardii CNCM I-745 changes lipidemic profile and gut microbiota in a hamster hypercholesterolemic model – F Briand – Beneficial Microbes

Animal microbiome

Gut microbial diversity increases with social rank in the African cichlid fish, Astatotilapia burtoni – Avehi Singh – Animal Behaviour

Amphibian Host and Skin Microbiota Response to a Common Agricultural Antimicrobial and Internal Parasite – Obed Hernández-Gómez – Microbial Ecology

Pre-print: Space, time, and captivity: quantifying the factors influencing the fecal microbiome of an alpine ungulate – Sarah E Haworth – bioRxiv

Plant, root, and soil microbiome

Interaction between root hairs and soil phosphorus on rhizosphere priming of soil organic matter – Gabriel Boilard – Soil Biology and Biochemistry

Green manures of Indian mustard and wild rocket enhance cucumber resistance to Fusarium wilt through modulating rhizosphere bacterial community composition – Xue Jin – Plant and Soil

Ozone dose-response relationships for soil microbial dynamics of winter wheat in North China – Enzhu Hu – Atmospheric Environment

Water and extremophile microbiome

Filamentous calcareous alga provides substrate for coral-competitive macroalgae in the degraded lagoon of Dongsha Atoll, Taiwan – Carolin Nieder – PLOS ONE

Food microbiology

Roles of microbes in supporting sustainable rice production using the system of rice intensification – Febri Doni – Applied Microbiology and Biotechnology

Microbes in the news

Airway microbiome appears altered in severe asthma linked to neutrophils – EurekAlert

Coffee Consumption Alters Microbiome and Improves Gut Motility – Genetic Engineering & Biotechnology News

Researchers receive $1.94 million to study connection between autism, microbiome – EurekAlert

Novel Autonomous Biosampler Will Foster In Situ Aquatic Microbiome Monitoring – Eunice Sousa – Science Trends

Meta-study suggests anxiety can be reduced by altering gut bacteria, but not with probiotics – Rich Haridy – New Atlas

Science, career, and publishing

Pre-print: To Tweet or Not to Tweet, That is the Question: A Randomized Trial of Twitter Effects on Article Engagement in Medical Education – Lauren A Maggio – bioRxiv

January 15, 2019

Highlights today include the organisms in the healthy infant intestinal microbiome that protect against food allergy, an algorithm to predict aging based on the gut microbiome, and how bacteria adapt to life on the International Space Station. Enjoy!

Pregnancy and early life
Healthy infants harbor intestinal bacteria that protect against food allergy – Taylor Feehley – Nature Medicine

Human gut microbiome
Preprint: Human microbiome aging clocks based on deep learning and tandem of permutation feature importance and accumulated local effects – Fedor Galkin – bioRxiv
(Covered in popular press as Your Gut Microbiome Could Actually Reveal Your Age, Study Shows)

Preprint: The virome in adult monozygotic twins with concordant or discordant gut microbiomes – J. Leonardo Moreno-Gallego – bioRxiv

Human nearly-sterile sites
Review: Microbiome–metabolome reveals the contribution of gut–kidney axis on kidney disease – Yuan-Yuan Chen – Journal of Translational Medicine

Animal experiments
Lactobacillus sakei Alleviates High-fat Diet-induced Obesity and Anxiety in Mice by Inducing AMPK Activation and SIRT1 Expression and Inhibiting Gut Microbiota-mediated NF-κB Activation – Hyo-Min Jang – Molecular Nutrition and Food Research

Aqueous raw and ripe Pu-erh tea extracts alleviate obesity and alter cecal microbiota composition and function in diet-induced obese rats – Yun Xia – Applied Microbiology and Biotechnology

Impact of intramammary inoculation of inactivated Lactobacillus rhamnosus and antibiotics on the milk microbiota of water buffalo with subclinical mastitis – Carlotta Catozzi – PLOS One

Plant, root, and soil microbiome
Superior dispersal ability can lead to persistent ecological dominance throughout succession – Primrose J. Boynton – Applied and Environmental Microbiology

Plant growth-promoting rhizobacterium Pseudomonas PS01 induces salt tolerance in Arabidopsis thaliana – Thanh Nguyen Chu – BMC Research Notes

Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range – Dandan Cheng – PeerJ\

Antifungal potential of bacterial rhizosphere isolates associated with three ethno-medicinal plants (poppy, chamomile, and nettle) – Marija Mojicevic – International Microbiology

Analysis of uranium removal capacity of anaerobic granular sludge bacterial communities under different initial pH conditions – Taotao Zeng – Environmental Science and Pollution Research

Water and extremophile microbiomes
An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community – Po-Hsiang Wang – The ISME Journal

Bacterial community assembly in a typical estuarine marsh with multiple environmental gradients – Zhiyuan Yao – Applied and Environmental Microbiology

Effects of salinity on microbialite-associated production in Great Salt Lake, Utah – Melody R. Lindsay – Ecology

Preprint: Capturing the Diversity of Subsurface Microbiota – Choice of Carbon Source for Microcosm Enrichment and Isolation of Groundwater Bacteria – Xiaoqin Wu – bioRxiv

Genetic Evidence for Two Carbon Fixation Pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in Symbiotic and Free-Living Bacteria – Maxim Rubin-Blum – mSphere

Techniques
Generation of 13C-labeled MUC5AC mucin oligosaccharides for stable isotope probing of host-associated microbial communities – Clayton Evert – ACS Infectious Diseases

Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism – Hiroki Nishiguchi – Metabolic Engineering

Built environment/Microbes in Space
Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil – Ryan A. Blaustein – mSystems
(Covered in the popular press as Good news: space bacteria (probably) aren’t evolving to destroy us)

Science, publishing, and career
Preprint: Tracking the popularity and outcomes of all bioRxiv preprints – Richard J. Abdill – bioRxiv