January 12, 2022

General microbiome

[PERSPECTIVE]It’s the Economy, Stupid: Applying (Micro)economic Principles to Microbiome Science – Kashtan, Bushong and Leveau – mSystems

[PERSPECTIVE]Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes – Pfister et al. – mSystems

Human endometrial microbiome

Endometrial microbiota composition is associated with reproductive outcome in infertile patients – Moreno et al. – Microbiome

Human oral microbiome

[REVIEW]Temporal development of the infant oral microbiome – Blum et al. – Critical Reviews in Microbiology

Human gut microbiome

Effect of antibiotic pretreatment on bacterial engraftment after Fecal Microbiota Transplant (FMT) in IBS-D – Singh et al. – Gut Microbes

[REVIEW]The gut microbiota can orchestrate the signaling pathways in colorectal cancer – Bennedsen et al. – Journal of Pathology, Microbiology and Immunology

Age-Associated Gut Dysbiosis, Marked by Loss of Butyrogenic Potential, Correlates With Altered Plasma Tryptophan Metabolites in Older People Living With HIV – Ghare et al. – Journal of Acquired Immune Deficiency Syndrome

Intestinal Microbiota and Host Cooperate for Adaptation as a Hologenome – Zhou et al. – mSystems

The bacterial density of clinical rectal swabs is highly variable, correlates with sequencing contamination, and predicts patient risk of extraintestinal infection – Chanderraj et al. – Microbiome

Animal microbiome

Consistent changes in the intestinal microbiota of Atlantic salmon fed insect meal diets – Li et al. – Animal Microbiome

Maternal regulation of biliary disease in neonates via gut microbial metabolites – Jee et al. – Nature Communications

Reduced calorie diet combined with NNMT inhibition establishes a distinct microbiome in DIO mice – Dimet-Wiley et al. – Scientific Reports

Comparison of Gut Microbiota and Metabolic Status of Sows With Different Litter Sizes During Pregnancy – Chen et al. – Front. Vet. Sci.

Modulation of gut microbiota impacts diet-induced and drug-induced alopecia in mice – Lam et al. – Gut

Sex-specific differences in the gut microbiota and fecal metabolites in an adolescent valproic acid-induced rat autism model – Gu et al. – Frontiers in Bioscience Landmark

Host tp53 mutation induces gut dysbiosis eliciting inflammation through disturbed sialic acid metabolism – Lee et al. – Microbiome

Plant, root, and soil microbiome

Whole-Genome Duplication and Host Genotype Affect Rhizosphere Microbial Communities – Ponsford et al. – mSystems

Bioinformatics

A Goldilocks Principle for the Gut Microbiome: Taxonomic Resolution Matters for Microbiome-Based Classification of Colorectal Cancer – Armour et al. – mBio

Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer – Casimiro-Soriguer et al. – Scientifi Reports

Techniques

[PREPRINT]Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes – Poulsen et al. – bioRxiv

January 10, 2022

Today’s digest features studies on glycosaminoglycans degradation by urinary microbiome, social network of honeybees, improved DNA extraction for low biomass samples, the LotuS2 tool for amplicon sequencing analysis, and more. Happy Monday!


Gut microbiome

Review: The role of the microbiota in the management of intensive care patients – Piotr Szychowiak – Annals of Intensive Care

Review: The Gut Microbiome in Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS) – Rahel S. König – Frontiers in Immunology

Review: Opioid Use, Gut Dysbiosis, Inflammation, and the Nervous System – Richa Jalodia – Journal of Neuroimmune Pharmacology

Urinary microbiome

*A Semi-Quantitative Assay to Measure Glycosaminoglycan Degradation by the Urinary Microbiota – Vivian H. Nguyen – Frontiers in Cellular and Infection Microbiology

Vaginal microbiome

Composition and Stability of the Vaginal Microbiota of Pregnant Women With Inflammatory Bowel Disease – Janet E Hill – Inflammatory Bowel Diseases

Skin microbiome

*Anatomy promotes neutral coexistence of strains in the human skin microbiome – Arolyn Conwill – Cell Host & Microbe

Water microbiome

Tenets of a Holistic Approach to Drinking Water-Associated Pathogen Research, Management, and Communication – Caitlin Proctor – Water Research

Animal microbiome

Review: Possibilities and limits for using the gut microbiome to improve captive animal health – Jessica Diaz & Aspen T. Reese – Animal Microbiome

The mosquito microbiome includes habitat-specific but rare symbionts – Hans Schrieke – Computational and Structural Biotechnology Journal

*The gut microbiota affects the social network of honeybees – Joanito Liberti – bioRxiv

Techniques and methods

Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome – Guoshun Xu – BMC Genomics

Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics – Anna Pryszlak – Cell Report Methods

When to suspect contamination rather than colonization – lessons from a putative fetal sheep microbiome – Simone Bihl – Gut Microbes

*Microvolume DNA extraction methods for microscale amplicon and metagenomic studies – Anna R. Bramucci – ISME Communications

Bioinformatics

*LotuS2: An ultrafast and highly accurate tool for amplicon sequencing analysis – Ezgi Özkurt – bioRxiv

Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities – Derek M. Bickhart – Nature Biotechnology



January 7, 2022

Today’s digest covers a range of topics including a duplex qPCR assay to detect lung infections, an investigation into sand fly symbionts, and a characterization of a fermented soybean food (Pe poke). If you want to end the week on a good note, I’d suggest reading the two articles I’ve highlighted below. One demonstrates that flooding and ecological restoration of former cranberry farmland also restores wetland microbial communities and soil function. The second provides a new barcoding strategy for the phenotypic screening of mosquitos that can be applied towards malaria research.

Happy reading!

General microbiome

Controlled spatial organization of bacterial growth reveals key role of cell filamentation preceding Xylella fastidiosa biofilm formation – Anbumani et al. – npj Biofilms and Microbiomes

Bacteria can be selected to help beneficial plasmids spread – Dimitriu et al. – PLOS Biology

Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network – Urchueguía et al. – PLOS Biology

Human respiratory microbiome

Detection of Pneumocystis jirovecii and Toxoplasma gondii in patients with lung infections by a duplex qPCR assay – Wu et al. – PLOS Neglected Tropical Diseases

Animal experiments

***Barcoded Asaia bacteria enable mosquito in vivo screens and identify novel systemic insecticides and inhibitors of malaria transmission – Sturm et al. – PLOS Biology

Molecular phylogeny of heritable symbionts and microbiota diversity analysis in phlebotominae sand flies and Culex nigripalpus from Colombia – Vivero-Gomez – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar – Tamang et al. – PLOS One

***Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland – Rubin et al. – PLOS One

Water and extremophile microbiome

Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment – Remple et al. – npj Biofilms and Microbiomes

January 6, 2022

Human and General Microbiome

Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome – Xiaomin Liu – Nature Genetics

Determine independent gut microbiota-diseases association by eliminating the effects of human lifestyle factors – Congmin Zhu – BMC Microbiology

Comparing Published Gut Microbiome Taxonomic Data Across Multinational Studies – Brianna K Meeks – Nursing Research

A Comprehensive Review on the Role of the Gut Microbiome in Human Neurological Disorders – Shokufeh Ghasemian Sorboni – Clinical Microbiology Reviews

Beneficial Microbes and Compounds

Lactobacillus casei Zhang exerts anti-obesity effect to obese glut1 and gut-specific-glut1 knockout mice via gut microbiota modulation mediated different metagenomic pathways – Qiuwen He – European Journal of Nutrition

Administration of Human Derived Upper gut Commensal Prevotella histicola delays the onset of type 1 diabetes in NOD mice – Eric Marietta – BMC Microbiology

Probiotic supplementation in neonates with congenital gastrointestinal surgical conditions: a pilot randomised controlled trial – Shripada Rao – Pediatric Research

Dietary supplementation with low-dose xylooligosaccharide promotes the anti-Salmonella activity of probiotic Lactiplantibacillus plantarum ZS2058 in a murine model – Junsheng Liu – Food Research International 

Review: Recent understanding of human milk oligosaccharides in establishing infant gut microbiome and roles in immune system – Ravindra Pal Singh – Food Research International

Microbiome and Metabolism

Gut Microbiota Diversity and Overweight/Obesity in Infancy: Results from a Nested Case-control Study – Hong Mei – Current Medical Science

Microbiome and Cancer

Microbiome composition indicate dysbiosis and lower richness in tumor breast tissues compared to healthy adjacent paired tissue, within the same women – Maria Valeria Esposito – BMC Cancer

Changes in the gut bacterial communities in colon cancer surgery patients: an observational study – Mohamed Abbas – Gut Pathogens

Urinary and Reproductive Tract Microbiome

Endometrial microbiota composition is associated with reproductive outcome in infertile patients – Inmaculada Moreno – Microbiome

Dysbiosis of vaginal microbiota associated with persistent high-risk human papilloma virus infection – Ling Mei – Journal of Translational Medicine

Urogenital Microbiota:Potentially Important Determinant of PD-L1 Expression in Male Patients with Non-muscle Invasive Bladder Cancer – Chunxiao Chen – BMC Microbiology

Animal Microbiome

Destabilization of the Bacterial Interactome Identifies Nutrient Restriction-Induced Dysbiosis in Insect Guts – Ramona Marasco – Microbiology Spectrum

Specific Strains of Honeybee Gut Lactobacillus Stimulate Host Immune System to Protect against Pathogenic Hafnia alvei – Haoyu Lang – Microbiology Spectrum

Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing – Edna Chiang – Animal Microbiome

Metagenomic and metatranscriptomic analyses reveal minor-yet-crucial roles of gut microbiome in deep-sea hydrothermal vent snail – Yi Yang – Animal Microbiome

Host, microbiome, and complex space: applying population and landscape genetic approaches to gut microbiome research in wild populations – Claire E Couch – The Journal of Heredity

Antibiotic resistance and potential bacterial pathogens identified in red deer’s faecal DNA – Diana Dias – Transboundary and Emerging Diseases

Review: Gut microbiome-immune system interaction in reptiles – Ruqaiyyah Siddiqui – Journal of Applied Microbiology

Plant and Soil Microbiome

Contrasting Effects of Local Environmental and Biogeographic Factors on the Composition and Structure of Bacterial Communities in Arid Monospecific Mangrove Soils – T Thomson – Microbiology Spectrum

Review: Endophytic Microbiota of Rice and Their Collective Impact on Host Fitness – Santosh Kumar Jana – Current Microbiology

Other Microbes

Spaceflight Virology: What Do We Know about Viral Threats in the Spaceflight Environment? – Bruno Pavletić – Astrobiology

Microbiome Analysis Methods

Cell-Free Paper-Based Analysis of Gut Microbiota and Host Biomarkers – Melissa K Takahashi – Methods in Molecular Biology 

Bioinformatics

CACONET: a novel classification framework for microbial correlation networks – Yuanwei Xu – Bioinformatics

December 22, 2021

General microbiome

[PREPRINT]Unconstrained coevolution of bacterial size and the latent period of plastic phage – Bonachela, Choua & Heath – bioRxiv

Not a ‘they’ but a ‘we’: the microbiome helps promote our well-being – Ragsdale – Journal of Biological Chemistry

Microbial metabolite delta-valerobetaine is a diet-dependent obesogen – Liu et al. – Nature Metabolism

[EDITORIAL]15 years of microbial biotechnology: the time has come to think big—and act soon – de Lorenzo – Microbial Biotechnology

Pregnancy and early life

Microbial community networks across body sites are associated with susceptibility to respiratory infections in infants – Reyman et al. – Communications Biology

Human oral microbiome

Profiling the oral microbiomes in patients with Alzheimer’s disease – Guo et al. – Oral Diseases

Human skin microbiome

[REVIEW]Human Skin Microbiota in Health and Disease – Bay & Ring – Journal of Pathology, Microbiology and Immunology

Human vaginal microbiome

Human implantation: The complex interplay between endometrial receptivity, inflammation, and the microbiome – Sehring & Jeelani – Placenta

Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population – Ng et al. – NPJ Biofilms and Microbiomes

Human gut microbiome

The potential of gut microbiome as a non-invasive predictive biomarker for early detection of pancreatic cancer and hepatocellular carcinoma – Kaźmierczak-Siedlecka – European Review for Medical and Pharmacological Sciences

The effect of antibiotics on the human microbiome: a systematic review – van Zyl et al. – International Journal of Antimicrobial Agents

[REVIEW]Non-alcoholic fatty liver disease: the interplay between metabolism, microbes and immunity – Tilg et al. – Nature Metabolism

Clinical efficacy of fecal microbial transplantation treatment in adults with moderate-to-severe atopic dermatitis – Mashiah et al. – Immunity, Inflammation and Disease

Deviated and early unsustainable stunted development of gut microbiota in children with autism spectrum disorder – Lou et al. – Gut

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

Oat Fiber Modulates Hepatic Circadian Clock via Promoting Gut Microbiota-Derived Short Chain Fatty Acids – Han et al. – J. Agric. Food Chem.

Animal microbiome (for animals in the wild)

Effects of sublethal azadirachtin on the immune response and midgut microbiome of Apis cerana cerana (Hymenoptera: Apidae) – Zhao et al. – Ecotoxicology and Environmental Safety

Analysis of the microbial diversity in the fecal material of the critically endangered African wild dog, Lycaon pictus – Sanches et al. – Archives of Microbiology

Divergence together with microbes: A comparative study of the associated microbiomes in the closely related Littorina species – Maltseva et al. – PLOS One

Gut microbiome composition, not alpha diversity, is associated with survival in a natural vertebrate population – Worsley et al. – Animal Microbiome

Clinical health issues, reproductive hormones, and metabolic hormones associated with gut microbiome structure in African and Asian elephants – Keady et al. – Animal Microbiome

Early life skin microbial trajectory as a function of vertical and environmental transmission in Bornean foam-nesting frogs – McGrath-Blaser et al. – Animal Microbiome

Plant, root, and soil microbiome

[PRERPINT]Disentangling the genetic basis of rhizosphere microbiome assembly in tomato – Oyserman et al. – bioRxiv

[PREPRINT]Amino acid availability determines plant immune homeostasis in the rhizosphere microbiome – Liu et al. – bioRxiv

Techniques

Ancient Metagenomic Studies: Considerations for the Wider Scientific Community – der Sarkissian et al. – mSystems

Assessing the impact of storage time on the stability of stool microbiota richness, diversity, and composition – Holzhausen et al. – Gut Pathogens

December 20, 2021

Today’s digest is a grab bag that includes research articles on the vaginal microbiota, the gut microbiota of dairy calves, microbial loads in medical waste, and more! I’ve also highlighted a non-microbiology article that found that pet dog owners were significantly less depressed than non-pet owners during the pandemic. So if you’re looking for more reasons to adopt a new furry friend, you can add this one to the list!

General microbiome

Genomic comparison and phenotypic profiling of small colony variants of Burkholderia pseudomallei – Zulkefli et al. – PLOS One

Human vaginal microbiome

Vaginal microbiota of American Indian women and associations with measures of psychosocial stress – Borgogna et al. – PLOS One

Human gut microbiome

Gut microbiota features associated with Clostridioides difficile colonization in dairy calves – Redding et al. – PLOS One

Animal microbiome

Culicoides Latreille (Diptera: Ceratopogonidae) as potential vectors for Leishmania martiniquensis and Trypanosoma sp. in northern Thailand – Sunantaraporn et al. – PLOS Neglected Tropical Diseases

Migratory wild birds carrying multidrug-resistant Escherichia coli as potential transmitters of antimicrobial resistance in China – Yuan et al. – PLOS One

Plant, root, and soil microbiome

Characterization of soils conducive and non-conducive to Prunus replant disease – Khan et al. – Plos One

Built environment

Disposal habits and microbial load of solid medical waste in sub-district healthcare facilities and households in Yilo-Krobo municipality, Ghana – Egbenyah et al. – PLOS One

Phages and viruses

A systematic review and meta-analysis of the potential non-human animal reservoirs and arthropod vectors of the Mayaro virus – Celone et al. – PLOS Neglected Tropical Diseases

Bioinformatics

Genomic prediction using low-coverage portable Nanopore sequencing – Lamb et al. – PLOS One

Development of an efficient Sanger sequencing-based assay for detecting SARS-CoV-2 spike mutations – Lim et al. – PLOS One

Kara’s non-microbiology pick

***Depression, anxiety, and happiness in dog owners and potential dog owners during the COVID-19 pandemic in the United States – Martin et al. – PLOS One

December 08, 2021

General microbiome

Clinical medicine journals lag behind science journals with regards to “microbiota sequence” data availability – Pryor et al. – Clinical and Translational Medicine

Role of the Microbiome in Regulating Bone Metabolism and Susceptibility to Osteoporosis – Cronin et al. – Calcified Tissue International

Defining and quantifying the core microbiome: Challenges and prospects – Neu, Allen & Roy – PNAS

Clean room microbiome complexity impacts planetary protection bioburden – Hendrickson et al. – Microbiome

[PREPRINT]Community Composition of Bacteria Isolated from Swiss Banknotes Varies Depending on Collection Environment – Bischofberger & Hall – bioRxiv

Microbiota and stress: a loop that impacts memory – Kraimi et al. – Psychoneuroendocrinology

Species- and site-specific genome editing in complex bacterial communities – Rubin et al. – Nature Microbiology

Human respiratory microbiome

Integrated metabolic and microbial analysis reveals host–microbial interactions in IgE-mediated childhood asthma – Chiu et al. – Scientific Reports

Human oral microbiome

Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome – Liu et al. – Cell Discovery

Human gut microbiome

Interaction Between Intestinal Microbiota, Immunology Molecular Mimicry, and AID – Pan et al. – Journal of Immunology Research

[REVIEW]The Gut Microbiome and Hepatocellular Carcinoma – Akkiz – Journal of Gastrointestinal Cancel

Anaerostipes hominis sp. nov., a novel butyrate-producing bacteria isolated from faeces of a patient with Crohn’s disease – Lee et al. – International Journal of Systematic and Evolutionary Microbiology

Gut microbiome is associated with the clinical response to anti-PD-1 based immunotherapy in hepatobiliary cancers – Mao et al. – Journal for ImmunoTherapy of Cancer

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

Time-restricted feeding induces Lactobacillus- and Akkermansia-specific functional changes in the rat fecal microbiota – Palomba et al. – NPJ Biofilms and Microbiomes

Animal microbiome (for animals in the wild)

Diet-driven mercury contamination is associated with polar bear gut microbiota – Watson et al. – Scientific Reports

Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development – Blyton et al. – Environmental Microbiology

[PREPRINT]Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi – McMurtie et al. – bioRxiv

Age-Based Variations in the Gut Microbiome of the Shennongjia (Hubei) Golden Snub-Nosed Monkey (Rhinopithecus roxellana hubeiensis) – Yao et al. – BioMed Research International

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

Looking through the FOG: microbiome characterization and lipolytic bacteria isolation from a fatberg site – Court et al. – Microbiology

The Baltic Sea methane pockmark microbiome: The new insights into the patterns of relative abundance and ANME niche separation – Iasakov et al. – Marine Environmental Research

Bioinformatics

3MCor: an integrative web server for metabolome-microbiome-metadata correlation analysis – Sun et al. – Bioinformatics

Techniques

Microbiome Methods in Experimental Autoimmune Encephalomyelitis – Daberkow et al. – Current Protocols

[PREPRINT]A wipe-based stool collection and preservation kit for microbiome community profiling – Hua et al. – bioRxiv

December 2, 2021

Happy December from Pittsburgh!

Today’s digest includes original research on the impacts of fungal entomopathogens on Wolbacia infections and the influence of nutrient status on the response of a diatom to oil and dispersant. I have also included a study protocol for oral microbiome transplant for the treatment of dental caries and periodontal disease as well as preprints on a variety of topics. Finally, I want to highlight two articles I included that are little different from my usual content: the first is on predictors of willingness to receive the COVID-19 vaccination and the second is focused on transparency in peer review.

Enjoy!

COVID-19

***To vaccinate or not to vaccinate!? Predictors of willingness to receive Covid-19 vaccination in Europe, the U.S., and China – Brailovskaia et al. – PLOS One

General microbiome

Preprint: Copper nanoparticles as modulator of active bacterial population and their physiology in ecosphere – Alboloushi et al. – bioRxiv

Preprint: Metabolite Damage and Damage-Control in a Minimal Genome – Haas et al. – bioRxiv

Development and characterization of an oral microbiome transplant among Australians for the treatment of dental caries and periodontal disease: A study protocol – Nath et al. – PLOS One

Preprint: Heat activation and inactivation of bacterial spores. Is there an overlap? – Wen et al. – bioRxiv

Animal experiments

Inferring Mycobacterium bovis transmission between cattle and badgers using isolates from the Randomised Badger Culling Trial – van Tonder et al. – PLOS Pathogens

Animal microbiome

Impacts of fungal entomopathogens on survival and immune responses of Aedes albopictus and Culex pipiens mosquitoes in the context of native Wolbachia infections – Ramirez et al. – PLOS Neglected Tropical Diseases

Water and extremophile microbiome

Influence of nutrient status on the response of the diatom Phaeodactylum tricornutum to oil and dispersant – Kamalanathan et al. – PLOS One

Preprint: Community-wide epigenetics provides novel perspectives on the ecology and evolution of marine microbiome – Seong et al. – bioRxiv

Preprint: Microbial cysteine degradation is a source of hydrogen sulfide in oxic freshwater lakes – Tran et al. – bioRxiv

Bioinformatics

When and why direct transmission models can be used for environmentally persistent pathogens – Benson – PLOS Computational Biology

Techniques

Preprint: The processing of staphylococcal biofilm images from Fluorescence and Confocal Microscopy to assess in vitro efficacy of antiseptic molecules – Krasowski et al. – bioRxiv

Science, publishing, and career

***Transparency in peer review: Exploring the content and tone of reviewers’ confidential comments to editors – O’Brien et al. – PLOS One

December 01, 2021

General microbiome

Searching for New Microbiome-Targeted Therapeutics through a Drug Repurposing Approach – Barone et al. – Journal of Medicinal Chemistry

Current status of intratumour microbiome in cancer and engineered exogenous microbiota as a promising therapeutic strategy – Chen et al. – Biomedicine & Pharmacotherapy

Regulation of blood–brain barrier integrity by microbiome-associated methylamines and cognition by trimethylamine N-oxide – Hoyles et al. – Microbiome

Modeling host-associating microbes under selection – Bansept et al. – The ISME Journal

Human oral microbiome

Bacterial variation in the oral microbiota in multiple sclerosis patients – Zangeneh – PLOS One

Human gut microbiome

[REVIEW]Gut microbiota as a transducer of dietary cues to regulate host circadian rhythms and metabolism – Choi, Rao & Chang – Nature Reviews Gastroenterology & Hepatology

[REVIEW]Gut microbiota-derived short-chain fatty acids and colorectal cancer: Ready for clinical translation? – Hou et al. – Cancer Letters

Analysis of changes in microbiome compositions related to the prognosis of colorectal cancer patients based on tissue-derived 16S rRNA sequences – Coi et al. – Journal of Translational Medicine

The Fecal Microbiome and Metabolome of Pitt Hopkins Syndrome, a Severe Autism Spectrum Disorder – Dilmore et al. – mSystems

Characterization of gut microbial structural variations as determinants of human bile acid metabolism – Wang et al. – Cell Host & Microbe

Animal microbiome

Microbial regulation of hexokinase 2 links mitochondrial metabolism and cell death in colitis – Hinrichsen et al. – Cell Metabolism

Bacterial communities from vagina of dairy healthy heifers and cows with impaired reproductive performance – Moreno et al. – Research in Veterinary Science

Plant, root, and soil microbiome

Artificial Selection on Microbiomes To Breed Microbiomes That Confer Salt Tolerance to Plants – Mueller et al. – mSystems

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations – ter Horst et al. – Microbiome

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

Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments – Castro et al. – The ISME Journal

Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients – Schauberger et al. – The ISME Journal

Bioinformatics

Disentangling environmental effects in microbial association networks – Deutschmann et al. – Microbiome

Negative Binomial factor regression with application to microbiome data analysis – Muller, Mishra

Techniques

Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses – Chen et al. – The ISME Journal

October 29, 2021

Sorry for the delayed post, WordPress was playing some mean tricks on me today and there were no treats! Good morning all and happy spooky season! It’s been a moment since I’ve written a post and I write to you now as a freshly (pepper)minted PhD! I’m feeling gourd and can’t wait to pumpkin spice things up with some fangtastic papers.

Some of the highlights include a paper by McAlpine et al. examining interkingdom relationships between bacteria and fungi. Specifically, they found that the gut commensal species Lactobacillus can produce a small molecule that blocks filamentous growth of the opportunistic pathogen Candida albicans. Another interesting paper comes from Michael Adams lab at the University of Georgia, Athens which showed that members of the gut microbiota have the capacity to assimilate the metal tungsten which, in turn, allows these microbes to oxidize a broad range of aldehydes in the gut. Additionally, a paper by Plummer et al. looked at the vaginal microbiota of women who have recurrent bacterial vaginosis as well as the penile microbiota of their partners, and found that when males also underwent antibiotic treatment it led to a decrease in bacterial vaginosis in their female partners.

Hope you enjoy reading these fa-boo-lous papers and may you eat, drink, and be scary this Halloween!

General Microbiome
A small molecule produced by Lactobacillus species blocks Candida albicans filamentation by inhibiting a DYRK1-family kinase. – MacAlpine, J. et al., Nature Communications.

Pregnancy and Early-Life
Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut. – Laursen, M.F. et al., Nature Microbiology.

Bifidobacterium catabolism of human milk oligosaccharides overrides endogenous competitive exclusion driving colonization and protection. – Heiss, B.E. et al., Gut Microbes.

Mother’s Milk Microbiome Shaping Fecal and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Analysis. – Gołębiewski. M. et al., Nutrients.

Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load. – Pärnänen, K.M.M. et al., The American Journal of Clinical Nutrition.

Human Vaginal Microbiome
A Prospective, Open-Label Pilot Study of Concurrent Male Partner Treatment for Bacterial Vaginosis. – Plummer, E.L. et al., mBio.

Human Gut Microbiome
Tungsten enzymes play a role in detoxifying food and antimicrobial aldehydes in the human gut microbiome. – Schut, G.J. et al., PNAS.

Commensal bacteria promote endocrine resistance in prostate cancer through androgen biosynthesis. – Pernigoni, N. et al., Science.

Vertebrate host phylogeny influences gut archaeal diversity. – Youngblut, N.D. et al., Nature Microbiology.

Gut microbiota dysbiosis contributes to the development of chronic obstructive pulmonary disease. – Li, N. et al., Respiratory Research.

Oral Administration of Latilactobacillus sakei ADM14 Improves Lipid Metabolism and Fecal Microbiota Profile Associated With Metabolic Dysfunction in a High-Fat Diet Mouse Model. – Won, S.-M. et al., Frontiers in Microbiology.

Human Oral Microbiome
Discrimination of Bacterial Community Structures among Healthy, Gingivitis, and Periodontitis Statuses through Integrated Metatranscriptomic and Network Analyses. – Nemoto, T. et al., mSystems.

Animal Experiments
Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection. – Woo, V. et al., Cell Host & Microbe.

Intestinal microbiota shapes gut physiology and regulates enteric neurons and glia. – Vicentini, F.A. et al., Microbiome.

Lactobacillus rhamnosus GG Derived Extracellular Vesicles Modulate Gut Microbiota and Attenuate Inflammatory in DSS-Induced Colitis Mice. – Tong, L. et al., Nutrients.

Animal Microbiome
Phage Treatment Trial to Eradicate LA-MRSA from Healthy Carrier Pigs. – Tuomala, H. et al., Viruses.

Characterization of the Eukaryotic Virome of Mice from Different Sources. – Zhang, C. et al., Microorganisms.

Supplemental L-Arginine Improves the Embryonic Intestine Development and Microbial Succession in a Chick Embryo Model. – Dai, D. et al., Frontiers in Nutrition.

Water and Extremophile Microbiome
Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends. – Zrimec, J. et al., mBio.

Acrylate protects a marine bacterium from grazing by a ciliate predator. – Teng, Z.-J. et al., Nature Microbiology.

Plant, Root, and Soil Microbiome
The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. – Mahdi, L.K. et al., ISME Journal.

Spatial Characterization of Microbial Communities on Multi-Species Leafy Greens Grown Simultaneously in the Vegetable Production Systems on the International Space Station. – Hummerick, M.E. et al., Life (Basel).

Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms. – Jones, M.L. et al., Elife.

Probiotics
High-efficiency delivery of CRISPR-Cas9 by engineered probiotics enables precise microbiome editing. – Neil, K. et al., Molecular Systems Biology.

Techniques
Visualizing transfer of microbial biomolecules by outer membrane vesicles in microbe-host-communication in vivo. – Bittel, M. et al., Journal of Extracellular Vesicles.