September 18, 2020


Legal agreements: barriers and enablers to global equitable COVID-19 vaccine access – Phelan et al. -The Lancet

Science news

‘Scientific American’ Breaks 175 Years Of Tradition, Endorses A Presidential Nominee – NPR

Human microbiome

Early origin and global colonisation of foot-and-mouth disease virus – Aiewsakun et al. – Scientific Reports

Human gut microbiome

Alteration of Gut Microbiota in Patients With Epilepsy and the Potential Index as a Biomarker – Gong et al. – Frontiers in Microbiology

Plant, root, and soil microbiome

Amazonian soil metagenomes indicate different physiological strategies of microbial communities in response to land use change – Khan et al. – bioRxiv

Deciphering the Role of Trehalose in Tripartite Symbiosis Among Rhizobia, Arbuscular Mycorrhizal Fungi, and Legumes for Enhancing Abiotic Stress Tolerance in Crop Plants – Sharma et al. – Frontier in Microbiology

Animal experiments

Diet posttranslationally modifies the mouse gut microbial proteome to modulate renal function – Lobel et al. – Science

Investigation into the effect of divergent feed efficiency phenotype on the bovine rumen microbiota across diet and breed – McGovern et al. – Scientific Reports

September 17, 2020

Another broad selection of microbiome papers for you this morning. Several papers today show how microbial communities are influenced by pollution, water depth, and El Niño, plus a study that found ants use signals from soil microbes to decide where to nest.

Human gut microbiome

Lactobacillus strains vary in their ability to interact with human endometrial stromal cells, Shiroda and Manning, PLOS ONE

A predictive index for health status using species-level gut microbiome profiling, Vinod K. Gupta et al., Nature Communications

Gut Microbiota and Metabolome Alterations Associated with Parkinson’s Disease, Sarah Vascellari et al., mSystems

Human nearly sterile sites

Metagenome analysis using serum extracellular vesicles identified distinct microbiota in asthmatics, Lee and Choi et al., Scientific Reports

Animal microbiome

The nesting preference of an invasive ant is associated with the cues produced by actinobacteria in soil, Hongmei Huang et al., PLOS Pathogens

Influence of host genetics in shaping the rumen bacterial community in beef cattle, Abbas and Howard et al., Scientific Reports

Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System, Charlotte B. Francoeur et al., mBio

Plant, root, and soil microbiome

Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts, Shawn M. Higdon et al., PLOS ONE

Water and extremophile microbiome

Pollution shapes the microbial communities in river water and sediments from the Olifants River catchment, South Africa, Angel Valverde et al., Archives of Microbiology

Persistent El Niño driven shifts in marine cyanobacteria populations, Alyse A. Larkin et al., PLOS ONE

Depth-Dependent Variables Shape Community Structure and Functionality in the Prince Edward Islands, Phoma and Makhalanyane, Environmental Microbiology


Preprint: Tracking strains predicts personal microbiomes and reveals recent adaptive evolution, Shijie Zhao et al., bioRxiv

September 16, 2020

Greetings from Chile! Today, in this Digest, it is worth to highlight: a study showing associations between the use of antibiotics and the risk of appendicitis, a review about microbiota and colorectal cancer (CRC) risk and another review about markers for diabetes-associated chronic kidney disease. In addition, there are a set of papers about microbiome changes under short- and long-term antibiotic use in the animal lab, and microbiota changes in the treatment of non-model animals, such as the sika deer.   

Human Microbiome

Antibiotics during childhood and development of appendicitis-a nationwide cohort study – Jacob Antonsen – Alimentary Pharmacology and Therapeutics

Review: Bacteria-related changes in host DNA methylation and the risk for CRC – Iradj Sobhani – Gut Microbes

Review: Potential for Novel Biomarkers in Diabetes-Associated Chronic Kidney Disease: Epigenome, Metabolome, and Gut Microbiome – Ashani Lecamwasam – Biomedicines

Microbiota-Mitochondria Inter-Talk: A Potential Therapeutic Strategy in Obesity and Type 2 Diabetes – Teresa Vezza – Antioxidants

Preprint: Impact of sleep fragmentation, heart failure, and their combination, on the gut microbiome – Olfat Khannous-Lleiffe – BioRxiv

Microbiome and Diet

Relative abundance of the Prevotella genus within the human gut microbiota of elderly volunteers determines the inter-individual responses to dietary supplementation with wheat bran arabinoxylan-oligosaccharides – Wing Sun Faith Chung – BMC Microbiology

Animal Microbiome

Acute and long-term effects of antibiotics commonly used in laboratory animal medicine on the fecal microbiota – Scott W. Korte – Veterinary Research

The impact of anthelmintic treatment on gut bacterial and fungal communities in diagnosed parasite-free sika deer Cervus nippon – Xiaolong Hu – Applied genetics and molecular biotechnology

On the way to specificity – Microbiome reflects sponge genetic cluster primarily in highly structured populations – Cristina Díez‐Vives – Molecular Ecology

The gut microbiota may be a novel pathogenic mechanism in loosening of orthopedic implants in rats – Meghan M. Moran – The FASEB Journal

Characterization of Gut Microbiota in Prenatal Cold Stress Offspring Rats by 16S rRNA Sequencing – Jiasan Zheng – Animals

Obesity Worsens Gulf War Illness Symptom Persistence Pathology by Linking Altered Gut Microbiome Species to Long-Term Gastrointestinal, Hepatic, and Neuronal Inflammation in a Mouse Model – Dipro Bose – Nutrients

Beneficial Microbes and Compounds

Influence of a cholesterol-lowering strain Lactobacillus plantarum LP3 isolated from traditional fermented yak milk on gut bacterial microbiota and metabolome of rats fed with a high-fat diet – Zitong Ding – Food and Function

The Microbiota-Derived Metabolite of Quercetin, 3,4-Dihydroxyphenylacetic Acid Prevents Malignant Transformation and Mitochondrial Dysfunction Induced by Hemin in Colon Cancer and Normal Colon Epithelia Cell Lines – Mabel Catalán – Molecules


Constructing bi-plots for random forest: Tutorial – Lionel Blanchet – Analytica Chimica Acta

More Microbes

Cultural isolation of spore-forming bacteria in human feces using bile acids – Masaru Tanaka – Scientific Reports

Bed bugs shape the indoor microbial community composition of infested homes – Madhavi L. Kakumanu – Science of The Total Environment

Sept 15, 2020

We have got a human gut microbiome heavy edition today, with two reviews of the early life microbiome and its affects on physiological development.

I also want to highlight the work of Chen et al. 2020, who nicely demonstrate that the zebra finch early-life microbiome converges upon the microbiome of the parent that reared them (rather than their genetic parent) in cross-fostering experiments. This is important as cross-fostering experiments have been a staple in studies of avian micro-evolution and eco-physiology in captive and free-living system. Therefore, variation in offspring phenotypes attributable to the ‘early life environment’, ‘nest effects’, or ‘foster parent effects’ might in some cases be partly proximately driven by microbiome variation. This is an important point of clarification since, as Chen et al. 2020 and other researchers have demonstrated, the microbiome can be vertically transmitted—unlike most early-life environment sources of phenotypic variation. Thanks for indulging me in my musings 😉

Enjoy today’s list!

Human respiratory microbiome
Adhesion of Staphylococcus aureus to epithelial cells: an in vitro approach to study interactions within the nasal microbiota – Ménard et al. 2020 – Journal of Medical Microbiology

Human skin microbiome
Early development of the skin microbiome: therapeutic opportunities – Casterline and Paller 2020 – Pediatric Research

Human gut microbiome
Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria – Seelbinder et al. 2020 – Microbiome

Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease – Leonard et al. 2020 – Microbiome

The effects of different dietary fiber pectin structures on the gastrointestinal immune barrier: impact via gut microbiota and direct effects on immune cells – Beukema et al. 2020 – Experimental & Molecular Medicine

Roles of the Polyphenol–Gut Microbiota Interaction in Alleviating Colitis and Preventing Colitis-Associated Colorectal Cancer – Zhao and Jiang – Advances in Nutrition

Stomach microbiota, Helicobacter pylori, and group 2 innate lymphoid cells – Ohno and Satoh-Takayama 2020 – Experimental & Molecular Medicine

Maternal supplementation with Bifidobacterium breve M-16V prevents their offspring from allergic airway inflammation accelerated by the prenatal exposure to an air pollutant aerosol – Terada-Ikeda et al. 2020 – PLOS ONE

[Review] Early Life Stress and the Development of the Infant Gut Microbiota: Implications for Mental Health and Neurocognitive Development – Vogel et al. 2020 – Current Psychiatry Reports

[Review] Early life interaction between the microbiota and the Enteric Nervous System – Foong et al. 2020 – Gastrointestinal and Liver Physiology

Animal experiments
Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests – Chen et al. 2020 – Microbiome

Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter – McKenna et al. 2020 –

Animal microbiome
Elucidation of Gut Microbiota in Mud Crab Scylla paramamosain Challenged to WSSV and Aeromonas hydrophila – Lin et al. 2020 – Marine Biotechnology

Plant, root, and soil microbiome
Soil microbial communities respond to an environmental gradient of grazing intensity in south Patagonia Argentina – Santiago et al. 2020 – Journal of Arid Environments

Different maturities drive proteomic and metabolomic changes in Chinese black truffle – Zhang et al. 2020 – Food Chemistry: X

Fungal Volatile Organic Compounds: More Than Just a Funky Smell? – Inamdar et al. 2020 – Annual Review of Microbiology

Phages and viruses
Potential applications of human viral metagenomics and reference materials: 2 considerations for current and future viruses – Santiago-Rodriguez and Hollister 2020 – Applied and Environmental Microbiology

Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC – Saary et al. 2020 – Genome Biology

Hill-based dissimilarity indices and null models for analysis of microbial community assembly – Modin et al. 2020 –

A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model – Fu et al. 2020 – Communications Biology

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


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


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 12, 2020

Human vaginal microbiome
Lactobacillus species signature in association with term and preterm births from low-income group of Pakistan – Aslam et al. – The Journal of Maternal-Fetal & Neonatal Medicine

Human gut microbiome
Long-term use of antibiotics and risk of type 2 diabetes in women: a prospective cohort study – Yuan et al. – International Journal of Epidemiology

The Impact of Diabetes on the Gut and Salivary IgA Microbiomes – Brown et al. – Infection and Immunity

Animal experiments
Effects of dietary replacement of soybean meal with dried distillers grains with solubles on the microbiota occupying different ecological niches in the rumen of growing Hu lambs – Shen et al. – Journal of Animal Science and Biotechnology

Pathogen identification and epidemiological assessment in recirculation aquaculture system based on Illumina sequencing technology – Sugachenko et al. – Limnology and Freshwater Biology

How oral probiotics affect the severity of an experimental model of progressive multiple sclerosis? Bringing commensal bacteria into the neurodegenerative process – Mestre et al. – Gut Microbes

Animal microbiome
General Microbiota of the Soft TickOrnithodoros turicataParasitizing the Bolson Tortoise(Gopherus flavomarginatus) in the Mapimi BiosphereReserve, Mexico – Barraza-Guerrero et al. – Biology

Water and extremophile microbiome
Bioturbation by the marine polychaete Capitella teleta alters sediment microbial community by ingestion and defecation of sediment particles – Jang et al. – Science of the Total Environment

Bacteria in the lakes of the Tibetan Plateau and polar regions – Liu et al. – Science of the Total Enivornment

Sulfate-reducing bacterial community shifts in response to acid mine drainage in the sediment of the Hengshi watershed, South China – Bao et al. – Environmental Science and Pollution Research

Review: Predictive interactome modeling for precision microbiome engineering – Kessell et al – Current Opinion in Chemical Engineering

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!


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.


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


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

September 10, 2020

Good morning from smokey, apocalyptic San Francisco! The world outside my window may be in sepia tones, but the articles I’m highlighting here are helping to brighten my day. Today’s digest has some fascinating insect and environmental microbiome research including a paper about the gut microbiota of a beetle that lives in the mixed forest of northeastern Asia and its capacity to efficiently degrade polystyrene. Additionally, there’s a paper characterizing the community structure and metabolic capacity of a biofilm-like microbial community lining the wall of the Yumugi river cave in a remote part of Western New Guinea. I’ve also included a paper examining availability of microbial community sequencing data which found that much of this data is not available and offers suggestions for improving data archiving practices. Finally, there is a very interesting technique paper about an orally ingestible microdevice that can be used to sample the gut microbiota in the upper gastrointestinal tract. Happy reading!

General Microbiome
Influence of Intratumor Microbiome on Clinical Outcome and Immune Processes in Prostate Cancer. – Ma, J. et al., Cancers

Experimental (co)evolution in a multi-species microbial community results in local maladaptation. – Castledine, M. et al., Ecology Letters

Pregnancy and Early Life
Mothers of Preterm Infants Have Individualized Breast Milk Microbiota that Changes Temporally Based on Maternal Characteristics. – Asbury, M.R et al., Cell Host Microbe

The meconium microbiota shares more features with the amniotic fluid microbiota than the maternal fecal and vaginal microbiota. – He, Q. et al., Gut Microbes

Skin microbiome
Stratum Corneum Lipidomics Analysis Reveals Altered Ceramide Profile in Atopic Dermatitis Patients Across Body Sites With Correlated Changes in Skin Microbiome. – Emmert, H. et al., Experimental Dermatology

Vaginal microbiome
Diverse vaginal microbiome was associated with pro-inflammatory vaginal milieu among pregnant women in Uganda. – Bayigga, L. et al. Human Microbiome Journal

Gut microbiome
Diet Diurnally Regulates Small Intestinal Microbiome-Epithelial-Immune Homeostasis and Enteritis. – Tuganbeav, T. et al., Cell

Microbiota-modulated CART + enteric neurons autonomously regulate blood glucose. – Muller, P.A. et al., Science

Succinate Produced by Intestinal Microbes Promotes Specification of Tuft Cells to Suppress Ileal Inflammation. -Banerjee, A. et al., Gastroenterology

Animal Experiments
Gut microbiome improves postoperative cognitive function by decreasing permeability of the blood-brain barrier in aged mice. – Wen, J. et al., Brain Research Bulletin

Indolepropionic Acid, a Metabolite of the Microbiome, Has Cytostatic Properties in Breast Cancer by Activating AHR and PXR Receptors and Inducing Oxidative Stress. – Sári, Z. et al., Cancers

Angiogenin maintains gut microbe homeostasis by balancing α-Proteobacteria and Lachnospiraceae. – Sun, D. et al., Gut

Gut Microbiota-Associated Activation of TLR5 Induces Apolipoprotein A1 Production in the Liver. – Yiu, J.H.C. et al., Circulation Research

Animal and insect microbiome
Cross-generational effects of climate change on the microbiome of a photosynthetic sponge. – Luter, H.M. et al., Environmental Microbiology

Symbionts shape host innate immunity in honeybees. – Horak, R.D. et al., Proceedings Biological Sciences

Parental Microbiota Modulates Offspring Development, Body Mass and Fecundity in a Polyphagous Fruit Fly. – Nguyen, B. et al. Microorganisms

Fast and Facile Biodegradation of Polystyrene by the Gut Microbial Flora of Plesiophthalmus davidis Larvae. – Woo, S. et al., Applied and Environmental Microbiology

Gut microbiota protects honey bees (Apis mellifera L.) against polystyrene microplastics exposure risks. – Wang, K. et al., Journal of Hazardous Materials

Plant, root, and soil microbiome
Characteristics of microbial community of soil subjected to industrial production of antibiotics. – Borčinová, M. et al., Folia Microbiologica

Host selection shapes crop microbiome assembly and network complexity. -Xiong, C. et al., The New Phytologist

Microbiome of root vegetables-a source of gluten-degrading bacteria. – Kõiv, V. et al., Applied Microbiology and Biotechnology

Water and extremophile microbiome
Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity. – Wang, Z. et al., ISME Journal

Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth. – Xue, C-X et al., Microorganisms

The microbial community of a biofilm lining the wall of a pristine cave in Western New Guinea. – Turrini, P. et al., Microbiological Research

Built environment
Airborne bacteria in outdoor air and air of mechanically ventilated buildings at city-scale in Hong Kong across seasons. – Zhou, Y. et al., Environmental Science and Technology

Phages and viruses
Review: Phages and their potential to modulate the microbiome and immunity. Federici, S. et al., Cellular and Molecular Immunology

Generalized estimating equation modeling on correlated microbiome sequencing data with longitudinal measures. – Chen, B. and Xu, W., PLoS Computational Biology

The Nubeam reference-free approach to analyze metagenomic sequencing reads. – Dai, H. and Guan, Y., Genome Research

The archives are half-empty: an assessment of the availability of microbial community sequencing data. – Jurburg, S.D. et al., Communications Biology

An effective culturomics approach to study the gut microbiota of mammals. – Pereira, A.C. and Cunha, M.V., Research in Microbiology

Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment. – Reichart, N.J. et al., ISME Journal

An Ingestible Self-Polymerizing System for Targeted Sampling of Gut Microbiota and Biomarkers. – Chen, L. et al., ACS Nano

September 9, 2020


[PREPRINT] Long-term survival of salmon-attached SARS-CoV-2 at 4°C as a potential source of transmission in seafood markets – Dai et al. – bioarxiv

Human gut microbiome

[REVIEW] Predictive values of colon microbiota in the treatment response to colorectal cancer – Galan-Ros et al. – Pharmacogenomics

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

Long-term effects of western diet consumption in male and female mice – Hasegawa et al. – Scientific Reports

Young versus aged microbiota transplants to germ-free mice: increased short-chain fatty acids and improved cognitive performance – Lee et al. – Gut Microbes

Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet – Hennessy et al. – Plos One

Plant, root, and soil microbiome

Comparison of the microbial diversity during two different wine fermentation processes – Böhmer et al. – FEMS Microbiology Letters

[PREPRINT] Functional metagenomics of bark microbial communities from avocado trees (Persea americana Mill.) reveals potential for bacterial primary productivity – Aguirre-von-Wobeser – bioarxiv


[PREPRINT] BacAnt: the combination annotation server of antibiotic resistance gene, insertion sequences, integron, transposable elements for bacterial DNA sequences – Hua et al. – bioarxiv

Microbes in the news

Plant-based diets shine when looking at the gut microbiome – Zimlich

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


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


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