April 2, 2021

Good morning and happy Friday!

In my last blog post I requested reader contributions and many of you reached out! Below are some of the highlights which include a commentary on phylogenetic core groups, a preprint on viral RNA methylation in Wolbachia, a database for the murine oral bacterial community, and a research article on fungal modification in the leaf-cutter ant fungal garden ecosystem.

Events and jobs

Biological Sciences Laboratory Instructor Position at Smith College in Northampton, MA

General microbiome

***Commentary: Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework – Pascual-García – Microbiome

Animal microbiome

***Preprint: Differential viral RNA methylation contributes to pathogen blocking in Wolbachia-colonized arthropod – Bhattacharya et al. – bioRxiv

Preprint: Isolation and characterization of a novel Wolbachia bacteriophage from Allonemobius socius crickets in Missouri – Fischer et al. – bioRxiv

***From plants to ants: Fungal modification of leaf lipids for nutrition and communication in the leaf-cutter ant fungal garden ecosystem – Khadempour et al. – mSystems

Plant, root, and soil microbiome

Preprint: Experimental evolution-driven identification of Arabidopsis rhizosphere competence genes in Pseudomonas protegens – Zhang et al. – bioRxiv

Built environment

Metagenomic profile of microbial communities in a drinking water storage tank sediment after sequential exposure to monochloramine, free chlorine, and monochloramine – Gomez-Alvarez et al. – ACS EST Water

Bioinformatics

***A 16S rRNA gene and draft genome database for the murine oral bacterial community – Joesph et al. – mSystems

March 18, 2021

Greetings from Pittsburgh!

Today’s digest has a lot of food and agriculture associated articles. Several articles focus on the effects of various pathogens on dairy cows, beef steers, and poultry breeds! For those of us who are more interested in plants, there is an article on biogas production from tomato waste and a preprint on how the microbial community of food waste changes during the composting process. Finally, I included a research article about social media during the pandemic since I’m sure I’m not the only one who has relied on it a little too heavily over the last year…

Happy reading!

General microbiome

Preprint: Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations – Conrad et al. – bioRxiv

BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE – Demo et al. – PLOS ONE

Review: The gut microbiota–brain axis in behaviour and brain disorders – Morais et al. – Nature Reviews Microbiology

Preprint: Cross-species evolutionary rewiring in the enteric bacterium Campylobacter – Taylor et al. – bioRxiv

Human gut microbiome

Gut microbiota profiles in diarrheic patients with co-occurrence of Clostridioides difficile and Blastocystis – Vega et al. – PLOS ONE

Animal experiments

Preprint: Low pathogenic avian influenza virus infection retards colon microbiome diversification in two different chicken lines – Chrzastek et al. – bioRxiv

Preprint: Borrelia infection in rodent host has dramatic effects on the microbiome of ticks – Hamilton et al. – bioRxiv

Animal microbiome

Preprint: The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe – Wallace et al. – bioRxiv

Plant, root, and soil microbiome

Effects of precipitation change and nitrogen addition on the composition, diversity, and molecular ecological network of soil bacterial communities in a desert steppe – Jia et al. – PLOS ONE

Preprint: Changes and composition of microbial community during aerobic composting of household food waste – Jin et al. – bioRxiv

Preprint: What’s under the Christmas tree? Soil acidification alters fir tree rhizosphere bacterial and eukaryotic communities, their interactions, and functional traits – Steven et al. – bioRxiv

A comparative analysis of biogas production from tomato bio-waste in mesophilic batch and continuous anaerobic digestion systems – Szilágyi et al. – PLOS ONE

Food microbiology

Red seaweed (Asparagopsis taxiformis) supplementation reduces enteric methane by over 80 percent in beef steers – Roque et al. – PLOS ONE

Prevalence and distribution of multilocus sequence types of Staphylococcus aureus isolated from bulk tank milk and cows with mastitis in Pennsylvania – Thomas et al. – PLOS ONE

Multidrug-resistant enterobacteria in newborn dairy calves in Germany – Waade et al. – PLOS ONE

Phages and viruses

Review: Viral and host heterogeneity and their effects on the viral life cycle – Jones et al. – Nature Review Microbiology

Bioinformatics

Dcmd: Distance-based classification using mixture distributions on microbiome data – Shestopaloff et al. – PLOS Computational Biology

Kara’s non-microbiology pick

Don’t put all social network sites in one basket: Facebook, Instagram, Twitter, TikTok, and their relations with well-being during the COVID-19 pandemic – Masciantonio et al. – PLOS ONE

February 4, 2021

Greetings from a very snowy Pittsburgh!

If you like getting dirty, today’s digest is for you! It includes a review on bat guano, two research articles about compost, four focused on soil research, and a preprint about fertilization with poultry manure.

Happy reading!

Events and jobs

February 1st to 14th: If you’re on twitter, check out #MicrobeValentinesDay! @AnneAMadden is posting 14 days of pink microbes in honor of Valentine’s Day under this hashtag!

Human skin microbiome

Gut microbiome profile in psoriatic patients treated and untreated with biologic therapy – Valentini et al. – The Journal of Dermatology

Human gut microbiome

Preprint – Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement – Barrasso et al. – bioRxiv

Review: Gut microbiota-mediated pesticide toxicity in humans: methodological issues and challenges in risk assessment of pesticides – Utembe and Kamng’ona – Chemosphere

Animal experiments

Effects of thallium exposure on intestinal microbial community and organ functions in zebrafish (Danio rerio) – Wang et al. – Elementa: Science of the Anthropocene

Is intestinal bacterial diversity enhanced by trans-species spread in the mixed-species flock of hooded crane (Grus monacha) and bean goose (Anser fabalis) wintering in the lower and middle Yangtze river floodplain? – Yang and Zhou – Animals

Animal microbiome

Review: The microbiome of bat guano: for what is this knowledge important? – Dimkić et al. – Applied Microbiology and Biotechnology

Tick microbiomes in neotropical forest fragments are best explained by tick-associated and environmental factors rather than host blood source – Kueneman et al. – Microbial Ecology

Plant, root, and soil microbiome

Survival rates of microbial communities from livestock waste to soils: a comparison between compost and digestate – Akari and Uchida – Applied and Environmental Soil Science

Year, location, and variety impact on grape-, soil-, and leaf-associated fungal microbiota of Arkansas-grown table grapes – Cureau et al. – Microbial Ecology

Preprint: Agricultural fertilization with poultry manure results in persistent environmental contamination with the pathogen Clostridioides difficile – Frentrup et al. – bioRxiv

Impacts of invasive Australian Acacias on soil bacterial community composition, microbial enzymatic activities, and nutrient availability in Fynbos soils – Keet et al. – Microbial Ecology

A novel carboxylesterase derived from a compost metagenome exhibiting high stability and activity towards high salinity – Lu and Daniel – Genes

A two-year field study of nickel-agromining using Odontarrhena chalcidica co-cropped with a legume on an ultramafic soil: temporal variation in plant biomass, nickel yields and taxonomic and bacterial functional diversity – Saad et al. – Plant and Soil

Bacterial response to soil property changes caused by wood ash from wildfire in forest soils around mining areas: Relevance of bacterial community composition, carbon and nitrogen cycling – Zhang et al. – Journal of Hazardous Materials

Water and extremophile microbiome

Microcystis blooms aggravate the diurnal alternation of nitrification and nitrate reduction in the water column in Lake Taihu – Chen et al. – Science of the Total Environment

Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs – He et al. – Science of the Total Environment

Cadmium sulfide nanoparticle biomineralization and biofilm formation mediate cadmium resistance of the deep‐sea bacterium Pseudoalteromonas sp. MT33b – Ma and Sun – Environmental Microbiology Reports

Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession – Shabarova et al. – Nature Microbiology

Built environment

Preprint: Half-life of biodegradable plastics in the marine environment depends on material, habitat, and climate zone – Lott et al. – bioRxiv

Water flushing irremovable biofilms on support material in dynamic membrane bioreactor: formation, composition, and microbial community – Huang et al. – Chemosphere

Phages and viruses

Preprint: Rampant prophage movement among transient competitors drives rapid adaptation during infection – Marshall et al. – bioRxiv

January 14, 2021

Greetings from Pittsburgh!

Today’s digest contains lots of microbial ecology articles focused on everything from the impacts of sleep on dental biofilm to the response of soil microbiota to high petroleum pollution. Also included are two articles focused on insect-plant interactions, with the first focusing on gall induction in insects and the second on the intestinal microbiota of the pine defoliator C. chuxiongica.


General microbiome

Novel cyanotoxin-producing Synechococcus in tropical lakes – Yew-Hoong et al. – Water Research

Multi-site human microbiome

Impacts of sleep on the characteristics of dental biofilm – Sotozono et al. – Scientific Reports

Animal experiments

Dysbiosis of rat vagina is efficiently rescued by the vaginal microbiota transplantation or probiotic combination: Vaginal microbiota transplantation rescues dysbiosis in rat vagina – Chen et al. – International Journal of Antimicrobial Agents

Are bacterial symbionts associated with gall induction in insects? – Hammer et al. – Arthropod-Plant Interactions

The diversity and function of intestinal microorganisms in four geographic Cephalcia chuxiongica (a pine defoliator) populations – Yu et al. – Journal of Applied Entomology

Animal microbiome

Linking bacterial communities associated with the environment and the ecosystem engineer Orchestia gammarellus at contrasting salt marsh elevations – Hernández et al. – Microbial Ecology

Plant, root, and soil microbiome

Response of bacterial and fungal communities to high petroleum pollution in different soils – Galitskaya et al. – Scientific Reports

Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing – Hu et al. – AMB Express

First reported quantitative microbiota in different livestock manures used as organic fertilizers in the Northeast of Thailand – Wongsaroj et al. – Scientific Reports

Water and extremophile microbiome

Coastal bacterial community response to glacier melting in the Western Antarctic Peninsula – Alcamán-Arias et al. – Microorganisms

Microbial necromass formation, enzyme activities and community structure in two alpine elevation gradients with different bedrock types – Bhople et al. – Geoderma

Exploring the taxonomical and functional profile of As Burgas hot spring focusing on thermostable β-galactosidases – DeCastro et al. – Scientific Reports

The effect of an adsorbent matrix on recovery of microorganisms from hydrocarbon-contaminated groundwater – Taylor et al. – Microorganisms

Built environment

Electrochemical performance and response of bacterial community during phenanthrene degradation in single-chamber air-cathode microbial fuel cells – Hua et al. – Environmental Science and Pollution Research

Food microbiology

Combination of Flos Sophorae and chili pepper as a nitrite alternative improves the antioxidant, microbial communities and quality traits in Chinese sausages – Tang et al. – Food Research International

December 18, 2020

Greetings from cold and snowy Pittsburgh!

As I type this, my housemate (who is an essential healthcare worker) should be getting the first dose of her COVID-19 vaccine! Although I’m not sure what the distribution of COVID-19 vaccines is expected to look like, today’s digest includes an article mapping routine measles vaccination coverage in low- and middle- income countries. I’ve also highlighted a few interesting environmental microbiology preprints, including one on the role of ecosystem engineers in shaping arid soil bacterial communities.

Happy holidays and happy reading!


Events and jobs

Danone North America Gut Microbiome, Yogurt and Probiotics Fellowship Grant – Applications for the 2020-2021 grant are currently open and are due on February 24, 2021.

General microbiome

Mapping routine measles vaccination in low- and middle-income countries – Local Burden of Disease Vaccine Coverage Collaborators – Nature

The functional proteome landscape of Escherichia coli – Mateus et al. – Nature

Preprint: Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae – Shaw et al. – bioRxiv


Plant, root, and soil microbiome

Preprint: The role of ecosystem engineers in shaping the diversity and function of arid soil bacterial communities – Baubin et al. – bioRxiv

Preprint: Environmental interactions with amoebae as drivers of bacterial-fungal endosymbiosis and pathogenicity – Itabangi et al. – bioRxiv

November 5, 2020

Hello, friends!

I’m an American who grew up in North Carolina, lived in Georgia for many years, and now counts Pennsylvania as home. All of this is to say, I’ve been especially consumed by the US election this morning and so today’s digest is tailor made to distract me for a few hours. It contains a heavy dose of general microbiome, environmental microbiology, and microbial ecology articles. If you need a bigger distraction than usual, I’ve highlighted a few articles that I am particularly looking forward to reading and am using this space as an opportunity to reintroduce myself and share why these articles have peaked my interest.

I completed my PhD research on the cockroach gut microbiome and through this work, I realized how complex microbiome-host-environmental interactions can be. Because of this, my first highlighted article is a review about cockroach-associated microbes. Currently, I work in a national lab studying environmental-associated microbes (and their functional capacity!) in a variety of different energy-associated environments. It’s no wonder I’m excited to read the second highlighted article focused on novel soil microbes found in an abandoned coal mine! I’m also very hungry at the moment, so as soon I read the phrase “smoked cow cheese” I was motivated to explore my cheese drawer as well as think more about microbial food safety and the microbial production of favor compounds. Finally, I love musical theater and science outreach, so I’m delighted to share a mouldy article that combines both passions.

Happy reading, everyone!


General microbiome

Review: The pneumococcal social network – Aggarawal et al. – PLOS Pathogens

Expanding magnetic organelle biogenesis in the domain Bacteria – Lin et al. – Microbiome

Gene duplication drives genome expansion in a major lineage of Thaumarchaeota – Sheridan et al. – Nature Communications

Metatranscriptomic analysis reveals active microbes and genes responded to short-term Cr(VI) stress – Yu et al. – Ecotoxicology

Effects of heavy ion particle irradiation on spore germination of Bacillus spp. from extremely hot and cold environments – Zammuto et al. – Life
Human gut microbiome

Gut microbiome

Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging – Sala et al. – PLOS ONE

Implication of gut microbiota in the physiology of rats intermittently exposed to cold and hypobaric hypoxia – Ramos-Romero et al. – PLOS ONE

Animal microbiome

Exploring the resident gut microbiota of stranded odontocetes: high similarities between two dolphin species Tursiops truncatus and Stenella coeruleoalba – Abdelrhman et al. – Journal of the Marine Biological Association of the UK

**Review: Bacteria associated with cockroaches: health risk or biotechnological opportunity? – Guzman & Vilcinskas – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Impact of land uses, drought, flood, wildfire, and cascading events on water quality and microbial communities: A review and analysis – Mishra et al. – Journal of Hydrology

Dams shift microbial community assembly and imprint nitrogen transformation along the Yangtze River – Gao et al. – Water Research

Built environment

**Isolation and characterization of soil bacteria from an abandoned coal mine in southeast Kansas – Bechtold et al. – BioOne Complete

Review: Understanding building-occupant-microbiome interactions toward healthy built environments – Li et al. – Frontiers of Environmental Science & Engineering

Food microbiology

**Microbial quality of smoked cow cheese “Parencia” – Kačániová et al. – Scientific Papers: Animal Science and Biotechnologies

Phages and viruses

Virome of bat guano from nine northern California roosts – Li et al. – Journal of Virology

Bioinformatics

The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities – Chen et al. – Nucleic Acids Research

PhANNs, a fast and accurate tool and web server to classify phage structural proteins – Cantu et al. – PLOS Computational Biology

Techniques

Low-cost biofuel-powered autoclaving machine for use in rural health care centres – Ahmed et al. – Journal of Medical Engineering & Technology

**‘The Mould that Changed the World’: Quantitative and qualitative evaluation of children’s knowledge and motivation for behavioural change following participation in an antimicrobial resistance musical – Hall et al. – PLOS ONE

Harnessing the power of eDNA metabarcoding for the detection of deep-sea fishes – McClenaghan et al. – PLOS ONE

October 27, 2020

Greetings from Pittsburgh, PA!

Today’s digest a contains articles focused on the oral microbiome, koala symbionts, soil microbial communities, and more. For those of you who are a bit too tired to digest cutting-edge research, I suggest using the 10 simple steps outlined in the highlighted editorial to colorize your own data visualizations. Finally, if you just need a break, I suggest bookmarking the article on the whale skin microbiome and revisiting the film Star Trek IV: The Voyage Home.

Happy reading (or movie watching)!

General microbiome

Taxonomic profiling and functional characterization of the healthy human oral bacterial microbiome from the north Indian urban sub-population – Verma et al. – Archives of Microbiology

Pregnancy and early life

Maternal and cord blood vitamin D level and the infant gut microbiota in a birth cohort study – Kassem et al. – Maternal Health, Neonatology and Perinatology

Human gut microbiome

Review: A review on preventive role of ketogenic diet (KD) in CNS disorders from the gut microbiota perspective – Rawat et al. – Reviews in Neurosciences

Animal experiments

Challenges in microbiological identification of aerobic bacteria isolated from the skin of reptiles – Brockmann et al. – PLOS ONE

Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum – Dahlhausen et al. – Peer J

Vertical transmission of zika virus in Aedes albopictus – Lai et al. – PLOS Neglected Tropical Diseases

Cultured-dependent and cultured-independent study of bacteria associated with Thai commercial stingless bee Lepidotrigona terminata – Suphaphimol et al. – Journal of Apicultural Research

Animal microbiome

**Skin microbiome of beluga whales: spatial, temporal, and health-related dynamics – Van Cise et al. – Animal Microbiome

Diversity of bacterial symbionts associated with Myzus persicae (Sulzer) (Hemiptera: Aphididae: Aphidinae) revealed by 16S rRNA Illumina sequencing – Xu et al. – Microbial Ecology

Plant, root, and soil microbiome

Protists and collembolans alter microbial community composition, C dynamics and soil aggregation in simplified consumer–prey systems – Erktan et al. – Biogeosciences

Responses of soil bacteria and fungi after 36 years fertilizer, straw cover, and irrigation management practices in northwest China – Zhang et al. – Soil Use and Management

Water and extremophile microbiome

Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance – Herold et al. – Nature Communications

Islands in the sand: Are all hypolithic microbial communities the same? – Lebre et al. – FEMS Microbiology Ecology

Shifts of sediment bacterial community and respiration along a successional gradient in a typical karst plateau lake wetland (China) – Xia et al. – Journal of Oceanology and Limnology

Salinity controls soil microbial community structure and function in coastal estuarine wetlands – Zhang et al. – Environmental Microbiology

Phages and viruses

Association of host proteins with the broad host range filamentous phage NgoΦ6 of Neisseria gonorrhoeae – Piekarowicz et al. – PLOS ONE

Bioinformatics

**Editorial: Ten simple rules to colorize biological data visualization – Hattab et al. – PLOS Computational Biology

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy – de Koning et al. – GigaScience

Predicting antimicrobial resistance using conserved genes – Nguyen et al. – PLOS Computational Biology

Techniques

Review: Innovations to culturing the uncultured microbial majority – Lewis et al. – Nature Reviews Microbiology

Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods – Wang et al. – PeerJ

Science, publishing, and career

Comment: Crowdsourcing virtual summer research opportunities to support minorities in microbiology – Johnson et al. – Nature Microbiology

October 1, 2020

Greetings, friends!

Today’s digest contains a wealth of microbiology articles focused on everything from the dog ear canal microbiome to estuarine methanogen communities. Rather than highlight a specific research article, today I’d like to encourage you to check out this week’s New York Times article profiling the organizers of Black in Micro Week and this commentary published by one of the organizers in mSphere. Black in Micro week began this Monday and programming is scheduled to continue through October 4th. If you missed earlier events, you’re in luck! The organizers have already uploaded videos of all completed events at the Black in Micro youtube channel.

Enjoy!


Events

Black in Micro Week is this week (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.

Human respiratory microbiome

Airway microbiota is associated with the severity of non‐CF bronchiectasis – Li et al. – The Clinical Respiratory Journal

Human gut microbiome

Systematic analysis of gut microbiota in pregnant women and its correlations with individual heterogeneity – Yang et al. – npj Biofilms and Microbiomes

Review: Implication of gut microbiota in cardiovascular diseases – Zhou et al. – Oxidative Medicine and Cellular Longevity

Animal experiments

Changes in the ear canal microbiota of dogs with otitis externa – Kasai et al. – Journal of Applied Microbiology

Plant, root, and soil microbiome

Soil borne Fusarium solani exhibited pathogenic effect on tomato cultivars in Nigeria – Abiala et al. – Archives of Phytopatholgy and Plant Protection

A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium, Microcoleus vaginatus – Nelson et al. – The ISME Journal

Successional change of the fungal microbiome pine seedling roots inoculated with Tricholoma matsutake – Park et al. – Frontiers in Microbiology

Review: Arbuscular mycorrhizal fungi: an ecological accelerator of phytoremediation of metal contaminated soils – Tiwari et al. – Archives of Agronomy and Soil Science

Co‐occurrence history increases ecosystem stability and resilience in experimental plant communities – van Moorsel et al. – Ecology

Quantitative estimation of stochastic and deterministic processes for soil prokaryotic community assembly in the Yellow River floodplain – Yu et al. – European Journal of Soil Science

Water and extremophile microbiome

Homogeneous environmental selection dominates microbial community assembly in the oligotrophic South Pacific Gyre – Allen et al. – Molecular Ecology

An unexpectedly broad thermal and salinity-tolerant estuarine methanogen community – Blake et al. – Microorganisms

Microbial communities responded to tetracyclines and Cu(II) in constructed wetlands microcosms with Myriophyllum aquaticum – Guo et al. – Ecotoxicology and Environmental Safety

Built environment

Microbial community and function in nitrogen transformation of ectopic fermentation bed system for pig manure composting – Chen et al. – Bioresource Technology

Effect of hydrothermal hot-compression method on the antimicrobial performance of green building materials from heterogeneous cellulose wastes – Echeverria et al. – Journal of Cleaner Production

Nitrous oxide emission and microbial community of full-scale anoxic/aerobic membrane bioreactors at low dissolved oxygen setpoints – Wen et al. – Journal of Water Process Engineering

Response of Cyperus involucratus to sulfamethoxazole and ofloxacin-contaminated environments: Growth physiology, transportation, and microbial community – Xu et al. – Ecotoxicology and Environmental Safety

Microbes in the news

Black microbiologists push for visibility amid a pandemic – Wu – New York Times

Science, publishing, and career

Commentary: mSphere of influence: That’s racist—COVID-19, biological determinism, and the limits of hypotheses – Taylor – mSphere

September 8, 2020

Greetings, friends!

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

Happy reading!

General microbiome

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

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

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

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

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

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

Multi-site human microbiome

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

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

Human respiratory microbiome

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

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

Human gut microbiome

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

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

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

Animal experiments

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

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

Plant, root, and soil microbiome

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

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

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

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

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

Water and extremophile microbiome

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

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

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

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

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

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

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

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

Built environment

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

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

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

Food microbiology

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

Bioinformatics

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

Techniques

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

August 28, 2020

Greetings!

Today’s microbiome digest has something for everyone. We have several articles focused on the human microbiome, a few animal studies, and quite a few articles focused on environmental bacteria found in soil, water, and even a cave! I want to highlight one article focused on the impact of spatial proximity on territory among bacteria. Although the article specifically focuses on skin bacteria, it’s relevant to anyone studying microbial communities!

Enjoy!

General microbiome

Horizontal transmission and recombination maintain forever young bacterial symbiont genomes – Russel et al. – PLOS GENETICS

Human skin microbiome

Impact of spatial proximity on territoriality among human skin bacteria – Hernandez-Valdes et al. – npj BIofilms and Microbiomes

Human gut microbiome

Gut microbiota and dysbiosis in Alzheimer’s disease: Implications for pathogenesis and treatment – Liu et al. – Molecular Neurobiology

Animal experiments

Caecal microbiota compositions from 7-day-old chicks reared in high-performance and low-performance industrial farms and systematic culturomics to select strains with anti-Campylobacter activity – Duquenoy et al. – PLOS ONE

Effect of FHA and Prn on Bordetella pertussis colonization of mice is dependent on vaccine type and anatomical site – Zeddeman et al. – PLOS ONE

Animal microbiome

Lactobacilli and other gastrointestinal microbiota of Peromyscus leucopus, reservoir host for agents of Lyme disease and other zoonoses in North America – Milovic et al. – PLOS ONE

Plant, root, and soil microbiome

Simple kinetics, assay, and trends for soil microbial catalases – Chabot et al. – Analytical Biochemistry

Sustaining the growth of Pinaceae trees under nutrient-limited edaphic conditions via plant-beneficial bacteria – Puri et al. – PLOS ONE

Soil properties, bacterial and fungal community compositions and the key factors after 5-year continuous monocropping of three minor crops – Yang et al. – PLOS ONE

Water and extremophile microbiome

Oleaginous potential of indigenously isolated fresh water microalgae for biofuel production – Saraf & Dutt – International Journal of Sustainable Energy

Bacteria and archaea communities in Cerrado natural pond sediments – Silveira et al. – Microbiology of Aquatic Systems

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

On microbial community of Pyropia haitanensis by metagenomic analysis – Wang et al. – Journal of Oceanology and Limnology