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

June 15, 2020

We’ve got a belated post for you today (sorry all!) with a good balance of recent research on plant, animal and free-living microbiomes. Rather than highlight specific pieces of literature, I would encourage any who are interested in the microbiome from an evolutionary perspective to check out the recording of the ERC funded IDEM group’s recent discussion of the Holobiont Concept, featuring some preeminent proponents and critics of this model.

Seminar Recordings

ERC IDEM Group Holobiont Discussion – Dr. Scott Gilbert (7:17), Dr. Joan Roughgarden (1:05:03), Dr. Ford Doolittle (2:04:42)

General microbiome

Intestinal fermentation in vitro models to study food- induced gut microbiota shift: an updated review – Nissen et al. – FEMS Microbiology Letters

Human gut microbiome

Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions – Baldini et al. – BMC Biology

High Oscillospira abundance indicates constipation and low BMI in the Guangdong Gut Microbiome Project – Chen et al. – Scientific Reports

Animal microbiome

Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house mice – Belheouane et al. – The ISME Journal

Competitive traits of coral symbionts may alter the structure and function of the microbiome – McIlroy et al. – The ISME Journal

Evolutionary development and co‐phylogeny of primate‐associated bifidobacteria – Lugli et al. – Environmental Microbiology

Plant, root, and soil microbiome

Microbial functional traits in phyllosphere are more sensitive to anthropogenic disturbance than in soil – Xiang et al. – Environmental Pollution

Water and extremophile microbiome

Eutrophication as a driver of microbial community structure in lake sediments – Han et al. – Environmental Microbiology


MetaFS: Performance assessment of biomarker discovery in metaproteomics – Tang et al. – Briefings in Bioinformatics

Microbes on the market

(Radio) Using our Microbiome to Change the Way We Live – KPCW

May 15th, 2020

We have got a balanced mix for folks today of human, animal, plant, and free-living microbiome research. In particular I want to highlight the work of Inagaki et al., who tracked gut microbiome dynamics within Japanese termites (Reticulitermes speratus) during dispersal and colony formation. They observed a rapid increase then decrease of gut protozoa coinciding with larval hatching of a pioneering termite pair’s first brood; a pattern they call a ‘gut microbial pulse’ (what a wonderfully evocative term!). This is a neat example of how host-associated microbiomes might play a integral role in the ecology of free-living organisms.

General microbiome

Dynamic metabolic adaptation can promote species coexistence in competitive communities– Leonardo Pacciani-Mori et al. – PLOS Computational Biology

The role of the microbiota in periodontal disease – Mike A. Curtis et al. – Periodontology 2000

Human respiratory microbiome

Oral‐lung microbiome interactions in lung diseases– Manoj J. Mammen et al. – Periodontology 2000

Human nearly-sterile sites

Microbiome and Schizophrenia: Current Evidence and Future Challenges – Thiago Macedo e Cordeiro et al. – Current Behavioural Neuroscience Reports

Human gut microbiome

Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota – Sivaranjani Namasivayam et al. – PLOS Neglected Tropical Diseases

A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type – Alan Le Goallec et al. – PLOS Computational Biology

The role of small intestinal bacterial overgrowth and false positive diagnosis of lactose intolerance in southwest Hungary — A retrospective observational study – Péter Varjú et al. – PLOS One

The Bacterial Gut Microbiota of Adult Patients Infected, Colonized or Noncolonized by Clostridioides difficile – Monique J.T Crobach et al. – Microorganisms

Animal experiments

Effect of age and the individual on the gastrointestinal bacteriome of ponies fed a high-starch diet– Philippa K. Morrison et al. – PLOS One

Animal microbiome

Gut microbial pulse provides nutrition for parental provisioning in incipient termite colonies – Tatsuya Inagaki et al. – Behavioural Ecology and Sociology

The role of the gut microbiome in mediating standard metabolic rate after dietary shifts in the viviparous cockroach, Diploptera punctata – Paul A. Ayayee et al. – Journal of Experimental Biology

Plant, root, and soil microbiome

Genome reconstruction of the non-culturable spinach downy mildew Peronospora effusa by metagenome filteringJoël Klein et al. – PlOS One

Unraveling the Microbiota of Natural Black cv. Kalamata Fermented Olives through 16S and ITS Metataxonomic Analysis – Maria Kazou et al. – Microorganisms

Quantifying Plant-Borne Carbon Assimilation by Root-Associating Bacteria – Spenser Waller et al. – Microorganisms

Water and extremophile microbiome

Community-level signatures of ecological succession in natural bacterial communities – Alberto Pascual-Garcia & Thomas Bell – Nature Communications

Instigation of indigenous thermophilic bacterial consortia for enhanced oil recovery from high temperature oil reservoirs – Leha Sharma et al. – PLOS One

Microplastics affect sedimentary microbial communities and nitrogen cycling – Meredith E. Seeley et al. – Nature Communications

Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient – James Seward et al. – Environmental Microbiology


Confocal Raman microscopy to identify bacteria in oral subgingival biofilm models – Lukas Simon Kriem et al. – PLOS One


April 15, 2020

Hi folks! Another new volunteer poster here up from the ranks of the recently recruited. Today’s post is pre-print and plant/soil heavy. If up until now you’ve focused your reading on animal microbiomes, now’s a great time to check in on our photosynthesizing friends. Lots of great work today on the affect of management strategies on plant-associated and soil microbes. If the transition into the world of the leafy green is too jarring, perhaps try easing yourself in with Marchese et al.’s work on the mycobiome of sea cucumbers – a critter which is plant in common name only.


Pregnancy and early life

Review: Breast Milk, a Source of Beneficial Microbes and Associated Benefits for Infant Health – Lyons et al. – Nutrients

Human respiratory microbiome

Comment: Microbiota and chronic lung disease in preterm infants. Where is the truth? – Nandakumar and Aly – Journal of Perinatology

Human skin microbiome

The cutaneous microbiome in hospitalized patients with pressure ulcers – de Wert Luuk et al. – Scientific Reports

Human vaginal microbiome

Inflammatory and antimicrobial properties differ between vaginal Lactobacillus isolates from South African women with non-optimal versus optimal microbiota – Manhanzva et al. – Scientific Reports

A meta-analysis of mannose-binding lectin gene polymorphisms with the risk of recurrent vulvovaginal infections – Kalia et al. – Scientific Reports

Human gut microbiome

Review: Gut Microbial Metabolites of Aromatic Amino Acids as Signals in Host–Microbe Interplay – Liu et al. – Trends in Endocrinology & Metabolism

Preprint: Computational Modeling of the Gut Microbiota Predicts Metabolic Mechanisms of Recurrent Clostridioides difficile Infection – Henson – bioRxiv

Preprint: Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica – Liao et al. – bioRxiv


Animal experiments

Preprint: Validating the use of bovine buccal sampling as a proxy for the rumen microbiota using a time course and random forest classification approach – Young et al. – bioRxiv

Animal microbiome

Gut microbial diversity across a contact zone for California voles: implications for lineage divergence of hosts and mito‐nuclear mismatch in the assembly of the mammalian gut microbiome – Lin et al. – Molecular Ecology

Diversity and bioactivity of fungi associated with the marine sea cucumber Holothuria poli: disclosing the strains potential for biomedical applications – Marchese et al. – Journal of Applied Microbiology

Perspective: Microbiome maturation during a unique developmental window – Videvall – Molecular Ecology

Preprint: Microbial interactions in the mosquito gut determine Serratia colonization and blood feeding propensity – Kozlova et al. – bioRxiv

Plant, root, and soil microbiome

Reduced microbial diversity induces larger volatile organic compound emissions from soils – Abis et al. – Scientific Reports

Increased temperatures alter viable microbial biomass, ammonia oxidizing bacteria and extracellular enzymatic activities in Antarctic soils – Barnard et al. – FEMS Microbiology Ecology

One ring to rule them all: an ecosystem engineer fungus fosters plant and microbial diversity in a Mediterranean grassland – Zotti et al. – New Phytologist

Changes in soil fungal communities following anthropogenic disturbance are linked to decreased lodgepole pine seedling performance – Beck et al. – Journal of Applied Ecology

Long-term effects of stump removal and tree species composition on the diversity and structure of soil fungal communities – Modi et al. – FEMS Microbiology Ecology

Effect of treated sewage characteristics on duckweed biomass production and microbial communities – Iwano et al. – Water Science and Technology

Review: Functional roles of microbial symbionts in plant cold tolerance – Acuña‐Rodríguez et al. – Ecology Letters

Preprint: Dryland cropping system, weed communities, and disease status modulate the effect of climate conditions on wheat soil bacterial communities – Ishaq et al. – bioRxiv

Preprint: Cropping systems that improve richness convey greater resistance and resilience to soil fungal, relative to prokaryote, communities – Finn et al. – bioRxiv

Water and extremophile microbiome

Diverse groups of fungi are associated with plastics in the surface waters of the Western South Atlantic and the Antarctic Peninsula – Lacerda et al. – Molecular Ecology

Nitrification kinetics and microbial community dynamics of attached biofilm in wastewater treatment – Skoyles et al. – Water Science and Technology



Data normalization strategies in metabolomics: Current challenges, approaches, and tools – Misra – European Journal of Mass Spectrometry


Microbes on the market

Blog: COVID-19: Impact of Coronavirus Pandemic on Human Microbiome Market 2020. Top Leaders are Dohme Corp, Seres Therapeutics, Synthetic Biologics Inc, Synlogic – Publicist 360