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


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