Volume 1 Issue 12, December 2016

Dysbiosis, an imbalance in the microbiota, has been a major organizing concept in microbiome science. Here, we discuss how the balance concept, a holdover from prescientific thought, is irrelevant to — and may even distract from — useful microbiome research.

Plasmids are well known for spreading antibiotic-resistance genes between bacterial strains. Recent experiments show that they can also act as catalysts for evolutionary innovation, promoting rapid evolution of novel antibiotic resistance.

Microorganisms produce antibiotics, which can exclude competitors, but bacteria typically only synthesize modest amounts of these compounds. New work suggests this may be an evolutionary strategy to balance the benefits of antimicrobial warfare against inadvertently providing help to resistant free-loaders.

7.7 million non-redundant genes have been documented in the pig gut microbiome gene catalogue, revealing a 96% similarity in functional pathways to the human catalogue and influences from sex, age, host genetics and antibiotic treatments.

Immunization with inactivated Japanese encephalitis vaccine generates cross-reactive antibodies that enhance immunogenicity on subsequent immunization with live attenuated yellow fever vaccine, demonstrating antibody-dependent enhancement of infection in a clinical trial.

Mutations in two previously unreported Plasmodium falciparum genes, acetyl-CoA transporter (pfact) and UDP-galactose transporter (pfugt), convey resistance to two imidazolopiperazine antimalarial compounds.

A symbiosis between the root-inhabiting Enterobacter sp. M6 and the finger millet creates a physical barrier around the roots, trapping and killing the fungus Fusarium graminearum via M6-derived release of fungicides into the barrier matrix.

Whole-genome sequencing suggests that the spread of multidrug-resistant Enterobacter cloacae infections in the UK and Ireland is driven by a diverse community-based pool of strains.

Intermediate colistin production in E. coli maximizes the benefit of inhibiting sensitive neighbours while minimizing competition from resistant cheaters.

A hybrid conjugative plasmid is found to mediate one-step co-transfer of bla_NDM-5 and mcr-1 and confer β-lactam and colistin resistance.

The Verstraetearchaeota encode divergent methyl-coenzyme M reductase genes, which are required for methylotrophic methanogenesis, increasing methanogen diversity and the complexity of the global methane cycle.

The Pseudomonas aeruginosa quorum-sensing molecule 2-aminoacetophenone (2-AA) upregulates HDAC1 to reduce acetylation at cytokine promoters and promote host tolerance during infection.

Inflammatory bowel disease dysbiosis networks were different between humans and dogs, with some species switching from positive to negative between groups. Stool samples were sufficient for dog-classification, whereas mucosal samples are required in humans.

Hydraulic conditions result in selective taxonomic pressures that determine the formation of biofilm or aggregate communities in experimental fluvial systems.

Optimization of culturing techniques has allowed the identification of 1,057 prokaryotic species within the human gut microbiome repertoire, doubling the previous number of isolated species from the human gut.