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Food supply is one of the major drivers of animal behavior, and the gut microbiome is an important mediator between food supply and its effects on physiology. However, predicting the outcome of diet change on microbiome and consequences for the animal has proven extremely challenging. We propose this reflects processes occurring at different scales. Inadequate accounting for the multi‐level complexity of nutrition (nutrients, foods, diets) obscures the diet influence on microbiome and subsequently animal. Here, we present a detailed year‐round, multi‐level analysis of diet and microbiome changes in a wild population of a temperate primate, the rhesus macaque (Macaca mulatta). Total daily food and nutrient intake of 6 male and 6 female macaques was monitored in each of the 4 seasons (total 120 days observations). For each individual, we found significant variation in the microbiome between all 4 seasons. This response was more strongly correlated with changes in macronutrient intake than with food items and much of the response could be explained at the level of 6 ecological guilds—sets of taxa sharing similar responses to nutrient intake. We conclude that study of diet, microbiome, and animal performance in ecology will more effectively identify patterns if diet is recorded at the level of nutrient intake. Although microbiome response to diet does show variation in species‐level taxa in response to food items, there is greater commonality in response at the level of guilds. A goal for microbiome researchers should be to identify genes encoding microbial attributes that can define such guilds. [ABSTRACT FROM AUTHOR]

The integron-gene cassette system contributes to multiple antibiotic resistance in bacteria and is likely to be of broader evolutionary significance. However, the majority of integron diversity consists of chromosomal integrons (CIs), with mostly unknown phenotypes, which are poorly characterized. A pUC-based reporter plasmid (pUS23) was developed containing a recombination site [aadB 59 base element (59-be)] upstream of promoterless aadB [gentamicin (Gm) resistance] and gfp (green fluorescence) genes, and this construct was used to investigate the recombination and expression activities of the CI in Pseudomonas stutzeri strain Q. Electroporation of pUS23 into P. stutzeri Q gave ampicillin-resistant transformants, which yielded [Gm.sup.R] green fluorescent recombinants after plating on Gm medium. Site-specific integration of pUS23 at attl was detected by [P.sub.c]R in 8% of [Gm.sup.R] colonies and the frequency of attl integration was estimated as 2.0 x [10.sup.-8] per P. stutzeri Q(pUS23) cell. RT-[P.sub.c]R confirmed integron-mediated expression of aadB in one recombinant strain (Q23-17) and a promoter ([P.sub.c]) was localized to the 5' end of the intl gene. The integrated pUS23 and flanking integron DNA were cloned from genomic DNA of strain Q23-17 and sequenced, confirming that site-specific integration of the entire reporter plasmid had occurred at the attl site. An insertion sequence (ISPst5; IS5 family) was discovered in the vector backbone of the reporter plasmid integrated at attl and also in a pUS23 derivative recovered as a plasmid in Escherichia coli JM 109. This is the first demonstration that wild-type CIs can capture gene cassettes and express cassette-associated genes.

Author(s): Jessica L. Green (corresponding author) [1, 4]; Andrew J. Holmes [2]; Mark Westoby [1]; Ian Oliver [3]; David Briscoe [1]; Mark Dangerfield [1]; Michael Gillings [1]; Andrew J. Beattie [...]

Researchers have developed a technique for detecting bacterial genes in environmental samples even when a genetic sequence is lacking. It is a PCR assay based on the gene cassettes associated with integrons. Most of the gene cassettes contained open reading frames that were not homologous to any known sequence.

Researchers have discovered an unknown group of methanotrophic bacteria that participates in the soil sink for atmospheric methane. Monooxygenase gene analysis indicates that the bacteria belong to the alpha subclass of Proteobacteria and are only distantly related to other methane-oxidizing strains.

The methanotrophs have a lot of biotechnological potential and are important in the global methane cycle. In an experiment, methane-oxidizing bacteria were utilized to assess the specificity and efficiency of rRNA-targeted group-specific probes. Methanotroph group specific probes did not give a signal with samples from these enrichments, though a methanol dehydrogenase structural gene was detected. Enrichment on methane combined with the screening with the broad specific methanol dehydrogenase probe facilitated detection of novel methanotrophs that were not detected with the original suit of methanotroph group-specific probes.