Exploration of mobile genetic elements in the ruminal microbiome of Nellore cattle.

Metagenomics has made it feasible to elucidate the intricacies of the ruminal microbiome and its role in the differentiation of animal production phenotypes of significance. The search for mobile genetic elements (MGEs) has taken on great importance, as they play a critical role in the transfer of genetic material between organisms. Furthermore, these elements serve a dual purpose by controlling populations through lytic bacteriophages, thereby maintaining ecological equilibrium and driving the evolutionary progress of host microorganisms. In this study, we aimed to identify the association between ruminal bacteria and their MGEs in Nellore cattle using physical chromosomal links through the Hi-C method. Shotgun metagenomic sequencing and the proximity ligation method ProxiMeta were used to analyze DNA, getting 1,713,111,307 bp, which gave rise to 107 metagenome-assembled genomes from rumen samples of four Nellore cows maintained on pasture. Taxonomic analysis revealed that most of the bacterial genomes belonged to the families Lachnospiraceae, Bacteroidaceae, Ruminococcaceae, Saccharofermentanaceae, and Treponemataceae and mostly encoded pathways for central carbon and other carbohydrate metabolisms. A total of 31 associations between host bacteria and MGE were identified, including 17 links to viruses and 14 links to plasmids. Additionally, we found 12 antibiotic resistance genes. To our knowledge, this is the first study in Brazilian cattle that connect MGEs with their microbial hosts. It identifies MGEs present in the rumen of pasture-raised Nellore cattle, offering insights that could advance biotechnology for food digestion and improve ruminant performance in production systems.

Designing a synthetic microbial community through genome metabolic modeling to enhance plant-microbe interaction.

BACKGROUND: Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynComs, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and carefully selecting compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed multi-genome metabolic modeling of 270 previously described metagenome-assembled genomes from Campos rupestres to design a synthetic microbial community to improve the yield of important crop plants. RESULTS: We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, exopolysaccharide production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our in-silico selection for the SymComs, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla. CONCLUSION: Overall, the study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.

Conservation of locomotor behavior in the golden hamster: effects of light cycle and a circadian period mutation.

Locomotor activity in rodents is restricted temporally by the animal' s circadian system. The relative stability of both the species-specific pattern and the amount of locomotor activity per cycle suggested that this behavior may be regulated by conservative mechanisms. In these experiments, the wheel-running behavior of golden hamsters carrying the circadian period mutation, tau, was analyzed in animals housed in a 24-h light:dark cycle (LD) and in constant dark (DD) conditions to determine which aspects of this behavior were conserved. In DD, apart from the change in period which defines the mutation, no main effects of allele combination were found in either average amount of activity, activity profile, or length of the activity phase. In LD, wild-type behavior did not differ from that in DD; however, heterozygous mutants exhibited early onsets of activity, significant fragmentation of both activity and rest, an increase in the duration of the active phase, and an overall decrease in the amount of activity. Despite these differences, the total amount of time spent on the wheel in LD or DD was the same for all environment/genotype combinations. The data show that a conservative mechanism that may influence daily patterns of locomotor behavior is related more to a drive to perform the behavior than the quantity or timing of the behavior itself.