Characterization of the Ruminal Microbiome of Water Buffaloes (Bubalus bubalis) Kept in Different Ecosystems in the Eastern Amazon

Simple Summary Maximizing ruminant production relies on enhancing rumen fermentation efficiency, necessitating an understanding of the ruminal microbiome and its environmental impacts. This study aimed to characterize buffalo microbiomes in the eastern Amazon across seasons and ecosystems. The study included three grazing systems: Baixo Amazonas (BA), Continente do Pará (CP), Ilha do Marajó (IM), and a confinement system: Tomé-Açu (TA). Seventy-one samples from male crossbred buffaloes were analyzed for ruminal microbial community structure, along with the compositions of their diets. Bacterial and Archaeal taxa were identified, with 61 genera recognized. Taxonomic composition similarities were observed across ecosystems. Twenty-three bacterial genera significantly differed between the confinement and other ecosystems. Among Archaea, abundances of Methanomicrobium and Methanosarcina varied between ecosystems. Diet (available or offered) exerted the most influence on the ruminal microbiota. This research provides insights into buffalo microbiomes in the Amazon, vital for optimizing ruminant production sustainably. Abstract Increasing the efficiency of rumen fermentation is one of the main ways to maximize the production of ruminants. It is therefore important to understand the ruminal microbiome, as well as environmental influences on that community. However, there are no studies that describe the ruminal microbiota in buffaloes in the Amazon. The objective of this study was to characterize the rumen microbiome of the water buffalo (Bubalus bubalis) in the eastern Amazon in the dry and rainy seasons in three grazing ecosystems: Baixo Amazonas (BA), Continente do Pará (CP), Ilha do Marajó (IM), and in a confinement system: Tomé-Açu (TA). Seventy-one crossbred male buffaloes (Murrah × Mediterranean) were used, aged between 24 and 36 months, with an average weight of 432 kg in the rainy season and 409 kg in the dry season, and fed on native or cultivated pastures. In the confinement system, the feed consisted of sorghum silage, soybean meal, wet sorghum premix, and commercial feed. Samples of the diet from each ecosystem were collected for bromatological analysis. The collections of ruminal content were carried out in slaughterhouses, with the rumen completely emptied and homogenized, the solid and liquid fractions separated, and the ruminal pH measured. DNA was extracted from the rumen samples, then sequenced using Restriction Enzyme Reduced Representation Sequencing. The taxonomic composition was largely similar between ecosystems. All 61 genera in the reference database were recognized, including members of the domains Bacteria and Archaea. The abundance of 23 bacterial genera differed significantly (p < 0.01) between the Tomé-Açu confinement and other ecosystems. Bacillus, Ruminococcus, and Bacteroides had lower abundance in samples from the Tomé-Açu system. Among the Archaea, the genus Methanomicrobium was less abundant in Tomé-Açu, while Methanosarcina was more abundant. There was a difference caused by all evaluated factors, but the diet (available or offered) was what most influenced the ruminal microbiota.