The Cervidae family has a wide distribution due to its adaptation to numerous ecological environments, which allows it to develop a diverse microbial community in its digestive tract. Recently, research has focused on the taxonomic composition and functionality of the intestinal and faecal microbiota of different cervid species worldwide, as well as their microbial diversity and variation under different associated factors such as age, sex, diet, distribution, and seasonal variation. In addition, there is special interest in knowing how cervids act as reservoirs of zoonotic pathogenic microorganisms, which represent a threat to public health. This review provides a synthesis of the growing field of microbiota determination in cervids worldwide, focusing on intestinal and faecal samples using 16S next-generation sequencing. It also documents factors influencing microbial diversity and composition, the microorganisms reported as pathogenic/zoonotic, and the perspectives regarding the conservation of these species. Knowing the interactions between bacteria and cervid health can drive management and conservation strategies for these species and help develop an understanding of their evolutionary history and the interaction with emerging disease-causing microorganisms.

The Mexican wolf (Canis lupus baileyi) was once distributed in southern United States and northern Mexico. It is an endangered subspecies detached from the gray wolf, and likely exemplifies one of the original migration waves of C. lupus into the new world. This is a canine whose individuals survive in specialized facilities, zoos, and museums as part of captive-breeding programs. In order to contribute to the improvement of the management of this species and favor its long-term conservation in Mexico, we aimed to evaluate the diversity and abundance of the fecal bacterial microbiota in two populations exposed to different types of diet: (1) Michilia (23° N, 104° W); kibble daily and raw meat sporadically, and (2) Ocotal (19° N, 99° W); raw meat daily and live animals periodically. Next generation sequencing (V3-V4 16S rRNA gene) by Illumina was implemented. The operational taxonomic units (OTUs) in Michilia resulted in 9 phyla, 19 classes, 34 orders, 61 families, 204 genera, and 316 species, while in Ocotal there were 12 phyla, 24 classes, 37 orders, 69 families, 232 genera, and 379 species. Higher estimated Chao1 richness, Shannon diversity, and core microbiota were observed in Ocotal. Differences (p < 0.05) between populations occurred according to the Bray–Curtis beta diversity index. In the Michilia, dominance of bacteria that degrade carbohydrates (Firmicutes, Lachnospiraceae, Blautia, Clostrodium, Eisenbergiella, Romboutsia, and Ruminococcus) was observed; they are abundant in kibble diets. In contrast, the Ocotal microbiota was dominated by protein-degrading bacteria (Fusobacteria, Fusobacteriaceae, and Fusobacteria), indicating a possible positive relation with a raw meat diet. The information generated in this study is fundamental to support the implementation of better management plans in the two populations considered here, as well as in different facilities of southern United States and Mexico, where this subspecies is kept in captivity for conservation purposes.

In Mexico, information on the bovine fecal microbiota (Bos taurus) is scarce. The present study describes the diversity and abundance of bacteria in fecal samples from rangeland bovines, collected in the Mapimi Biosphere Reserve in the central part of the Chihuahuan desert. Fecal samples were analysed using high-throughput next generation massive sequencing using V3-V4 16S rRNA on Illumina Miseq. A total of 17 phyla, 24 classes, 33 orders, 50 families, 281 genera, and 297 species were identified. Firmicutes and Verrucomicrobia were the most abundant phyla. The most abundant genera were Sporobacter, PAC000748_g (genera into the Ruminococcaceae family) and Eubacterium_g23. Three genera (Clostridium, Corynebacterium and Fusobacterium) and one species (Campylobacter fetus) potentially pathogenic bovine bacteria were registered. This information represents a bacteriological baseline for monitoring the grazing bovine intestinal health status, and to trace possible interactions with the fecal microbiota of native roaming wildlife in the area.

Urban pigeons (Columba livia) are widely distributed synanthropic birds closely associated with environments of intense human activity, raising interest in their role in urban microbial dynamics. Here, we characterized the fecal bacterial microbiota of urban pigeons from northern Mexico using 16S rRNA gene amplicon sequencing (V3–V4). A total of 1479 amplicon sequence variants (ASVs) were identified across five pooled samples. Alpha diversity varied among pools, with observed richness ranging from 228 to 514 ASVs. The bacterial community was dominated by Proteobacteria and Firmicutes, particularly Escherichia–Shigella and Enterococcus. PICRUSt2-based functional predictions suggested a predominance of predicted metabolic pathways related to carbohydrate degradation and energy acquisition. Conservative taxonomic screening identified 58 gut-associated taxa, including 15 bacteria previously reported in association with humans; however, only three (Clostridium perfringens, Enterococcus faecalis, and Proteus mirabilis) showed reported zoonotic associations, all at very low relative abundances (<0.07%). These findings indicate that the fecal bacterial communities characterized in this study were dominated by taxa commonly associated with the avian gastrointestinal tract, whereas taxa that could be conservatively linked to documented zoonotic reports represented only a minor fraction of the detected microbiota. Overall, the results contribute to a more ecologically informed understanding of urban pigeon-associated microbiota within a One Health framework.

Bovine-associated microbial communities play important roles in animal physiology, immune regulation, and mammary health. However, knowledge regarding bacterial populations associated with blood and milk remains limited in healthy dairy cattle exposed to different environmental conditions. In this study, we characterized and compared blood- and milk-associated bacterial communities from clinically healthy Holstein cows during summer and winter in an intensive commercial dairy production system located in northern Mexico using 16S rRNA metabarcoding. Significant differences in alpha and beta diversity metrics were observed according to sample type and season. Milk samples exhibited higher microbial richness and diversity than blood samples, and comparative analyses revealed significant differences in bacterial community composition between sample types and seasonal sampling periods. Bacterial communities were mainly dominated by Proteobacteria, Firmicutes, Actinobacteriota, and Bacteroidota. Differential abundance analyses identified genera associated with environmental exposure or opportunistic infections, including Staphylococcus, Streptococcus, Corynebacterium, Pseudomonas, and Acinetobacter. Overall, the observed bacterial community patterns varied according to sample type and seasonal environmental conditions, highlighting the complexity of host-associated microbial ecosystems in dairy cattle.