Traditional methods for studying microbial communities have been limited due to difficulties in culturing and sequencing all microbial species. Recent advances in third-generation sequencing technologies, particularly PacBio’s high-fidelity (HiFi) sequencing, have significantly advanced metagenomics by providing accurate long-read sequences. This review explores the role of HiFi sequencing in overcoming the limitations of previous sequencing methods, including high error rates and fragmented assemblies. We discuss the benefits and applications of HiFi sequencing across various environments, such as the human gut and soil, which provides broader context for further exploration. Key studies are discussed to highlight HiFi sequencing’s ability to recover complete and coherent microbial genomes from complex microbiomes, showcasing its superior accuracy and continuity compared to other sequencing technologies. Additionally, we explore the potential applications of HiFi sequencing in quantitative microbial analysis, as well as the detection of single nucleotide variations (SNVs) and structural variations (SVs). PacBio HiFi sequencing is establishing a new benchmark in metagenomics, with the potential to significantly enhance our understanding of microbial ecology and drive forward advancements in both environmental and clinical applications.

The interaction between bacteria and fungi is one of the key interactions of microbial ecology, including mutualism, antagonism, and competition, which profoundly affects the balance and functions of animal microbial ecosystems. This article reviews the interactive dynamics of bacteria and fungi in more concerned microenvironments in animals, such as gut, rumen, and skin. Moreover, we summarize the molecular mechanisms and ecological functions of the interaction between bacteria and fungi. Three major bacterial–fungal interactions (mutualism, antagonism, and competition) are deeply discussed. Understanding of the interactions between bacteria and fungi allows us to understand, modulate, and maintain the community structure and functions. Furthermore, this summarization will provide a comprehensive perspective on animal production and veterinary medicine, as well as guide future research directions.

In piglets, the gut microbiota matures in a segment-specific manner during the nursing period, while fecal-based studies provide limited functional resolution across intestinal sites. We profiled the ileum using 16s rRNA gene sequencing and assessed segmental functions by shotgun metagenomics at selected ages. Ileal species richness and diversity were relatively stable across days. Lactobacillus were prominent from day 7, with stage-associated taxa including Lactobacillus johnsonii, Lactobacillus delbrueckii, Ligilactobacillus salivarius, and Limosilactobacillus pontis. Through metagenomic functional analysis, at 21 days, genes were enriched in butanoate metabolism, and Limosilactobacillus pontis as a potential probiotic played an important role in it. At day 28, metagenomic analysis indicated higher relative abundance in the ileum of pathways linked to cysteine and methionine metabolism and lysine biosynthesis, largely carried by Limosilactobacillus mucosae, Limosilactobacillus oris, and Limosilactobacillus pontis. These data describe the composition and function of the ileum in the intestines of piglets and indicate a differentiation period around day 21 to day 28.

Umami is a key determinant of pork flavor, but the association between the intestinal microbial community and umami differences remains unclear. Here, we used the taste-sensing electronic tongue system to divide the Duroc × Landrace × Yorkshire pigs into high, medium and low groups. We combined 16S rRNA gene and shotgun metagenomic sequencing to study the differences in the microbial community composition and functional genes. The results showed that the microorganisms in the cecum of different groups had a similar core microbial community. The Shannon diversity analysis showed that there were no significant differences among the different groups. The Bray–Curtis distance indicated that there were differences in the bacterial communities between the high umami group and the other two groups. The LEfSe analysis and Spearman correlation analysis revealed that the uncultured species CAG-632 sp900539185 maintained a high abundance in the high umami group and was significantly correlated with umami. Metagenomic functional analysis revealed distinct functional signatures among umami groups, with enrichment of genes related to carbohydrate transport and metabolism, butanoate and other short-chain fatty acid pathways, nitrogen utilisation, cell-surface structures, adhesion and RNA metabolism in high umami groups. These research findings indicate that the differences in the delicious flavor of pork are more likely to be associated with specific microbial species and the functional characteristics of the cecal microbial community, rather than the overall situation of the entire microbial community.

Unique skin microbial communities have been shaped by the harsh climatic conditions in high-altitude areas, such as intense ultraviolet radiation and low oxygen concentration. However, it is unknown whether high altitude contributes to shaping common microbiota inhabiting the skin across different mammals. The skin microbial communities of humans and horses living in high-altitude (Tibetan) and low-altitude areas were analyzed using full-length 16S rRNA sequencing technology. Alpha diversity differed between high- and low-altitude groups (p < 0.01). Skin microbial community composition also differed between high- and low-altitude areas (p < 0.05). Some of the common taxa present in the skin of humans and horses in high-altitude areas were identified as extreme microorganisms capable of adapting to the harsh high-altitude environment. Five bacterial taxa, including the genera Sphingomonas, Brevundimonas, and Kocuria, as well as the species Acinetobacter guillouiae and Arboricoccus pini, were significantly enriched (p < 0.01) on the skin of both humans and horses in high-altitude areas. Meanwhile, some taxa enriched on the skin surface at the same altitude showed preferences for mammalian species. Acinetobacter johnsonii, Anaerococcus nagyae, and Anaerococcus octavius were significantly enriched (p < 0.05) in the skin of humans at both high and low altitudes, whereas Acinetobacter pseudolwoffii and Armatimonas rosea, Archangium gephyra and Acinetobacter lwoffii were significantly enriched (p < 0.05) in the skin of horses at both high and low altitudes. In the network analyses, a positive correlation (p < 0.01) was shown between the skin taxa enriched in high-altitude areas and each other, while a negative correlation (p < 0.01) was found between the skin microorganisms enriched in high-altitude areas and those enriched in low-altitude areas. Overall, our findings indicate that high-altitude extreme environments drive convergent evolution of skin microbiota across mammals, reflecting the joint effects of environmental selection and host-related filtering on community assembly. This cross-species comparison provides a framework for understanding skin microbiome responses to extreme environments in plateau mammals.