Bin Zuo

The rise of sequencing technologies has greatly contributed to our knowledge of the microbiota and its role in animal health and production. However, many members of the microbiota have historically been considered “unculturable.” Culturomics can be utilized to bring these fastidious microbes into cultivation and can be used in conjunction with culture-independent methods to study the microbiota in a more comprehensive manner. This review paper details culturomics’ role in revolutionizing human, swine, and bovine microbiota research and how its use has greatly increased the bacterial repertoire. Additionally, it describes how culturomics can be applied to develop microbiota-derived therapeutics, such as next-generation probiotics, and to study the role of the microbiota. Finally, this review provides potential methods and considerations for designing future culturomics studies.

DNA extraction for downstream molecular diagnostic applications can be an expensive, time-consuming process. We devised a method to quickly extract total bacterial DNA from environmental samples based on the sodium hydroxide lysis of cells with or without capture by magnetic beads for subsequent PCR or quantitative PCR. The final DNA extraction method using NaOH is extremely low-cost and can be completed in as little as 10 min at room temperature with dilution, or the DNA can be further purified using silica-coated paramagnetic beads. NaOH extraction was effective for Gram-negative and Gram-positive bacteria in samples from air, soil, sewage, food, laboratory surfaces, and chicken cloacal swabs. The NaOH extraction method was comparable to commercial kits for extraction of DNA from pig fecal samples for 16S amplicon sequencing analyses. We demonstrated that an impinger and portable pump can efficiently capture bacteria from the air in poultry facilities for rapid NaOH extraction to quantify total bacteria and for detection of specific species using qPCR. The air sampling and NaOH extraction procedures are well suited for routine, high-throughput screening and for metagenomic analyses for specific pathogens, even in resource-limited situations.

DNA extraction for downstream molecular diagnostic applications can be an expensive, time-consuming process. We devised a method to quickly extract genomic DNA from environmental samples based on sodium hydroxide lysis of cells with or without capture by magnetic beads, for subsequent PCR or quantitative PCR. The final DNA extraction method using NaOH is extremely low-cost and can be completed in 10 minutes at room temperature. NaOH extraction was effective for Gram-negative and Gram-positive bacteria in samples from air, soil, sewage, food, laboratory surfaces, and chicken cloacal swabs. The NaOH extraction method was comparable to commercial kits for extraction of DNA from pig fecal samples for 16S amplicon sequencing analyses. We demonstrate that an impinger and portable pump can efficiently capture bacteria in poultry facilities for rapid DNA extraction for quantification of total bacteria and for detection of specific species using qPCR. The air sampling and NaOH extraction procedures are well-suited for routine, high throughput screening, and for metagenomic analyses for specific pathogens, even in resource-limited situations.

Journal of Animal Science and Technology (JAST) is a peer-reviewed, open access journal publishing original research, review articles and notes in all fields of animal science. Topics covered by the journal include: genetics and breeding, physiology, nutrition of monogastric animals, nutrition of ruminants, animal products (milk, meat, eggs and their by-products) and their processing, grasslands and roughages, livestock environment, animal biotechnology, animal behavior and welfare.

Background: The application of fecal microbiota transplantation (FMT) to improve swine growth performance has been sporadically studied. Most of these studies used a single microbiota source and thus the effect of donor characteristics on recipient pigs’ fecal microbiota development and growth performance is largely unknown. Results: In this study, we collected feces from six donors with heavy (H) or light (L) body weight and different ages (d 42, nursery; d 96, growing; and d 170, finisher) to evaluate their effects on the growth performance and fecal microbiota development of recipient pigs. Generally, recipients that received two doses of FMT from nursery and finisher stages donor at weaning (21 ± 2 days of age) inherited the donor’s growth pattern, while the pigs gavaged with grower stage material exerted a numerically greater weight gain than the control pigs regardless of donor BW. FMT from heavier donors (NH, GH, and FH) led to the recipients to have numerically increased growth compared to their lighter counterparts (NL, GL, and FL, respectively) throughout the growing and most finishing stages. This benefit could be attributed to the enrichment of ASV25 Faecalibacterium, ASV61 Faecalibacterium, ASV438 Coriobacteriaceae_unclassified, ASV144 Bulleidia, and ASV129 Oribacterium and decrease of ASV13 Escherichia during nursery stage. Fecal microbiota transplantation from growing and finishing donors influenced the microbial community significantly in recipient pigs during the nursery stage. FMT of older donors’ gut microbiota expedited recipients’ microbiota maturity on d 35 and 49, indicated by increased estimated microbiota ages. The age-associated bacterial taxa included ASV206 Ruminococcaceae, ASV211 Butyrivibrio, ASV416 Bacteroides, ASV2 Streptococcus, and ASV291 Veillonellaceae. The body weight differences between GL and GH pigs on d 104 were associated with the increased synthesis of the essential amino acid, lysine and methionine, mixed acid fermentation, expedited glycolysis, and sucrose/galactose degradation. Conclusions: Overall, our study provided insights into how donor age and body weight affect FMT outcomes regarding growth performance, microbiota community shifts, and lower GI tract metabolic potentials. This study also provided guidance to select qualified donors for future fecal microbiota transplantation.

To evaluate the effects of lactylate and Bacillus subtilis on growth performance, complete blood cell count, and microbial changes, 264 weaning pigs were assigned to four treatments (1) control (Con) basal diets that met the nutrient requirement for each phase, (2) 0.2% lactylate (LA), (3) 0.05% Bacillus subtilis strains mixtures (BM), or (4) the combination of LA and BM (LA+BM) added to the control basal diet at their respective inclusion rates in each of the three phases. Dietary lactylate tended to increase weight gain, significantly increased feed intake, and reduced fecal total E. coli and enterotoxigenic E. coli counts during Phase 1. Pigs fed Bacillus subtilis had a greater gain to feed ratio (G:F) during Phases 1 and 2. Pigs fed lactylate had an increased peripheral absolute neutrophil count on D14 but a decreased eosinophil percentage. Pigs fed Bacillus subtilis had an elevated peripheral total white blood cell count at study completion. The addition of lactylate increased microbiota richness, reduced E. coli, and increased Prevotella, Christensenellaceae, and Succinivibrio. Bacillus subtilis supplementation-enriched f_Ruminococcaceae_unclassified and S24-7_ unclassified had positive relationships with feed efficiency. Collectively, these findings suggested that lactylate can be added to diets to balance gut microbiota and improve growth performance during the early postweaning period. The combination of lactylate and Bacillus subtilis strains exerted a synergic effect on the growth performance of nursery pigs.