Identification of microflora related to growth performance in pigs based on 16S rRNA sequence analyses

Knowledge graph-derived feed efficiency analysis via pig gut microbiota

Feed efficiency (FE) is essential for pig production, has been reported to be partially explained by gut microbiota. Despite an extensive body of research literature to this topic, studies regarding the regulation of feed efficiency by gut microbiota remain fragmented and mostly confined to disorganized or semi-structured unrestricted texts. Meanwhile, structured databases for microbiota analysis are available, yet they often lack a comprehensive understanding of the associated biological processes. Therefore, we have devised an approach to construct a comprehensive knowledge graph by combining unstructured textual intelligence with structured database information and applied it to investigate the relationship between pig gut microbes and FE. Firstly, we created the pgmReading knowledge base and the domain ontology of pig gut microbiota by annotating, extracting, and integrating semantic information from 157 scientific publications. Secondly, we created the pgmPubtator by utilizing PubTator to expand the semantic information related to microbiota. Thirdly, we created the pgmDatabase by mapping and combining the ADDAGMA, gutMGene, and KEGG databases based on the ontology. These three knowledge bases were integrated to form the Pig Gut Microbial Knowledge Graph (PGMKG). Additionally, we created five biological query cases to validate the performance of PGMKG. These cases not only allow us to identify microbes with the most significant impact on FE but also provide insights into the metabolites produced by these microbes and the associated metabolic pathways. This study introduces PGMKG, mapping key microbes in pig feed efficiency and guiding microbiota-targeted optimization.

Parabacteroides faecalis sp. nov. Isolated from Swine Faeces

A Gram-negative, obligate anaerobic, non-motile, non-spore-forming, rod-shaped bacterial strain designated AGMB00274^T was isolated from swine faeces. An 16S rRNA gene analysis indicated that strain AGMB00274^T belonged to the genus Parabacteroides, with the highest similarity to Parabacteroides johnsonii (P. johnsonii) DSM 18315^T (sequence similarity of 94.9%). The genome size of strain AGMB00274^T was 4,308,683 bp, with a DNA G+C content of 42.5 mol%. The biochemical analysis of strain AGMB00274^T showed that it was positive for gelatin hydrolysis and α-fucosidase, but negative for the acid production from D-glucose, D-mannitol, D-maltose, salicin, glycerol, D-cellobiose, D-mannose, D-melezitose, D-sorbitol, D-trehalose, and negative for α-arabinosidase, glutamic acid decarboxylase, and pyroglutamic acid arylamidase. The dominant cellular fatty acids (> 10%) of the isolate were anteiso-C_{15: 0} (23.2%), iso-C_{15: 0} (16.6%), C_{18: 1} ω9c (16.4%), summed feature 11 (iso-C_{17: 0} 3-OH and/or C_{18: 2} DMA) (12.5%), and C_{16: 0} (11.3%). The major respiratory quinones of strain AGMB00274^T were MK-9 (55.4%) and MK-10 (44.6%). The major polar lipid was phosphatidylethanolamine. Based on phylogenetic, genetic, physiological, and chemotaxonomic analyses, as a novel species of the genus Parabacteroides, strain AGMB00274^T was proposed with the name Parabacteroides faecalis sp. nov. The type strain used was AGMB00274^T (= KCTC 25286^T = GDMCC 1.2742^T).

Gut microbiota and growth performance of offspring are influenced by wet nurse in pigs using cross-fostering trial

BACKGROUND

Nursing mom can regulate the gut microbiome succession in offspring. However, it remains unclear whether these effects are long-term and what effect it has on the growth performance of piglets. This study aimed to develop a cross-fostering model of piglets and investigate the effect of maternal environment on gut microbiota, even the growth performance of the offspring, and if this effect could be maintained in the long term.

RESULTS

Four groups of piglets were generated as follows (n = 12): Duroc piglets nursed by their birth mom (Dd) or Yorkshire sows (Yd), Yorkshire piglets nursed by Duroc sows (Dy) or their birth mom (Yy). The study found that cross-fostering improved the growth performance of piglets for a long time. The gut microbiota of piglets was mainly determined by the breeds of nursing moms before weaning, and it was more and more influenced by their breeds after weaning, but the influence of birth mom breeds still existed. The linear discriminant analysis (LDA) effect size (LEfSe) analysis and Spearman correlation analysis showed that Sutterella, Butyricimonas and Alistipes, which were affected by nursing mom before weaning, had a strong positive correlation with the growth performance of piglets before weaning. Candidatus_Soleaferrea and Treponema, which were affected by both nursing mom and piglet breed after weaning, were significantly negatively correlated with the growth performance of piglets long after weaning.

CONCLUSION

Our results revealed that both the breeds of piglets and their birth moms influence the gut microbiota of piglets for a long time, even after weaning. Additionally, this effect might be related to the growth performance of piglets. © 2022 Society of Chemical Industry.

Dietary supplementation of squalene increases the growth performance of early-weaned piglets by improving gut microbiota, intestinal barrier, and blood antioxidant capacity

This study aimed to investigate the effects of dietary squalene (SQ) supplementation on the growth performance of early-weaned piglets. Twenty early-weaned piglets were randomly divided into two groups, the squalene group (SQ) and the control group (CON). The CON group was fed a basal diet, and the SQ group was fed a basal diet with 250 mg/kg squalene. The feeding period lasted 21 days. The results showed that SQ significantly increased the final body weight (FWB, P < 0.05), average daily gain (ADG, P < 0.05), and average daily feed intake (ADFI, P < 0.05) and significantly decreased the F/G ratio (feed intake/gain, P < 0.05) and diarrhea index (DI, P < 0.05). In terms of blood biochemical indicators, SQ significantly increased anti-inflammatory factors such as transforming growth factor-β (TGF-β, P < 0.001), interleukin-10 (IL-10, P < 0.001), and interferon-γ (IFN-γ, P < 0.01), and decreased pro-inflammatory factors such as tumor necrosis factor-α (TFN-α, P < 0.001) and interleukin-6 (IL-6, P < 0.001). Furthermore, SQ significantly increased blood antioxidant indexes (P < 0.001) such as superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), catalase (CAT), and total antioxidant capacity (T-AOC) and significantly decreased the level of malondialdehyde (MDA) (P < 0.001). The villus height (P < 0.001) and V/C ratio (villus height/crypt depth, P < 0.001) of the jejunum were significantly increased in the SQ group, while the crypt depth (P < 0.01) was decreased compared to the CON group. The intestinal permeability indexes, namely diamine oxidase (DAO), D-lactic acid (D-Lac), regenerative insulin-derived protein 3 (REG-3), and FITC-Dextran 4 (FD₄), significantly decreased the concentrations in the treatment group (P < 0.001), and the antioxidant indexes of the jejunum, such as SOD, GSH-Px, CAT, and MDA, were improved by adding SQ. The qPCR results showed that adding SQ could significantly increase the mRNA expression of jejunal tight-junction proteins, such as zonula occludens-1 (ZO-1, P < 0.001), Occludin (P < 0.001), Claudin (P < 0.001), glucagon-like peptide-2 (GLP-2, P < 0.001), and insulin-like growth factor-1 (IGF-1, P < 0.001). Then, we used Western blotting experiments to further confirm the qPCR results. In addition, it was found that adding SQ increased the abundance of beneficial bacteria such as Gemmiger (P < 0.01) and decreased the abundance of harmful bacteria such as Alloprevotella (P < 0.05), Desulfovibrio (P < 0.05), and Barnesiella (P < 0.05). It was interesting that there was a very close correlation among the fecal microbes, growth performance parameters, intestinal barrier, and blood biochemical indicators. In conclusion, the data suggest that SQ supplementation could effectively improve the growth performance of early-weaned piglets by improving the gut microbiota, intestinal barrier, and antioxidant capacity of the blood and jejunal mucosa.

Different creep compound feed formulations for new born piglets: influence on growth performance and health parameters

The aim of this study was to compare the influence of different compositions of creep compound feed (CCF) (C-I – control group; TG-II – a CCF containing wheat bran extruded and fermented with L. paracasei; TG-III – a creep compound feed containing sugar beet pulp) on the piglets' growth performance, blood parameters, fecal microbial profile and physicochemical characteristics. Moreover, the fecal volatile compound (VC) profile was analyzed as a possible chemical marker related to changes in the fecal microbial profile and physicochemical characteristics. A 21-day experiment was conducted using 1-day-old 300 Large White/Norwegian Landrace piglets. The highest body weight (at the 21st day) was found in piglets of the TG-III group, and both treated groups showed lower feed conversion ratios. At the end of the experiment, significantly higher lactobacillus counts in the feces of both treated groups were found, and a correlation between fecal textural hardness and the lactobacillus count was established (r = 0.475). Significant correlations of piglets' individual fecal VC with microbiological parameters and fecal pH were established [lactobacilli with 3-n-nonadecanol-1; enterobacteria with butyric acid &lt;2-methyl-&gt;; pentanoic acid, 4-methyl-; eicosene(E)-, etc.]. It can be concluded that local material could be successfully incorporated into CCF preparation without impairing animal metabolism.

Comparative Analyses of Antibiotic Resistance Genes in Jejunum Microbiota of Pigs in Different Areas

Antibiotic resistance genes (ARGs) are emerging environmental contaminants that threaten human and animal health. Intestinal microbiota may be an important ARGs repository, and intensive animal farming is a likely contributor to the environmental burden of ARGs. Using metagenomic sequencing, we investigated the structure, function, and drug resistance of the jejunal microbial community in Landrace (LA, Kunming), Saba (SB, Kunming), Dahe (DH, Qujing), and Diannan small-ear piglets (DS, Xishuangbanna) from different areas in Yunnan Province, China. Remarkable differences in jejunal microbial diversity among the different pig breeds, while the microbial composition of pig breeds in close areas tends to be similar. Functional analysis showed that there were abundant metabolic pathways and carbohydrate enzymes in all samples. In total, 32,487 ARGs were detected in all samples, which showed resistance to 38 categories of drugs. The abundance of ARGs in jejunum was not significantly different between LA and SB from the same area, but significantly different between DS, DH and LA or SB from different areas. Therefore, the abundance of ARGs was little affected by pig breeds and microorganism community structure, but it was closely related to geographical location. In addition, as a probiotic, Lactobacillus amylovorus is also an important ARGs producing bacterium. Our results revealed the antibiotic exposure and intestinal microbial resistance of farms in the study areas, which could provide basic knowledge and potential strategies for rational use of antibiotics and reducing the risk of ARGs transmission in animal husbandry.

Faecal microbiota transplantation alleviates early-life antibiotic-induced gut microbiota dysbiosis and mucosa injuries in a neonatal piglet model

Faecal microbiota transplantation (FMT) is a promising approach to modulate the gut microbiota. Gut microbiota dysbiosis caused by antibiotic administration is a universal problem. This study aimed to evaluate the effect of FMT on the dysbiosis of gut microbiota and metabolic profiles and injury of the intestinal barrier induced by antibiotics and used a neonatal piglet model. Neonatal piglets were administered ampicillin for 3 days, and antibiotic-induced dysbiosis was evaluated by the occurrence of diarrhoea and alteration of gut microbiota. Then, FMT was conducted for 3 days to rebuild the gut microbiota. High-throughput sequencing and a mass spectrometry platform were used for integrated microbiome-metabolome analysis. The results showed that antibiotics led to a decline in the diversity of gut microbiota. Furthermore, there was an increase in the relative abundance of potential pathogenic bacteria, such as Oscillibacter, Pseudomonas and Eubacterium, and an increase in the relative abundance of tetracycline resistance genes (tet genes). FMT restored the diversity and promoted the relative abundance of beneficial bacteria, such as Parabacteroides, Dorea and Parasutterella, while decreasing the relative abundance of tet genes. Untargeted metabolomics analysis found that alpha linolenic acid and linoleic acid metabolism were the key metabolic pathways utilized in the FMT group, and targeted metabolomics analysis further verified the variation in the associated metabolites arachidonic acid and conjugated linoleic acid. FMT also significantly enhanced the relative expression of tight junction (ZO-1, claudin-1 and occludin) and adherens junction (β-catenin, E-cadherin) proteins and anti-inflammatory cytokines (IL-10, TGF-β1) and reduced the production of proinflammatory cytokines (IL-6, IL-1β, TNF-α and IFN-γ) in the colon. FMT not only modulated the gut microbiota composition and microbial metabolism but also reduced the relative abundance of tet genes, improving the intestinal barrier function and inflammatory responses in antibiotic-treated piglets.

Effects of Partially Hydrolyzed Guar Gum Supplementation on the Fecal Microbiotas of Piglets

Probiotics and prebiotics have become viable alternatives of growth-promoting antimicrobials in animal production. Here, we tested partially hydrolyzed guar gum (PHGG) as a possible prebiotic for piglets in the commercial farm. Five hundred and ninety-four piglets were used for the experiments, with 293 given a normal pig feed (control), while the rest the feed plus 0.06% (w/w) of PHGG (PHGG). One and three months post-PHGG supplementation, fecal samples were collected from randomly selected 20 piglets in each group and analyzed for microbiota and organic acid concentrations. Notably, the abundance of Streptococcus, and unclassified Ruminococcaceae were lower (p < 0.05) in PHGG than in control, one-month post-supplementation. Lactobacillus and Prevotella were higher (p < 0.05), while Streptococcus was lower (p < 0.05), in PHGG than in control, three months post-supplementation. The concentrations of acetate, propionate, and butyrate were greater in PHGG than in control, three months post-supplementation. Finally, PHGG grew faster and had fewer deaths until slaughter time (p < 0.05), than control. We concluded that PHGG not only was an effective prebiotic to alter gut microbiota of weanling piglets but also can possibly promote body weight accretion and health.

Black Soldier Fly (Hermetia illucens) Larvae Meal Modulates Intestinal Morphology and Microbiota in Xuefeng Black-Bone Chickens

The addition of Hermetia illucens larvae meal (HILM) to the feed could contribute to particular antimicrobial and intestinal health in animal husbandry. This study was conducted to investigate the effects of HILM on intestinal morphology and microbial diversity in different intestinal segments of Xuefeng black-bone chickens. All of 432 birds (45 weeks old) were randomly assigned to four equal groups with six replicates and 18 hens in each replicate: (A) basal diet, (B) basal diet with 1% HILM, (C) basal diet with 3% HILM, and (D) basal diet with 5% HILM. The results showed that, compared with the basal diet group, the HILM supplement significantly increased the abundance-based coverage estimator (ACE) and Chao index in cecum (p < 0.05). Diet with 1% HILM significantly increased the villus height (VH) of the duodenum (p < 0.05) and cecum microbial diversity as represented by the Simpson index (p < 0.05). In particular, 1% HILM displayed a markedly increase in the genus unclassified Bacteroidales (cecum, p < 0.05). A basal diet with 3% HILM markedly increased the beneficial genus Romboutsia (jejunum, p < 0.05). Also, principal component analysis (PCA) cluster analysis showed that 3% of HILM was more individual than other groups (p < 0.05). However, 5% HILM decreased the VH and the ratio of villus height to crypt depth (VH/CD) of the jejunum and increased beneficial bacteria such as Staphylococcus (p < 0.05), which was regarded as pathogenetic genera. In conclusion, we found that HILM improved intestinal morphology and increased microbiological diversity and species abundance. Together, dietary supplementation of 1 or 3% HILM might benefit the intestinal morphology and intestinal microbiota of Xuefeng black-bone chicken. However, the addition of 5% HILM could decrease VH and the ratio of VH/CD of the jejunum and increased pathogenetic genera. HILM was an excellent protein substitute for Xuefeng black-bone chickens, which could meet the nutritional requirements under the condition of less feed. These results provide information for HILM meal as an alternative source of soybean meal in Xuefeng black-bone chickens’ feed.