Fecal Microbiota and Its Correlation With Fatty Acids and Free Amino Acids Metabolism in Piglets After a Lactobacillus Strain Oral Administration

Comparative Analysis of Metabolic Dysfunctions Associated with Pristine and Aged Polyethylene Microplastic Exposure via the Liver-Gut Axis in Mice

The accumulation of plastic waste in the environment has raised widespread concern about the impact of microplastics (MPs) on human and environmental health, particularly regarding aged MPs. This study investigated the effects of subchronic dietary intake on pristine and aged polyethylene microplastics (PE-MPs) in C57BL/6J mice. Results revealed that both pristine and aged PE-MPs, at doses of 0.01 and 1 mg/day, induced plasma metabolic changes primarily associated with lipid metabolism and digestive processes. These alterations were reflected in the expression changes of proteins involved in unsaturated fatty acid pathways in the liver as well as a reduction in beneficial gut microbiota. Key contributors in the toxicity of aged PE-MPs included ATP-binding cassette transporters, gut bacteria alterations (notably Lactobacillus, Akkermansia, Parasutterella, and Turicibacter), and significantly altered proteins related to fatty acid elongation, such as acyl-CoA thioesterase enzyme family and elongation of very long chain fatty acid protein 5. These disruptions exacerbated lipid metabolism disorders, potentially contributing to metabolic diseases. Additionally, decreased levels of glutathione S-transferase A proteins, along with reduced hepatic glutathione and increased reactive oxygen species in both the small intestine and liver, suggested that aged PE-MPs aggravated hepatic and intestinal damage through oxidative stress. These findings indicated that aged PE-MPs caused more severe hepatic dysfunction and gut microbiota disruption. This effect was likely mediated by the transfer of fatty acids and signaling molecules through the gut-liver axis, ultimately leading to hepatic lipid metabolism disorders and oxidative stress.

Gut Metagenome Reveals the Microbiome Signatures in Tibetan and Black Pigs

The harsh conditions of the Qinghai-Tibet Plateau pose significant physiological challenges to local fauna, often resulting in gastrointestinal disorders. However, Tibetan pigs have exhibited remarkable adaptability to the high-altitude stress of the Tibetan Plateau, a phenomenon that remains not fully understood in terms of their gastrointestinal microbiota. This study collected 57 gastrointestinal tract samples from Tibetan pigs (n = 6) and plain black pigs (n = 6) with comparable genetic backgrounds. Samples from the stomach, jejunum, cecum, colon, and rectum, underwent comprehensive metagenomic analysis to elucidate the gut microbiota-related adaptive mechanisms in Tibetan pigs to the extreme high-altitude environment. A predominance of Pseudomonadota was observed within gut microbiome of Tibetan pigs. Significant differences in the microbial composition were also identified across the tested gastrointestinal segments, with 18 genera and 141 species exhibiting differential abundance. Genera such as Bifidobacterium, Megasphaera, Fusobacterium, and Mitsuokella were significantly more abundant in Tibetan pigs than in their lowland counterparts, suggesting specialized adaptations. Network analysis found greater complexity and modularity in the microbiota of Tibetan pigs compared to black pigs, indicating enhanced ecological stability and adaptability. Functional analysis revealed that the Tibetan pig microbiota was particularly enriched with bacterial species involved in metabolic pathways for propionate and butyrate, key short-chain fatty acids that support energy provision under low-oxygen conditions. The enzymatic profiles of Tibetan pigs, characterized by elevated levels of 4-hydroxybutyrate dehydrogenase and glutaconyl-CoA decarboxylase, highlighted a robust fatty acid metabolism and enhanced tricarboxylic acid cycle activity. In contrast, the gut microbiome of plain black pigs showed a reliance on the succinate pathway, with a reduced butyrate metabolism and lower metabolic flexibility. Taken together, these results demonstrate the crucial role of the gastrointestinal microbiota in the adaptation of Tibetan pigs to high-altitude environments by optimizing carbohydrate metabolism and short-chain fatty acid production for efficient energy utilization. This study not only highlights the metabolic benefits conferred by the gut microbiota of Tibetan pigs in extreme environments, but also advances our understanding of the adaptive gastrointestinal mechanisms in plateau-dwelling animals. These insights lay the foundation for exploring metabolic interventions to support health and performance in high-altitude conditions.

Fecal Microbiota Characteristics in Constipation-Predominant and Mixed-Type Irritable Bowel Syndrome

BACKGROUND

Irritable bowel syndrome (IBS) is a common condition that affects the lifestyle of patients. It is associated with significant changes in the composition of the gut microbiome, but the underlying microbial mechanisms remain to be fully understood. We study the fecal microbiome of patients with constipation-predominant IBS (IBS-C) and mixed-type IBS (IBS-M).

METHODS

We sequenced the V3 region of the 16S rRNA on the Ion Torrent PGM sequencing platform to study the microbiome.

RESULTS

In the patients with IBS-C and IBS-M, an increase in alpha diversity was found, compared to the healthy group, and differences in beta diversity were also noted. At the phylum level, both IBS subtypes showed an increase in the Firmicutes/Bacteroidetes ratio, as well as an increase in the abundance of Actinobacteria and Verrucomicrobiota. Changes in some types of bacteria were characteristic of only one of the IBS subtypes, while no statistically significant differences in the composition of the microbiome were detected between IBS-C and IBS-M.

CONCLUSIONS

This study was the first to demonstrate the association of Turicibacter sanguinis, Mitsuokella jalaludinii, Erysipelotrichaceae UCG-003, Senegalimassilia anaerobia, Corynebacterium jeikeium, Bacteroides faecichinchillae, Leuconostoc carnosum, and Parabacteroides merdae with IBS subtypes.

Bifidobacterium longum S3 alleviates loperamide-induced constipation by modulating intestinal acetic acid and stearic acid levels in mice

Constipation is a major gastrointestinal (GI) symptom worldwide, with diverse causes of formation, and requires effective and safe therapeutic measures. In the present study, we used loperamide hydrochloride to establish a constipation model and assessed the effect of Bifidobacterium on constipation and its possible mechanism of relief. The results showed that B. longum S3 exerted a constipation-relieving effect primarily by improving the gut microbiota, enriching genera including Lactobacillus, Alistipes, and Ruminococcaceae UCG-007, and decreasing the bacteria Lachnospiraceae NK4B4 group. These changes may thereby increase acetic acid and stearic acid (C18:0) levels, which significantly increase the expression levels of ZO-1 and MUC-2, repair intestinal barrier damage and reduce inflammation (IL-6). Furthermore, it also inhibited oxidative stress levels (SOD and CAT), decreased the expression of water channel proteins (AQP4 and AQP8), significantly elevated the Gas, 5-HT, PGE2, and Ach levels, and reduced nNOS and VIP levels to improve the intestinal luminal transit time and fecal water content. Collectively, these changes resulted in the alleviation of constipation.

Antibiotics and probiotics-induced effects on the total fatty acid composition of feces in a rat model

Fatty acids (FAs) play important roles as membrane components and signal transduction molecules. Changes in short chain FA (SCFA) composition are associated with gut microbiota modifications. However, the effect of bacteria-driven changes on the detailed FA spectrum has not been explored yet. We investigated the effect of antibiotics (ABx) and/or probiotics, in four treatment groups on rat stool FA composition. Principal component analysis indicated that the chromatogram profiles of the treatment groups differ, which was also observed at different time points. Linear mixed effects models showed that in the parameters compared (sampling times, treatments. and their interactions), both the weight percentage and the concentration of FAs were affected by ABx and probiotic administration. This study found that the gut microbiome defines trans and branched saturated FAs, most saturated FAs, and unsaturated FAs with less carbon atoms. These results are among the first ones to demonstrate the restoring effects of a probiotic mixture on a substantial part of the altered total FA spectrum, and also revealed a previously unknown relationship between gut bacteria and a larger group of FAs. These findings suggest that intestinal bacteria produce not only SCFAs but also other FAs that may affect the host's physiological processes.

A first characterization of the microbiota-resilience link in swine

BACKGROUND

The gut microbiome plays a crucial role in understanding complex biological mechanisms, including host resilience to stressors. Investigating the microbiota-resilience link in animals and plants holds relevance in addressing challenges like adaptation of agricultural species to a warming environment. This study aims to characterize the microbiota-resilience connection in swine. As resilience is not directly observable, we estimated it using four distinct indicators based on daily feed consumption variability, assuming animals with greater intake variation may face challenges in maintaining stable physiological status. These indicators were analyzed both as linear and categorical variables. In our first set of analyses, we explored the microbiota-resilience link using PERMANOVA, α-diversity analysis, and discriminant analysis. Additionally, we quantified the ratio of estimated microbiota variance to total phenotypic variance (microbiability). Finally, we conducted a Partial Least Squares-Discriminant Analysis (PLS-DA) to assess the classification performance of the microbiota with indicators expressed in classes.

RESULTS

This study offers four key insights. Firstly, among all indicators, two effectively captured resilience. Secondly, our analyses revealed robust relationship between microbial composition and resilience in terms of both composition and richness. We found decreased α-diversity in less-resilient animals, while specific amplicon sequence variants (ASVs) and KEGG pathways associated with inflammatory responses were negatively linked to resilience. Thirdly, considering resilience indicators in classes, we observed significant differences in microbial composition primarily in animals with lower resilience. Lastly, our study indicates that gut microbial composition can serve as a reliable biomarker for distinguishing individuals with lower resilience.

CONCLUSION

Our comprehensive analyses have highlighted the host-microbiota and resilience connection, contributing valuable insights to the existing scientific knowledge. The practical implications of PLS-DA and microbiability results are noteworthy. PLS-DA suggests that host-microbiota interactions could be utilized as biomarkers for monitoring resilience. Furthermore, the microbiability findings show that leveraging host-microbiota insights may improve the identification of resilient animals, supporting their adaptive capacity in response to changing environmental conditions. These practical implications offer promising avenues for enhancing animal well-being and adaptation strategies in the context of environmental challenges faced by livestock populations. Video Abstract.

Lactobacillus-driven feed fermentation regulates microbiota metabolism and reduces odor emission from the feces of pigs

IMPORTANCE

Our present study showed that dietary supplementation with feed fermented by Lactobacillus could promote the growth performance of pigs, regulate the microbiota, and inhibit the growth of harmful bacteria. It could prevent the accumulation of toxic substances and reduce odor emission from pig feces, thereby reducing environmental pollution. In addition, one key triumph of the present study was the isolation of Weissella cibaria ZWC030, and the strain could inhibit the production of skatole in vitro in our present results.

Probiotics alleviate constipation and inflammation in late gestating and lactating sows

Constipation and systemic inflammation are common in late pregnant and lactating sows, which cause health problems like uteritis, mastitis, dystocia, or even stillbirth, further influencing piglets' survival and growth. Probiotic supplementation can improve such issues, but the beneficial mechanism of relieving constipation and enhancing gut motility remains underexplored. This study aimed to investigate the effects and mechanism of probiotic supplementation in drinking water to late pregnant sows on constipation, inflammation, and piglets' growth performance. Seventy-four sows were randomly allocated to probiotic (n = 36) and control (n = 38) groups. Probiotic treatment significantly relieved sow constipation, enhanced serum IL-4 and IL-10 levels while reducing serum IL-1β, IL-12p40, and TNF-α levels, and increased piglet daily gain and weaning weight. Furthermore, probiotic administration reshaped the sow gut bacteriome and phageome structure/diversity, accompanied by increases in some potentially beneficial bacteria. At 113 days of gestation, the probiotic group was enriched in several gut microbial bioactive metabolites, multiple carbohydrate-active enzymes that degrade pectin and starch, fecal butyrate and acetate, and some serum metabolites involved in vitamin and amino acid metabolism. Our integrated correlation network analysis revealed that the alleviation of constipation and inflammation was associated with changes in the sow gut bacteriome, phageome, bioactive metabolic potential, and metabolism.

Endogenous chitinase might lead to differences in growth performance and intestinal health of piglets fed different levels of black soldier fly larva meal

This study aimed to investigate the effects of different levels of black soldier fly (BSF) replacing soybean meal (SBM) in diets on the performance and health condition of piglets. A total of 180 weaned piglets were allocated into 5 treatments: BSF0 (corn-soybean meal basal diet), BSF25 (BSF replacing 25% SBM), BSF50 (BSF replacing 50% SBM), BSF75 (BSF replacing 75% SBM) and BSF100 (BSF replacing 100% SBM). During the whole period, in comparison with BSF0, average daily gain (ADG) and average daily feed intake increased in the BSF25 and BSF50 groups, whereas ADG decreased in the BSF75 and BSF100 groups (P < 0.05). The result of quadratic fitting curve showed that piglets exhibited the highest ADG when BSF replaced around 20% SBM. Compared with BSF0, organic matter and dry matter digestibility improved in the BSF25 group, whereas ether extract digestibility decreased in the BSF100 group (P < 0.05). In comparison with BSF0, piglets from the BSF25 group showed a higher duodenal ratio of villus height to crypt depth, increased jejunal sucrase activity, serum neuropeptide Y and ghrelin levels, elevated ileal immunoglobulin (Ig) A, IgG and IgM contents and a lower leptin level, and piglets from the BSF100 group exhibited an increased relative weight of kidney (P < 0.05). However, no significant differences were observed in the expression level of tight junction proteins and chitin-degrading enzyme. Additionally, compared with BSF0, the abundance of short chain fatty acid producing bacteria such as Ruminococcaceae, Faecalibacterium and Butyricicoccus increased, and potential pathogenic bacteria decreased in piglets from the BSF25 group, whereas piglets from the BSF100 group had a greater abundance of harmful bacteria. In conclusion, BSF replacing 25% SBM in diets could improve digestive parameters, immune function and intestinal microbiota, and thus improved growth performance of piglets. However, BSF replacing 100% SBM showed an adverse effect on piglet performance, and the reason might be related to the limited amount of chitin-degrading enzyme.

β-mannanase supplementation in diets reduced in 85 kcal metabolizable energy/kg containing xylanase-phytase improves gain to feed ratio, nutrient usage, and backfat thickness in finisher pigs

This study aimed to assess the effects of β-mannanase supplementation in metabolizable energy (ME)-reduced diets containing xylanase-phytase on performance, fecal score, blood biochemical and immunological profile, apparent total tract digestibility (ATTD), digesta passage rate, fecal microbiome, carcass traits and meat quality in finisher pigs (n = 40 entire male hybrid, 26.0 ± 0.9 kg) randomly assigned to 1 of 4 dietary treatments: a control diet containing isolated phytase and xylanase valued at 40 kcal of ME/kg (CD0), CD0 + β-mannanase (0.3 g/kg valued at 30 kcal of ME/kg) (CD70), CD0 + β-mannanase (0.3 g/kg valued at 45 kcal of ME/kg) (CD85), and CD0 + β-mannanase (0.3 g/kg valued at 60 kcal of ME/kg) (CD100), with 10 pen replicates. Pigs fed CD0 diet showed (P = 0.002) greater ADFI. However, pigs fed CD0 diet showed (P = 0.009) lower G:F than those provided CD70 or CD85 diets. A greater (P &lt; 0.001) superoxide dismutase concentration was observed in pigs fed CD70 diet. Pigs fed CD85 diet showed (P = 0.002) greater digestible protein than pigs fed CD0 or CD100 diets. Pigs fed CD70 diet showed an increase of 11.3% in digestible protein than those fed CD0 diet. In addition, greater (P &lt; 0.001) digestible energy was observed in pigs fed CD85 diet. Pigs fed CD0 or CD100 diets showed greater (P &lt; 0.05) Firmicutes:Bacteroidota ratio than those fed CD85 diet. The Muribaculaceae was more abundant (P = 0.030) in pigs fed CD70 diet than in those fed CD0 diet. The Prevotella was more abundant (P = 0.045) in pigs fed CD85 diet than in those fed CD100 diet. In conclusion, β-mannanase supplementation in diets containing xylanase-phytase allows reducing 85 kcal of ME/kg because it improves gain to feed ratio, energy and protein usage, and backfat thickness without metabolic and intestinal ecosystem disorders in finisher pigs.

Effects of Exposure to Low Zearalenone Concentrations Close to the EU Recommended Value on Weaned Piglets’ Colon

Pigs are the most sensitive animal to zearalenone (ZEN) contamination, especially after weaning, with acute deleterious effects on different health parameters. Although recommendations not to exceed 100 µg/kg in piglets feed exists (2006/576/EC), there are no clear regulations concerning the maximum limit in feed for piglets, which means that more investigations are necessary to establish a guidance value. Due to these reasons, the present study aims to investigate if ZEN, at a concentration lower than the EC recommendation for piglets, might affect the microbiota or induce changes in SCFA synthesis and can trigger modifications of nutritional, physiological, and immunological markers in the colon (intestinal integrity through junction protein analysis and local immunity through IgA production). Consequently, the effect of two concentrations of zearalenone were tested, one below the limit recommended by the EC (75 µg/kg) and a higher one (290 µg/kg) for comparison reasons. Although exposure to contaminated feed with 75 µg ZEN/kg feed did not significantly affect the observed parameters, the 290 µg/kg feed altered several microbiota population abundances and the secretory IgA levels. The obtained results contribute to a better understanding of the adverse effects that ZEN can have in the colon of young pigs in a dose-dependent manner.

Avenanthramide Improves Colonic Damage Induced by Food Allergies in Mice through Altering Gut Microbiota and Regulating Hsp70-NF-κB Signaling

Food allergies can cause intestinal damage that can exacerbate allergic symptoms, and gut microbiota have been shown to influence allergic development. This study was intended to investigate the effects of Avenanthramide (AVA) on colonic damage induced by food allergy and its mechanism. In Exp. 1, AVA administrations alleviated colonic inflammation in mice challenged with ovalbumin, as shown by decreased concentrations of TNF-α, IL-25 and IL-33. Additionally, the AVA supplementations improved intestinal barrier damage by elevating occludin, ZO-1 and claudin-1 levels. Moreover, AVA inhibited NF-κB phosphorylation and enhanced heat shock protein 70 (Hsp70) expression in the colon. In Exp. 2, apoptozole as a Hsp70 inhibitor was used to explore the Hsp70-NF-κB signaling contribution to AVA function. The AVA additions increased the productions of acetate and butyrate, but decreased propionate. Notably, AVA reduced the colonic abundance of propionate-producing microbes such as Muribaculaceae, but elevated butyrate-producing microbes including Roseburia, Blautia, and Lachnospiraceae_NK4A136_group. Microbial alteration could be responsible for the increased butyrate, and thus the up-regulated Hsp70. However, apoptozole treatment eliminated the effects of AVA. Our study revealed that AVA improved colonic injury and inflammation induced by food allergies, and this mechanism may be mediated by the increased microbial-derived butyrate and involved in the Hsp70-NF-κB signaling.

Lactobacillus plantarum ZJUIDS14 alleviates non-alcoholic fatty liver disease in mice in association with modulation in the gut microbiota

This present study was designed to explore the protective role of Lactobacillus plantarum ZJUIDS14 against Non-alcoholic Fatty Liver Disease (NAFLD) in a high-fat-diet (HFD)-induced C57BL/6 mice model. The probiotic (10⁹ CFU/every other day) was administered by oral gavage for 12 weeks. We found that L. plantarum ZJUIDS14 intervention significantly alleviated HFD related hepatic steatosis, liver damage, insulin resistance, and increased hepatic expression of peroxisome proliferator activated receptor α (PPAR-α) while stimulating the activation of AMP-activated protein kinase (AMPK). Furthermore, L. plantarum ZJUIDS14 improved mitochondrial function as reflected by an increase in dynamin related protein 1 (DRP1) and a decrease of proteins associated with oxidative phosphorylation (OXPHOS) after the treatment. Additionally, mice from the L. plantarum ZJUIDS14 group had a restored intestinal flora and homeostasis involving Coprostanoligenes group, Ruminococcaceae UCG-014, Allobaculum, Ruminiclostridium 1, and Roseburia. Meanwhile, these five genera exhibited a significant (negative or positive) association with ileum inflammation mRNA levels and SCFA contents, by Spearman's correlation analysis. In general, our data demonstrated that L. plantarum ZJUIDS14 mitigates hepatic steatosis and liver damage induced by HFD. Specifically, they strengthened the integrity of the intestinal barrier, regulated gut microbiota, and improved mitochondrial function. Our data provide an experimental basis for L. plantarum ZJUIDS14 as a promising candidate to prevent NAFLD.

Limosilactobacillus reuteri Regulating Intestinal Function: A Review

Probiotics have extensive use in daily life, due to the function of the changing intestinal metabolism and material conversion processes, wherein they remodel the intestinal microbiota, regulate the intestinal function and affect the organism’s health. Limosilactobacillus reuteri (L. reuteri), originally discovered in breast milk and currently reported to be present within the gut of almost all vertebrates and mammals, is an intestinal probiotic with prebiotic efficacy. Most L. reuteri have good intestinal colonization and bacteriocin secretion abilities, which can increase the expression of the mucin (mucoprotein) genes 2 MUC2 and MUC13, which in turn promote the development and maturation of intestinal organoids, and augment mucin secretion. In enteritis patients, L. reuteri downregulates α Tumor necrosis factor-α, (TNF-α), Interleukin-6 (IL-6), IL-8, and IL-12 expression to attenuate inflammation. It also induces the host’s production of immunoglobulin A (IGA), which manipulates the intestinal microbial community, inhibiting the growth of pathogens. L. reuteri has been widely used in daily life. with in-depth studies having been conducted on the prebiotic effects of L. reuteri. However, the complexity of its application in a clinical setting is still unclear because the pathogenesis of various diseases still requires a large amount of data and theoretical support.

Spraying compound probiotics improves growth performance and immunity and modulates gut microbiota and blood metabolites of suckling piglets

One factor that shapes the establishment of early neonatal intestinal microbiota is environmental microbial exposure, and probiotic application has been shown to promote health and growth of piglets. Thus, this study hypothesized that environmental probiotic application in early days of life would be beneficial to newborn piglets. This study aimed to investigate the effect of spraying a compound probiotic fermented liquid (CPFL) into the living environment of piglets on their early growth performance and immunity. This work included 68 piglets, which were randomized into probiotic and control groups. Blood and fecal samples were collected at 0, 3, 7, 14, and 21 days of age. Spraying CPFL significantly reshaped the microbiota composition of the delivery room environment, increased piglets' daily weight gain and weaning weight (P<0.001), and modulated piglets' serum cytokine levels (increases in IgA, IgG, and IL-10; decrease in IFN-γ; P<0.05 in each case) in piglets. Additionally, spraying CPFL during early days of life modified piglets' gut microbiota structure and diversity, increased the abundance of some potentially beneficial bacteria (such as Bacteroides uniformis, Butyricimonas virosa, Parabacteroides distasonis, and Phascolarctobacterium succinatutens) and decreased the abundance of Escherichia coli (P<0.05). Interestingly, CPFL application also significantly enhanced the gut microbial bioactive potential and levels of several serum metabolites involved in the metabolism of vitamins (B2, B3, B6, and E), medium/long-chain fatty acids (caproic, tetradecanoic, and peptadecanoic acids), and dicarboxylic acids (azelaic and sebacic acids). Our study demonstrated that spraying CPFL significantly could improve piglets' growth performance and immunity, and the beneficial effects are associated with changes in the gut microbiota and host metabolism. Our study has provided novel data for future development of probiotic-based health-promoting strategies and expanded our knowledge of probiotic application in animal husbandry.

Lactobacillus reuteri improves the development and maturation of fecal microbiota in piglets through mother-to-infant microbe and metabolite vertical transmission

BACKGROUND

The immature neonatal fecal microbiota substantially impacts the development of gut health and greatly increases the risk of disease. Developing effective strategies to modulate the development of neonatal fecal microbiota has great significance. Herein, we investigated whether the maternal dietary supplementation and oral administration of Lactobacillus reuteri could effectively promote the development and maturation of the fecal microbiome in piglets from birth to weaning.

RESULTS

Metagenomic analysis of colostrum showed that maternal dietary L. reuteri supplementation influenced the overall microbiota composition, decreased the abundance of the phylum Proteobacteria and increased that of the species Bifidobacterium choerinum. KEGG pathway analysis revealed that maternal L. reuteri supplementation enriched the lysine biosynthesis and glycolysis/gluconeogenesis pathways and downregulated the bacterial invasion of epithelial cells in the colostrum. In addition, L. reuteri supplementation significantly altered the metabolite features and modules in umbilical cord blood serum based on metabolomics. Further, a significant covariation was observed between these differential metabolites and the species in colostrum. Maternal dietary L. reuteri supplementation also significantly influenced the microbiota composition and increased the meconium abundance of beneficial bacteria (such as Romboutsia, Lactobacillus, Blautia, Butyricicoccus, and Ruminococcus), some of which were markedly associated with several differential metabolites in umbilical cord blood serum between two groups. Notably, both the maternal dietary supplementation and oral intake of L. reuteri had strong impacts on the overall microbial composition and maturation of fecal microbiota in piglets during early life, and these effects were dependent on the growth stage. Oral administration of L. reuteri promoted diarrhea resistance in neonates, while maternal supplementation of L. reuteri enhanced the abilities of antioxidants and decreased inflammation. Moreover, the administration of L. reuteri via both methods in combination improved the growth performances of piglets.

CONCLUSION

Overall, our data demonstrated that L. reuteri had the ability to modulate the composition of fecal microbiota in newborn piglets by influencing the microbial community and functional composition in the colostrum and by altering several key metabolites in the umbilical cord blood serum. Also, both the maternal dietary supplementation and oral administration of L. reuteri effectively promoted the development and maturation of the fecal microbiome in piglets during early life. Both the maternal dietary supplementation and oral administration of L. reuteri in combination optimized the growth performances of piglets. Video Abstract.

TangNaiKang, herbal formulation, alleviates obesity in diabetic SHR/cp rats through modulation of gut microbiota and related metabolic functions

CONTEXT

Tangnaikang (TNK) is a Chinese herbal formulation that has lipid-lowering effects, but its effect on reducing obesity has not been studied.

OBJECTIVE

To observe the effect of TNK on obesity and explore its effect on gut microbiota of obese rats.

MATERIALS AND METHODS

The SHR/NDmcr-cp rats were divided into three groups: (1) 3.24 g/kg TNK (High TNK), (2) 1.62 g/kg TNK (Low TNK), and (3) an untreated control (CON). Wistar-Kyoto rats were used as normal controls (WKY). After 8 weeks of TNK oral administration, body weight, abdominal circumference, triglycerides (TC) and total cholesterol (CHO) were measured. Gut microbiota diversity was studied by 16S rDNA sequencing, and metagenomes analysis was conducted to determine alteration in functional gene expression.

RESULTS

The body weight (496.60 ± 6.0 g vs. 523.40 ± 5.6 g), abdomen circumference (24.00 ± 0.11 cm vs. 24.87 ± 0.25 cm), TC (3.04 ± 0.16 mmol/L vs. 4.97 ± 0.21 mmol/L), CHO (2.42 ± 0.15 mmol/L vs. 2.84 ± 0.09 mmol/L) of rats in the High TNK group were decreased significantly (all p < 0.05). TNK administration regulates intestinal flora, up-regulates Eisenbergiella and down-regulates Clostridium_sensu_stricto_1, which is beneficial to the production of short-chain fatty acids (SCFAs). Metagenomes analysis shows that TNK is closely related to the fatty acid synthesis pathway.

DISCUSSION AND CONCLUSIONS

TNK can regulate gut microbiota to reduce obesity, which may be related to fatty acid metabolism. Our research supports the clinical application of TNK preparation and provides a new perspective for the treatment of obesity.

Effect of feeding raw potato starch on the composition dynamics of the piglet intestinal microbiome

OBJECTIVE

Raw potato starch (RPS) is resistant to digestion, escapes absorption, and is metabolized by intestinal microflora in the large intestine and acts as their energy source. In this study, we compared the effect of different concentrations of RPS on the intestinal bacterial community of weaned piglets.

METHODS

Male weaned piglets (25-days-old, 7.03±0.49 kg) were either fed a corn/soybean-based control diet (CON, n = 6) or two treatment diets supplemented with 5% RPS (RPS5, n = 4) or 10% RPS (RPS10, n = 4) for 20 days and their fecal samples were collected. The day 0 and 20 samples were analyzed using a 16S rRNA gene sequencing technology, followed by total genomic DNA extraction, library construction, and high-throughput sequencing. After statistical analysis, five phyla and 45 genera accounting for over 0.5% of the reads in any of the three groups were further analyzed. Furthermore, short-chain fatty acids (SCFAs) in the day 20 fecal samples were analyzed using gas chromatography.

RESULTS

Significant changes were not observed in the bacterial composition at the phylum level even after 20 d post feeding (dpf); however, the abundance of Intestinimonas and Barnesiella decreased in both RPS treatment groups compared to the CON group. Consumption of 5% RPS increased the abundance of Roseburia (p<0.05) and decreased the abundance of Clostridium (p<0.01) and Mediterraneibacter (p< 0.05). In contrast, consumption of 10% RPS increased the abundance of Olsenella (p<0.05) and decreased the abundance of Campylobacter (p<0.05), Kineothrix (p<0.05), Paraprevotella (p<0.05), and Vallitalea (p<0.05). Additionally, acetate (p<0.01), butyrate (p<0.05), valerate (p = 0.01), and total SCFAs (p = 0.01) were upregulated in the RPS5 treatment group.

CONCLUSION

Feeding 5% RPS altered bacterial community composition and promoted gut health in weaned piglets. Thus, resistant starch as a feed additive may prevent diarrhea in piglets during weaning.

Intestinal microbial composition changes induced by Lactobacillus plantarum GBL 16, 17 fermented feed and intestinal immune homeostasis regulation in pigs

In this study, Rubus coreanus (R. coreanus) byproducts with high polyphenol content were fermented with R. coreanus-derived lactic acid bacteria (Lactobacillus plantarum GBL 16 and 17). Then the effect of R. coreanus-derived lactic acid bacteria fermented feed (RC-LAB fermented feed) with probiotics (Bacillus subtills, Aspergillus oryzae, Yeast) as a feed additive for pigs on the composition of intestinal microbes and the regulation of intestinal immune homeostasis was investigated. Seventy-two finishing Berkshire pigs were randomly allotted to four different treatment groups and 18 replicates. RC-LAB fermented feed with probiotics increased the genera Lactobacillus, Streptococcus, Mitsuokella, Prevotella, Bacteroides spp., Roseburia spp., and Faecalibacterium prausnitzii, which are beneficial bacteria of the digestive tract of pigs. Also, RC-LAB fermented feed with probiotics decreased the genera Clostridium, Terrisporobacter, Romboutsia, Kandleria, Megasphaera and Escherichia, which are harmful bacteria. In particular, the relative abundance of the genera Lactobacillus and Streptococcus increased by an average of 8.51% and 4.68% in the treatment groups and the classes Clostridia and genera Escherichia decreased by an average of 27.05% and 2.85% in the treatment groups. In mesenteric lymph nodes (MLN) and spleens, the mRNA expression of transcription factors and cytokines in Th1 and Treg cells increased and the mRNA expression of Th2 and Th17 transcription factors and cytokines decreased, indicating a regulatory effect on intestinal immune homeostasis. RC-LAB fermented feed regulates gut immune homeostasis by influencing the composition of beneficial and detrimental microorganisms in the gut and regulating the balance of Th1/Th2 and Th17/Treg cells.

Lactobacillus (LA-1) and butyrate inhibit osteoarthritis by controlling autophagy and inflammatory cell death of chondrocytes

Osteoarthritis (OA) reduces the quality of life as a result of the pain caused by continuous joint destruction. Inactivated Lactobacillus (LA-1) ameliorated osteoarthritis and protected cartilage by modulating inflammation. In this study, we evaluated the mechanism by which live LA-1 ameliorated OA. To investigate the effect of live LA-1 on OA progression, we administered LA-1 into monosodium iodoacetate (MIA)-induced OA animals. The pain threshold, cartilage damage, and inflammation of the joint synovial membrane were improved by live LA-1. Furthermore, the analysis of intestinal tissues and feces in the disease model has been shown to affect the systems of the intestinal system and improve the microbiome environment. Interestingly, inflammation of the intestinal tissue was reduced, and the intestinal microbiome was altered by live LA-1. Live LA-1 administration led to an increase in the level of Faecalibacterium which is a short-chain fatty acid (SCFA) butyrate-producing bacteria. The daily supply of butyrate, a bacterial SCFA, showed a tendency to decrease necroptosis, a type of abnormal cell death, by inducing autophagy and reversing impaired autophagy by the inflammatory environment. These results suggest that OA is modulated by changes in the gut microbiome, suggesting that activation of autophagy can reduce aberrant cell death. In summary, live LA-1 or butyrate ameliorates OA progression by modulating the gut environment and autophagic flux. Our findings suggest the regulation of the gut microenvironment as a therapeutic target for OA.

Effect of Lactobacillus reuteri S5 Intervention on Intestinal Microbiota Composition of Chickens Challenged with Salmonella enteritidis

To understand the mechanism of lactic acid bacteria against Salmonella enteritidis infection; we examined how lactic acid bacteria regulated the intestinal microbiota to resist infection by pathogenic bacteria. The probiotic strain Lactobacillus reuteri S5 was used to construct an animal model of S. enteritidis infected broilers. A high-throughput sequencing technology was used to analyze the regulatory effects of L. reuteri S5 on the structure of the intestinal microbiota of broilers infected with S. enteritidis; and to examine the possible defense mechanism they used. Our results showed that the administration of L. reuteri S5 reduced colonization of S. enteritidis (p < 0.05), decreased intestinal permeability (p < 0.05), and reduced the bacterial displacement likely due by S. enteritidis colonization (p < 0.05), suggesting some enhancement of the intestinal barrier function. Furthermore, L. reuteri S5 increased the number of operational taxonomic units (OTUs) in the chicken cecal microflora and the relative abundance of Lactobacillaceae and decreased the relative abundance of Enterobacteriaceae. These results suggest that the lactic acid bacterium L. reuteri S5 protected the intestinal microbiota of chickens against S. enteritidis infection.

Gut Microbiota Composition and Diversity in Different Commercial Swine Breeds in Early and Finishing Growth Stages

The gut microbiota affects the metabolism, health and growth rate of pigs. Understanding the characteristics of gut microbiota of different pig breeds at each growth stage will enable the design of individualized feeding strategies. The present study aimed to compare the growth curves and development patterns of pigs of three different breeds (Duroc, Landrace and Yorkshire) using the mathematical models Gompertz, Logistic, Von Bertalanffy and Richards. For Duroc pigs, the Gompertz model showed the highest prediction accuracy (R2 = 0.9974). In contrast, the best models for Landrace and Yorkshire pigs were Richards (R2 = 0.9986) and Von Bertalanffy (R2 = 0.9977), respectively. Path analysis showed that body length (path coefficient  =  0.507) and chest circumference (path coefficient  =  0.532) contributed more significantly to the body weight of pigs at the early growth stage, while hip circumference (path coefficient  =  0.312) had a greater influence on pig body weight in the late growth stage. Moreover, the composition of the gut microbiota of pigs at two growth stages (60 kg of body weight in the early growth stage and 120 kg in the finishing stage) was studied using 16S rRNA sequencing technology. Variations in gut microbiota composition of pigs at different growth stages were observed. KEGG pathway enrichment analysis of annotated metagenomes revealed that protein synthesis and amino acid metabolism pathways were significantly enriched in pigs at the early growth stage, which may be related to nutritional requirements of pigs during this stage. This study confirmed longitudinal variation in the gut microbiota of pigs pertaining to age as well as lateral variation related to pig breed. The present findings expand the current understanding of the variations in swine gut microbiota during production stages.

The Responses of Lactobacillus reuteri LR1 or Antibiotic on Intestinal Barrier Function and Microbiota in the Cecum of Pigs

This study aimed to investigate responses of the Lactobacillus reuteri or an antibiotic on cecal microbiota and intestinal barrier function in different stages of pigs. A total of 144 weaned pigs (Duroc × Landrace × Yorkshire, 21 days of age) were randomly assigned to the control group (CON, fed with a basal diet), the antibiotic group (AO, fed with basal diet plus 100 mg/kg olaquindox and 75 mg/kg aureomycin), and the L. reuteri group (LR, fed with the basal diet + 5 × 10¹⁰ CFU/kg L. reuteri LR1) throughout the 164-d experiment. A total of 45 cecal content samples (5 samples per group) from different periods (14th, 42th, and 164th days) were collected for 16S rRNA gene amplification. The results revealed that although LR and AO did not change the diversity of cecal microbiota in pigs, the abundance of some bacteria at the genus level was changed with age. The proportion of Lactobacillus was increased by LR in early life, whereas it was decreased by AO compared with the control group. The relative abundance of Ruminococcaceae was increased along with age. In addition, the gas chromatography results showed that age, not AO or LR, has significant effects on the concentrations of SCFAs in the cecum of pigs (P < 0.05). However, the mRNA expression of tight junction proteins zonula occluden-1 (ZO-1) and occludin were increased by AO in the cecum of pigs on day 14, while LR increased the mRNA expression of intestinal barrier-related proteins ZO-1, occludin, mucin-1, mucin-2, PG1-5, and pBD2 in the cecum of pigs on days 14 and 164 (P < 0.05). In conclusion, LR and AO have different effects on the intestinal barrier function of the cecum, and neither LR nor AO damaged the intestinal barrier function of pig cecum. In addition, LR and AO have little effects on cecal microflora in different stages of the pigs. The microflora and their metabolite SCFAs were significantly changed along with age. These findings provide important information to understand the homeostasis of the cecum of pigs after antibiotic or probiotic treatment.

Developmental Profiling of Dietary Carbohydrate Digestion in Piglets

Carbohydrates are the main source of energy in the diet, accounting for the largest proportion in the diets of humans and monogastric animals. Although recent progress has been made in the study of intestinal carbohydrate digestion in piglets, there is a lack of comprehensive study on the dynamic changes in intestinal carbohydrate digestion with age in the early growth stage of piglets. To fill in this gap of knowledge, we collected samples of the small intestine, pancreatic tissues, and colonic digesta from 42 piglets during newborn [day (d) 0], lactation (d 7, 14), weaning (d 21), and nursery (d 28, 35, and 42) stages. Intestinal and pancreatic tissues and colonic digesta were collected at necropsy and analyzed for morphology, digestive enzyme activities, short-chain fatty acids (SCFA), and microbial abundance. Villus height reached a maximum at 1 week (d 7) in the duodenum and jejunum (P <0.01), and a higher ratio of villus height to crypt depth and lactase activity were observed on d 0 and 7 (P < 0.001) compared to other ages. However, the sucrase and maltase activities were increased with piglets' age. Similar activities of sucrase and maltase were found in the small intestine. In addition, amylase, lipase, and protease activities were assayed in the pancreas. The activity of amylase increased with age, while lipase and protease decreased gradually from birth to weaning (d 21, 28) and then increased after weaning (d 35, 42). Compared with d 0, d 42 increased the abundance of Firmicutes and Bacteroidetes with a higher concentration of total SCFA (P < 0.001) and decreased the abundance of Proteobacteria, but weaning (d 21, 28) increased the abundance of Proteobacteria in the colon. These results indicate that with the increase in piglet age, the carbohydrate digestive function gradually increased, but weaning hindered the development of intestinal function. These results provide us with new insights into the healthy development of piglets' intestines, which may help us to better regulate the physiological health of piglets in the future.

Effects of Fenugreek Seed Extracts on Growth Performance and Intestinal Health of Broilers

The purpose of this experiment was to study the effects of fenugreek seed extract (FSE) on the growth performance, intestinal morphology, intestinal immunity and cecal micro-organisms in yellow-feathered broilers. A total of 240 one-day-old male yellow-feathered broilers were selected and randomly assigned to four treatments with 6 replicates per group and ten broilers per replicate. Started from the third day, birds were fed with basal diet (CON group) or basal diet supplemented with 30 mg/kg Zinc bacitracin (ZB group), or basal diet supplemented with 50 (D-FSE group) or 100 (H-FSE group) mg/kg FSE, respectively. The experiment lasted for 56 d. The results showed that dietary FSE supplementation improved average daily weight gain (ADG) and ratio of feed to weight gain (F: G) (P < 0.01), increased intestinal villus height (VH), villus height to crypt depth ratio (V/C) (P < 0.05), serum concentrations of IL-10, and the contents of secretory immunoglobulin A (sIgA) (P < 0.05), as well as decreased the activity of iNOS (P < 0.05). The high-throughput sequencing results showed that dietary FSE supplementation increased the alpha diversity of cecal microbes, and Firmicutes, Bacteroidetes, Verrucomicrobia and Proteobacteria taken up 95% of all phyla detected, FSE significantly reduced Campylobacter, Synergistes, and Lachnoclostridium abundance (P ≤ 0.05). There were significant difference in more than 30 KEGG pathways between FSE added group and control group or ZB group. FSE supplementation, in other words, maintained gut microbiota homeostasis while improving broiler growth performance. As a result, FSE has the potential to replace prophylactic antibiotic use in poultry production system.

Two untargeted metabolomics reveals yogurt-associated metabolic alterations in women with multiple metabolic disorders from a randomized controlled study

The beneficial role of yogurt on metabolic profile has been widely reported. Yet, few studies have intended to describe the integrated metabolic alterations in response to yogurt. Yogurt and milk (220 g/d) were given to 48 and 44 obese women with metabolic syndrome and nonalcoholic fatty liver disease for 24 weeks in a randomized controlled trial (registered at http://www.chictr.org.cn as ChiCTR-IPR-15006801). Fasting serum samples were collected before and after intervention for global, untargeted metabolomics based on ¹H nuclear magnetic resonance (NMR) and ultra-high-performance liquid chromatography coupled with electrospray ionization time-of-flight mass spectrometry (UPLC-Q-TOF-MS) (in positive and negative ion modes). Multivariable statistical analysis and pathway analysis were conducted. In both ¹H NMR and UPLC-Q-TOF-MS metabolomics, no clustering was observed between the two groups at baseline. While, a clear clustering was shown after intervention, and the yogurt group had significantly different metabolic status from the milk. The metabolites that contributed mostly to class separation were identified, and involved into pathway analysis. Pathways on amino acids metabolism, fatty acid oxidation, cholesterol catabolism and choline metabolism significantly changed after yogurt intervention. The study revealed the integrated metabolic alterations in response to yogurt via two metabolomics approaches, suggesting the potential mechanisms of yogurt against metabolic disorders. TRIAL REGISTRATION: Chinese Clinical Trial Registry, ChiCTR-IPR-15006801. Registered 20 July 2015, http://www.chictr.org.cn/ ChiCTR-IPR-15006801. SIGNIFICANCE: Both review from prospective studies and our randomized clinical trial showed the protective role of yogurt against multiple metabolic disorders. However, they were focus on targeted glucose, lipid, and other metabolic indicators, which were only part of human metabolism, failing to show an integrated metabolic feature on yogurt. Therefore, two global, untargeted metabolomics were applied in our current randomized clinical trial, trying to uncover the significant metabolic alterations characterizing the effects of yogurt on obese women with multiple metabolic disorders, and to explore the potential biological mechanisms of yogurt. The finding will shed light on a more comprehensive picture of how yogurt affects host metabolism, and provide theoretical foundation for dietary prevention of chronic diseases.

Biological characteristics and whole-genome analysis of the potential probiotic, Lactobacillus reuteri S5

Lactic acid bacteria are microorganisms used for probiotic purposes and form major parts of human and mammalian intestinal microbiota, exerting important health-promoting effects on the host. Here, we evaluated L. reuteri strain S5 isolated from the intestines of healthy white feather broilers. L. reuteri S5 grew best after 20 h of incubation in MRS medium. Lactic acid production was 1.42 mmol L^-1 at 24 h, which was well tolerated. Activities of T-AOC, GSH-Px and T-SOD in the cell-free fermentation supernatant of L. reuteri S5 were higher than those in the bacteria, and the strain showed good hydrophobicity in vitro. The dominant carbon and nitrogen sources of L. reuteri S5 were glucose and soybean meal. A high-quality complete genome map of L. reuteri S5 was obtained using a Pacbio nanopore third-generation sequencing platform. The results showed that L. reuteri S5 possesses a complete primary metabolic pathway, encoding the main functional enzymes of the glycolysis pathway and pentose phosphate pathway. The genome contains genes encoding antioxidants and conferring tolerance to inorganic salt ions, acids and bile salts. This study shows that L. reuteri S5 is a probiotic strain with excellent probiotic characteristics and has great potential for the development of feed additives to promote animal health.

Dietary ferulic acid and vanillic acid on inflammation, gut barrier function and growth performance in lipopolysaccharide-challenged piglets

Ferulic acid (FA) and vanillic acid (VA) are considered as major phenolic metabolites of cyanidin 3-glucoside, a polyphenol that widely exists in plants that possess a protective effect against oxidative stress and inflammation in our previous study. This study aimed to investigate the effect of FA and VA on inflammation, gut barrier function, and growth performance in a weaned piglet model challenged with lipopolysaccharide (LPS). Thirty-six piglets (PIC 337 × C48, 28 d of age) were randomly allocated into 3 treatments with 6 replicate pens (2 piglets per pen). They were fed with a basal diet or a diet containing 4,000 mg/kg of FA or VA. Dietary supplementation of VA significantly increased average daily gain (ADG) (P < 0.05). Both FA and VA decreased serum levels of thiobarbituric acid reactive substances (TBARS), interlukin (IL)-1β, IL-2, IL-6, and tumor necrosis factor (TNF)-α (P < 0.05), and enhanced the expression of tight junction protein oclaudin (P < 0.05). Analysis of gut microbiota indicated that both FA and VA increased the Firmicutes/Bacteroidetes ratio alongside reducing the relative abundance of the Prevotellaceae family including Prevotella 9 and Prevotella 2 genera, but enriched the Lachoiraceaea family including the Lachnospiraceae FCS020 group (P < 0.05). Moreover, VA reduced the relative abundance of Prevotella 7 and Prevotella 1 but enriched Lachnospira, Eubacterium eligens group, and Eubacterium xylanophilum group (P < 0.05), while FA showed a limited effect on these genera. The results demonstrated that both VA and FA could alleviate inflammation and oxidative stress, but only VA has a significant positive effect on the growth performance of LPS-challenged piglets potentially through modulating gut microbiota.

Influenza A H1N1 Induced Disturbance of the Respiratory and Fecal Microbiome of German Landrace Pigs - a Multi-Omics Characterization

Seasonal influenza outbreaks represent a large burden for the health care system as well as the economy. While the role of the microbiome has been elucidated in the context of various diseases, the impact of respiratory viral infections on the human microbiome is largely unknown. In this study, swine was used as an animal model to characterize the temporal dynamics of the respiratory and gastrointestinal microbiome in response to an influenza A virus (IAV) infection. A multi-omics approach was applied on fecal samples to identify alterations in microbiome composition and function during IAV infection. We observed significantly altered microbial richness and diversity in the gastrointestinal microbiome after IAV infection. In particular, increased abundances of Prevotellaceae were detected, while Clostridiaceae and Lachnospiraceae decreased. Moreover, our metaproteomics data indicated that the functional composition of the microbiome was heavily affected by the influenza infection. For instance, we identified decreased amounts of flagellin, correlating with reduced abundances of Lachnospiraceae and Clostridiaceae, possibly indicating involvement of a direct immune response toward flagellated Clostridia during IAV infection. Furthermore, enzymes involved in short-chain fatty acid (SCFA) synthesis were identified in higher abundances, while metabolome analyses revealed rather stable concentrations of SCFAs. In addition, 16S rRNA gene sequencing was used to characterize effects on the composition and natural development of the upper respiratory tract microbiome. Our results showed that IAV infection resulted in significant changes in the abundance of Moraxellaceae and Pasteurellaceae in the upper respiratory tract. Surprisingly, temporal development of the respiratory microbiome structure was not affected. IMPORTANCE Here, we used swine as a biomedical model to elucidate the impact of influenza A H1N1 infection on structure and function of the respiratory and gastrointestinal tract microbiome by employing a multi-omics analytical approach. To our knowledge, this is the first study to investigate the temporal development of the porcine microbiome and to provide insights into the functional capacity of the gastrointestinal microbiome during influenza A virus infection.

Reduced Feeding Frequency Improves Feed Efficiency Associated With Altered Fecal Microbiota and Bile Acid Composition in Pigs

A biphasic feeding regimen exerts an improvement effect on feed efficiency of pigs. While gut microbiome and metabolome are known to affect the host phenotype, so far the effects of reduced feeding frequency on fecal microbiota and their metabolism in pigs remain unclear. Here, the combination of 16S rRNA sequencing technique as well as untargeted and targeted metabolome analyses was adopted to investigate the fecal microbiome and metabolome of growing–finishing pigs in response to a biphasic feeding [two meals per day (M2)] pattern. Sixty crossbred barrows were randomly assigned into two groups with 10 replicates (three pigs/pen), namely, the free-access feeding group (FA) and the M2 group. Pigs in the FA group were fed free access while those in the M2 group were fed ad libitum twice daily for 1 h at 8:00 and 18:00. Results showed that pigs fed biphasically exhibited increased feed efficiency compared to FA pigs. The Shannon and Simpson indexes were significantly increased by reducing the feeding frequency. In the biphasic-fed pigs, the relative abundances of Subdoligranulum, Roseburia, Mitsuokella, and Terrisporobacter were significantly increased while the relative abundances of unidentified_Spirochaetaceae, Methanobrevibacter, unidentified_Bacteroidales, Alloprevotella, Parabacteroides, and Bacteroides were significantly decreased compared to FA pigs. Partial least-square discriminant analysis (PLS-DA) analysis revealed an obvious variation between the FA and M2 groups; the differential features were mainly involved in arginine, proline, glycine, serine, threonine, and tryptophan metabolism as well as primary bile acid (BA) biosynthesis. In addition, the changes in the microbial genera were correlated with the differential fecal metabolites. A biphasic feeding regimen significantly increased the abundances of primary BAs and secondary BAs in feces of pigs, and the differentially enriched BAs were positively correlated with some specific genera. Taken together, these results suggest that the improvement effect of a reduced feeding frequency on feed efficiency of pigs might be associated with the altered fecal microbial composition and fecal metabolite profile in particular the enlarged stool BA pool.

Time-course alterations of gut microbiota and short-chain fatty acids after short-term lincomycin exposure in young swine

Increasing evidence suggests that antibiotic administration causes gut injury, negatively affecting nutrient digestion, immune regulation, and colonization resistance against pathogens due to the disruption of gut microbiota. However, the time-course effects of therapeutic antibiotics on alterations of gut microbes and short-chain fatty acids (SCFAs) in young swine are still unknown. In this study, twenty piglets were assigned into two groups and fed commercial diets with or without lincomycin in the first week for a 28-day trial period. Results showed that 1-week lincomycin exposure (LE) did reduce the body weight on day 14 (p = 0.0450) and 28 (p = 0.0362). The alpha-diversity notably reduced after 1-week LE, and then gradually raised and reached the control group level in the second week on cessation of LE, indicated by the variation of Sobs, Chao, Shannon, and ACE index (p < 0.05). Beta-diversity analysis revealed that the distinct microbial cluster existed persistently for the whole trial period between two groups (p < 0.001). The relative abundance of most microbes including fiber-degrading (e.g., Agathobacter and Coprococcus), beneficial (e.g., Lactobacillus and Mitsuokella), or pathogenic bacteria (e.g., Terrisporobacter and Lachnoclostridium) decreased (LDA score > 3), and the concentration of SCFAs also diminished in the feces of 1-week lincomycin-administrated young swine, indicating that therapeutic LE killed most bacteria and reduced SCFA production with gut dysbiosis occurring. After the LE stopped, the state of gut dysbiosis gradually attenuated and formed new gut-microbe homeostasis distinct from microbial homeostasis of young pigs unexposed to lincomycin. The increased presence of potential pathogens, such as Terrisporobacter, Negativibacillus, and Escherichia-Shigella, and decreased beneficial bacteria, such as Lactobacillus and Agathobacter, were observed in new homeostasis reshaped by short-lincomycin administration (LDA score > 3 or p < 0.05), adversely affecting gut development and health of young pigs. Collectively, these results suggested that severe disruption of the commensal microbiota occurred after short-term LE or termination of LE in young swine. KEY POINTS: • Therapeutic lincomycin exposure induced gut dysbiosis, killing most bacteria and reducing short-chain fatty acid production. • Gut dysbiosis gradually attenuated and formed new homeostasis after lincomycin exposure stopped. • The new homeostasis, increased Escherichia-Shigella etc. and decreased Lactobacillus etc., was potentially harmful to gut health.

Effects of cadmium on organ function, gut microbiota and its metabolomics profile in adolescent rats

Cadmium (Cd) exposure in adult animals can result in multi-organ damages and gut microbiota disturbance. However, Cd's consequences on health and gut microbiota during adolescence are obscure. In the present study, three-week-old SD rats were exposed to Cd at doses of 0, 0.25, 1, and 4 mg/kg body weight for eight weeks, and the changes of liver, kidney, and ovary function, as well as gut microbiota and its metabolomics profile, were analyzed. After transplantation of fecal bacteria from the 4 mg/kg Cd-treated group into age-matched rats (4 mg/kg-Cd recipients), the organ function and inflammatory reaction were evaluated. The results indicated that Cd perturbed gut microbiota composition, significantly decreased the abundance of Prevotella and Lachnoclostridium but increased Escherichia coli_Shigella. The fecal metabolome profile was altered and was closely correlated with some specific genera. These changes were accompanied by the inflammatory response, dyslipidemia, kidney dysfunction, and abnormal estrogen level. In 4 mg/kg-Cd recipients, the serum triglyceride (TG), lipopolysaccharide (LPS), and inflammatory cytokines were increased with the expressions of IL-1β, IL-6, TNF-α genes up-regulated in liver and kidney. Overall, this study demonstrated that Cd exposure during adolescence could cause disturbance of gut microbiota, dysfunction of liver, kidney, and ovary, which may be correlated with the activation of Cd-induced inflammatory response.

Composition of the Fecal Microbiota of Piglets at Various Growth Stages

Gastrointestinal (GI) microbiota play an important role in promoting growth in piglets. However, studies on microbiota composition at various growth stages are lacking. We measured body weights of Jinfen White and Mashen piglets every 7 days and collected their fecal samples by rectal swabbing at nine time points during suckling (1-28 days) and nursery (35-70 days) stages to gain insight into microbiota variability during piglet growth. The fecal microbiota were characterized via 16S rRNA gene sequencing to analyze the effects of microbial diversity on piglet growth and development preliminarily. The results showed that although the two breeds of piglets have similar body weights at birth, weaned Jinfen White piglets demonstrated a significantly greater body weight and daily weight gain than weaned Mashen piglets (P < 0.01). A total of 1,976 operational taxonomic units (OTUs) belonging to 27 phyla and 489 genera were uncovered, in which the highest numbers of OTUs belong to the phyla Firmicutes and Bacteroidetes. Lactobacillus, Bacteroides, and Prevotellaceae NK3B31 groups accounting for 12.4, 8.8, and 5.8% of OTUs, respectively, showed relatively high abundance at the genus level. Nine sampling time points were divided into three growth stages, namely, immediate postfarrowing (1 day old), suckling (7, 14, and 21 days old), and nursery (28, 35, 49, 63, and 70 days old), on the basis of the results of microbial diversity, principal coordinate, and co-occurrence network analyses. In addition, it identified 54 discriminative features in the microbiota between two breeds of piglets by LEfSe analysis, in which 17 genera enriched the microbiota community of Jinfen White piglets. Finally, abundances of 29 genera showed significant positive correlations with body weights and daily weight gain of piglets. Conversely, abundances of 12 genera demonstrated significant negative correlations with body weights of piglets. The results of our study will provide a theoretical basis for succession patterns in fecal microbiota of piglets and suggest the need for meticulous management of piglets in pig production.

Metabolome-Microbiome Responses of Growing Pigs Induced by Time-Restricted Feeding

Time-restricted feeding (TRF) mode is a potential strategy in improving the health and production of farm animals. However, the effect of TRF on microbiota and their metabolism in the large intestine of the host remains unclear. Therefore, the present study aimed to investigate the responses of microbiome and metabolome induced by TRF based on a growing-pig model. Twelve crossbred growing barrows were randomly allotted into two groups with six replicates (1 pig/pen), namely, the free-access feeding group (FA) and TRF group. Pigs in the FA group were fed free access while the TRF group were fed free access within a regular time three times per day at 07:00–08:00, 12:00–13:00, and 18:00–19:00, respectively. Results showed that the concentrations of NH4-N, putrescine, cadaverine, spermidine, spermine, total biogenic amines, isobutyrate, butyrate, isovalerate, total SCFA, and lactate were increased while the pH value in the colonic digesta and the concentration of acetate was decreased in the TRF group. The Shannon index was significantly increased in the TRF group; however, no significant effects were found in the Fisher index, Simpson index, ACE index, Chao1 index, and observed species between the two groups. In the TRF group, the relative abundances of Prevotella 1 and Eubacterium ruminantium group were significantly increased while the relative abundances of Clostridium sensu sticto 1, Lactobacillus, and Eubacterium coprostanoligenes group were decreased compared with the FA group. PLS-DA analysis revealed an obvious and regular variation between the FA and TRF groups, further pathway enrichment analysis showed that these differential features were mainly enriched in pyrimidine metabolism, nicotinate and nicotinamide metabolism, glycerolipid metabolism, and fructose and mannose metabolism. In addition, Pearson's correlation analysis indicated that the changes in the microbial genera were correlated with the colonic metabolites. In conclusion, these results together indicated that although the overall microbial composition in the colon was not changed, TRF induced the gradient changes of the nutrients and metabolites which were correlated with certain microbial genera including Lactobacillus, Eubacterium_ruminantium group, Eubacterium coprostanoligenes group, Prevotella 1, and Clostridium sensu sticto 1. However, more studies are needed to understand the impacts of TRF on the health and metabolism of growing pigs.

Sex-dependent changes in the microbiota profile, serum metabolism, and hormone levels of growing pigs after dietary supplementation with Lactobacillus

Dietary supplementation with Lactobacillus can improve the intestinal microbial balance and exerts beneficial effects on pig health. However, whether these effects in pigs show differences between the sexes remains poorly understood. Therefore, we analyzed the sex-dependent patterns in the fecal microbiota after dietary supplementation with Lactobacillus acidophilus ZLA012 through high-throughput sequencing, determined the metabolomic profile of serum in barrows (immature castrated males) and gilts (sexually immature females) through nontargeted liquid chromatography-mass spectrometry, and measured the levels of various hormones, such as insulin, growth hormone, serotonin, triiodothyronine, and thyroxine. Lactobacillus supplementation resulted in more obvious effects on the microbial diversity and composition in barrows than in gilts. Specifically, supplementation with L. acidophilus ZLA012 significantly increased the abundance of the phylum Bacteroidetes and decreased that of Firmicutes in barrows. In contrast, more notable effects on metabolites, particularly those involved in lipid metabolism and glycerophospholipid metabolism, were observed in gilts than in barrows after Lactobacillus supplementation. Megasphaera, Dialister, Gemmiger, Faecalibacterium, Bulleidia, and Prevotella were the core functional genera associated with the significantly affected metabolites, which are involved in the biosynthesis, degradation, and elongation of fatty acids. L. acidophilus ZLA012 treatment increased the serum insulin, total bile acid, lipoprotein lipase, and nicotinamide adenine dinucleotide (NAD)⁺ levels in gilts, whereas higher serotonin levels were found in barrows than in gilts. The results indicated that the separate housing of barrows and gilts might be beneficial for targeted dietary supplementation and application of Lactobacillus in pig production. KEY POINTS: • L. acidophilus exerted obvious effects on microbiota profiles for barrows than gilts. • Gilts treated by L. acidophilus had a greater variety of lipid metabolism compared with barrows. • Lactobacillus regulated the dynamic balance among the microbiota, metabolism, and hormone in pigs.

Introduction of Colonic and Fecal Microbiota From an Adult Pig Differently Affects the Growth, Gut Health, Intestinal Microbiota and Blood Metabolome of Newborn Piglets

Microbiota transplantation is a rapid and effective method for changing and reshaping the intestinal microbiota and metabolic profile in humans and animals. This study compared the different influences of the introduction of fecal microbes and colonic microbes from a fat, adult pig in newborn pigs. Both colonic microbiota transplantation (CMT) and fecal microbiota transplantation (FMT) promoted growth and improved gut functions in suckling pigs up to weaning. FMT was more beneficial for body weight gain and body fat deposition in piglets, while CMT was more beneficial for intestinal health and mucosal immunity. 16S rDNA sequence analysis indicated that both CMT and FMT significantly increased the abundances of beneficial or functional bacteria, such as Lactobacillus and Prevotella_2 genera, in the piglets, and reduced the abundances of harmful bacteria, such as Escherichia-Shigella. Blood metabolome analysis showed that transplantation, especially FMT, enhanced lipid metabolism in piglets. In addition, while CMT also changed amino acid metabolism and increased anti-inflammatory metabolites such as 3-indoleacetic acid and 3-indolepropionic acid in piglets, FMT did not. Of note, FMT damaged the intestinal barrier of piglets to a certain extent and increased the levels of inflammatory factors in the blood that are potentially harmful to the health of pigs. Taken together, these results suggested that intestinal and fecal microbiota transplantations elicited similar but different physiological effects on young animals, so the application of microbiota transplantation in animal production requires the careful selection and evaluation of source bacteria.

Dissection of the gut microbiota in mothers and children with chronic Trichuris trichiura infection in Pemba Island, Tanzania

Background

Soil-transmitted helminthiases are important neglected tropical diseases that result in a notably high number of disability-adjusted life years worldwide. Characterizing the interactions between the human intestinal microbiome and helminths is of interest in the development of alternative treatments that do not rely on chemotherapeutics and do not lead to drug resistance.

Methods

We recruited and obtained fecal samples from 32 pairs of mothers and children on Pemba Island and monitored their intestinal microbiota using 16S rRNA gene sequencing.

Results

We observed that microbial changes occur in the gut microbiota of infected mothers and children. Some short-chain fatty acid (SCFA)-producing bacteria and carbohydrate-degrading bacteria exhibited lower abundance in the infected individuals. Potentially pathogenic Campylobacter and proinflammatory Methanobrevibacter in infected mothers and opportunistic Enterococcus in infected children exhibited greater abundance.

Conclusions

Our findings could reveal the microbiota profiling in T. trichiura-infected individuals, indicate the potential roles of key microbiota in the host and aid to the development of novel strategies to control T. trichiura infection.

Graphic abstract

A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function

Swine are regarded as promising biomedical models, but the dynamics of their gastrointestinal microbiome have been much less investigated than that of humans or mice. The aim of this study was to establish an integrated multi-omics protocol to investigate the fecal microbiome of healthy swine. To this end, a preparation and analysis protocol including integrated sample preparation for meta-omics analyses of deep-frozen feces was developed. Subsequent data integration linked microbiome composition with function, and metabolic activity with protein inventories, i.e., 16S rRNA data and expressed proteins, and identified proteins with corresponding metabolites. 16S rRNA gene amplicon and metaproteomics analyses revealed a fecal microbiome dominated by Prevotellaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae and Clostridiaceae. Similar microbiome compositions in feces and colon, but not ileum samples, were observed, showing that feces can serve as minimal-invasive proxy for porcine colon microbiomes. Longitudinal dynamics in composition, e.g., temporal decreased abundance of Lactobacillaceae and Streptococcaceae during the experiment, were not reflected in microbiome function. Instead, metaproteomics and metabolomics showed a rather stable functional state, as evident from short-chain fatty acids (SCFA) profiles and associated metaproteome functions, pointing towards functional redundancy among microbiome constituents. In conclusion, our pipeline generates congruent data from different omics approaches on the taxonomy and functionality of the intestinal microbiome of swine.

Dietary Supplementation of ε-Polylysine Beneficially Affects Ileal Microbiota Structure and Function in Ningxiang Pigs

Intestinal microbiota plays an important role in the health of animals. However, little is known about the gut microbiota in Ningxiang pigs. Thus, we investigated how dietary supplementation with different ε-polylysine concentrations (0, 20, 40, 80, and 160 ppm) affected the ileal microbiota in Ningxiang pigs using a replicated 5 × 5 Latin square method. Each experimental period included 10 days for diet adaptation, 3 days for feces collection and 2 days for digesta collection. The ileal contents were collected and used for sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. The results revealed that ε-polylysine significantly decreased the digestibility of crude protein and crude fiber, as well as the utilization of metabolizable energy (P < 0.05). The relative abundances of 19 bacterial genera significantly increased, while those of 26 genera significantly decreased (P < 0.05). In addition, ε-polylysine increased the abundance of some bacteria (e.g., Faecalibacterium, Bifidobacterium, and lactic acid bacteria) and inhibited some other bacteria (e.g., Micrococcaceae, Acinetobacter, Anaerococcus, Peptoniphilus, Dehalobacterium, Finegoldia, Treponema, and Brevundimonas). Furthermore, based on the 16S rRNA gene data and data from the precalculated GreenGenes database, bacterial communities in the ileal contents exhibited enhanced functional maturation, including changes in the metabolism of carbohydrates, amino acids (e.g., alanine, lysine, tryptophan, cysteine, and methionine), cofactors, and vitamins (e.g., biotin, thiamine, and folate), as well as in the activity of the insulin signaling pathway. This study suggests that ε-polylysine may influence the utilization of feed nutrients by Ningxiang pigs, including proteins, lipids, metabolizable energy, and fiber, by regulating the gut microbiota.

Protective effect of Lactobacillus salivarius Li01 on thioacetamide-induced acute liver injury and hyperammonaemia

The gut microbiota plays pivotal roles in liver disease onset and progression. The protective effects of Lactobacillus salivarius Li01 on liver diseases have been reported. In this study, we aimed to detect the protective effect of L. salivarius Li01 on thioacetamide (TAA)-induced acute liver injury and hyperammonaemia. C57BL/6 mice were separated into three groups and given a gavage of L. salivarius Li01 or phosphate-buffered saline for 7 days. Acute liver injury and hyperammonaemia were induced with an intraperitoneal TAA injection. L. salivarius Li01 decreased mortality and serum transaminase levels and improved histological liver damage caused by TAA. Serum inflammatory cytokine and chemokine and lipopolysaccharide-binding protein (LBP) concentrations, nuclear factor κB (NFκB) pathway activation and macrophage and neutrophil infiltration into the liver were significantly alleviated by L. salivarius Li01. L. salivarius Li01 also reinforced gut barrier and reshaped the perturbed gut microbiota by upregulating Bacteroidetes and Akkermansia richness and downregulating Proteobacteria, Ruminococcaceae_UCG_014 and Helicobacter richness. Plasma and faecal ammonia levels declined noticeably in the Li01 group, accompanied by improvements in cognitive function, neuro-inflammation and relative brain-derived neurotrophic factor (BDNF) gene expression. Our results indicated that L. salivarius Li01 could be considered a potential probiotic in acute liver injury and hepatic encephalopathy (HE).

Dietary protocatechuic acid ameliorates inflammation and up-regulates intestinal tight junction proteins by modulating gut microbiota in LPS-challenged piglets

Background

Weaning is one of the major factors that cause stress and intestinal disease in piglets. Protocatechuic acid (PCA) is an active plant phenolic acid which exists in Chinese herb, Duzhong (Eucommia ulmoides Oliver), and is also considered as the main bioactive metabolite of polyphenol against oxidative stress and inflammation. This study aimed to investigate the effect of PCA on growth performance, intestinal barrier function, and gut microbiota in a weaned piglet model challenged with lipopolysaccharide (LPS).

Methods

Thirty-six piglets (Pig Improvement Company line 337 × C48, 28 d of age, 8.87 kg ± 0.11 kg BW) were randomly allocated into 3 treatments and fed with a basal diet (CTL), a diet added 50 mg/kg of aureomycin (AUR), or a diet supplemented with 4000 mg/kg of PCA, respectively. The piglets were challenged with LPS (10 μg/kg BW) on d 14 and d 21 by intraperitoneal injection during the 21-d experiment. Animals (n = 6 from each group) were sacrificed after being anesthetized by sodium pentobarbital at 2 h after the last injection of LPS. The serum was collected for antioxidant indices and inflammatory cytokines analysis, the ileum was harvested for detecting mRNA and protein levels of tight junction proteins by PCR and immunohistochemical staining, and the cecum chyme was collected for intestinal flora analysis using 16S rRNA gene sequencing.

Results

Dietary supplementation of PCA or AUR significantly increased the expression of tight junction proteins including ZO-1 and claudin-1 in intestinal mucosa, and decreased the serum levels of thiobarbituric acid reactive substances (TBARS) and IL-6, as compared with CTL group. In addition, PCA also decreased the serum levels of IL-2 and TNF-α (P < 0.05). Analysis of gut microbiota indicated that PCA increased the Firmicutes/Bacteroidetes ratio (P < 0.05). Spearman’s correlation analysis at the genus level revealed that PCA reduced the relative abundance of Prevotella 9, Prevotella 2, Holdemanella, and Ruminococcus torques group (P < 0.05), and increased the relative abundance of Roseburia and Desulfovibrio (P < 0.05), whereas AUR had no significant effect on these bacteria.

Conclusions

These results demonstrated that both PCA and AUR had protective effect on oxidative stress, inflammation and intestinal barrier function in piglets challenged with LPS, and PCA potentially exerted the protective function by modulating intestinal flora in a way different from AUR.

Holdemanella

Chemical Reporters for Exploring Microbiology and Microbiota Mechanisms

The advances made in bioorthogonal chemistry and the development of chemical reporters have afforded new strategies to explore the targets and functions of specific metabolites in biology. These metabolite chemical reporters have been applied to diverse classes of bacteria including Gram-negative, Gram-positive, mycobacteria, and more complex microbiota communities. Herein we summarize the development and application of metabolite chemical reporters to study fundamental pathways in bacteria as well as microbiota mechanisms in health and disease.

Toxicity, Pharmacokinetics, and Gut Microbiome of Oral Administration of Sesterterpene MHO7 Derived from a Marine Fungus

Sesterterpene MHO7 derived from mangrove fungus is a novel estrogen receptor degrader for the treatment of breast cancer. To explore its safety and pharmacokinetics in vivo, Log P/D values, stability in simulated gastric/intestinal (SGF/SIF), toxicity, and pharmacokinetics studies were carried mainly by liquid chromatography technique coupled with tandem mass spectrometry (LC–MS/MS) method in mice, and the effect of MHO7 on mice gut microbiota at different time points was revealed by 16S rRNA sequencing. Log P/D values ranged 0.93–2.48, and the compound in SGF and SIF is stable under the concentration of 5 mM·L⁻¹. The maximum tolerance dose (MTD) of oral administration in mice was 2400 mg·kg⁻¹. The main pharmacokinetics parameters were as following: C_max of 1.38 μg·mL⁻¹, T_max of 8 h, a half-life (t_1/2) of 6.97 h, an apparent volume of mean residual time (MRT) of 8.76 h, and an area under the curve (AUC) of 10.50 h·μg·mL⁻¹. MHO7 displayed a wide tissue distribution in mice, with most of the compound in liver (3.01 ± 1.53 μg·g⁻¹) at 1 h, then in fat (5.20 ± 3.47 μg·g⁻¹) at 4 h, and followed by reproductive organs with the concentrations of 23.90 ± 11.33 μg·g⁻¹,13.69 ± 10.29 μg·g⁻¹, 1.46 ± 1.23 μg·g⁻¹, and 0.36 ± 0.46 μg·g⁻¹ at 8, 12, 20 and 30 h, respectively. The most influenced genera of gut microbiome belonged to phylum Firmicutes (21 of 28), among which 18 genera originated from the order Clostridiales, class Clostridia, and families of Ruminococcaceae (11 of 18) and Lachnospiraceae (4 of 18). These results provide that MHO7 is suitable for oral administration in the treatment of breast cancer with the target organs of reproductive organs and regulation on Ruminococcaceae and Lachnospiraceae.