Structure and Function of the Fecal Microbiota in Diarrheic Neonatal Piglets

Relationship between the components of mare breast milk and foal gut microbiome: shaping gut microbiome development after birth

The gut microbiota (GM) is essential for mammalian health. Although the association between infant GM and breast milk (BM) composition has been well established in humans, such a relationship has not been investigated in horses. Hence, this study was conducted to analyze the GM formation of foals during lactation and determine the presence of low-molecular-weight metabolites in mares' BM and their role in shaping foals' GM. The fecal and BM samples from six pairs of foals and mares were subjected to 16S ribosomal RNA metagenomic and metabolomic analyses, respectively. The composition of foal GM changed during lactation time; hierarchical cluster analysis divided the fetal GM into three groups corresponding to different time points in foal development. The level of most metabolites in milk decreased over time with increasing milk yield, while threonic acid and ascorbic acid increased. Further analyses revealed gut bacteria that correlated with changes in milk metabolites; for instance, there was a positive correlation between Bacteroidaceae in the foal's gut microbiota and serine/glycine in the mother's milk. These findings help improve the rearing environment of lactating horses and establish artificial feeding methods for foals.

Role of immunomodulatory probiotics in alleviating bacterial diarrhea in piglets: a systematic review

Diarrhea is a common enteric disease in piglets that leads to high mortality and economic losses in swine production worldwide. Antibiotics are commonly used to prevent or treat diarrhea in piglets. However, irrational antibiotic use contributes to the development of resistance in bacteria and antibiotic residues in animal products, threatening public health, while causing gut microbiota dysbiosis and antibiotic-resistant bacterial infection in piglets. Therefore, the quest for alternative products (such as probiotics, prebiotics, organic acids, enzymes, essential oils, medium-chain fatty acids, zinc, and plant extracts) has recently been clearly emphasized through the increase in regulations regarding antibiotic use in livestock production. These antibiotic alternatives could lower the risk of antibiotic-resistant bacteria and meet consumer demand for antibiotic-free food. Several antibiotic alternatives have been proposed, including immunomodulatory probiotics, as candidates to reduce the need for antimicrobial therapy. Many studies have revealed that probiotics can avert and cure bacterial diarrhea by regulating the gut function and immune system of piglets. In this review, we focus on the major pathogenic bacteria causing piglet diarrhea, the research status of using probiotics to prevent and treat diarrhea, their possible mechanisms, and the safety issues related to the use of probiotics. Supplementation with probiotics is a possible alternative to antibiotics for the prevention or treatment of bacterial diarrhea in piglets. Furthermore, probiotics exert beneficial effects on feed efficiency and growth performance of piglets. Therefore, appropriate selection and strategies for the use of probiotics may have a positive effect on growth performance and also reduce diarrhea in piglets. This review provides useful information on probiotics for researchers, pig nutritionists, and the additive industry to support their use against bacterial diarrhea in piglets.

Bamboo fiber improves piglet growth performance by regulating the microbial composition of lactating sows and their offspring piglets

Introduction

Feeding bamboo powder is a kind of fiber raw material mainly composed of insoluble dietary fiber (IDF). In this study, IDF-based rice husk meal and feeding bamboo powder were used to compare the effects of bamboo fiber on fecal microflora and the performance of lactating sows and their offspring piglets.

Methods

Thirty healthy crossbred gilts (Yorkshire × Landrace) at day 105 of gestation were randomly allocated into three groups: CON, TRE1 supplemented with 2% BBF1 (feeding bamboo powder), and TRE2 supplemented with 2% BBF2 (99% feeding bamboo powder +1% bamboo fiber polymer material). The reproductive performance, serum indexes, and fecal microbiota of sows and piglets were analyzed. The results showed that, compared with CON, the average feed intake of sows in TRE1 during the second week of lactation was significantly increased by 21.96% (p < 0.05), the average daily gain (ADG) per litter in TRE1 on 11-21 days and 3-21 days of lactation was significantly increased by 50.68 and 31.61%, respectively (p < 0.05), and the serum triglyceride content of sows in TRE1 on the 21st day of lactation was significantly increased (p < 0.05). The 16S rRNA analysis showed that dietary bamboo fiber significantly increased the fecal microbial richness index Ace, Chao, and Sobs of sows (p < 0.05) and tended to increase the Sobs index of suckling piglets on day 21 (p < 0.10). Compared with CON, BBF1 supplementation significantly decreased the abundance of Christensenellaceae_R-7_group in feces of sows on days 7 and 21 after delivery (p < 0.05), while BBF2 decreased the genera Christensenellaceae_R-7_group on days 7 (p < 0.10) and 21 (p < 0.05) after delivery. Spearman correlation analysis showed that the abundance of Phascolarctobacterium in the feces of piglets on the 21st day after delivery was significantly positively correlated with diarrhea rate and significantly negatively correlated with ADG per litter, day 21 litter weight, and 3- to 21-day survival rate. In contrast, Christensenellaceae_R-7_group was significantly negatively correlated with diarrhea rate and positively correlated with ADG per litter.

Discussion

These results indicated that maternal BBF1 supplementation improved the litter weight gain of suckling piglets, which was associated with the improvement of diversity and structure of the fecal microbiota in the piglets.

Lactiplantibacillus argentoratensis AGMB00912 alleviates salmonellosis and modulates gut microbiota in weaned piglets: a pilot study

This study aimed to evaluate the efficacy of Lactiplantibacillus argentoratensis AGMB00912 (LA) in reducing Salmonella Typhimurium infection in weaned piglets. The investigation focused on the influence of LA on the gut microbiota composition, growth performance, and Salmonella fecal shedding. The results indicated that LA supplementation significantly improved average daily gain and reduced the prevalence and severity of diarrhea. Fecal analysis revealed reduced Salmonella shedding in the LA-supplemented group. Furthermore, LA notably altered the composition of the gut microbiota, increasing the levels of beneficial Bacillus and decreasing those of harmful Proteobacteria and Spirochaetes. Histopathological examination showed less intestinal damage in LA-treated piglets than in the controls. The study also observed that LA affected metabolic functions related to carbohydrate, amino acid, and fatty acid metabolism, thereby enhancing gut health and resilience against infection. Short-chain fatty acid concentrations in the feces were higher in the LA group, suggesting improved gut microbial activity. LA supplementation enriched the population of beneficial bacteria, including Streptococcus, Clostridium, and Bifidobacterium, while reducing the number of harmful bacteria, such as Escherichia and Campylobacter. These findings indicate the potential of LA as a probiotic alternative for swine nutrition, offering protective effects to the gut microbiota against Salmonella infection.

Swine farm environmental microbiome: exploring microbial ecology and functionality across farms with high and low sanitary status

Introduction

Stringent regulations in pig farming, such as antibiotic control and the ban on certain additives and disinfectants, complicate disease control efforts. Despite the evolution of microbial communities inside the house environment, they maintain stability over the years, exhibiting characteristics specific to each type of production and, in some cases, unique to a particular company or farm production type. In addition, some infectious diseases are recurrent in specific farms, while other farms never present these diseases, suggesting a connection between the presence of these microorganisms in animals or their environment. Therefore, the aim of this study was to characterise environmental microbiomes of farms with high and low sanitary status, establishing the relationships between both, health status, environmental microbial ecology and its functionality.

Methods

For this purpose, 6 pig farms were environmentally sampled. Farms were affiliated with a production company that handle the majority of the pigs slaughtered in Spain. This study investigated the relationship among high health and low health status farms using high throughput 16S rRNA gene sequencing. In addition, to identify ecologically relevant functions and potential pathogens based on the 16S rRNA gene sequences obtained, functional Annotation with PROkaryotic TAXa (FAPROTAX) was performed.

Results and Discussion

This study reveals notable differences in microbial communities between farms with persistent health issues and those with good health outcomes, suggesting a need for protocols tailored to address specific challenges. The variation in microbial populations among farms underscores the need for specific and eco-friendly cleaning and disinfection protocols. These measures are key to enhancing the sustainability of livestock farming, ensuring safer products and boosting competitive edge in the market.

Simulated Swine Digestion and Gut Microbiota Fermentation of Hydrolyzed Copra Meal

This study aimed to compare the effects of hydrolyzed copra meal (HCM) inclusion at 1% on its in vitro digestibility and the microbiota and cecum fermentation using the gut microbiota of weaned swine, targeting microbial community and short-chain fatty acids (SCF). For this reason, three treatments were considered: control (no copra meal), 1% non-hydrolyzed copra meal (CM), and 1% HCM. Non-defatted copra meal was hydrolyzed and analyzed (reducing sugars and total carbohydrates) in our laboratory. For digestion, microbiota identification, and fermentation assays, fresh fecal samples from two weaned pigs (1 month old) were used. Three replicates of each treatment were employed. HCM was more digestible, with approximately 0.68 g of hydrolysate recovered after simulated digestion compared to 0.82 g of hydrolysate recovered from CM. This was shown by Scanning Electron Microscope (SEM) images. Also, the three swine shared the majority of microbial species identified at the phylum and family levels. There were no differences (p > 0.05) between treatments in the microbial community and SCFA during fermentation. However, higher Chao-1 and Shannon indexes were observed in CM and HCM treatments. HCM was also found to be capable of preserving Actinobacterota and Proteobacteria at the phylum level, while at the family level, both treatments may help Lactobacillaceae, Peptostreptococcaceae, Lachnospiraceae, and Ruminococcaceae survive in the long term. Also, there was a potential trend of increasing acetic acid and butyric acid in the CM and HCM treatments. While HCM shows promise in potentially modulating the gut microbiota of weaned swine, additional research is required to investigate the effects of higher doses of HCM on swine performance parameters.

Tryptophan metabolism and piglet diarrhea: Where we stand and the challenges ahead

The intestinal architecture of piglets is vulnerable to disruption during weaning transition and leads to diarrhea, frequently accompanied by inflammation and metabolic disturbances (including amino acid metabolism). Tryptophan (Trp) plays an essential role in orchestrating intestinal immune tolerance through its metabolism via the kynurenine, 5-hydroxytryptamine, or indole pathways, which could be dictated by the gut microbiota either directly or indirectly. Emerging evidence suggests a strong association between piglet diarrhea and Trp metabolism. Here we aim to summarize the intricate balance of microbiota-host crosstalk by analyzing alterations in both the host and microbial pathways of Trp and discuss how Trp metabolism may affect piglet diarrhea. Overall, this review could provide valuable insights to explore effective strategies for managing piglet diarrhea and the related challenges.

Effects of Enterotoxigenic Escherichia coli Challenge on Jejunal Morphology and Microbial Community Profiles in Weaned Crossbred Piglets

Pathogenic enterotoxigenic Escherichia coli (ETEC) is a major cause of bacterial diarrhea in weaning piglets, which are vulnerable to changes in environment and feed. This study aimed to determine the effects of the ETEC challenge on piglet growth performance, diarrhea rate, jejunal microbial profile, jejunal morphology and goblet cell distribution. A total of 13 piglets from one litter were selected on postnatal day 21 and assigned to treatments with or without ETEC challenge at 1 × 108 CFUs, as ETEC group or control group, respectively. On postnatal day 28, samples were collected, followed by the detection of serum biochemical indexes and inflammatory indicators, HE staining, PAS staining and 16S rDNA gene amplicon sequencing. Results showed that the growth performance decreased, while the diarrhea rate increased for the ETEC group. The jejunum is the main segment of the injured intestine during the ETEC challenge. Compared with the control, the ETEC group displayed fewer goblet cells in the jejunum, where goblet cells are more distributed at the crypt and less distributed at the villus. In addition, ETEC piglets possessed higher abundances of the genus Desulfovibrio, genus Oxalobacter and genus Peptococus and lower abundances of the genus Prevotella 2, genus Flavonifractor and genus Blautra. In terms of alpha diversity, Chao 1 and observed features indexes were both increased for the ETEC group. Our study provides insights into jejunal histopathological impairment and microbial variation in response to ETEC infection for weaned piglets and is a valuable reference for researchers engaged in animal health research to select stress models.

Metagenomic characterization of the cecal microbiota community and functions in finishing pigs fed fermented Boehmeria nivea

Ramie (Boehmeria nivea, BN) is used as livestock forage through suitable silage fermentation owing to its nutritional value. To date, relatively few studies have investigated the effects of dietary fermented BN (FBN) on gut health in finishing pigs. The aim of the present study was to investigate the effects of dietary supplementation with 20% FBN on intestinal morphology, gene expression, and the functional response of the gut microbiota in finishing pigs. We found that FBN did not significantly affect serum antioxidant enzyme activities, ileal morphology, or the expression of genes encoding antioxidant enzymes, inflammatory cytokines, or tight junction proteins in the liver of the pigs. However, the gene expression levels of aryl hydrocarbon receptor (AHR) and interleukin 6 (IL6) were significantly downregulated in the ileum. A metagenomic analysis demonstrated that, compared with that seen in the control group, the cecal microbiota of pigs in the FBN treatment group was more closely clustered and contained a greater number of unique microbes. Bacteria were the predominant kingdom in the cecal microbiota, while Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phyla, and Streptococcus, Lactobacillus, and Prevotella were the dominant genera. Dietary FBN significantly increased the abundance of the probiotic bacterium Roseburia inulinivorans (p < 0.05). Functional analysis of the cecal microbiota showed that ABC transporter levels and glycolysis/gluconeogenesis-associated functions were diminished in FBN-fed pigs. Meanwhile, CAZyme analysis revealed that dietary FBN significantly downregulated the contents of carbohydrate-active enzymes, such as GT2, GH1, GH25, and GH13_31. In addition, cytochrome P450 analysis revealed that the abundance of CYP51 and CYP512 decreased with FBN treatment. An assessment of antibiotic resistance based on the Comprehensive Antibiotic Resistance Database (CARD) annotation indicated that the cecal microbes from pigs in the FBN treatment group had increased resistance to lincosamide, streptogramin, and chloramphenicol and reduced resistance to amikacin, isepamicin, neomycin, lividomycin, gentamicin, paromomycin, ribostamycin, and butirosin. Finally, virulence factor-related analysis showed that putative hemolysin-associated functions were decreased, whereas fibronectin-binding protein, flagella, and alginate-associated functions were increased. Taken together, our data showed that FBN supplementation exerted only minor effects on intestinal morphology and microbial community composition, suggesting that it is potentially safe for use as a supplement in the diets of finishing pigs. However, more studies are needed to validate its functionality.

The Effect of Prebiotic Supplements on the Gastrointestinal Microbiota and Associated Health Parameters in Pigs

Establishing a balanced and diverse microbiota in the GIT of pigs is crucial for optimizing health and performance throughout the production cycle. The post-weaning period is a critical phase, as it is often associated with dysbiosis, intestinal dysfunction and poor performance. Traditionally, intestinal dysfunctions associated with weaning have been alleviated using antibiotics and/or antimicrobials. However, increasing concerns regarding the prevalence of antimicrobial-resistant bacteria has prompted an industry-wide drive towards identifying natural sustainable dietary alternatives. Modulating the microbiota through dietary intervention can improve animal health by increasing the production of health-promoting metabolites associated with the improved microbiota, while limiting the establishment and proliferation of pathogenic bacteria. Prebiotics are a class of bioactive compounds that resist digestion by gastrointestinal enzymes, but which can still be utilized by beneficial microbes within the GIT. Prebiotics are a substrate for these beneficial microbes and therefore enhance their proliferation and abundance, leading to the increased production of health-promoting metabolites and suppression of pathogenic proliferation in the GIT. There are a vast range of prebiotics, including carbohydrates such as non-digestible oligosaccharides, beta-glucans, resistant starch, and inulin. Furthermore, the definition of a prebiotic has recently expanded to include novel prebiotics such as peptides and amino acids. A novel class of -biotics, referred to as "stimbiotics", was recently suggested. This bioactive group has microbiota-modulating capabilities and promotes increases in short-chain fatty acid (SCFA) production in a disproportionally greater manner than if they were merely substrates for bacterial fermentation. The aim of this review is to characterize the different prebiotics, detail the current understating of stimbiotics, and outline how supplementation to pigs at different stages of development and production can potentially modulate the GIT microbiota and subsequently improve the health and performance of animals.

The Effect of Maternal Probiotic or Synbiotic Supplementation on Sow and Offspring Gastrointestinal Microbiota, Health, and Performance

The increasing prevalence of antimicrobial-resistant pathogens has prompted the reduction in antibiotic and antimicrobial use in commercial pig production. This has led to increased research efforts to identify alternative dietary interventions to support the health and development of the pig. The crucial role of the GIT microbiota in animal health and performance is becoming increasingly evident. Hence, promoting an improved GIT microbiota, particularly the pioneer microbiota in the young pig, is a fundamental focus. Recent research has indicated that the sow's GIT microbiota is a significant contributor to the development of the offspring's microbiota. Thus, dietary manipulation of the sow's microbiota with probiotics or synbiotics, before farrowing and during lactation, is a compelling area of exploration. This review aims to identify the potential health benefits of maternal probiotic or synbiotic supplementation to both the sow and her offspring and to explore their possible modes of action. Finally, the results of maternal sow probiotic and synbiotic supplementation studies are collated and summarized. Maternal probiotic or synbiotic supplementation offers an effective strategy to modulate the sow's microbiota and thereby enhance the formation of a health-promoting pioneer microbiota in the offspring. In addition, this strategy can potentially reduce oxidative stress and inflammation in the sow and her offspring, enhance the immune potential of the milk, the immune system development in the offspring, and the sow's feed intake during lactation. Although many studies have used probiotics in the maternal sow diet, the most effective probiotic or probiotic blends remain unclear. To this extent, further direct comparative investigations using different probiotics are warranted to advance the current understanding in this area. Moreover, the number of investigations supplementing synbiotics in the maternal sow diet is limited and is an area where further exploration is warranted.

Probiotic Escherichia coli Nissle 1917 protect chicks from damage caused by Salmonella enterica serovar Enteritidis colonization

As a foodborne pathogen of global importance, Salmonella enterica serovar Enteritidis (S. Enteritidis) is a threat to public health that is mainly spread by poultry products. Intestinal Enterobacteriaceae can inhibit the colonization of S. Enteritidis and are regarded as a potential antibiotic substitute. We investigated, in chicks, the anti-S. Enteritidis effects of Escherichia coli (E. coli) Nissle 1917, the most well-known probiotic member of Enterobacteriaceae. Eighty 1-d-old healthy female AA broilers were randomly divided into 4 groups, with 20 in each group, namely the negative control (group P), the E. coli Nissle 1917-treated group (group N), the S. Enteritidis-infected group (group S) and the E. coli Nissle 1917-treated and S. Enteritidis-infected group (group NS). From d 5 to 7, chicks in groups N and NS were orally gavaged once a day with E. coli Nissle 1917 and in groups P and S were administered the same volume of sterile PBS. At d 8, the chicks in groups S and NS were orally gavaged with S. Enteritidis and in groups P and N were administered the same volume of sterile PBS. Sampling was conducted 24 h after challenge. Results showed that gavage of E. coli Nissle 1917 reduced the spleen index, Salmonella loads, and inflammation (P < 0.05). It improved intestinal morphology and intestinal barrier function (P < 0.05). S. Enteritidis infection significantly reduced mRNA expression of angiotensin-converting enzyme 2 (ACE2) and solute carrier family 6-member 19 (SLC6A19) in the cecum and the content of Gly, Ser, Gln, and Trp in the serum (P < 0.05). Pretreatment with E. coli Nissle 1917 yielded mRNA expression of ACE2 and SLC6A19 in the cecum and levels of Gly, Ser, Gln, and Trp in the serum similar to that of uninfected chicks (P < 0.05). Additionally, E. coli Nissle 1917 altered cecum microbiota composition and enriched the abundance of E. coli, Lactobacillales, and Lachnospiraceae. These findings reveal that the probiotic E. coli Nissle 1917 reduced S. Enteritidis infection and shows enormous potential as an alternative to antibiotics.

The gut microbiome and resistome of conventionally vs. pasture-raised pigs

Conventional swine production typically houses pigs indoors and in large groups, whereas pasture-raised pigs are reared outdoors at lower stocking densities. Antimicrobial use also differs, with conventionally raised pigs often being exposed to antimicrobials directly or indirectly to control and prevent infectious disease. However, antimicrobial use can be associated with the development and persistence of antimicrobial resistance. In this study, we used shotgun metagenomic sequencing to compare the gut microbiomes and resistomes of pigs raised indoors on a conventional farm with those raised outdoors on pasture. The microbial compositions as well as the resistomes of both groups of pigs were significantly different from each other. Bacterial species such as Intestinibaculum porci, Pseudoscardovia radai and Sharpea azabuensis were relatively more abundant in the gut microbiomes of pasture-raised pigs and Hallella faecis and Limosilactobacillus reuteri in the conventionally raised swine. The abundance of antimicrobial resistance genes (ARGs) was significantly higher in the conventionally raised pigs for nearly all antimicrobial classes, including aminoglycosides, beta-lactams, macrolides-lincosamides-streptogramin B, and tetracyclines. Functionally, the gut microbiomes of the two group of pigs also differed significantly based on their carbohydrate-active enzyme (CAZyme) profiles, with certain CAZyme families associated with host mucin degradation enriched in the conventional pig microbiomes. We also recovered 1043 dereplicated strain-level metagenome-assembled genomes (≥90 % completeness and <5 % contamination) to provide taxonomic context for specific ARGs and metabolic functions. Overall, the study provides insights into the differences between the gut microbiomes and resistomes of pigs raised under two very different production systems.

Maternal and/or post-weaning supplementation with Bacillus altitudinis spores modulates the microbial composition of colostrum, digesta and faeces in pigs

This study examined the effects of maternal and/or post-weaning Bacillus altitudinis supplementation on the microbiota in sow colostrum and faeces, and offspring digesta and faeces. Sows (n = 12/group) were assigned to: (1) standard diet (CON), or (2) CON supplemented with probiotic B. altitudinis spores (PRO) from day (d)100 of gestation to weaning (d26 of lactation). At weaning, offspring were assigned to CON or PRO for 28d, resulting in: (1) CON/CON, (2) CON/PRO, (3) PRO/CON, and (4) PRO/PRO, after which all received CON. Samples were collected from sows and selected offspring (n = 10/group) for 16S rRNA gene sequencing. Rothia was more abundant in PRO sow colostrum. Sow faeces were not impacted but differences were identified in offspring faeces and digesta. Most were in the ileal digesta between PRO/CON and CON/CON on d8 post-weaning; i.e. Bacteroidota, Alloprevotella, Prevotella, Prevotellaceae, Turicibacter, Catenibacterium and Blautia were more abundant in PRO/CON, with Firmicutes and Blautia more abundant in PRO/PRO compared with CON/CON. Lactobacillus was more abundant in PRO/CON faeces on d118 post-weaning. This increased abundance of polysaccharide-fermenters (Prevotella, Alloprevotella, Prevotellaceae), butyrate-producers (Blautia) and Lactobacillus likely contributed to previously reported improvements in growth performance. Overall, maternal, rather than post-weaning, probiotic supplementation had the greatest impact on intestinal microbiota.

Butyrogenic effect of galactosyl and mannosyl carbohydrates and their regulation on piglet intestinal microbiota

Diarrhea is a global problem that causes economic losses in the pig industry. There is a growing attention on finding new alternatives to antibiotics to solve this problem. Hence, this study aimed to compare the prebiotic activity of low-molecular-weight hydrolyzed guar gum (GMPS) with commercial manno-oligosaccharide (MOS) and galacto-oligosaccharide (GOS). We further identified their combined effects along with probiotic Clostridium butyricum on regulating the intestinal microbiota of diarrheal piglet by in vitro fermentation. All the tested non-digestible carbohydrates (NDCs) showed favorable short-chain fatty acid-producing activity, and GOS and GMPS showed the highest production of lactate and butyrate, respectively. After 48 h of fermentation, the greatest enhancement in the abundance of Clostridium sensu stricto 1 was observed with the combination of GMPS and C. butyricum. Notably, all the selected NDCs significantly decreased the abundances of pathogenic bacteria genera Escherichia-Shigella and Fusobacterium and reduced the production of potentially toxic metabolites, including ammonia nitrogen, indole, and skatole. These findings demonstrated that by associating with the chemical structure, GMPS exhibited butyrogenic effects in stimulating the proliferation of C. butyricum. Thus, our results provided a theoretical foundation for further application of galactosyl and mannosyl NDCs in the livestock industry. KEY POINTS: • Galactosyl and mannosyl NDCs showed selective prebiotic effects. • GMPS, GOS, and MOS reduced pathogenic bacteria and toxic metabolites production. • GMPS specifically enhanced the Clostridium sensu stricto 1 and butyrate production.

Dynamic distribution of gut microbiota in cattle at different breeds and health states

Weining cattle is a precious species with high tolerance to cold, disease, and stress, and accounts for a large proportion of agricultural economic output in Guizhou, China. However, there are gaps in information about the intestinal flora of Weining cattle. In this study, high-throughput sequencing were employed to analyze the intestinal flora of Weining cattle (WN), Angus cattle (An), and diarrheal Angus cattle (DA), and explore the potential bacteria associated with diarrhea. We collected 18 fecal samples from Weining, Guizhou, including Weining cattle, Healthy Angus, and Diarrheal Angus. The results of intestinal microbiota analysis showed there were no significant differences in intestinal flora diversity and richness among groups (p > 0.05). The abundance of beneficial bacteria (Lachnospiraceae, Rikenellaceae, Coprostanoligenes, and Cyanobacteria) in Weining cattle were significantly higher than in Angus cattle (p < 0.05). The potential pathogens including Anaerosporobacter and Campylobacteria were enriched in the DA group. Furthermore, the abundance of Lachnospiraceae was very high in the WN group (p < 0.05), which might explain why Weining cattle are less prone to diarrhea. This is the first report on the intestinal flora of Weining cattle, furthering understanding of the relationship between intestinal flora and health.

Intestine microbiota and SCFAs response in naturally Cryptosporidium-infected plateau yaks

Diarrhea is a severe bovine disease, globally prevalent in farm animals with a decrease in milk production and a low fertility rate. Cryptosporidium spp. are important zoonotic agents of bovine diarrhea. However, little is known about microbiota and short-chain fatty acids (SCFAs) changes in yaks infected with Cryptosporidium spp. Therefore, we performed 16S rRNA sequencing and detected the concentrations of SCFAs in Cryptosporidium-infected yaks. Results showed that over 80,000 raw and 70,000 filtered sequences were prevalent in yak samples. Shannon (p<0.01) and Simpson (p<0.01) were both significantly higher in Cryptosporidium-infected yaks. A total of 1072 amplicon sequence variants were shared in healthy and infected yaks. There were 11 phyla and 58 genera that differ significantly between the two yak groups. A total of 235 enzymes with a significant difference in abundance (p<0.001) were found between healthy and infected yaks. KEGG L3 analysis discovered that the abundance of 43 pathways was significantly higher, while 49 pathways were significantly lower in Cryptosporidium-infected yaks. The concentration of acetic acid (p<0.05), propionic acid (p<0.05), isobutyric acid (p<0.05), butyric acid (p<0.05), and isovaleric acid was noticeably lower in infected yaks, respectively. The findings of the study revealed that Cryptosporidium infection causes gut dysbiosis and results in a significant drop in the SCFAs concentrations in yaks with severe diarrhea, which may give new insights regarding the prevention and treatment of diarrhea in livestock.

Influence of dietary n-3 long-chain fatty acids on microbial diversity and composition of sows' feces, colostrum, milk, and suckling piglets' feces

Introduction

Very little is known about the impact of n-3 long-chain fatty acids (n-3 LCFAs) on the microbiota of sows and their piglets. The aim of this study was to evaluate the effect of n-3 LCFA in sow diets on the microbiota composition of sows' feces, colostrum, and milk as well as that of piglets' feces.

Methods

Twenty-two sows were randomly assigned to either a control or an n-3 LCFA diet from service to weaning. Sows' and piglets' performance was monitored. The gestating and lactating sows' microbiomes in feces, colostrum, and milk were characterized by 16s ribosomal RNA gene sequencing. The fecal microbiome from the two lowest (>800 g) and the two highest birth weight piglets per litter was also characterized, and the LPS levels in plasma were analyzed at weaning.

Results and Discussion

n-3 LCFA increased microbiota alpha diversity in suckling piglets' and gestating sows' feces. However, no effects were observed in colostrum, milk, or lactating sows' feces. Dietary n-3 LCFA modified the microbiota composition of gestating sows' feces, milk, and suckling piglets' feces, without affecting lactating sows' feces or colostrum. In gestating sows' feces and milk, the decrease in genus Succinivibrio and the increase of Proteobacteria phylum, due to the increased genera Brenneria and Escherichia, respectively, stand out. In the feces of suckling piglets, the higher abundance of the beneficial genus Akkermansia and Bacteroides, and different species of Lactobacillus are highlighted. In addition, positive correlations for families and genera were found between lactating sows' feces and milk, milk and suckling piglets' feces, and lactating sows' feces and suckling piglets' feces. To conclude, dietary n-3 LCFA had a positive impact on the microbiome of suckling piglet's feces by increasing microbial diversity and some beneficial bacteria populations, had a few minor modifications on the microbiome of milk and gestating sows' feces and did not change the microbiome in lactating sows' feces or colostrum. Therefore, this study shows the effect of dietary n-3 LCFA on the microbiota of sows, colostrum, milk, and suckling piglets during the lactation period providing crucial information on the microbiota status at the early stages of life, which have an impact on the post-weaning.

Remodeling of the microbiota improves the environmental adaptability and disease resistance in Tibetan pigs

Introduction

The establishment of intestinal microbiota and the maintenance of its equilibrium structure plays an important role in Tibetan pigs during different growth stages. Understanding the structure and function of the intestinal microbiota at different growth stages of Tibetan pigs can provide a theoretical basis for guiding nutritional regulation and feeding management in different stages.

Methods

Fecal samples were collected from the Tibetan piglets at different growth stages, and the 16S rRNA was sequenced to analyze the changes of intestinal microbiota.

Results

Alpha and Beta diversity indexes showed that the diversity of the intestinal microbiota did not change during the three growth stages, and the main components of intestinal microbiota were not significantly different. At the phylum level, Firmicutes and Bacteroidetes were dominant and abundant at different growth stages and were not restricted by age. At the genus level, Streptococcus, Lactobacillus, and Bifidobacterium were the most dominant in the TP10d and TP40d groups, Streptococcus was the most dominant in the TP100d group, followed by Treponema_2 and Lactobacillus. Fusobacteria, Gluconobacter, and Synergistetes were found to be specific genera of 10-day-old Tibetan piglets by LEfSe combined with LDA score. The change of diet made Tenericutes and Epsilonbacteraeota, which are closely related to digestive fiber, become specific bacteria at the age of 40 days. With the consumption of oxygen in the intestine, obligate anaerobes, such as Verrucomicrobia, Fibrobacter, and Planctomycetes, were the characteristic genera of 100 days. KEGG function prediction analysis showed that the intestinal microbiota function of Tibetan pigs changed dynamically with the growth and development of Tibetan piglets.

Discussion

In conclusion, the structure and composition of the intestinal microbiota of Tibetan pigs are significantly different at different growth and development stages, which plays an important role in their immune performance.

Lower abundance of Bacteroides and metabolic dysfunction are highly associated with the post-weaning diarrhea in piglets

Growing evidences show a direct link between diarrhea and disorders of gut microbiota in pigs. However, whether there are microbial markers associated with post-weaning diarrhea remains unknown. In the current study, we compared the microbial community, functions and metabolites between healthy weaned piglets (group H, n=7) and piglets with post-weaning diarrhea (group D, n=7), in order to find out diarrhea associated microbial markers. Each of 7 fecal samples was collected from H and D piglets (weaned at 21 d and sampled at 26 d). The metagenomic and untargeted metabolomic analysis revealed that the microbial composition, function and metabolic profile in D pigs was considerably reshaped, including the reduced abundance and number of Bacteroides, which significantly correlated with the diarrhea status of host. The carbohydrate metabolism, biosynthesis and metabolism, lipid metabolism, amino acid metabolism, and the activity of glycan and carbohydrates digestion related enzymes showed extensively down-regulated in D pigs compared with H pigs. Diarrhea significantly changed the metabolic profiles of fecal microbiota, and most of the altered metabolites were negatively or positively correlated with the change in the abundance of Bacteroides. In conclusion, the lower abundance of Bacteroides and its associated metabolic dysfunction may be regarded as microbial markers of physiological post-weaning diarrhea in piglets.

Maternal Dietary Forsythia suspensa Extract Supplementation Induces Changes in Offspring Antioxidant Status, Inflammatory Responses, Intestinal Development, and Microbial Community of Sows

This experiment aims to investigate the effect of maternal diet supplemented with Forsythia suspensa extract (FSE) on the performance, antioxidant status, inflammatory responses, intestinal development, and microbial community of sows. A total of 24 gestating sows (Landrace × Yorkshire) were assigned to 2 treatments with 12 sows per treatment. From d 107 of gestation to d 21 of lactation, sows were supplemented with a basal diet as control (CON) or an FSE diet (basal diet + 100 mg/kg FSE). Compared with CON, sows fed FSE showed lower (P &lt; 0.05) wean-to-estrus interval, body weight loss, and higher (P &lt; 0.05) average daily gain of suckling piglet. Sows fed FSE had reduced (P &lt; 0.05) serum malondialdehyde (MDA) content and enhanced (P &lt; 0.05) catalase and glutathione peroxidase (GSH-Px) contents at farrowing and weaning compared with CON. The suckling piglets of FSE-fed sows had increased (P &lt; 0.05) mRNA expressions of nuclear factor erythroid-2 related factor 2, heme oxygenase-1 in the liver, and lower (P &lt; 0.05) serum MDA content on d 0, 7, and 14 of lactation. Sows fed FSE had lower (P &lt; 0.05) serum tumor necrosis factor-α (TNF-α) and interleukin-8 (IL-8) contents at farrowing and reduced (P &lt; 0.05) serum IL-6 and IL-8 contents at weaning compared with CON. Piglets from FSE-fed sows had enhanced (P ≤ 0.05) villus height and villus height to crypt depth ratio in the jejunum, and higher (P &lt; 0.05) protein expression of Occludin in jejunal mucosa compared with CON. Sows fed FSE tended to have higher (P = 0.09) relative abundance of Lactobacillus at genus level in feces at weaning compared with CON. Our results showed maternal diet supplemented with FSE in lactating sows could effectively induce improvement of performance, antioxidant status, anti-inflammatory function, intestinal morphology, barrier function, and microbial community.

Early Weaning and Milk Substitutes Affect the Gut Microbiome, Metabolomics, and Antibody Profile in Goat Kids Suffering From Diarrhea

Early weaning and milk substitutes increase the incidence of diarrhea in young ruminants, which may modify their gut microbiota, metabolism, immunity, and health. The aim of the study was to determine if early weaning and milk substitutes affect the gut microbiota, metabolism, and immunological status of goat kids suffering from diarrhea. The 16S rRNA gene and metagenomic sequencing in feces and serum metabolomics of early-weaned and artificially reared goat kids suffering from diarrhea (DK group) and healthy goat kids reared by their mothers (HK group) were analyzed. The serum biochemistry and immunoglobulin concentration were also determined. Several probiotics, such as Streptococcus and Lactobacillus, were higher in the feces of the DK group than in feces of the HK group. Ruminococcus sp. was elevated in the feces of HKs, likely being a biomarker for goat health. Taking all the carbohydrate-active enzyme (CAZyme) families into consideration, 20 CAZyme families were different between the groups. Compared with the DK group, the relative quantity of glycoside hydrolases (GH) and glycosyltransferase (GT) families in the HK group decreased. GT70 was only identified in HK kids participating in the activity of β-glucuronosyltransferase during the carbohydrate metabolism. Overall, 24 metabolites were different between the groups, which were mainly involved in protein digestion and absorption, cyanoamino acid metabolism, and cholesterol metabolism. The concentrations of immunoglobulins G and M were significantly lower in the DK than in the HK group. In conclusion, our study characterized the fecal microbiota, metabolism, and immunological status of early-weaned and artificially reared goat kids suffering from diarrhea.

Comparative analysis of gut microbiota in healthy and diarrheic yaks

BACKGROUND

Yak (Bos grunniens) mainly inhabiting Tibet Plateau, displayed a high incidence of diarrhea due to harsh living environment and nutritional deficit. Gut microbial community has been reported to be closely related to many diseases including diabetes, obesity and inflammatory bowel disease, but information regarding diarrheic influence on gut microbiota in yaks remains scarce. Here, this study was performed to investigate the gut bacterial and fungal alternations of diarrheic yaks.

RESULTS

Results revealed that the gut bacterial and fungal communities of diarrheic yaks showed a distinct decline in alpha diversity, accompanied by significant shifts in taxonomic compositions. Specifically, diarrhea caused a distinct increase in the relative abundance of 1 phylum and 8 genera as well as a distinct decrease in 3 phyla and 30 genera. Fungal taxonomic analysis indicated that the relative richness of 1 phylum and 2 genera dramatically increased, whereas the relative richness of 2 phylum and 43 genera significantly decreased during diarrhea. Surprisingly, 2 bacterial genera and 5 fungal genera even cannot be detected in the gut microbiota of diarrheic yaks.

CONCLUSIONS

In summary, this study indicated that the gut bacterial and fungal compositions and diversities of yaks altered significantly during diarrhea. Moreover, these findings also contribute to understanding the gut microbial composition and diversity of yaks and developing strategies to alleviate and prevent diarrhea from gut microbial perspective.

Disordered Gut Microbiota Correlates With Altered Fecal Bile Acid Metabolism and Post-cholecystectomy Diarrhea

Post-cholecystectomy diarrhea (PCD) is a common complication of gallbladder removal, and gut microbiota changes have been determined in PCD patients. Bile acid diarrhea (BAD) is supposed to be the main pathogenic factor for PCD due to the disrupted fecal bile acid metabolism in diarrheal patients. However, the profiling of bile acid metabolite alteration in PCD is unclear and whether changed gut microbiota and fecal bile acid metabolism are correlated is also underdetermined. The fecal bile acid metabolites from fecal samples were profiled by targeted UPLC/MS (ultra-high-performance liquid chromatography coupled with a triple-quadrupole mass spectrometer) and the composition of fecal bile acid metabolites in PCD patients was demonstrated to be distinct from those in Non-PCD and HC groups. In addition, the quantification of bile acid excretion in feces of diarrheal patients was significantly elevated. Furthermore, 16S rRNA sequencing results revealed that PCD patients had the lowest operational taxonomic units (OTU) and significant reduction in microbial richness and evenness. Bacterial composition was remarkably shifted in PCD patients, which mainly lay in dominated phyla Firmicutes and Bacteroidota. Besides, the co-abundance network among genus bacteria declined in PCD. Among the genera, Prevotella, Enterococcus, and Erysipelotrichaceae_UCG-003 were enriched, but Alistipes, Bacteroides, Ruminococcus, and Phascolarctobacterium were reduced. Moreover, these disease-linked genera were closely associated with several diarrheal phenotypes. Notably, changed bile acid metabolites exhibited strong correlations with gut microbiota as well. Conclusively, this study reveals associations between PCD-linked microbes and bile acid metabolites, which may synergistically correlate to postoperative diarrhea.

Immunomodulation Potential of Probiotics: A Novel Strategy for Improving Livestock Health, Immunity, and Productivity

Over the past decade, the use of probiotics as feed supplements in animal production has increased considerably due to the ban on antibiotic growth promoters in livestock. This review provides an overview of the current situation, limitation, and prospects for probiotic formulations applied to livestock. Recently, the use of probiotics in livestock has been suggested to significantly improve their health, immunity, growth performance, nutritional digestibility, and intestinal microbial balance. Furthermore, it was reported that the use of probiotics in animals was helpful in equilibrating their beneficial microbial population and microbial turnover via stimulating the host immune response through specific secretions and competitive exclusion of potentially pathogenic bacteria in the digestive tract. Recently, there has been great interest in the understanding of probiotics targeted diet and its ability to compete with harmful microbes and acquire their niches. Therefore, the present review explores the most commonly used probiotic formulations in livestock feed and their effect on animal health. In summary, this article provides an in-depth knowledge about the formulation of probiotics as a step toward a better alternative to antibiotic healthy growth strategies.

Alterations of Suckling Piglet Jejunal Microbiota Due to Infection With Porcine Epidemic Diarrhea Virus and Protection Against Infection by Lactobacillus salivarius

The high mortality of neonatal piglets due to porcine epidemic diarrhea virus (PEDV) infection has caused huge economic losses to the pig industry. The intestinal microbiota is an important barrier against invaders entering the gastrointestinal route. In this study, we examined the differences between intestinal microbiota of PEDV-infected and healthy piglets. According to the viral copy numbers, 16 crossbred (Landrace-Yorkshire) piglets were divided into three groups: uninfected, low virus load, and high virus load groups. Next, 16S rRNA sequencing was performed to determine the microbiota composition in jejunal content and jejunal mucosal samples from the three groups. PEDV infection induced an imbalance in the microbiota of both jejunal content and jejunal mucosa. The abundance of phylum Firmicutes was higher in uninfected piglets than in infected piglets, whereas the abundance of Proteobacteria was lower in uninfected piglets. Principal coordinate analysis showed significant separation of jejunal microbiota between different groups. Linear discriminant analysis (LDA) effect size (LEfSe) identified Lactobacillus salivarius as a potential biomarker among three groups at the level of species. Then, in vitro, L. salivarius was able to suppress the infection of PEDV to IPEC-J2 cells and decreased the expression of GRP78 (Glucose-regulating protein 78). In addition, we detected the mRNA expression of genes involved in the FAK/PI3K/Akt signaling pathway. When IPEC-J2 cells were treated with L. salivarius before PEDV infection, the mRNA expression levels of ITGA1, ITGA5, ITGB5, FAK, PIK3R1, PIK3CA and AKT1 were significantly higher than those in the control cells (without treatment) at different times post-infection, indicating that L. salivarius may upregulate the FAK/PI3K/Akt signaling pathway in IPEC-J2 cells to resist PEDV infection. In summary, PEDV infection altered microbial communities in both jejunal content and jejunal mucosa. L. salivarius has a protective effect against PEDV infection in IPEC-J2 cells. This study provides a potentially effective strategy to prevent the occurrence and control the spread of PED in the pig production.

Impacts of feeding organic acid-based feed additives on diarrhea, performance, and fecal microbiome characteristics of pigs after weaning challenged with an enterotoxigenic strain of Escherichia coli

Post weaning diarrhea (PWD) caused by enterotoxigenic strains of E. coli (ETEC) remains a major problem in the industry, causing decreases in performance and survival of weaned pigs. Traditionally, antimicrobials have been used for its mitigation/control. This study tested the hypothesis that a combination of two organic acid (OA)-based commercial feed additives, Presan FX [an OA, medium-chain fatty acid (MCFA) and phenolic compound-based product] and Fysal MP (free and buffered OA based on formic acid), would reduce PWD and improve post-weaning performance in pigs challenged with an F4-ETEC. This combination was assessed against a Negative control diet without any feed additives and a diet containing amoxicillin. Combined with a reduction in temperature during the infection period, inoculation with F4-ETEC resulted in 81% of pigs developing diarrhea, but with no differences between treatments (P > 0.05). However, between days 14 to 20 of the study and due to colonization by Salmonella serovars, pigs fed the combination of Presan FX and Fysal MP showed less (P = 0.014) diarrhea commensurate with a lower (P = 0.018) proportion of Salmonella numbers relative to total bacterial numbers. This caused less (P = 0.049) therapeutic antibiotic administrations relative to the diet with amoxicillin during this time. The diversity of bacteria within amoxicillin-treated pigs was lower (P = 0.004) than the diversity in control or Presan FX + Fysal MP-treated pigs (P = 0.01). Pair-wise comparisons showed that amoxicillin-treated pigs had altered (P < 0.001) fecal microbial communities relative to both Presan FX + Fysal MP-treated pigs and control pigs. Amoxicillin-treated pigs were characterized by an increased abundance of bacterial families generally linked to inflammation and dysbiosis in the gastrointestinal tract (GIT), whereas Presan FX + Fysal MP-treated pigs had an increased abundance of bacterial families considered beneficial commensals for the GIT. Control pigs were characterized by an increased abundance of Spirochaetaceae associated with healthy piglets, as well as bacterial families associated with reduced feed intake and appetite. The combination of two OA-based feed additives did not reduce the incidence of F4 ETEC-associated diarrhea nor enhance performance. However, the combination markedly reduced diarrhea caused by Salmonella that occurred following the ETEC infection, commensurate with less therapeutic administrations relative to the diet with amoxicillin.

Gut Microbial Alterations in Diarrheal Baer's Pochards (Aythya baeri)

The structure and composition of gut microbiota correlate with the occurrence and development of host health and disease. Diarrhea can cause alterations in gut microbiota in animals, and the changes in the gut microbial structure and composition may affect the development of diarrhea. However, there is a scarcity of information on the effects of diarrhea on gut fungal composition and structure, particularly in Baer's pochard (Aythya baeri). The current study was performed for high-throughput sequencing of the fungal-specific internal transcribed spacer 1 (ITS-1) to detect the differences of gut mycobiota in healthy and diarrheal Baer's pochard. Results showed that the gut mycobiota not only decreased significantly in diversity but also in structure and composition. Statistical analysis between two groups revealed a significant decrease in the abundance of phylum Rozellomycota, Zoopagomycota, Mortierellomycota, and Kickxellomycota in diarrheal Baer's pochard. At the genus levels, fungal relative abundance changed significantly in 95 genera, with 56 fungal genera, such as Wickerhamomyces, Alternaria, Penicillium, Cystofilobasidium, and Filobasidium, increasing significantly in the gut of the diarrheal Baer's pochard. In conclusion, the current study revealed the discrepancy in the gut fungal diversity and community composition between the healthy and diarrheal Baer's pochard, laying the basis for elucidating the relationship between diarrhea and the gut mycobiota in Baer's pochard.

Neonatal Piglets Are Protected from Clostridioides difficile Infection by Age-Dependent Increase in Intestinal Microbial Diversity

While Clostridioides difficile is recognized as an important human pathogen, it is also a significant cause of gastroenteritis and associated diarrhea in neonatal pigs. Since clinical disease is rarely diagnosed in piglets older than 1 week of age, it is hypothesized that natural resistance is associated with the increased complexity of the intestinal microbiota as the animals age. To test this, piglets were challenged with C. difficile (ribotype 078/toxinotype V) at times ranging from 2 to 14 days of age, and the severity of disease and microbial diversity of the cecal microbiota were assessed. Half of the piglets that were challenged with C. difficile at 2 and 4 days of age developed clinical signs of disease. The incidence of disease decreased rapidly as the piglets aged, to a point where none of the animals challenged after 10 days of age showed clinical signs. The cecal microbial community compositions of the piglets also clustered by age, with those of animals 2 to 4 days old showing closer relationships to one another than to those of older piglets (8 to 14 days). This clustering occurred across litters from 4 different sows, providing further evidence that the resistance to C. difficile disease in piglets greater than 1 week old is directly related to the diversity and complexity of the intestinal microbiota. IMPORTANCE C. difficile is an important bacterial pathogen that is the most common cause of infections associated with health care in the United States. It also causes significant morbidity and mortality in neonatal pigs, and currently there are no preventative treatments available to livestock producers. This study determined the age-related susceptibility of piglets to C. difficile over the first 2 weeks of life, along with documenting the natural age-related changes that occurred in the intestinal microbiota over the same time period in a controlled environment. We observed that the populations of intestinal bacteria within individual animals of the same age, regardless of litter, showed the highest degree of similarity. Identifying bacterial species associated with the acquisition of natural resistance observed in older pigs could lead to the development of new strategies to prevent and or treat disease caused by C. difficile infection.

Integrated Bacterial and Fungal Diversity Analysis Reveals the Gut Microbial Alterations in Diarrheic Giraffes

Gut microbiota has been demonstrated to be associated with multiple gastrointestinal diseases, but information regarding the gut microbial alternations in diarrheic giraffe remains scarce. Here, 16S rDNA and ITS gene amplicon sequencing were conducted to investigate the gut microbial composition and variability in diarrheic giraffes. Results demonstrated that Firmicutes and Proteobacteria were the most dominant phyla in the gut bacterial community, whereas Ascomycota and Basidiomycota were observed to be predominant in the gut fungal community regardless of health status. However, the species and relative abundance of preponderant bacterial and fungal genera in healthy and diarrheic giraffes were different. In contrast to the relatively stabilized gut fungal community, gut bacterial community displayed a significant decrease in the alpha diversity, accompanied by distinct changes in taxonomic compositions. Bacterial taxonomic analysis revealed that the relative abundances of eight phyla and 12 genera obviously increased, whereas the relative abundances of two phyla and eight genera dramatically decreased during diarrhea. Moreover, the relative richness of five fungal genera significantly increased, whereas the relative richness of seven fungal genera significantly declined in diarrheic giraffes. Taken together, this study demonstrated that diarrhea could cause significant alternations in the gut microbial composition of giraffes, and the changes in the gut bacterial community were more significant than those in the gut fungal community. Additionally, investigating the gut microbial characteristics of giraffes in different health states is beneficial to provide a theoretical basis for establishing a prevention and treatment system for diarrhea from the gut microbial perspective.

The Impact of Weaning Stress on Gut Health and the Mechanistic Aspects of Several Feed Additives Contributing to Improved Gut Health Function in Weanling Piglets-A Review

Simple Summary

The current review aimed to provide an overview on the problems associated with weaning with a special focus on gut health, and also highlighted the nutritional approach using different kinds of feed additives and their mechanistic aspects in mitigating production inefficiencies and gut health dysfunction in weanling pigs.

Abstract

Newly weaned pig encounters psychosocial, physical, and nutritional stressors simultaneously when their immune system is not fully developed. These stressors have a cumulative effect on the immune response that contributes to the post-weaning growth lag which is characterized by depression in feed intake, reduced or negative growth rates, and increased susceptibility to pathogens in the first 24 to 48 h post-weaning. Consequently, the intestinal integrity, and digestive and absorptive capacity are impaired, and there is an increase in intestinal oxidative stress. It also causes the shifts in the taxonomic and functional properties of intestinal microbiome abruptly, thereby adversely affecting the health and performance of animals. It has been suggested that the effects of weaning stress on immune functions, intestinal barrier functions, and nervous system function in early weaned pigs extends into adulthood. The inclusion of different types of feed additives into the diet have been reported to alleviate the negative effects of weaning stress. The objective of this paper was to provide an overview on how the weaning stress affects gut health and the impact it has on production efficiencies, as well as the mechanistic aspects of several feed additives applied in reducing the weaning associated gut health problems and performance inefficiencies.

Characterization of the fecal microbiota of sows and their offspring from German commercial pig farms

Strategies to combat microbiota-associated health problems are of high interest in pig production. Successful intervention strategies with beneficial long-term effects are still missing. Most studies on pig microbiota have been conducted under standardized experimental conditions, but the situation in commercial farms differs dramatically. This study describes the fecal microbiota in German commercial pig farms under practical conditions. The study is part of the larger project "Optibiom" that aims to use bacterial composition and farm metadata to formulate tailor-made solutions for farm-specific health maintenance strategies. Special consideration is given to the sow-piglet relationship. Fecal samples from sows and their piglets were collected at two time points each in 20 different farms (sows ante- and postpartum and piglets before and after weaning). The extracted DNA was sequenced with Illumina 16S rDNA sequencing. For data analysis and visualization, differential abundance analyses, as well as hierarchical clustering and nonmetric multidimensional scaling (NMDS) were performed. A new "family unit" was implemented to compare farms based on the association between the microbiota in sows and their offspring. There are distinct changes in the microbial communities in sows before and after birth as well as in suckling and post-weaning piglets. The suckling pig microbiota is particularly different from all other groups and shows a lower bacterial diversity. While dominant genera in antepartum sows further displace the abundance of non-dominant genera postpartum, the opposite was true for piglets, where non-dominant bacteria in the suckling phase became dominant after weaning. The family unit for sows and their piglets led to separate cluster formation for some farms. The results indicate that the sow-piglet relationship is one driving force for the observed differences of the pig farms. The next step in the analysis will be the combination of metadata (feeding, housing and management practices) to find farm-specific differences that can be exploited to formulate a farm-specific health maintenance strategy.

Effects of Dietary Supplementation with Protected Sodium Butyrate on Gut Microbiota in Growing-Finishing Pigs

Simple Summary

The addition of protected sodium butyrate to the diet of fattening pigs during the whole fattening period (≈90 days) at a dose of 3 kg per ton of feed, did not modify the overall richness of microbiota composition of the pigs at slaughter, but may have caused some significant changes in specific taxa that could be associated with better gut health parameters. In any case, these results should be taken with caution, as the role of a given taxon on the pig’s gut health is influenced by numerous variables such as age, diet, environment, treatments, other taxa present, infections, or even the physiological status of the animal.

Abstract

The study assessed changes in the gut microbiota of pigs after dietary supplementation with protected sodium butyrate (PSB) during the growing-fattening period (≈90 days). One gram of colon content from 18 pigs (9 from the treatment group -TG- and 9 from the control group -CG-) was collected. Bacterial DNA was extracted and 16S rRNA high-throughput amplicon sequencing used to assess microbiota changes between groups. The groups shared 75.4% of the 4697 operational taxonomic units identified. No differences in alpha diversity were found, but significant differences for some specific taxa were detected between groups. The low-represented phylum Deinococcus-Thermus, which is associated with the production of carotenoids with antioxidant, anti-apoptotic, and anti-inflammatory properties, was increased in the TG (p = 0.032). Prevotellaceae, Lachnospiraceae, Peptostreptococcaceae, Peptococcaceae, and Terrisporobacter were increased in the TG. Members of these families have the ability to ferment complex dietary polysaccharides and produce larger amounts of short chain fatty acids. Regarding species, only Clostridium butyricum was increased in the TG (p = 0.048). Clostridium butyricum is well-known as probiotic in humans, but it has also been associated with overall positive gut effects (increased villus height, improved body weight, reduction of diarrhea, etc.) in weanling pigs. Although the use of PSB did not modify the overall richness of microbiota composition of these slaughter pigs, it may have increased specific taxa associated with better gut health parameters.

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.

Evaluation of Tannin Extracts, Leonardite and Tributyrin Supplementation on Diarrhoea Incidence and Gut Microbiota of Weaned Piglets

The effects of the dietary administration of a combination of Quebracho and Chestnut tannins, leonardite and tributyrin were evaluated in weaned piglets. A total of 168 weaned piglets (Landrace × Large White) were randomly allotted to two experimental groups (6 pens/group, 14 piglets/pen). Animals were fed a basal control diet (CTRL) and a treatment diet (MIX) supplemented with 0.75% tannin extracts, 0.25% leonardite and 0.20% tributyrin for 28 days. Individual body weight and feed intake were recorded weekly. Diarrhoea incidence was recorded by a faecal scoring scale (0-3; considering diarrhoea ≥ 2). At 0 and 28 days, faecal samples were obtained from four piglets/pen for microbiological and chemical analyses of faecal microbiota, which were then assessed by V3-V4 region amplification sequencing. At 28 days, blood from two piglets/pen was sampled to evaluate the serum metabolic profile. After 28 days, a reduction in diarrhoea incidence was observed in the MIX compared to CTRL group (p < 0.05). In addition, compared to CTRL, MIX showed a higher lactobacilli:coliform ratio and increased Prevotella and Fibrobacter genera presence (p < 0.01). The serum metabolic profile showed a decreased level of low-density lipoproteins in the treated group (p < 0.05). In conclusion, a combination of tannin extract, leonardite and tributyrin could decrease diarrhoea incidence and modulate the gut microbiota.

Microbiome Analysis Reveals the Dynamic Alternations in Gut Microbiota of Diarrheal Giraffa camelopardalis

The ruminant gut microbial community's importance has been widely acknowledged due to its positive roles in physiology, metabolism, and health maintenance. Diarrhea has been demonstrated to cause adverse effects on gastrointestinal health and intestinal microecosystem, but studies regarding diarrheal influence on gut microbiota in Giraffa camelopardalis have been insufficient to date. Here, this study was performed to investigate and compare gut microbial composition and variability between healthy and diarrheic G. camelopardalis. The results showed that the gut microbial community of diarrheal G. camelopardalis displayed a significant decrease in alpha diversity, accompanied by distinct alterations in taxonomic compositions. Bacterial taxonomic analysis indicated that the dominant bacterial phyla (Proteobacteria, Bacteroidetes, and Firmicutes) and genera (Escherichia Shigella and Acinetobacter) of both groups were the same but different in relative abundance. Specifically, the proportion of Proteobacteria in the diarrheal G. camelopardalis was increased as compared with healthy populations, whereas Bacteroidetes, Firmicutes, Tenericutes, and Spirochaetes were significantly decreased. Moreover, the relative abundance of one bacterial genus (Comamonas) dramatically increased in diarrheic G. camelopardalis, whereas the relative richness of 18 bacterial genera decreased compared with healthy populations. Among them, two bacterial genera (Ruminiclostridium_5 and Blautia) cannot be detected in the gut bacterial community of diarrheal G. camelopardalis. In summary, this study demonstrated that diarrhea could significantly change the gut microbial composition and diversity in G. camelopardalis by increasing the proportion of pathogenic to beneficial bacteria. Moreover, this study first characterized the distribution of gut microbial communities in G. camelopardalis with different health states. It contributed to providing a theoretical basis for establishing a prevention and treatment system for G. camelopardalis diarrhea.

The Gastrointestinal Microbiota of the Common Marmoset (Callithrix jacchus)

The microbiota is heavily involved in both health and disease pathogenesis, but defining a normal, healthy microbiota in the common marmoset has been challenging. The aim of this review was to systematically review recent literature involving the gastrointestinal microbiome of common marmosets in health and disease. Twelve sources were included in this review. The gut microbiome composition was reviewed across institutions worldwide, and taxonomic shifts between healthy individuals were described. Unlike the human gut microbiome, which is dominated by Firmicutes and Bacteroidetes, the marmoset gut microbiome shows great plasticity across institutions, with 5 different phyla described as dominant in different healthy cohorts. Genera shared across institutions include Anaerobiospirillum, Bacteroides, Bifidobacterium, Collinsella, Fusobacterium, Megamonas, Megasphaera, Phascolarctobacterium, and Prevotella. Shifts in the abundance of Prevotella or Bifidobacterium or invasion by pathogens like Clostridium perfringens may be associated with disease. Changes in microbial composition have been described in healthy and diseased marmosets, but factors influencing the severe changes in microbial composition have not been established. Multi-institutional, prospective, and longitudinal studies that utilize multiple testing methodologies are required to determine sources of variability in the reporting of marmoset microbiomes. Furthermore, methods of microbial manipulation, whether by diet, enrichment, fecal microbiome transplantation, etc, need to be established to modulate and maintain robust and resilient microbiome communities in marmoset colonies and reduce the incidence of idiopathic gastrointestinal disease.

Dietary osteopontin-enriched algal protein as nutritional support in weaned pigs infected with F18-fimbriated enterotoxigenic Escherichia coli

This study investigated the effects of dietary osteopontin (OPN)-enriched algal protein on growth, immune status, and fecal fermentation profiles of weaned pigs challenged with a live infection of F18-fimbriated enterotoxigenic E. coli (ETEC). At 21 d of age, 54 pigs (5.95 ± 0.28 kg BW; blocked by BW) were allotted to 1 of 3 experimental groups combining dietary and health statuses. A control diet, containing 1% wild-type algal protein, was fed to both sham-inoculated (NC) and ETEC-inoculated (PC) pigs, while the test diet contained 1% OPN-enriched algal protein as fed only to ETEC-inoculated pigs (OA). All pigs received their assigned dietary treatment starting at study initiation to permit a 10-d acclimation period prior to inoculation. Growth performance, fecal dry matter, as well as hematological, histopathological, immune, and microbiota outcomes were analyzed by ANOVA, where treatment and time were considered as fixed effects and pig as a random effect; significance was accepted at P < 0.05. Overall, ETEC-inoculated pigs (PC and OA) exhibited decreased (P < 0.05) ADG and G:F, as well as increased (P < 0.05) peripheral blood helper T-cells and total leukocyte counts, compared with NC pigs during the postinoculation period. The OA treatment also elicited the highest (P < 0.05) concentrations of circulating tumor necrosis factor-α and volatile fatty acid concentrations in luminal contents at various postinoculation time-points, compared with other treatments. A principal coordinate analysis based on Unifrac weighted distances indicated that NC and OA groups had similar overall bacterial community structures, while PC pigs exhibited greater diversity, but infection status had no impact on α-diversity. Osteopontin-specific effects on microbial community structure included enrichment within Streptococcus and Blautia genera and decreased abundance of 12 other genera as compared with PC pigs. Overall, ETEC-infected pigs receiving 1% OPN-enriched algal protein exhibited changes immunity, inflammatory status, and colonic microbial community structure that may benefit weanling pigs experiencing F18 ETEC infection.

The Dynamic Changes of Gut Microbiota during the Perinatal Period in Sows

Simple Summary

The gut microbiota in sows is important for the health of the host, and potential benefits may also be transferred to piglets during pregnancy. Therefore, systematic studies investigating the changes in the gut microbiota of sows are needed to elucidate the microbial compositions and functions. This study was conducted at 12 time points to investigate the temporal variations in the gut microbiota of sows using 16S rRNA sequencing. The results provided important information for the gut microbiota of sows during different perinatal periods.

Abstract

The gut microbiota in sows is important for the health of the host, and potential benefits may also be transferred to piglets during pregnancy. Therefore, systematic studies investigating the changes in the gut microbiota of sows are needed to elucidate the microbial compositions and functions. This study was conducted at 12 time points to investigate the temporal variations in gut microbiota on Days 27, 46, 64, 81, 100, and 113 during gestation (G) and Days 3, 5, 7, 10, 14, and 21 during lactation (L). Results suggested that the gut microbiota changed across the perinatal period with microbial function and abundance varying between the prenatal and postnatal periods. The alpha diversity was higher in the postnatal period than in the prenatal period. Thirty-eight genera were distributed between the two periods with Methanobrevibacter, Desulfovibrio, Akkermansia, and Turicibacter being enriched in the prenatal period while Eubacterium, Actinobacillus, Paludibacter, Butyricimonas, Megasphaera, Succiniclasticum, Acidaminococcus, and Rummeliibacillus were enriched in the postnatal period. Analysis done at the different time points of the prenatal period suggested that Days 27 and 113 had more microbial biomarkers than other days. Bacteroidales, Bacteroidia, and Prevotella were enriched on the 27th day, while bacteria belonging to the Clostridium and Ruminococcaceae were enriched on the 113th day. On the other hand, Clostridiales, Ruminococcaceae, Clostridia, and unclassified Christensenellaceae were enriched three days after delivery. Predicted microbial KO functions were also more enriched on Day 27 of the gestation period and Day 3 of the lactation period. Random forest, a machine learning method, was used to identify the top five important genera of Megasphaera, Stenotrophomonas, Phyllobacterium, Catenibacterium, and Turicibacter, while the most important function was arginine and proline metabolism. These systematic results provide important information for the gut microbiota of sows.

Effects of Dietary Supplementation of Humic Acid Sodium and Zinc Oxide on Growth Performance, Immune Status and Antioxidant Capacity of Weaned Piglets

Simple Summary

Weaning of piglets can destroy the piglet’s intestinal health and immune function, leading to diarrhea and a reduction in growth rate eventually. Considering drug resistance and residues, new alternatives, such as sodium humate (HNa), have attracted considerable research interest over recent decades. Our study was designed to explore the effect of HNa on the growth performance, diarrhea rate, antioxidative, inflammation, and immunity of weaned piglets and the possibility of HNa replacing antibiotics and zinc oxide. The obtained results indicate that HNa reduces stress, protects the intestinal barrier, and improves the performance of weaned piglets.

Abstract

At present, the widespread use of high-dose zinc oxide and antibiotics to prevent post-weaning diarrhea (PWD) in piglets has caused serious environmental problems. To solve this problem, we studied the effect of HNa as a substitute for zinc oxide (ZnO) and antibiotics on the growth performance, immune status, and antioxidant capacity of piglets. Seventy-two weaned piglets (body weight = 7.42 ± 0.85 kg, 26-d-old) were distributed in a randomized 2 × 3 factorial design (two sexes and three treatments) with six replicates of four piglets each. The three treatments were the control diet (basic diet), HNa diet (basic diet + 2000 mg/kg sodium humate), and ZoA group (basic diet + 1600 mg/kg zinc oxide + 1000 mg/kg oxytetracycline calcium). ANOVA and Chi-square tests were applied to compare the means (p < 0.05) between treatments. The results showed that body weight at 16 and 30 d and the average daily gain of piglets fed with HNa or ZoA were significantly higher (p < 0.05) than the control group. Supplementing HNa or ZoA significantly increased (p < 0.05) the level of immunoglobulin M and G, and reduced (p < 0.05) the concentration of inflammatory factors such as tumor necrosis factor-alpha (TNF-α), interleukins IL-6 and IL-1β, myeloperoxidase (MPO), and diamine oxidase (DAO). Furthermore, dietary HNa or ZnO significantly reduced (p < 0.05) the level of total antioxidant capacity (T-AOC) and malondialdehyde (MDA) compared with the control group. ZoA treatment showed an upward trend of IgA level and a downward trend of the concentration of lipopolysaccharide (LPS) and catalase (CAT). Overall, the study demonstrated that the addition of HNa in the diet partially replaced antibiotics and ZnO to improve the growth performance, immune function, and antioxidant capacity of weaned piglets, and maintained a good preventive effect on piglet diarrhea.

Antimicrobial, Antioxidant, Sensory Properties, and Emotions Induced for the Consumers of Nutraceutical Beverages Developed from Technological Functionalised Food Industry By-Products

This study aims to develop nutraceutical beverages containing food processing by-products in their formulation, and determine the opinion of consumers. This is done by testing whether they know that the main ingredients of the product are by-products, performing an overall acceptability test of the developed beverages, and evaluating the emotions induced by the newly developed beverages for consumers. The main ingredients used for the preparation of added-value beverages were fermented milk permeate (containing galactooligosaccharides), extruded and fermented wheat bran (WB) (containing ≥6.0 log₁₀ CFU g⁻¹ viable antimicrobial properties showing lactic acid bacteria (LAB) strains), and different fruit/berry by-products (FBB) (as a source of compounds showing antioxidant properties). The definition of the quantities of bioactive ingredients was based on the overall acceptability of the prepared beverages, as well as on emotions induced in consumers by the tested beverages. Functional properties of the developed beverages were proofed by the evaluation of their antimicrobial and antioxidant properties, as well as viable LAB count during storage. Desirable changes in extruded and fermented WB were obtained: Fermentation reduced sugar concentration and pH in samples with predominant lactic acid isomer L(+). In addition, the viable LAB count in the substrate was higher than 6.0 log₁₀ CFU g⁻¹, and no enterobacteria remained. By comparing the overall acceptability of the beverages enriched with WB, the highest overall acceptability was shown for the samples prepared with 10 g of the extruded and fermented WB (7.9 points). FBB showed desirable antimicrobial activity: Shepherd inhibited—2, sea buckthorn—3, blueberries—5, and raspberries—7 pathogens from the 10 tested. Comparing different beverage groups prepared with different types of FBB, in most cases (except sea buckthorn), by increasing FBB content the beverages overall acceptability was increased, and the highest score (on average, 9.5 points) was obtained for the samples prepared with 5.0 and 7.5 g of blueberries FBB. Moreover, a very strong positive correlation (r = 0.8525) was found between overall acceptability and emotion “happy” induced in consumers by the prepared beverages enriched with extruded and fermented WB and FBB. By comparing the samples prepared with the addition of WB with samples prepared with WB and FBB, it was observed that most FBB increased total phenolic compounds (TPC) content (on average, by 9.0%), except in the case of samples prepared with sea buckthorn. A very high positive correlation (r = 0.9919) was established between TPC and antioxidant activity. Finally, it can be stated that the newly developed nutraceutical beverages were acceptable for consumers, induced positive emotions, and possessed desirable antimicrobial and antioxidant properties, while being prepared in a sustainable and environmentally friendly manner.

Combination of Antimicrobial Starters for Feed Fermentation: Influence on Piglet Feces Microbiota and Health and Growth Performance, Including Mycotoxin Biotransformation in vivo

The aim of this study was to apply a combination of the microbial starters Lactobacillus uvarum LUHS245, Lactobacillus casei LUHS210, Pediococcus acidilactici LUHS29, and Pediococcus pentosaceus LUHS183 for feed fermentation and to evaluate the influence of fermentation on feed acidity and microbiological characteristics, as well as on the piglet feces microbiota, health, and growth performance. Additionally, mycotoxin biotransformation was analyzed, including masked mycotoxins, in feed and piglet feces samples. The 36-day experiment was conducted using 25-day-old Large White/Norwegian Landrace (LW/NL) piglets with an initial body weight of 6.9–7.0 kg, which were randomly distributed into two groups (in each 100 piglets): control group, fed with basal diet (based on barley, wheat, potato protein, soybean protein concentrate, and whey powder), and treated group, fed with fermented feed at 500 g kg⁻¹ of total feed. Compared to a commercially available lactic acid bacteria (LAB) combination, the novel LAB mixture effectively reduced feed pH (on average pH 3.65), produced a 2-fold higher content of L(+) lactic acid, increased viable LAB count [on average 8.8 log₁₀ colony-forming units (CFU) g⁻¹], and led to stable feed fermentation during the entire test period (36 days). Fecal microbiota analysis showed an increased number of probiotic bacteria in the treated group, particularly Lactobacillus, when compared with the control group at the end of experiment. This finding indicates that fermented feed can modify microbial profile change in the gut of pigs. In treated piglets' blood (at day 61), the serum high-density lipoprotein (HDL) cholesterol and triglycerides (TG) were significantly higher, but the levels of T4, glucose, K, alkaline phosphatase (AP), and urea were significantly decreased (p ≤ 0.05) compared with the control group. Mycotoxin analysis showed that alternariol monomethyl ether (AME) and altenuene were found in 61-day-old control piglets' feces and in fermented feed samples. However, AME was not found in treated piglets' feces. Feed fermentation with the novel LAB combination is a promising means to modulate piglets' microbiota, which is essential to improve nutrient absorption, growth performance, and health parameters. The new LAB composition suggests a novel dietary strategy to positively manipulate fermented feed chemicals and bio-safety and the piglet gut microbial ecology to reduce antimicrobials use in pig production and increase local feed stock uses and economical effectiveness of the process.

Prevotella in Pigs: The Positive and Negative Associations with Production and Health

A diverse and dynamic microbial community (known as microbiota) resides within the pig gastrointestinal tract (GIT). The microbiota contributes to host health and performance by mediating nutrient metabolism, stimulating the immune system, and providing colonization resistance against pathogens. Manipulation of gut microbiota to enhance growth performance and disease resilience in pigs has recently become an active area of research in an era defined by increasing scrutiny of antimicrobial use in swine production. In order to develop microbiota-targeted strategies, or to identify potential next-generation probiotic strains originating from the endogenous members of GIT microbiota in pigs, it is necessary to understand the role of key commensal members in host health. Many, though not all, correlative studies have associated members of the genus Prevotella with positive outcomes in pig production, including growth performance and immune response; therefore, a comprehensive review of the genus in the context of pig production is needed. In the present review, we summarize the current state of knowledge about the genus Prevotella in the intestinal microbial community of pigs, including relevant information from other animal species that provide mechanistic insights, and identify gaps in knowledge that must be addressed before development of Prevotella species as next-generation probiotics can be supported.

Comparison of Productivity and Fecal Microbiotas of Sows in Commercial Farms

Sow productivity, that is, the number of weaned piglets per sow per year, depends on their health status. The gut microbiota is considered a crucial factor in the health of pigs and may affect sow productivity. In the present study, we aimed to investigate the relationship between productivity and the fecal microbiotas of sows in different farms. Feces of sows were collected from 18 farms (10 samples/farm). A total of 90 fecal samples of high-reproductive performance farms were labeled as group H, and 90 fecal samples from low-reproductive performance farms were labeled as group L. Fecal microbiotas were analyzed by 16S rRNA metagenomics, and the organic acids and putrefactive metabolites of the microbiotas were measured. β-diversity was significantly different between groups H and L (P < 0.01), and the relative abundances of 43 bacterial genera, including short-chain fatty acid-producing and fiber-degrading bacteria such as Ruminococcus, Fibrobacter and Butyricicoccus, significantly differed between groups (P < 0.05). In addition, the concentrations of acetate, propionate and n-butyrate were significantly higher in group H than in group L (P < 0.05). In conclusion, sow productivity in farms was likely associated with the compositions of the fecal microbiotas.

The Influence of Essential Oils on Gut Microbial Profiles in Pigs

Simple Summary

In recent years, the intake of ultra-processed foods has increased dramatically worldwide. Missing natural foods in the diet raise the need of biologically active food components that could compensate for this deficiency and help maintain proper immune status. In this study, the microbial changes in pigs as experimental animals were assessed as influenced by consumption of oregano extract combination with peppermint and thyme essential oils. The results demonstrated that the combination of plant extracts had a positive effect on the gastrointestinal tract of animals by increasing the number of probiotic bacteria. Based on the results obtained it may be outlined that the combination of oregano extract and peppermint and thyme essential oils can be promising ingredient as a functional component for the development of the new nutraceutical preparation.

Abstract

In recent years, the intake of ultra-processed foods has increased dramatically worldwide. Missing natural foods in the diet raise the need of biologically active food components that could compensate for this deficiency and help maintain proper immune status. This study used pigs as an animal model for the assessment of the impact of consumption of Origanum vulgare plant extract combined with Mentha piperita and Thymus vulgaris essential oils on microbial profile in intestines. A single group of weaned pigs received basal diet, while the other group basal diet supplemented with plant extract and two essential oils in the form of bilayer tablets prepared using “liquid/solid” phase technology. Metagenomic sequencing was performed with the aim to investigate changes of microbial communities in ileum, caecum, and colon. The results demonstrated that the combination of essential oils was non cytotoxic, and had a positive effect on the microbial composition in the large intestine of pigs due to significant increase in the number of probiotic bacteria. The amount of Lactobacillus was 2.5 times and Bifidobacterium 1.9 times higher in the animal group fed with supplement. The combination, however, had some negative impact on the variety of minor species in the distal part of the ileum. Additional studies need to be performed to obtain knowledge on how combinations of essential oils can change bacterial variety in the proximal part of the gastrointestinal tract.

Comparison of Gut Microbiota Diversity and Predicted Functions Between Healthy and Diseased Captive Rana dybowskii

The gut microbiota plays a key role in host health, and disruptions to gut bacterial homeostasis can cause disease. However, the effect of disease on gut microbiota assembly remains unclear and gut microbiota-based predictions of health status is a promising yet poorly established field. Using Illumina high-throughput sequencing technology, we compared the gut microbiota between healthy (HA and HB) and diarrhoeic (DS) Rana dybowskii groups and analyzed the functional profiles through a phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis. In addition, we estimated the correlation between gut microbiota structures and predicted the functional compositions. The results showed significant differences in the phylogenetic diversity (Pd), Shannon, and observed richness (Sobs) indices between the DS and HB groups, with significant differences observed in the gut microbiota composition between the DS group and the HA and HB groups. Linear discriminant analysis (LDA) effect size (LEfSe) results revealed that Proteobacteria were significantly enriched in the DS group; Bacteroidetes were significantly enriched in the HA and HB groups; and Aeromonas, Citrobacter, Enterococcus, Hafnia-Obesumbacterium, Morganella, Lactococcus, Providencia, Vagococcus, and Staphylococcus were significantly enriched in the DS group. Venn diagrams revealed that there were many more unique genera in the DS group than the HA and HB groups. Among 102 sensitive species selected using the indicator method, 33 indicated a healthy status and 69 (e.g., Acinetobacter, Aeromonas, Legionella, Morganella, Proteus, Providencia, Staphylococcus, and Vagococcus) indicated a diseased status. There was a significant and positive association between the composition and functional composition of the gut microbiota, thus indicating low functional redundancy of the frog gut bacterial community. Rana dybowskii disease was associated with changes in the gut microbiota, which subsequently disrupted bacterial-mediated functions. The results of this study can aid in revealing the effect of the R. dybowskii gut microbiota on host health and provide a basis for elucidating the mechanism of the occurrence of R. dybowskii disease.

Porcine circovirus type 2 (PCV2) and Campylobacter infection induce diarrhea in piglets: Microbial dysbiosis and intestinal disorder

Diarrhea is considered to be associated with microbial dysbiosis caused by infection of pathogens but poorly understood. We herein characterized the colonic microbiota of diarrheal early-weaning piglets infected with porcine circovirus type 2 (PCV2) and Campylobacter. Campylobacter infection significantly decreased species richness and Shannon diversity index of colonic microbiota together with a significant increase in the proportion of Campylobacter and Enterobacteriaceae, whereas no significant difference on the above indexes was observed in piglets infected with PCV2 compared with healthy piglets. PCV2 and Campylobacter infection could disturb the homeostasis of colonic microbiota through deterioration of ecological network within microbial community, and specially Campylobacter performed as a module hub in ecological networks. The microbial dysbiosis caused metabolic dysfunction and led to a remarkable reduction in production of short chain fatty acids, following by a higher pH level in colon cavity. Campylobacter infection disturbed the function of colonic tract barrier observed in terms of significant lower relative expression of claudin-1, occluding, and zonula occludens protein-1 genes, and PCV2 infection induced intestinal inflammation together with a higher permeability of colon. Generally, these results suggested that PCV2 and Campylobacter infection could induce microbial dysbiosis and metabolic dysfunction, and cause intestinal disorder, all of which finally were associated to contribute to the diarrhea of early-weaning piglets.

Shifts in the Fecal Microbial Community of Cystoisospora suis Infected Piglets in Response to Toltrazuril

The protozoan parasite Cystoisospora suis causes diarrhea and reduced weight gain in suckling piglets. Infections occur in the first days of life; it is transient but can lead to dysbiosis, exacerbating disease and increasing mortality. Cystoisosporosis is effectively controlled by toltrazuril treatment; however, alterations of the gut microbial composition upon infection and treatment have not been investigated. This study evaluated the development of fecal microbiota of C. suis infected piglets in response to treatment with toltrazuril. Thirty-eight conventional piglets were infected with C. suis on the first day of life (dol 1). Twenty-six of them received either parenteral or oral toltrazuril 2 days later. Fecal samples were collected pre- and post-weaning (dol 1-15 and 31-38) for microbiota analysis using 16S rRNA amplicon sequencing and during dol 5-18 to determine fecal consistency and parasite excretion. All control animals shed parasites at least once and the majority developed diarrhea, while toltrazuril-treated piglets did not excrete parasites and only had low levels of diarrhea. Age-related shifts in the fecal microbiota composition and increase in diversity and species richness were seen until after weaning. Parasite infection disrupted bacterial maturation 2 weeks after infection. Irrespective of the route of administration, fecal communities of piglets in the treated groups clustered separately and were more diverse compared to that of control piglets during the acute phase of infection on dol 11. Control piglet feces showed higher levels of Fusobacteriaceae and Veillonellaceae, while Ruminococcaceae, Lachnospiraceae, S24-7, Clostridiaceae, and Erysipelotrichaceae were more abundant in feces of treated piglets on dol 11. Thereafter, treatment-related effects on the microbial communities were small and mainly detectable on dol 34 (5 days post-weaning), potentially indicating that the oral toltrazuril treatment might have had long-term effects on host physiological responses post-weaning. Irrespective of the administration route, toltrazuril prevented C. suis-related dysbiosis and maintained species richness and diversity on dol 11. In addition to cystoisosporosis prevention, toltrazuril seems to contribute to the stabilization of the gut microbial development during the suckling phase and thus may reduce the need for antibiotics to control infections with secondary bacterial enteropathogens in C. suis-infected suckling piglets.

Weaning Alters Intestinal Gene Expression Involved in Nutrient Metabolism by Shaping Gut Microbiota in Pigs

Weaning transition usually impairs intestinal architecture and functions and results in gut-associated disorders in pigs. Understanding the changes in intestinal transcriptome and gut microbiota during weaning transition is important for elucidating the underlying mechanism of weaning stress. In the present study, we performed RNA-seq to determine the changes in intestinal transcriptome and 16S rRNA sequencing to measure the gut microbiota changes in the weaning transition. Transcriptome results indicated that weaning transition altered intestinal gene expression involved in nutrient transport and metabolism. Regarding fatty metabolism, fatty acid-binding protein 1 (FABP1), acyl-CoA dehydrogenase (ACADSB), and carnitine palmitoyltransferase 2 (CPT2) expression in the intestine was decreased by weaning. Genes related to bile acid metabolism were increased by weaning, including FABP6, farnesoid X receptor (FXR or NR1H4) and organic solute transporter-α (SLC51A). In addition, genes associated with oxidative stress were altered by weaning transition, including decreased catalase (CAT) and lactate dehydrogenase (LDHA) and increased glutathione peroxidase 2 (GPX2) and superoxide dismutase 3 (SOD3). Results of microbiota composition showed that the Firmicutes abundance and Firmicutes/Bacteroidetes ratio were increased and that the Proteobacteria abundance in the fecal microbiota was decreased by the weaning process; during the weaning transition, the Bacteroides and Fusobacterium abundances decreased markedly, and these bacteria nearly disappeared, while the Prevotella abundance showed a marked increase. Moreover, the levels of the microbial metabolites butyrate and acetate increased with changes in gut microbiota composition. In addition, predictive metagenome by PICRUSt analysis showed that the pathways related to D-glutamine and D-glutamate metabolism, citrate cycle (TCA cycle), peroxisome proliferators-activated receptor (PPAR) signaling, alpha-linolenic acid metabolism were decreased and the pathway related to retinol metabolism was increased in the gut microbiota of piglets during weaning transition. Our results showed that early weaning alters intestinal gene expression involved in nutrient metabolism, which may be due to the changes in microbiota composition.

Late weaning is associated with increased microbial diversity and Faecalibacterium prausnitzii abundance in the fecal microbiota of piglets

Background

In pig production systems, weaning is a crucial period characterized by nutritional, environmental, and social stresses. Piglets transition from a milk-based diet to a solid, more complex plant-based diet, and their gut physiology must adapt accordingly. It is well established that piglets weaned later display improved health, better wean-to-finish growth performance, and lower mortality rates. The aim of this study was to evaluate the impact of weaning age on fecal microbiota diversity and composition in piglets. Forty-eight Large White piglets were divided into 4 groups of 12 animals that were weaned at different ages: 14 days (early weaning), 21 days (a common weaning age in intensive pig farming), 28 days (idem), and 42 days (late weaning). Microbiota composition was assessed in each group by sequencing the 16S rRNA gene using fecal samples taken on the day of weaning, 7 days later, and at 60 days of age.

Results

In each group, there were significant differences in fecal microbiota composition before and after weaning (p < 0.05), confirming that weaning can drastically change the gut microbiota. Microbiota diversity was positively correlated with weaning age: microbial alpha diversity and richness were higher in piglets weaned at 42 days of age both on the day of weaning and 7 days later. The abundance of Faecalibacterium prausnitzii operational taxonomic units (OTUs) was also higher in piglets weaned at 42 days of age.

Conclusions

Overall, these results show that late weaning increased gut microbiota diversity and the abundance of F. prausnitzii, a microorganism with positive effects in humans. Piglets might thus derive a competitive advantage from later weaning because they have more time to accumulate a higher diversity of potentially beneficial microbes prior to the stressful and risky weaning period.