Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited

Exploring the Effect of Gastrointestinal Prevotella on Growth Performance Traits in Livestock Animals

Microorganisms in the rumen play a crucial role in determining the most efficient utilization rate of nutrients. Among these microorganisms, Prevotella stands out as one of the most representative bacteria within the rumen biological system. Prevotella is a common strict anaerobic bacterium that is found in the gastrointestinal tract of livestock. Prevotella plays a crucial role in breaking down and metabolizing complex nutrients like cellulose and protein during food digestion. Moreover, it is capable of working together with other bacteria in the body's digestive system. Several studies have shown a strong correlation between the abundance of Prevotella and livestock growth performance. This paper provides a comprehensive review of the current research on the function, mechanisms, and applications of Prevotella in the gastrointestinal tract. The insights provided in this review could serve as a theoretical basis for accurately classifying Prevotella, further investigating its effects and potential mechanisms on livestock growth performance, and exploring its practical applications.

Validation of a Combined In Vivo/In Vitro Ileal Fermentation Assay in the Growing Pig to be Used as a Model for Adult Humans

BACKGROUND

An in vivo/in vitro ileal fermentation assay using growing pigs has been developed but not yet formally validated.

OBJECTIVES

This study aimed to validate the in vivo/in vitro ileal fermentation assay by comparing in vitro fermentation values with those obtained in vivo in growing pigs. The effect of raising pigs under different environmental conditions was also investigated.

METHODS

Thirty piglets (1.59 ± 0.31 kg body weight, mean ± standard deviation) were subjected to 1 of 3 treatments: artificially reared (AR) (nonfarm, laboratory housing conditions) from postnatal day (PND) 7 (AR group), inoculated orally with human infant fecal extracts from birth until PND 8 and AR (AR+ group), or conventionally reared on a farm (control group). Starting at PND 7, the AR and AR+ pigs received human infant formula for 3 wk, followed by a human-type diet for 5 wk. Control pigs were weaned on the farm and, on PND 63, relocated to the laboratory animal facility. From PND 63, all pigs received a human-type diet. On PND 78, pigs were killed, after which ileal digesta were collected to perform an in vitro ileal fermentation (in vitro organic matter [OM] fermentability and organic acid production) and to determine digesta microbial composition and dietary OM fermentability in vivo.

RESULTS

The rearing regimen resulted in only a few differences in ileal microbial taxonomic composition. The rearing regimen generally did not affect the in vitro production of individual organic acids. The in vivo and in vitro OM fermentability of proximal ileal digesta (19.7 ± 2.04%; mean ± SEM) was similar (P > 0.05) for the AR and control pigs but not for the AR+ pigs.

CONCLUSIONS

The control-rearing regimen was preferred over AR or AR+ because of ease of implementation. The in vitro ileal fermentation assay accurately predicted the in vivo OM fermentability.

Swine Gastrointestinal Microbiota and the Effects of Dietary Amino Acids on Its Composition and Metabolism

Many researchers consider gut microbiota (trillions of microorganisms) an endogenous organ of its animal host, which confers a vast genetic diversity in providing the host with essential biological functions. Particularly, the gut microbiota regulates not only gut tissue structure but also gut health and gut functionality. This paper first summarized those common bacterial species (dominated by the Firmicutes, Bacteroidota, and Proteobacteria phyla) in swine gut and then briefly discussed their roles in swine nutrition and health, which include roles in nutrient metabolism, pathogen exclusion, and immunity modulation. Secondly, the current knowledge on how dietary nutrients and feed additives affect the gut bacterial composition and nutrient metabolism in pigs was discussed. Finally, how dietary amino acids affect the relative abundances and metabolism of bacteria in the swine gut was reviewed. Tryptophan supplementation promotes the growth of beneficial bacteria and suppresses pathogens, while arginine metabolism affects nitrogen recycling, impacting gut immune response and health. Glutamate and glutamine supplementations elevate the levels of beneficial bacteria and mitigate pathogenic ones. It was concluded that nutritional strategies to manipulate gut microbial ecosystems are useful measures to optimize gut health and gut functions. For example, providing pigs with nutrients that promote the growth of Lactobacillus and Bifidobacterium can lead to better gut health and growth performance, especially when dietary protein is limited. Further research to establish the mechanistic cause-and-effect relationships between amino acids and the dynamics of gut microbiota will allow swine producers to reap the greatest return on their feed investment.

Evaluation of Safety and Probiotic Traits from a Comprehensive Genome-Based In Silico Analysis of Ligilactobacillus salivarius P1CEA3, Isolated from Pigs and Producer of Nisin S

Ligilactobacillus salivarius is an important member of the porcine gastrointestinal tract (GIT). Some L. salivarius strains are considered to have a beneficial effect on the host by exerting different probiotic properties, including the production of antimicrobial peptides which help maintain a healthy gut microbiota. L. salivarius P1CEA3, a porcine isolated strain, was first selected and identified by its antimicrobial activity against a broad range of pathogenic bacteria due to the production of the novel bacteriocin nisin S. The assembled L. salivarius P1CEA3 genome includes a circular chromosome, a megaplasmid (pMP1CEA3) encoding the nisin S gene cluster, and two small plasmids. A comprehensive genome-based in silico analysis of the L. salivarius P1CEA3 genome reveals the presence of genes related to probiotic features such as bacteriocin synthesis, regulation and production, adhesion and aggregation, the production of lactic acid, amino acids metabolism, vitamin biosynthesis, and tolerance to temperature, acid, bile salts and osmotic and oxidative stress. Furthermore, the strain is absent of risk-related genes for acquired antibiotic resistance traits, virulence factors, toxic metabolites and detrimental metabolic or enzymatic activities. Resistance to common antibiotics and gelatinase and hemolytic activities have been discarded by in vitro experiments. This study identifies several probiotic and safety traits of L. salivarius P1CEA3 and suggests its potential as a promising probiotic in swine production.

Effects of dietary Glycyrrhiza polysaccharide supplementation on growth performance, intestinal antioxidants, immunity and microbiota in weaned piglets

The aim of this study was to evaluate the effects of dietary Glycyrrhiza polysaccharide (GCP) supplementation on growth performance, intestinal antioxidants, immunity and microbiota in weaned piglets. One hundred and twenty 28-day-old weaned piglets were randomly assigned into five groups (four replicates per group) and fed a basal diet with GCP at 0, 500, 1000, 2000 and 4000 mg/kg for four weeks, respectively. Results showed that 1000 mg/kg GCP improved piglets' ADG and ADFI and reduced FCR (p < .05). Thus, the 0 and 1000 mg/kg GCP dose were selected for subsequent experiments. We found that 1000 mg/GCP increased SOD and T-AOC and decreased MDA in the jejunal mucosa (p < .05). Dietary 1000 mg/kg GCP also resulted in high levels of sIgA, IL-10 and TGF-β, whereas IL-2 dropped dramatically (p < .05). The relative expression levels of ZO-1, CLDN, OCLDN, TLR-4, IL-10, TGF-β, Nrf-2, SOD1 and CAT increased in the jejunal mucosa, whereas INF-γ decreased (p < .05). 1000 mg/kg GCP treatment altered the diversity and community composition of cecal microbiota in pigs, with increasing relative abundance of Bacteroidota and Lactobacillus at phylum and genus levels (p < .05), respectively. The results suggested that dietary 1000 mg/kg GCP could improve growth performance and intestinal health of weaned piglets.

Characterization of the bacterial fecal microbiota composition of pigs preceding the clinical signs of swine dysentery

Swine dysentery (SD) is a worldwide production-limiting disease of growing-finishing pigs in commercial farms. The importance of the large intestinal microbiota in the swine dysentery pathogenesis has been established, but not well characterized. The objective of this study was to characterize the fecal bacterial microbiota of pigs immediately prior to developing clinical signs of swine dysentery. A total of 60 fecal samples were collected from 15 pigs with SD. Sampling times included a time point prior to SD (d0, n=15), 2 days before mucohaemorrhagic diarrhea was observed (d-2SD, n=15), 1 day before mucohaemorrhagic diarrhea was observed (d-1SD, n=15), and the day when pigs developed mucohemorragic diarrhea (MHD, n=15). Sequencing of cpn60 amplicons was used to profile the microbiome, and analyses were performed on QIIME2. Increased Chao1 index in d-1SD and MHD samples when compared to the d0 was the only change observed in alpha diversity. No differences between sampling times on beta diversity (Bray-Curtis dissimilarity) were found. Although a small sample size was investigated, differential abundance analysis revealed that Alistipes dispar and Parabacteroides gordonii were increased in MHD fecal samples when compared to d-2SD and d-1SD. It is suggested that these taxa may play a role in the pathogenesis of SD, which is known to require the presence of Brachyspira spp. and an anaerobe for severe disease development.

Potential application of Staphylococcus species detection in the specific identification of saliva

When found at crime scenes, saliva constitutes forensically relevant evidence. Although several tests have been developed to effectively identify saliva in such circumstances, most cannot discriminate between saliva and nasal secretion. Recently, studies have developed saliva tests involving oral bacteria as salivary markers. Although the specificity of such tests has been evaluated on most biological specimens, their specificity for nasal secretion samples remains to be tested. Herein, to improve the specificity of the saliva detection tests for nasal secretion samples, we reanalyzed a public microbiome dataset and conducted inhouse 16S rRNA sequencing to identify a new marker to distinguish between saliva and nasal secretions. The sequencing data indicated the existence of oral bacteria such as Streptococcus in nasal secretion samples, which may be responsible for the false positives in the saliva tests. Furthermore, we found that including the 16S rRNA gene of the genus Staphylococcus as a nasal secretion marker may improve the specificity of PCR-based saliva tests for nasal secretion samples. In addition, we assessed the specificity of previously developed salivary bacteria detection tests for nasal secretion samples and oral bacterial markers were detected in two of eight nasal secretion samples, which led to the false positive results for saliva detection. Thus, the specificity of such tests can be improved by adding Staphylococcus as a nasal marker, as revealed by our sequencing analysis.

Elucidating the Mechanisms of Cell-to-Cell Crosstalk in Probiotics Co-culture: A Proteomics Study of Limosilactobacillus reuteri ZJ625 and Ligilactobacillus salivarius ZJ614

Limosilactobacillus reuteri ZJ625 and Ligilactobacillus salivarius ZJ614 are potential probiotic bacteria with improved benefits when administered to the host as a multi-strain preparation. To elucidate the mechanisms of cell-to-cell crosstalk between these two strains, we studied their intracellular and extracellular proteomes in co-culture by liquid-chromatography mass-spectrometry (LC-MS) using Dionex Nano-RSLC and fusion mass spectrometer. The experiment consisted of five biological replicates, and samples were collected during the mid-exponential growth phase. The quantitative proteomic profiles revealed several differentially expressed proteins (DEPs), which are down- or up-regulated between and within groups for both the intracellular and extracellular proteomes. These DEPs include proteins synthesising autoinducer-2, a sensor compound for cell-to-cell bacterial crosstalk during quorum sensing in mixed culture. Other important DEPs identified include enolase, phosphoglycerate kinase, and l-lactate dehydrogenase, which play roles in carbohydrate metabolism. Proteins associated with transcription, ATP production and transport across the membrane, DNA repair, and those with the potential to bind to the host epithelium were also identified. The post-translational modifications associated with the proteins include oxidation, deamidation, and ammonia loss. Importantly, this study revealed a significant expression of S-ribosylhomocysteine lyase (luxS) involved in synthesising autoinducer-2 that plays important roles in quorum sensing, aiding bacterial cell-to-cell crosstalk in co-cultures. The proteome of L. salivarius ZJ614 was most affected when co-cultured with L. reuteri ZJ625. In contrast, omitting some medium components from the defined medium exerted more effects on L. reuteri ZJ625 than L. salivarius ZJ614.

Impact of Early Weaning on Development of the Swine Gut Microbiome

Considering that pigs are naturally weaned between 12 and 18 weeks of age, the common practice in the modern swine industry of weaning as early as between two and four weeks of age increases challenges during this transition period. Indeed, young pigs with an immature gut are suddenly separated from the sow, switched from milk to a diet consisting of only solid ingredients, and subjected to a new social hierarchy from mixing multiple litters. From the perspective of host gut development, weaning under these conditions causes a regression in histological structure as well as in digestive and barrier functions. While the gut is the main center of immunity in mature animals, the underdeveloped gut of early weaned pigs has yet to contribute to this function until seven weeks of age. The gut microbiota or microbiome, an essential contributor to the health and nutrition of their animal host, undergoes dramatic alterations during this transition, and this descriptive review aims to present a microbial ecology-based perspective on these events. Indeed, as gut microbial communities are dependent on cross-feeding relationships, the change in substrate availability triggers a cascade of succession events until a stable composition is reached. During this process, the gut microbiota is unstable and prone to dysbiosis, which can devolve into a diseased state. One potential strategy to accelerate maturation of the gut microbiome would be to identify microbial species that are critical to mature swine gut microbiomes, and develop strategies to facilitate their establishment in early post-weaning microbial communities.

Exploring the potential links between gut microbiota composition and natural populations management in wild boar (Sus scrofa)

We surveyed wild boar (Sus scrofa) populations using 16S rRNA gene analysis of the gut microbiota in fresh faeces taken from 88 animals hunted in 16 hunting estates. The wild boar is a very convenient model system to explore how environmental factors including game management, food availability, disease prevalence, and behaviour may affect different biological components of wild individuals with potential implications in management and conservation. We tested the hypotheses that diet (according to stable carbon isotopes analyses), gender (i.e., animal behaviour studying males and females), and both health (analyses of serum samples to detect exposure to several diseases) and form statutes (i.e., thoracic circumference in adults) are reflected in changes in the intestinal microbiota. We focused on a gut functional biomarker index combining Oscillospiraceae and Ruminococcaceae vs. Enterobacteriaceae. We found that gender and the estate (population) were explanatory variables (c.a. 28% of the variance), albeit a high degree of overlapping among individuals was observed. The individuals with higher abundance of Enterobacteriaceae showed a gut microbiota with low diversity, mostly in males. Significant statistical differences for thoracic circumference were not found between males and females. Interestingly, the thoracic circumference was significantly and inversely related to the relative abundance of Enterobacteriaceae in males. Overall, we found that diet, gender, and form status were major factors that could be related to the composition and diversity of the gut microbiota. A high variability was observed in the biomarker index for populations with natural diet (rich in C3 plants). Although, we noticed a marginally significant negative trend between the index (higher abundance of Enterobacteriaceae) and the continuous feeding of C4 plants (i.e., supplementary maize) in the diet of males. This result suggests that continuous artificial feeding in hunting estates could be one of the factors negatively influencing the gut microbiota and the form status of wild boars that deserves further investigations.

Fecal Microbial Structure and Metabolic Profile in Post-Weaning Diarrheic Piglets

(1) Background: Piglet diarrhea is one of the most serious diseases in pigs and has brought great economic losses to the pig industry. Alteration of the gut microbiota is an important factor in the etiology of piglet diarrhea. Therefore, this study aimed to analyze the differences in the gut microbial structures and fecal metabolic profile between post-weaning diarrhea and healthy Chinese Wannan Black pigs. (2) Methods: An integrated approach of 16S rRNA gene sequencing combined with LC/MS-based metabolomics was employed in this study. (3) Results: We found an increase in the relative abundance of the bacterial genus Campylobacter and a decrease in phylum Bacteroidetes and the species Streptococcus gallolyticus subsp. macedonicus. (S. macedonicus) in piglet diarrhea. Meanwhile, obvious changes in the fecal metabolic profile of diarrheic piglets were also detected, particularly higher levels of polyamines (spermine and spermidine). Moreover, there were substantial associations between the disturbed gut microbiota and the altered fecal metabolites, especially a strong positive relationship between spermidine and Campylobacter. (4) Conclusions: These observations may provide novel insights into potential etiologies related to post-weaning diarrhea and further enhance our understanding of the role of gut microbiota in host homeostasis and in modulating gut microbial structure.

Development of a novel definitive scoring system for an enteral feed-only model of necrotizing enterocolitis in piglets

Introduction

Necrotizing enterocolitis (NEC) is a complex inflammatory disorder of the human intestine that most often occurs in premature newborns. Animal models of NEC typically use mice or rats; however, pigs have emerged as a viable alternative given their similar size, intestinal development, and physiology compared to humans. While most piglet NEC models initially administer total parenteral nutrition prior to enteral feeds, here we describe an enteral-feed only piglet model of NEC that recapitulates the microbiome abnormalities present in neonates that develop NEC and introduce a novel multifactorial definitive NEC (D-NEC) scoring system to assess disease severity.

Methods

Premature piglets were delivered via Caesarean section. Piglets in the colostrum-fed group received bovine colostrum feeds only throughout the experiment. Piglets in the formula-fed group received colostrum for the first 24 h of life, followed by Neocate Junior to induce intestinal injury. The presence of at least 3 of the following 4 criteria were required to diagnose D-NEC: (1) gross injury score ≥4 of 6; (2) histologic injury score ≥3 of 5; (3) a newly developed clinical sickness score ≥5 of 8 within the last 12 h of life; and (4) bacterial translocation to ≥2 internal organs. Quantitative reverse transcription polymerase chain reaction was performed to confirm intestinal inflammation in the small intestine and colon. 16S rRNA sequencing was performed to evaluate the intestinal microbiome.

Results

Compared to the colostrum-fed group, the formula-fed group had lower survival, higher clinical sickness scores, and more severe gross and histologic intestinal injury. There was significantly increased bacterial translocation, D-NEC, and expression of IL-1α and IL-10 in the colon of formula-fed compared to colostrum-fed piglets. Intestinal microbiome analysis of piglets with D-NEC demonstrated lower microbial diversity and increased Gammaproteobacteria and Enterobacteriaceae.

Conclusions

We have developed a clinical sickness score and a new multifactorial D-NEC scoring system to accurately evaluate an enteral feed-only piglet model of NEC. Piglets with D-NEC had microbiome changes consistent with those seen in preterm infants with NEC. This model can be used to test future novel therapies to treat and prevent this devastating disease.

Assessment of cecal microbiota modulation from piglet dietary supplementation with copper

BACKGROUND

Swine production expanded in the last decades. Efforts have been made to improve meat production and to understand its relationship to pig gut microbiota. Copper (Cu) is a usual supplement to growth performance in animal production. Here, two performance studies were conducted to investigate the effects of three different sources of Cu on the microbiota of piglets. A total of 256 weaned piglets were randomly allocated into 4 treatments (10 replicates per treatment of 4 piglets per pen in Trial 1 and 8 replicates of 3 piglets per pen in Trial 2). Treatments included a control group (fed 10 mg/kg of Cu from CuSO₄), a group fed at 160 mg/kg of Copper (II) sulfate (CuSO₄) or tri-basic copper chloride (TBCC), and a group fed with Cu methionine hydroxy analogue chelated (Cu-MHAC) at 150, 80, and 50 mg/kg in Phases 1 (24-35 d), 2 (36-49 d), and 3 (50-70 d), respectively. At 70 d, the cecum luminal contents from one pig per pen were collected and polled for 16 S rRNA sequencing (V3/V4 regions). Parameters were analyzed in a completely randomized block design, in which each experiment was considered as a block.

RESULTS

A total of 1337 Operational Taxonomic Units (OTUs) were identified. Dominance and Simpson ecological metrics were statistically different between control and treated groups (P < 0.10) showing that different Cu sources altered the gut microbiota composition with the proliferation of some bacteria that improve gut health. A high abundance of Prevotella was observed in all treatments while other genera were enriched and differentially modulated, according to the Cu source and dosage. The supplementation with Cu-MHAC can modify a group of bacteria involved in feed efficiency (FE) and short chain fatty acids (SCFA) production (Clostridium XIVa, Desulfovibrio, and Megasphera). These bacteria are also important players in the activation of ghrelin and growth hormones that were previously reported to correlate with Cu-MHAC supplementation.

CONCLUSIONS

These results indicated that some genera seem to be directly affected by the Cu source offered to the animals. TBCC and Cu-MHAC (even in low doses) can promote healthy modifications in the gut bacterial composition, being a promising source of supplementation for piglets.

Nitrogen Fertilizer Type and Genotype as Drivers of P Acquisition and Rhizosphere Microbiota Assembly in Juvenile Maize Plants

Phosphorus (P) is an essential nutrient for plant growth and development, as well as an important factor limiting sustainable maize production. Targeted nitrogen (N) fertilization in the form of ammonium has been shown to positively affect Pi uptake under P-deficient conditions compared to nitrate. Nevertheless, its profound effects on root traits, P uptake, and soil microbial composition are still largely unknown. In this study, two maize genotypes F160 and F7 with different P sensitivity were used to investigate phosphorus-related root traits such as root hair length, root diameter, AMF association, and multiple P efficiencies under P limitation when fertilized either with ammonium or nitrate. Ammonium application improved phosphorous acquisition efficiency in the F7 genotype but not in F160, suggesting that the genotype plays an important role in how a particular N form affects P uptake in maize. Additionally, metabarcoding data showed that young maize roots were able to promote distinct microbial taxa, such as arbuscular mycorrhizal fungi, when fertilized with ammonium. Overall, the results suggest that the form of chemical nitrogen fertilizer can be instrumental in selecting beneficial microbial communities associated with phosphorus uptake and maize plant fitness.

Effects of different processing techniques of palm kernel cake on processing quality of pellet feed, nutrient digestibility, and intestinal microbiota of pigs

The present study was conducted to investigate the effects of extrusion, fermentation, and enzymolysis of palm kernel cake on processing quality of pellet feed, nutrient digestibility, and intestinal microbiota of pigs. First, the pretreatment parameters of extrusion, enzymolysis, and fermentation of palm kernel cake were optimized. Then, PKC after three processing techniques were used to prepare pellet feed. A total of 160 crossbred piglets (Duroc × Landrace × Yorkshire) with an average body weight of 28 ± 0.5 kg were used in an 8-wk feeding experiment. Pigs were randomly assigned to five treatments with four replicates per treatment and eight pigs per replicates. The five experimental groups were as follows: basal diet group (whole corn-soybean meal), 10% PKC group (PKC), 10% extrusion PKC group (PPKC), 10% enzymolysis PKC group (EPKC), and 10% fermented PKC group (FPKC), respectively. At the end of the experiment, four pigs from each treatment (randomly collected one pig per pen) were sacrificed by administering a pentobarbital overdose, the gut and blood samples were collected for the quantification analysis of microbiota, hematological parameters, and apparent total tract nutrient digestibility. The results showed that all three processing techniques significantly decreased the contents of crude fiber of PKC (P < 0.01), pulverization rate (P < 0.01), powder content (P < 0.01), and increased the hardness and gelatinization starch of pellet feed (P < 0.05) compared to PKC group. In addition, PPKC significantly improved the dry matter, crude protein, and ether extract content, blood indices and average daily feed intake compared to PKC group (P < 0.01), while the parameters were similar among FPKC, EPKC, and control group (P > 0.01). Furthermore, all three processing techniques significantly increased the Lactobacillus and decreased the Escherichia levels in feces or gut compared to PKC. Collectively, extrusion, fermentation, and enzymolysis of PKC had positively enhanced the pellet quality, growth performance, nutrient digestibility, and gut microbiota, extrusion exhibited a superior feeding effect compared to fermentation and enzymolysis.

Porcine spinal cord injury model for translational research across multiple functional systems

Animal models are necessary to identify pathological changes and help assess therapeutic outcomes following spinal cord injury (SCI). Small animal models offer value in research in terms of their easily managed size, minimal maintenance requirements, lower cost, well-characterized genomes, and ability to power research studies. However, despite these benefits, small animal models have neurologic and anatomical differences that may influence translation of results to humans and thus limiting the success of their use in preclinical studies as a direct pipeline to clinical studies. Large animal models, offer an attractive intermediary translation model that may be more successful in translating to the clinic for SCI research. This is largely due to their greater neurologic and anatomical similarities to humans. The physical characteristics of pig spinal cord, gut microbiome, metabolism, proportions of white to grey matter, bowel anatomy and function, and urinary system are strikingly similar and provide great insight into human SCI conditions. In this review, we address the variety of existing porcine injury models and their translational relevance, benefits, and drawbacks in modeling human systems and functions for neurophysiology, cardiovascular, gastrointestinal and urodynamic functions.

The microbiome shifts throughout the gastrointestinal tract of Bradford cattle in the Pampa biome

A deep understanding of the cattle gastrointestinal microbiome is crucial to selective breeding high-efficiency animals that produce more and generate less environmental damage. Here we performed the taxonomic identification of Bacterial and Archaeal communities using high throughput 16SrRNA gene sequencing from critical compartments of the gastrointestinal tract of Bradford cattle raised in a natural grassland in the Pampa biome, Brazil. We analyzed 110 samples, including saliva, ruminal fluid, and feces from 36 months old Bradford heifers (weighing on average 343 ± 30 kg by the sampling time). To reduce unexpected variation and confounders, we selected the animals from the same breed, submitted them to the same food source, and collected the samples for three consecutive years from different animals in the same season. Our main goal was to analyze the microbial shifts throughout the gastrointestinal tract to reference future works proposing management strategies and interventions to improve animal nutrition and increase production in the Pampa Biome. To accomplish our objective, we accessed the microbial community differences in groups with a high and low weight gain controlling for food ingestion and quality of grazed pasture. Few taxa were shared among the samples. About 40% of the phyla and 60% of the genera were unique from saliva samples, and 12.4% of the microbial genera were uniquely found in feces. All samples shared only 36.1% of phyla and 7.5% of genera. Differences in microbial diversity and taxa counts were observed. The ruminal fluid presented the lowest microbial richness, while saliva and feces presented the highest microbial richness. On the other hand, saliva and feces also presented more distinct communities between themselves when compared with ruminal samples. Our data showed that the saliva microbiome is not representative of the rumen microbiome and should not be used as an easy-to-collect sample for studies about the rumen microbiome.

Maintenance of gut microbiome stability for optimum intestinal health in pigs - a review

Pigs are exposed to various challenges such as weaning, environmental stressors, unhealthy diet, diseases and infections during their lifetime which adversely affects the gut microbiome. The inability of the pig microbiome to return to the pre-challenge baseline may lead to dysbiosis resulting in the outbreak of diseases. Therefore, the maintenance of gut microbiome diversity, robustness and stability has been influential for optimum intestinal health after perturbations. Nowadays human and animal researches have focused on more holistic approaches to obtain a robust gut microbiota that provides protection against pathogens and improves the digestive physiology and the immune system. In this review, we present an overview of the swine gut microbiota, factors affecting the gut microbiome and the importance of microbial stability in promoting optimal intestinal health. Additionally, we discussed the current understanding of nutritional interventions using fibers and pre/probiotics supplementation as non-antibiotic alternatives to maintain microbiota resilience to replace diminished species.

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

OBJECTIVE

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

METHODS

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

RESULTS

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

CONCLUSION

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

High-quality metagenome-assembled genomes from proximal colonic microbiomes of synbiotic-treated korean native black pigs reveal changes in functional capacity

Synbiotics are feed supplements with the potential to promote health and productivity in pigs partly, through modulation of the intestinal microbiome. Our study used shotgun sequencing and 16S rRNA gene sequencing techniques to characterize the effect of a synbiotic containing three Lactobacillus species and a fructo-oligosaccharide on the proximal colonic microbiome of 4- to 7-month-old Korean native black gilts. With shotgun sequencing we constructed unique metagenome-assembled genomes of gut microbiota in Native Black Pig for the first time, which we then used for downstream analysis. Results showed that synbiotic treatment did not alter microbial diversity and evenness within the proximal colons, but altered composition of some members of the Lactobacillaceae, Enterococcaceae and Streptococcaceae families. Functional analysis of the shotgun sequence data revealed 8 clusters of orthologous groups (COGs) that were differentially represented in the proximal colonic microbiomes of synbiotic-treated Jeju black pigs relative to controls. In conclusion, our results show that administering this synbiotic causes changes in the functional capacity of the proximal colonic microbiome of the Korean native black pig. This study improves our understanding of the potential impact of synbiotics on the colonic microbiome of Korean native black pigs.

Ammonium fertilization increases the susceptibility to fungal leaf and root pathogens in winter wheat

Nitrogen (N) fertilization is indispensable for high yields in agriculture due to its central role in plant growth and fitness. Different N forms affect plant defense against foliar pathogens and may alter soil-plant-microbe interactions. To date, however, the complex relationships between N forms and host defense are poorly understood. For this purpose, nitrate, ammonium, and cyanamide were compared in greenhouse pot trials with the aim to suppress two important fungal wheat pathogens Blumeria graminis f. sp. tritici (Bgt) and Gaeumannomyces graminis f. sp. tritici (Ggt). Wheat inoculated with the foliar pathogen Bgt was comparatively up to 80% less infested when fertilized with nitrate or cyanamide than with ammonium. Likewise, soil inoculation with the fungal pathogen Ggt revealed a 38% higher percentage of take-all infected roots in ammonium-fertilized plants. The bacterial rhizosphere microbiome was little affected by the N form, whereas the fungal community composition and structure were shaped by the different N fertilization, as revealed from metabarcoding data. Importantly, we observed a higher abundance of fungal pathogenic taxa in the ammonium-fertilized treatment compared to the other N treatments. Taken together, our findings demonstrated the critical role of fertilized N forms for host-pathogen interactions and wheat rhizosphere microbiome assemblage, which are relevant for plant fitness and performance.

Mixed silage with Chinese cabbage waste enhances antioxidant ability by increasing ascorbate and aldarate metabolism through rumen Prevotellaceae UCG-004 in Hu sheep

Silage is rich in nutrients, which can make up for the lack of seasonal roughage, and has a certain promotion effect on the intensive feeding of ruminants. In addition, silage can maintain the rumen function of ruminants to a certain extent and reduce the risk of rumen acidosis and abomasum translocation. The purpose of this study was to investigate the effects of the mixed silage of Chinese cabbage waste and rice straw (mixed silage) on antioxidant performance, rumen microbial population, and fermentation metabolism of Hu sheep. The 16 healthy Hu sheep (eight rams and eight ewes, 39.11 ± 1.16 kg, 5.5 months) were randomly divided into two groups (the control group and the mixed silage group) with eight animals (four rams and four ewes) in each group. The control group was fed with farm roughage (peanut seedlings, corn husk, and high grain shell) as forage, and the mixed silage group was fed with the mixed silage as forage. The results showed that the mixed silage had no effect on the growth performance of Hu sheep (p &gt; 0.05). Ruminal butyric acid, total volatile fatty acids (TVFA), and ammonia nitrogen (NH3-N) concentration in the mixed silage group were increased, whereas the pH was decreased (p &lt; 0.05). The blood and rumen total antioxidants capacity (T-AOC) concentration in the mixed silage group was higher, and the malondialdehyde (MDA) content in rumen, serum, liver, and kidney was lower than that in the control group (p &lt; 0.05). PCoA and ANOSIM results of Illumina sequencing indicated that the mixed silage affected the bacterial composition of the rumen microbes. The mixed silage increased the proportion of Prevotellaceae UCG-004 which was in a positive correlation with Vitamin C (Vc). In addition, PICRUSt functional prediction analysis showed that ascorbate and aldarate metabolism were up-regulated in the mixed silage group (p &lt; 0.05). In conclusion, higher contents of VC and acid detergent fiber (ADF) in the mixed silage were beneficial to the growth and reproduction of Prevotellaceae UCG-004, resulting in increased production of the butyric acid significantly upregulated the metabolism of ascorbate and aldarate metabolism, thereby improving the antioxidant properties of Hu sheep.

In vitro colonic fermentation characteristics of barley-koji differ from those of barley

Barley-koji is prepared by inoculating barley, a beneficial prebiotic source, with the fungi Aspergillus luchuensis mut. kawachii. In this study, the prebiotic effects of barley-koji on human colonic microbiota were evaluated in vitro compared with barley, using pig feces. The enzyme-resistant fraction of following sample groups each were added to respective fermenters: cellulose, barley (Commander and β104), and barley-koji (Commander-koji and β104-koji). Short-chain fatty acid and ammonia-nitrogen production increased and decreased, respectively, in barley-koji and barley groups. Furthermore, the propionate concentration increased in the barley group, showing a positive correlation with the abundance of the genus Dialister. In the barley-koji group, however, acetate and n-butyrate concentrations increased during the early stages of incubation, and the relative abundance of the genus Megasphaera was higher than those of the other genera. Therefore, this study demonstrated that barley-koji might possess beneficial physiological properties for colonic fermentation, which differ from those of barley.

Effects of Dietary Carbohydrases on Fecal Microbiome Composition of Lactating Sows and Their Piglets

Corn-soybean meal diets are commonly used in the pork industry as a primary source of energy and protein. However, such a diet generally contains non-starch polysaccharides (NSPs) which present a challenge in finding ways to improve their availability and digestibility. Dietary multi-carbohydrases (MCs) have been proposed as an efficient approach to utilize NSPs, and can result in improved growth performance and host intestinal fitness. In this study, we evaluated the effects of MC in lactation diets on gut microbiota composition of lactating sows and their litters. The experimental design contained two dietary treatments, a diet based on corn-soybean meal (CON), and CON supplemented with 0.01% multigrain carbohydrases (MCs). Sow and piglet fecal samples were collected on days 7 and 28 after farrowing. Based on the results from 16S rRNA gene amplicon sequencing, MC led to changes in species diversity and altered the microbial compositions in lactating sows and their piglets. Specifically, the MC treatment induced an increase in the proportions of Lactobacillus in piglets. Clostridium and Spirochaetaceae showed a significantly reduced proportion in MC-treated sows at day 28. Our results support the beneficial effects of dietary carbohydrases and their link with improved production due to better host fitness outcomes and gut microbiota composition.

Current State and Challenges of the Global Outcomes of Dental Caries Research in the Meta-Omics Era

Despite significant healthcare advances in the 21st century, the exact etiology of dental caries remains unsolved. The past two decades have witnessed a tremendous growth in our understanding of dental caries amid the advent of revolutionary omics technologies. Accordingly, a consensus has been reached that dental caries is a community-scale metabolic disorder, and its etiology is beyond a single causative organism. This conclusion was based on a variety of microbiome studies following the flow of information along the central dogma of biology from genomic data to the end products of metabolism. These studies were facilitated by the unprecedented growth of the next- generation sequencing tools and omics techniques, such as metagenomics and metatranscriptomics, to estimate the community composition of oral microbiome and its functional potential. Furthermore, the rapidly evolving proteomics and metabolomics platforms, including nuclear magnetic resonance spectroscopy and/or mass spectrometry coupled with chromatography, have enabled precise quantification of the translational outcomes. Although the majority supports ‘conserved functional changes’ as indicators of dysbiosis, it remains unclear how caries dynamics impact the microbiota functions and vice versa, over the course of disease onset and progression. What compounds the situation is the host-microbiota crosstalk. Genome-wide association studies have been undertaken to elucidate the interaction of host genetic variation with the microbiome. However, these studies are challenged by the complex interaction of host genetics and environmental factors. All these complementary approaches need to be orchestrated to capture the key players in this multifactorial disease. Herein, we critically review the milestones in caries research focusing on the state-of-art singular and integrative omics studies, supplemented with a bibliographic network analysis to address the oral microbiome, the host factors, and their interactions. Additionally, we highlight gaps in the dental literature and shed light on critical future research questions and study designs that could unravel the complexities of dental caries, the most globally widespread disease.

Postbiotic effects of Lactobacillus fermentate on intestinal health, mucosa-associated microbiota, and growth efficiency of nursery pigs challenged with F18+Escherichia coli

This study determined the supplemental effects of Lactobacillus fermentate (LBF, Adare Biome, France) on intestinal health and prevention of postweaning diarrhea caused by F18+Escherichia coli in nursery pigs. Sixty-four weaned pigs (6.6 ± 0.7 kg body weight) were allotted in a randomized complete block design to four treatments: NC: no challenge/no supplement; PC: E. coli challenge/no supplement; AGP: E. coli challenge/bacitracin (30 g/t feed); and PBT: E. coli challenge/LBF (2 kg/t feed). Bacitracin methylene disalicylate (BMD) was used as a source of bacitracin. On day 7, challenged groups were orally inoculated with F18+E. coli (2.4 × 1010 CFU), whereas NC received sterile saline solution. Growth performance was analyzed weekly, and pigs were euthanized at the end of 28 d feeding to analyze intestinal health. Data were analyzed using the Mixed procedure of SAS 9.4. During the post-challenge period, PC tended to decrease (P = 0.067) average daily gain (ADG) when compared with NC, whereas AGP increased (P < 0.05) when compared with PC; PBT tended to increase (P = 0.081) ADG when compared with PC. The PC increased fecal score (P < 0.05) during day 7 to 14 when compared with NC, whereas AGP decreased it (P < 0.05) during day 14 to 21 when compared with PC. The PC increased (P < 0.05) protein carbonyl, crypt cell proliferation, and the relative abundance of Helicobacter rodentium when compared with NC. However, AGP decreased (P < 0.05) crypt cell proliferation and H. rodentium and increased (P < 0.05) villus height, Bifidobacterium boum, Pelomonas spp., and Microbacterium ginsengisoli when compared with PC. The PBT reduced (P < 0.05) crypt cell proliferation and H. rodentium and increased (P < 0.05) Lactobacillus salivarius and Propionibacterium acnes when compared with PC. At the genus level, AGP and PBT increased (P < 0.05) the alpha diversity of jejunal mucosa-associated microbiota in pigs estimated with Chao1 richness estimator when compared with PC. Collectively, F18+E. coli reduced growth performance by adversely affecting microbiota and intestinal health. The LBF and BMD improved growth performance, and it was related to the enhanced intestinal health and increased diversity and abundance of beneficial microbiota in pigs challenged with F18+E. coli.

Sugarcane polyphenol and fiber to affect production of short-chain fatty acids and microbiota composition using in vitro digestion and pig faecal fermentation model

This study aimed to examine the effects of sugarcane polyphenol and fiber (Phytolin + Fiber) on gut microbiota, short-chain fatty acids (SCFAs) production and phenolic metabolites production using in vitro digestion and fermentation model. Microbial profiling by 16S rRNA sequencing was used to analyze the pig faecal microbiota profile. SCFAs were identified and quantified by GC-FID, and phenolic metabolites were characterized by LC-ESI-QTOF-MS/MS. The results showed that Phytolin + Fiber exert synergistic effects on the pig gut microbiota by increasing the relative abundances of Lactobacillus and Catenibacterium, and decreasing the relative abundances of Mogibacterium, Dialister, and Escherichia-Shigella. Phytolin + Fiber also significantly increased the total SCFAs production, particularly the propionic and butyric acids. Production of phenolic metabolites related to major polyphenols in Phytolin were tentatively identified. These results suggest that Phytolin + Fiber could be beneficial to human colon health given the similarities between pig and human intestine in terms of physiology and microbiome.

Perspectives and Advances in Probiotics and the Gut Microbiome in Companion Animals

As the number of households that raise dogs and cats is increasing, there is growing interest in animal health. The gut plays an important role in animal health. In particular, the microbiome in the gut is known to affect both the absorption and metabolism of nutrients and the protective functions of the host. Using probiotics on pets has beneficial effects, such as modulating the immune system, helping to reduce stress, protecting against pathogenic bacteria and developing growth performance. The goals of this review are to summarize the relationship between probiotics/the gut microbiome and animal health, to feature technology used for identifying the diversity of microbiota composition of canine and feline microbiota, and to discuss recent reports on probiotics in canines and felines and the safety issues associated with probiotics and the gut microbiome in companion animals.

Changes in the Microbiome Profile in Different Parts of the Intestine in Piglets with Diarrhea

Simple Summary

The most common genera in the piglet microbiome were Lactobacillus, Escherichia-Shigella, Enterococcus, Bacteroides, and Fusobacterium. Bacteria of the Lactobacillus genus dominated in healthy piglets. An increased number of Escherichia-Shigella and Enterococcus was detected in diarrheal pigs. This indicates an important role of these bacteria in the pathogenesis of diarrhea. A decreased number of Bacteroides was detected in diarrheal pigs. According to the assessment of the microbiome composition in different sections of the intestine, bacteria of the Lactobacillus genus were the most common in the ileum, while Fusobacterium and Bacteroides were more common in the rectum. Our results show that the gut microbiome may make a significant contribution to the pathogenesis of diarrhea.

Abstract

Determining the taxonomic composition of microbial consortia of the piglet intestine is of great importance for pig production. However, knowledge on the variety of the intestinal microbiome in newborn piglets is limited. Piglet diarrhea is a serious gastrointestinal disease with a high morbidity and mortality that causes great economic damage to the pig industry. In this study, we investigated the microbiome of various sections of the piglet intestine and compared the microbiome composition of healthy and diarrheal piglets using high-throughput sequencing of the 16S rRNA gene. The results showed that bacteria of the Lactobacillus genus were the most common in the ileum, while Fusobacterium and Bacteroides dominated in the rectum. Comparing the microbiome composition of healthy and diarrheal piglets revealed a reduced number of Lactobacillus bacteria as a hallmark of diarrhea, as did an increased content of representatives of the Escherichia-Shigella genus and a reduced number of Bacteroides, which indicates the contribution of these bacteria to the development of diarrhea in piglets. The relative abundance of Enterococcus bacteria was higher in the diarrhea group. Although some bacteria of this genus are commensals, a small number of species may be associated with the development of diarrhea in piglets. Therefore, our results indicate that the gut microbiome may be an important factor in the development of diarrhea in piglets.

Molecular diagnostics of Salmonella and Campylobacter in human/animal fecal samples remain feasible after long-term sample storage without specific requirements

Rapid advances in the development of sequencing technologies, numbers of commercial providers and diminishing costs have made DNA-based identification and diagnostics increasingly accessible to doctors and laboratories, eliminating the need for local investments in expensive technology and training or hiring of skilled technicians. However, reliable and comparable molecular analyses of bacteria in stool samples are dependent on storage and workflow conditions that do not introduce post-sampling bias, the most important factor being the need to keep the DNA at a stable detectable level. For that reason, there may remain other prohibitively costly requirements for cooling or freezing equipment or special chemical additives.

This study investigates the diagnostic detectability of Salmonella and Campylobacter DNA in human, pig and chicken stool samples, stored at different temperatures and with different preservation methods. Stool samples were spiked with 10⁶ CFU/mL of both Salmonella and Campylobacter strains stored at −20 °C, 5 °C and 20 °C (Room temperature, RT) and treated with either RNAlater, EDTA or Silica/ethanol. DNA was extracted at 9 different time points within 30 days and quantified by Qubit (total DNA) and qPCR (Salmonella and Campylobacter DNA). We found no statistically significant differences among the different preservation methods, and DNA from both species was easily detected at all time points and at all temperatures, both with and without preservation. This suggests that infections by these bacteria can be diagnosed and possibly also analysed in further detail simply by taking a stool sample in any suitable sealed container that can be transported to laboratory analysis without special storage or preservation requirements. We briefly discuss how this finding can benefit infection control in both developed and developing countries.

Sargassum plagiophyllum Extract Enhances Colonic Functions and Modulates Gut Microbiota in Constipated Mice

Constipation is a symptom that is widely found in the world’s population. Various dietary supplementations are used to relieve and prevent constipation. Seaweed is widely used for its health benefits. In this study, we aimed to investigate the effects of Sargassum plagiophyllum extract (SPE) on functions of the gastrointestinal tract and gut microbiota. The results show that SPE pretreatment increased the frequency of gut contraction, leading to reduce gut transit time. SPE pretreatment also significantly increased the secretion of Cl− and reduced Na+ absorption, increasing fecal water content in constipated mice (p < 0.05). In addition, the Bifidobacteria population in cecal contents was significantly higher in constipated mice pretreated with 500 mg/kg SPE for 14 days than in untreated constipated mice (p < 0.05). Our findings suggest that SPE can prevent constipation in loperamide-induced mice. This study may be useful for the development of human food supplements from S. plagiophyllum, which prevent constipation.

Gut Microbiota Implications for Health and Welfare in Farm Animals: A Review

Simple Summary

Farm animal health and welfare have been paid increasing concern in the world, which is generally assessed by the measurements of physical health, immune response, behavior, and physiological indicators, such as stress-related hormone, cortisone, and norepinephrine. Gut microbiota as a “forgotten organ” has been reported for its great influence on the host phenotypes through the immune, neural, and endocrine pathways to affect the host health and behavior. In addition, fecal microbiota transplantation as a novel approach is applied to regulating the composition and function of the recipient farm animals. In this review, we summarized recent studies that gut microbiota influenced health, immunity, behavior, and stress response, as well as the progress of fecal microbiota transplantation in farm animals. The review will provide new insights into the measurement of farm animal health and welfare concerning gut microbiota, and the implication of fecal microbiota transplantation to improve productivity, health, and welfare. Above all, this review suggests that gut microbiota is a promising field to evaluate and improve animal welfare.

Abstract

In the past few decades, farm animal health and welfare have been paid increasing concern worldwide. Farm animal health and welfare are generally assessed by the measurements of physical health, immune response, behavior, and physiological indicators. The gut microbiota has been reported to have a great influence on host phenotypes, possibly via the immune processes, neural functions, and endocrine pathways, thereby influencing host phenotypes. However, there are few reviews regarding farm animals’ health and welfare status concerning the gut microbiota. In this point of view, (1) we reviewed recent studies showing that gut microbiota (higher alpha diversity, beneficial composition, and positive functions) effectively influenced health characteristics, immunity, behaviors, and stress response in farm animals (such as pigs, chickens, and cows), which would provide a novel approach to measure and evaluate the health status and welfare of farm animals. In addition, fecal microbiota transplantation (FMT) as one of the methods can modulate the recipient individual’s gut microbiota to realize the expected phenotype. Further, (2) we highlighted the application of FMT on the improvement of the production performance, the reduction in disease and abnormal behavior, as well as the attenuation of stress in farm animals. It is concluded that the gut microbiota can be scientifically used to assess and improve the welfare of farm animals. Moreover, FMT may be a helpful strategy to reduce abnormal behavior and improve stress adaption, as well as the treatment of disease for farm animals. This review suggests that gut microbiota is a promising field to evaluate and improve animal welfare.

Isolation and probiotic potential of lactic acid bacteria from swine feces for feed additive composition

Animal microbiota is becoming an object of interest as a source of beneficial bacteria for commercial use. Moreover, the escalating problem of bacterial resistance to antibiotics is threatening animals and humans; therefore, in the last decade intensive search for alternative antimicrobials has been observed. In this study, lactic acid bacteria (LAB) were isolated from suckling and weaned pigs feces (376) and characterized to determine their functional properties and usability as pigs additives. Selection of the most promising LAB was made after each stage of research. Isolates were tested for their antimicrobial activity (376) and susceptibility to antibiotics (71). Selected LAB isolates (41) were tested for the production of organic acids, enzymatic activity, cell surface hydrophobicity and survival in gastrointestinal tract. Isolates selected for feed additive (5) were identified by MALDI-TOF mass spectrometry and partial sequence analysis of 16S rRNA gene, represented by Lentilactobacillus, Lacticaseibacillus (both previously classified as Lactobacillus) and Pediococcus genus. Feed additive prototype demonstrated high viability after lyophilization and during storage at 4 °C and − 20 °C for 30 days. Finally, feed additive was tested for survival in simulated alimentary tract of pigs, showing viability at the sufficient level to colonize the host. Studies are focused on obtaining beneficial strains of LAB with probiotic properties for pigs feed additive.

Effects of dietary fiber sources on bacterial diversity in separate segments of the gastrointestinal tract of native and exotic pig breeds raised in Vietnam

Background and Aim:

Dietary fiber has distinctive effects on the environment and microbiota of the pig’s intestinal tract. This study was conducted at the naturally ventilated facility of the experimental station, National Institute of Animal Sciences, Vietnam, to examine the effects of fiber sources in diets on the intestinal microbiota of two different pig breeds raised in Vietnam.

Materials and Methods:

A total of 18 native and 18 exotic pigs with average initial body weights of 9.5±0.4 and 16.5±0.4 kg, respectively, were each divided into three dietary treatments, including a low-fiber diet containing approximately 200 g NDF per kg dry matter (DM) and two high-fiber diets containing cassava by-products or brewer’s grains containing approximately 300 g NDF per kg DM. At the end of the experiment (28 days), the bacterial diversity of digesta samples collected from the stomach, ileum, and colon segments was analyzed through DGGE analysis of the V3 variable regions of 16S-rDNA and by cloning and sequencing.

Results:

Among the diets, significant differences were observed in the number of DNA bands in the stomach between the native and exotic pigs (p<0.05), but not in the ileum and colon. The dietary fiber affected the number of DNA bands in the ileum (p<0.05), but not in the stomach and colon. A significant interaction effect was found between diet and breed on the number of DNA bands in the ileum (p<0.05). Dietary fiber and breed had a greater effect on microbiota in the ileum and colon than that in the stomach.

Conclusion:

The fiber sources affected the number of DNA bands in the ileum, and breed affected the number of DNA bands in the stomach. The microbial compositions in the ileum and colon segments were significantly affected by the dietary fiber and breed.

Combined effects of BARLEYmax and cocoa polyphenols on colonic microbiota and bacterial metabolites in vitro

BARLEYmax, a barley variety, and cocoa polyphenols (CPPs) have been reported to affect bacterial metabolites in the colon. This study aimed to evaluate the combined effects of BARLEYmax and CPPs supplementation on fecal microbiota in vitro using pig feces for 48 h. The relative abundances of the family Clostridiaceae and the genus Clostridium and ammonia-nitrogen production were decreased by both BARLEYmax and CPP supplementation, and there was a positive correlation between their abundances and the ammonia-nitrogen concentration. Although acetate and n-butyrate production was decreased by CPP supplementation, their concentrations were maintained at a higher level in the BARLEYmax + CPP group than in the cellulose (control) and cellulose + CPP groups. Therefore, this study demonstrated that a combination of BARLEYmax and CPPs may be beneficial in maintaining higher short-chain fatty acid production and the elimination of potentially harmful factors.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-021-00959-z.

Resistant starch: Implications of dietary inclusion on gut health and growth in pigs: a review

Starch from cereal grains, pulse grains, and tubers is a major energy substrate in swine rations constituting up to 55% of the diet. In pigs, starch digestion is initiated by salivary and then pancreatic α-amylase, and has as final step the digestion of disaccharides by the brush-border enzymes in the small intestine that produce monosaccharides (glucose) for absorption. Resistant starch (RS) is the proportion of starch that escapes the enzymatic digestion and absorption in the small intestine. The undigested starch reaches the distal small intestine and hindgut for microbial fermentation, which produces short-chain fatty acids (SCFA) for absorption. SCFA in turn, influence microbial ecology and gut health of pigs. These fermentative metabolites exert their benefits on gut health through promoting growth and proliferation of enterocytes, maintenance of intestinal integrity and thus immunity, and modulation of the microbial community in part by suppressing the growth of pathogenic bacteria while selectively enhancing beneficial microbes. Thus, RS has the potential to confer prebiotic effects and may contribute to the improvement of intestinal health in pigs during the post-weaning period. Despite these benefits to the well-being of pigs, RS has a contradictory effect due to lower energetic efficiency of fermented vs. digested starch absorption products. The varying amount and type of RS interact differently with the digestion process along the gastrointestinal tract affecting its energy efficiency and host physiological responses including feed intake, energy metabolism, and feed efficiency. Results of research indicate that the use of RS as prebiotic may improve gut health and thereby, reduce the incidence of post-weaning diarrhea (PWD) and associated mortality. This review summarizes our current knowledge on the effects of RS on microbial ecology, gut health and growth performance in pigs.

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

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

Early life feeding accelerates gut microbiome maturation and suppresses acute post-weaning stress in piglets

Early life microbiome perturbations can have important effects on host development, physiology and behaviour. In this longitudinal study, we evaluated the impact of early feeding on gut microbiome colonization in neonatal piglets. Early‐fed (EF) piglets had access to a customized fibrous diet from 2 days after birth until weaning in addition to mother's milk, whereas control piglets suckled mother's milk only. Rectal swabs were collected at multiple time points until 6 weeks of age to investigate microbiota development using 16S rRNA gene profiling. The dynamic pre‐weaning microbiota colonization was followed by a relatively stable post‐weaning microbiota, represented by Prevotella, Roseburia, Faecalibacterium, Ruminococcus, Megasphaera, Catenibacterium and Subdoligranulum. EF piglets showed an accelerated microbiota maturation, characterized by increased microbial diversity, pre‐weaning emergence of post‐weaning‐associated microbes and a more rapid decline of typical pre‐weaning microbes. Furthermore, the individual eating behaviour scores of piglets quantitatively correlated with their accelerated microbiome. Importantly, EF piglets displayed a smoother relative weight gain and tended to reach a higher relative weight gain, in addition to reduced diarrhoea scores in the first week post‐weaning. Overall, these findings demonstrate the beneficial impact of early feeding on microbiota development as well as pig health and performance during the weaning transition.

Effect of dietary phytobiotic mixture on growth performance, nutrient utilization, and immunity in weaned piglets

This study investigated the effects of dietary phytobiotic mixture on growth performance, blood profiles, immune response, and fecal microorganisms in weaned piglets. Twenty four weaned crossbred piglets were equally divided into four groups in a completely randomized design. The animals in 4 groups were fed a basal diet added with (1) no antibiotics and phytobiotics (CON), (2) bacitracin (0.5 g/kg; AB), (3) a blend of Cinnamomum zeylanicum and Trachyspermum copticum essential oils (0.3 g/kg and 0.4 g/kg, respectively; EO), and (4) plant extracts (PEO) of Mikania micrantha and Garcinia lanceifolia (2.8 g/kg and 1.4 g/kg, respectively) and C. zeylanicum and T. copticum essential oils (0.3 g/kg and 0.4 g/kg, respectively). Inclusion of AB, EO, and PEO did not affect final body weight, average daily gain, feed intake, feed efficiency, and nutrient digestibility. Compared with the CON, serum protein profiles were not affected, but a few lipid profiles were improved, particularly cholesterol, low-density lipoprotein, and high-density lipoprotein in the EO and PEO groups. Lymphocyte proliferation index and concentrations of IgG and IgA and TNF-α were not affected by any treatments. The concentrations of IgM increased (P = 0.04) at 28 days and tended to increase (P = 0.10) at 56 days in the EO group. Serum IL-1β levels decreased on days 28 and 56 in the EO and PEO groups. Fecal Lactobacilli population generally increased (P < 0.01) in the AB, EO, and PEO groups compared with the CON. Fecal enterobacterial numbers were always greater for AB than for CON, EO, or PEO, but enterobacterial populations were sometimes lower in the EO group than the CON group. In conclusion, dietary EO or PEO has no effect on the growth performance, but it may improve a few lipid profiles, immune responses, and fecal microbial populations in piglets.

Overgrowth of Lactobacillus in gastric cancer

Dysbiosis of the gastric microbiome is involved in the development of gastric cancer (GC). A number of studies have demonstrated an increase in the relative abundance of Lactobacillus in GC. In this review, we present data that support the overgrowth of Lactobacillus in GC from studies on molecular and bacterial culture of the gastric microbiome, discuss the heterogenic effects of Lactobacillus on the health of human stomach, and explore the potential roles of the overgrowth of Lactobacillus in gastric carcinogenesis. Further studies are required to examine the association between Lactobacillus and GC at strain and species levels, which would facilitate to elucidate its role in the carcinogenic process.

Deciphering the colonic fermentation characteristics of agavin and digestion-resistant maltodextrin in a simulated batch fermentation system

Gut microbial fermentation of soluble dietary fibers promotes general and substrate-specific health benefits. In this study, the fermentation characteristics of two soluble branched-dietary fibers, namely, agavin (a type of agave fructans) and digestion-resistant maltodextrin (RD) were investigated against cellulose, using a simulated colonic fermenter apparatus employing a mixed culture of swine fecal bacteria. After 48 h of complete fermentation period, the microbial composition was different among all groups, where Bifidobacterium spp. and Lactobacillus spp. dominated the agavin treatment, while the members of the families Lachnospiraceae and Prevotellaceae dominated the RD treatment. Agavin treatment exhibited a clearly segregated two-phased prolonged fermentation trend compared to RD treatment as manifested by the fermentation rates. Further, the highest short-chain fatty acids production even at the end of the fermentation cycle, acidic pH, and the negligible concentration of ammonia accumulation demonstrated favorable fermentation attributes of agavin compared to RD. Therefore, agavin might be an effective and desirable substrate for the colonic microbiota than RD with reference to the expressed microbial taxa and fermentation attributes. This study revealed a notable significance of the structural differences of fermentable fibers on the subsequent fermentation characteristics.

Role of modified diet and gut microbiota in metabolic endotoxemia in mice

This study was aimed at investigating the effect of cultured gut microbiota (GM) from obese humans coupled HFD in inducing metabolic endotoxemia in humanized mice. In total, 30 strains were isolated from 10 stool samples of obese patients. Following morphological and biochemical characterization, 16S rRNA gene sequencing of six abundant isolates identified these Klebsiella aerogenes, Levilactobacillus brevis, Escherichia coli, Staphylococcus aureus, Bacillus cereus and Bacillus subtilis (MZ052089-MZ052094). In vivo trial using above isolates, known as human gut microbiota (HGM), was performed for six months. Sixteen mice were distributed into four groups, i.e., G1 (control) mice fed with chow diet, group 2 (G2) with HFD, group 3 (G3) with HFD + HGM and group 4 (G4) with chow diet + HGM. Body mass index (BMI) and plasma endotoxins were measured pre- and post-experiment. In vivo study revealed that HFD + HGM caused significant increase (3.9 g/cm at 20 weeks) in the body weight and BMI (0.4 g/cm post-experiment) of G3 mice compared to the other groups. One-way ANOVA showed significantly higher level of endotoxins (2.41, 4.08 and 3.7 mmol/L) in mice groups G2, G3 and G4, respectively, indicating onset of metabolic endotoxemia. Cecal contents of experimental mice groups showed a shift in microbial diversity as observed by all isolates belonging to either Firmicutes or Bacteroidetes phyla, respectively. In conclusion, current study reported that minor alteration in GM composition through HFD feeding and cultured GM transfer has significant impact in development of metabolic endotoxemia, possibly via modified intestinal permeability.

Fecal microbial composition and functional diversity of Wuzhishan pigs at different growth stages

The mammalian gut microbiome participates in almost all life processes in the host. In addition to diet, the breed is the main factor affecting changes in the swine gut microbiota. The composition of the gut microbiota changes significantly during different growth stages. Research on developmental changes in the gut microbiota of indigenous Chinese pig breeds is limited. In this study, the fecal microbiota of Wuzhishan pigs (a Chinese indigenous miniature pig) at different growth stages was investigated using high-throughput 16S rRNA sequencing. Firmicutes and Bacteroidetes were the two dominant phyla, accounting for more than 80% of all sequences. With increasing age, the fecal microbial diversity increased, and the proportion of Firmicutes increased, whereas the proportion of Bacteroidetes decreased. A total of 49 biomarkers with statistical differences were detected in the four growth stages. The different microbiota among groups enhanced the ability to degrade fiber, carbohydrates, and other substances during the growth stages. The endocrine system was different in multiple growth stage paired comparisons, which was attributed to the different body statuses in the growth stages. This study revealed developmental changes in the structure and function of gut microbes in local pigs.

Different Non-Structural Carbohydrates/Crude Proteins (NCS/CP) Ratios in Diet Shape the Gastrointestinal Microbiota of Water Buffalo

The microbiota of the gastrointestinal tract (GIT) are crucial for host health and production efficiency in ruminants. Its microbial composition can be influenced by several endogenous and exogenous factors. In the beef and dairy industry, the possibility to manipulate gut microbiota by diet and management can have important health and economic implications. The aims of this study were to characterize the different GIT site microbiota in water buffalo and evaluate the influence of diet on GIT microbiota in this animal species. We characterized and compared the microbiota of the rumen, large intestine and feces of water buffaloes fed two different diets with different non-structural carbohydrates/crude proteins (NSC/CP) ratios. Our results indicated that Bacteroidetes, Firmicutes and Proteobacteria were the most abundant phyla in all the GIT sites, with significant differences in microbiota composition between body sites both within and between groups. This result was particularly evident in the large intestine, where beta diversity analysis displayed clear clustering of samples depending on the diet. Moreover, we found a difference in diet digestibility linked to microbiota modification at the GIT level conditioned by NSC/CP levels. Diet strongly influences GIT microbiota and can therefore modulate specific GIT microorganisms able to affect the health status and performance efficiency of adult animals.

Functional Amino Acids in Pigs and Chickens: Implication for Gut Health

In pigs and broiler chickens, the gastrointestinal tract or gut is subjected to many challenges which alter performance, animal health, welfare and livability. Preventive strategies are needed to mitigate the impacts of these challenges on gut health while reducing the need to use antimicrobials. In the first part of the review, we propose a common definition of gut health for pig and chickens relying on four pillars, which correspond to the main functions of the digestive tract: (i) epithelial barrier and digestion, (ii) immune fitness, (iii) microbiota balance and (iv) oxidative stress homeostasis. For each pillar, we describe the most commonly associated indicators. In the second part of the review, we present the potential of functional amino acid supplementation to preserve and improve gut health in piglets and chickens. We highlight that amino acid supplementation strategies, based on their roles as precursors of energy and functional molecules, as signaling molecules and as microbiota modulators can positively contribute to gut health by supporting or restoring its four intertwined pillars. Additional work is still needed in order to determine the effective dose of supplementation and mode of administration that ensure the full benefits of amino acids. For this purpose, synergy between amino acids, effects of amino acid-derived metabolites and differences in the metabolic fate between free and protein-bound amino acids are research topics that need to be furtherly investigated.

Parasites, Drugs and Captivity: Blastocystis-Microbiome Associations in Captive Water Voles

(1) Background: Blastocystis is a microbial eukaryote inhabiting the gastrointestinal tract of a broad range of animals including humans. Several studies have shown that the organism is associated with specific microbial profiles and bacterial taxa that have been deemed beneficial to intestinal and overall health. Nonetheless, these studies are focused almost exclusively on humans, while there is no similar information on other animals. (2) Methods: Using a combination of conventional PCR, cloning and sequencing, we investigated presence of Blastocystis along with Giardia and Cryptosporidium in 16 captive water voles sampled twice from a wildlife park. We also characterised their bacterial gut communities. (3) Results: Overall, alpha and beta diversities between water voles with and without Blastocystis did not differ significantly. Differences were noted only on individual taxa with Treponema and Kineothrix being significantly reduced in Blastocystis positive water voles. Grouping according to antiprotozoal treatment and presence of other protists did not reveal any differences in the bacterial community composition either. (4) Conclusion: Unlike human investigations, Blastocystis does not seem to be associated with specific gut microbial profiles in water voles.

Co-Occurrence of Regulated and Emerging Mycotoxins in Corn Silage: Relationships with Fermentation Quality and Bacterial Communities

Sixty-four corn silages were characterized for chemicals, bacterial community, and concentrations of several fungal metabolites. Silages were grouped in five clusters, based on detected mycotoxins, and they were characterized for being contaminated by (1) low levels of Aspergillus- and Penicillium-mycotoxins; (2) low levels of fumonisins and other Fusarium-mycotoxins; (3) high levels of Aspergillus-mycotoxins; (4) high levels of non-regulated Fusarium-mycotoxins; (5) high levels of fumonisins and their metabolites. Altersetin was detected in clusters 1, 3, and 5. Rugulusovin or brevianamide F were detected in several samples, with the highest concentration in cluster 3. Emodin was detected in more than 50.0% of samples of clusters 1, 3 and 5, respectively. Kojic acid occurred mainly in clusters 1 and 2 at very low concentrations. Regarding Fusarium mycotoxins, high occurrences were observed for FB3, FB4, FA1, whereas the average concentrations of FB6 and FA2 were lower than 12.4 µg/kg dry matter. Emerging Fusarium-produced mycotoxins, such as siccanol, moniliformin, equisetin, epiequisetin and bikaverin were detected in the majority of analyzed corn silages. Pestalotin, oxaline, phenopirrozin and questiomycin A were detected at high incidences. Concluding, this work highlighted that corn silages could be contaminated by a high number of regulated and emerging mycotoxins.

Effect of Two Different Biochars as a Component of Compound Feed on Nutrient Digestibility and Performance Parameters in Growing Pigs

The objective of this study was to examine two different biochars as a component of compound feed regarding their effects on nutrient digestibility and performance parameters in growing pigs. A total of 18 male, intact piglets (N = 18) with 26 days of age and an initial bodyweight of 6.88 kg were divided into three homogeneous groups of six animals each (n = 6). Treatments were control (CON, no addition of biochar), 2% biochar 1 (BC 1, diet containing 2% biochar 1), and 2% biochar 2 (BC 2, diet containing 2% biochar 2). Before the start of the trials, the biochars were characterized regarding Brunnauer-Emmet-Teller (BET) surface area, surface energy, humidity, and ash content. During the first trial (weeks 1–6) a 3 × 3 Latin square was used to determine the apparent total tract digestibility (ATTD) of all three feed in each animal (N = 54, n = 18). By start of the second trial on day 42, three new homogenous groups were formed with two animals from each of the previous groups. Each group received one of the three diets for 4 weeks. In the first trial, the ATTD of dry matter, organic matter, ether extract, crude fiber, and N-free extract was higher (p &lt; 0.05) in pigs fed the biochar diets (BC1 and BC2) than in those animals fed the control diet. The greatest difference was found for ATTD of crude fiber, which was increased by 19.8 and 23.8%, respectively (CON: 30.8b ± 13.4%; BC 1: 38.4a ± 8.2%; BC 2: 40.4a ± 12.2%). ATTD of crude protein was only higher in BC 2 compared to CON (CON: 81.0b ± 4.1%; BC 1: 82.4ab ± 3.6%; BC 2: 84.2a ± 3.4%). In both trials, the different treatments revealed no effects on ADFI, ADWG or G:F (p &gt; 0.05). The results indicate that no negative effects can be expected when 2% biochar is included in the feed for growing pigs.

Isolation of <i>Lactobacillaceae</i> bacteria from feces of ostrich (<i>Struthio camelus</i>)

The ostrich (Struthio camelus) is an herbivorous bird with a long and developed hindgut. In the hindgut, there is a dense and highly diverse population of anaerobic bacteria, and active fermentation produces high concentrations of short-chain fatty acids. Bacteria in the hindgut of the ostrich are considered vital for both their nutritional contribution and health benefits, such as benefits to the immune and defense system of the host. We attempted to isolate Lactobacillaceae, which might be involved in improving immune function and in inhibiting pathogens. The number of colonies from ostrich feces observed on LBS agar medium was 3.64×10³ per gram of feces. Three strains of Lactobacillaceae were isolated from the feces. Nearly the entire length of the 16S ribosomal RNA gene of these isolates was sequenced, and a homology search showed high identity with L. brevis (identity=99.93%), L. coryniformis (98.39%), and L. paracasei (100.0%). These isolates may be deemed potential probiotics for the ostrich.