Dietary changes in nutritional studies shape the structural and functional composition of the pigs' fecal microbiome-from days to weeks

Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China

The gut microbiota is believed to be closely related to many important physical functions in the host. Comprehensive data on mammalian gut metagenomes has facilitated research on host-microbiome interaction mechanisms, but less is known about pig gut microbiome, especially the gut microbiome in industrialized feedlot pigs, compared with human microbiome. On the other hand, pig production, as an important source of food, is believed to exacerbate the antibiotic resistance in humans due to the abuse of antibiotics in pig production in various parts of the world. This study delineates an intricate picture of swine gut microbiome and antibiotic resistome in industrialized feedlots and may provide insight for the pig producing industry.

To characterize the diversity and richness and explore the function and structure of swine gut microbiome and resistome in common pig-farming feedlots, we sampled and metagenomic sequenced the feces of pigs from four different industrialized feedlots located in four distant provinces across China. Surprisingly, more than half of the nonredundant genes (1,937,648, 54.3%) in the current catalogue were newly found compared with the previously published reference gene catalogue (RGC) of the pig gut microbiome. Additionally, 16 high-completeness draft genomes were obtained by analyzing the dominant species on each feedlot. Notably, seven of these species often appeared in the human body sites. Despite a smaller number of nonredundant genes, our study identified more antibiotic resistance genes than those available in the RGC. Tetracycline, aminoglycoside, and multidrug resistance genes accounted for nearly 70% of the relative abundance in the current catalogue. Slightly higher sharing ratios were shown between the industrialized feedlot pig gut microbiomes and human gut microbiomes than that between the RGC and human counterpart (14.7% versus 12.6% in genes and 94.1% versus 87.7% in functional groups, respectively). Furthermore, a remarkably high number of the antibiotic resistance proteins (n =141) were identified to be shared by the pig, human, and mouse resistome, indicating the potential for horizontal transfer of resistance genes. Of the antibiotic resistance proteins shared by pigs and humans, 50 proteins were related to tetracycline resistance, and 49 were related to aminoglycoside resistance.

IMPORTANCE The gut microbiota is believed to be closely related to many important physical functions in the host. Comprehensive data on mammalian gut metagenomes has facilitated research on host-microbiome interaction mechanisms, but less is known about pig gut microbiome, especially the gut microbiome in industrialized feedlot pigs, compared with human microbiome. On the other hand, pig production, as an important source of food, is believed to exacerbate the antibiotic resistance in humans due to the abuse of antibiotics in pig production in various parts of the world. This study delineates an intricate picture of swine gut microbiome and antibiotic resistome in industrialized feedlots and may provide insight for the pig producing industry.

Effects of Bacillus subtilis C-3102 on sow and progeny performance, fecal consistency, and fecal microbes during gestation, lactation, and nursery periods1,2

This study evaluated the effects of providing a dietary probiotic, Bacillus subtilis C-3102, to sows during gestation and lactation and to progeny after weaning on performance, fecal consistency, and fecal microbes. For the sow portion of the study, 29 sows and litters were used from day 30 of gestation until weaning. Sow treatments consisted of control diet or probiotic diet with B. subtilis C-3102 at 500,000 cfu/g of gestation feed and 1,000,000 cfu/g of lactation feed. For the nursery portion of the study, 358 weaned pigs, progeny of sows on study, were used in a 42-d nursery study. Nursery treatments consisted of control diet or probiotic diet with B. subtilis C-3102 and prebiotics at 500,000 cfu/g of nursery feed. Treatments were arranged in a split-plot design with sow treatment (control or probiotic diet) as main plot and nursery treatment (control or probiotic diet) as subplot. Performance, fecal consistency by fecal score method, and fecal microbes by isolation and enumeration method were assessed. In lactation, probiotic-fed sows tended (P = 0.057) to have increased feed intake, but it did not improve (P > 0.05) sow or litter performance in lactation. In the nursery, there were no (P > 0.10) interactions or main effects of sow or nursery treatments on overall growth performance. However, pigs born from control-fed sows had greater (P < 0.05) average daily gain, average daily feed intake, and body weight in late nursery than pigs born from probiotic-fed sows. Fecal score evaluation of nursing and nursery pigs indicated no influence (P > 0.05) of sow or nursery treatments on fecal consistency. Fecal microbial analysis revealed a modest modification in fecal microbial population by increasing (P < 0.05) the number of total Bacillus sp. in probiotic-fed sows and nursery pigs. Nursing piglets born from probiotic-fed sows carried over (P < 0.05) this modification in fecal microbial population preweaning. In conclusion, providing a probiotic based on B. subtilis C-3102 to sows during gestation and lactation and to progeny after weaning did not elicit noteworthy improvements in performance or fecal consistency, but there was a benefit on sow lactation feed intake. Fecal microbial analysis indicated a maternal-progeny intestinal microbiota relationship with pigs born from probiotic-fed sows displaying similar fecal microbial population as sows. However, pigs born from probiotic-fed sows demonstrated reduced growth rate and feed consumption in late nursery.

Milk microbiota: Characterization methods and role in cheese production

Milk is a complex body fluid aimed at addressing the nutritional and defensive needs of the mammal's newborns. Harbored microbiota plays a pivotal role throughout the cheesemaking process and contributes to the development of flavor and texture typical of different type of cheeses. Understanding the dairy microbiota dynamics is of paramount importance for controlling the qualitative, sensorial and biosafety features of the dairy products. Although many studies investigated the contribution of single or few microorganisms, still there is some information lacking about microbial communities. The widespread of the omics platforms and bioinformatic tools enable the investigation of the cheese-associated microbial community in both phylogenetical and functional terms, highlighting the effects of the diverse cheesemaking variables. In this review, the most relevant literature is revised to provide an introduction of the milk- and cheese-associated microbiota, along with their structural and functional dynamics in relation to the diverse cheesemaking technologies and influencing variables. Also, we focus our attention on the latest omics technologies adopted in dairy microbiota investigation. Discussion on the key-steps and major drawbacks of each omics discipline is provided along with a collection of results from the latest research studies performed to unravel the fascinating world of the dairy-associated microbiota. SIGNIFICANCE: Understanding the milk- and cheese- associated microbial community is nowadays considered a key factor in the dairy industry, since it allows a comprehensive knowledge on how all phases of the cheesemaking process impact the harbored microflora; thus, predict the consequences in the finished products in terms of texture, organoleptic characteristics, palatability and biosafety. This review, collect the pioneering and milestones works so far performed in the field of dairy microbiota, and provide the basic guidance to whom approaching the cheese microbiota investigation by means of the latest omics technologies. Also, the review emphasizes the benefits and drawbacks of the omics disciplines, and underline how the integration of diverse omics sciences enhance a comprehensive depiction of the cheese microbiota. In turn, a better consciousness of the dairy microbiota might results in the application of improved starter cultures, cheesemaking practices and technologies; supporting a bio-safe and standardized production of cheese, with a strong economic benefit for both large-scale industries and local traditional dairy farms.

Effect of a synbiotic supplement on cecal microbial ecology, antioxidant status, and immune response of broiler chickens reared under heat stress

The aim of this study was to examine the effect of a dietary synbiotic supplement on the cecal microflora, antioxidant status, and immune response of broiler chickens under heat stress (HS). A total of 360 one-day-old male Ross 708 broiler chicks were randomly distributed among 3 dietary treatments containing a synbiotic (PoultryStar consists of Bifidobacterium animalis, Enterococcus faecium, Lactobacillus reuteri, Pediococcus acidilactici, and fructooligosaccharides) at 0 (control), 0.5 (0.5X), and 1.0 (1.0X) g/kg. Each treatment contained 8 replicates of 15 birds each housed in floor pens. Heat stimulation was at 32°C for 9 h daily from day 15 to 42. Heat stress-induced changes of cecal bacteria were detected using bacteria-specific agars, and spleen protein concentration and mRNA expression of interleukins and antioxidants were examined using ELISA and real-time PCR, respectively. Under the HS condition, synbiotic fed broilers regardless of dose had lower cecal enumerations of Escherichia coli and coliforms, and a lower heterophil/lymphocyte (H/L) ratio (P < 0.05) compared to controls. 1.0X group also had higher cecal enumerations of Bifidobacterium spp. and Lactobacillus spp., spleen glutathione peroxidase (GPx), and plasma nuclear factor erythroid 2-related factor 2 (Nrf-2), and a lower H/L ratio compared to both control and 0.5X groups (P < 0.05). However, there were no treatment effects on the levels of Enterococcus spp., the circulating monocytes, eosinophils, and basophils, Toll like receptor-4 (TLR-4), interleukin-6 (IL-6), interlukin-10 (IL-10), and their mRNA expression, as well as plasma Kelch-like ECH-associated protein 1 (Keap-1) (P > 0.05). These results suggest that the synbiotic could inhibit the negative effects of HS on broiler health through the reduction of cecal pathogens, regulation of stress reactions, and improvement of antioxidant status.

Simultaneous Improvement in the Precision, Accuracy, and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains

The label-free proteome quantification (LFQ) is multistep workflow collectively defined by quantification tools and subsequent data manipulation methods that has been extensively applied in current biomedical, agricultural, and environmental studies. Despite recent advances, in-depth and high-quality quantification remains extremely challenging and requires the optimization of LFQs by comparatively evaluating their performance. However, the evaluation results using different criteria (precision, accuracy, and robustness) vary greatly, and the huge number of potential LFQs becomes one of the bottlenecks in comprehensively optimizing proteome quantification. In this study, a novel strategy, enabling the discovery of the LFQs of simultaneously enhanced performance from thousands of workflows (integrating 18 quantification tools with 3,128 manipulation chains), was therefore proposed. First, the feasibility of achieving simultaneous improvement in the precision, accuracy, and robustness of LFQ was systematically assessed by collectively optimizing its multistep manipulation chains. Second, based on a variety of benchmark datasets acquired by various quantification measurements of different modes of acquisition, this novel strategy successfully identified a number of manipulation chains that simultaneously improved the performance across multiple criteria. Finally, to further enhance proteome quantification and discover the LFQs of optimal performance, an online tool (https://idrblab.org/anpela/) enabling collective performance assessment (from multiple perspectives) of the entire LFQ workflow was developed. This study confirmed the feasibility of achieving simultaneous improvement in precision, accuracy, and robustness. The novel strategy proposed and validated in this study together with the online tool might provide useful guidance for the research field requiring the mass-spectrometry-based LFQ technique.

Development and Function of the Intestinal Microbiome and Potential Implications for Pig Production

Simple Summary

Piglet preweaning mortality is a major economic loss and welfare concern for the global pork industry, with the industry average sitting at approximately 15%. As such, novel methods for reducing this mortality are needed. Since research into the intestinal microbiota has provided advances in human health, in particular the impact of early life factors, it was the logical next step to synthesise the existing literature to determine the potential relevance to the pig industry. It is evident from the literature that this area of research provides promising results. However, a large gap within the literature currently exists within the lactation period in pigs. Since optimal development within early life is proving to be critical for human infants, it is crucial that further research is invested into understanding the impact of early life events on a piglet’s microbiome. It is hoped that this review will enable access to critical information for those interested in the microbiome and its potential for improving herd health on the farm.

Abstract

The intestinal microbiota has received a lot of attention in recent times due to its essential role in the immune system development and function. Recent work in humans has demonstrated that the first year of life is the most critical time period for microbiome development with perturbations during this time being proven to have long term health consequences. In this review, we describe the literature surrounding early life events in humans and mice that contribute to intestinal microbiota development and function, and compare this to piglets predominantly during their lactation period, which focuses on the impact lactation management practices may have on the intestinal microbiota. Although extensive research has been conducted in this area in humans and mice, little research exists in pigs during perceivably the most critical time period of development, which is the lactation period. The research reviewed outlines the importance of appropriate intestinal microbiota development. However, further research is needed in order to understand the full extent routine farm practices have on a piglet’s intestinal microbiota.

Analysis of the Bacterial and Host Proteins along and across the Porcine Gastrointestinal Tract

Pigs are among the most important farm animals worldwide and research to optimize their feed efficiency and improve their welfare is still in progress. The porcine intestinal microbiome is so far mainly known from sequencing-based studies. Digesta and mucosa samples from five different porcine gastrointestinal tract sections were analyzed by metaproteomics to obtain a deeper insight into the functions of bacterial groups with concomitant analyses of host proteins. Firmicutes (Prevotellaceae) dominated mucosa and digesta samples, followed by Bacteroidetes. Actinobacteria and Proteobacteria were much higher in abundance in mucosa compared to digesta samples. Functional profiling reveals the presence of core functions shared between digesta and mucosa samples. Protein abundances of energy production and conversion were higher in mucosa samples, whereas in digesta samples more proteins were involved in lipid transport and metabolism; short-chain fatty acids production were detected. Differences were also highlighted between sections, with the small intestine appearing more involved in carbohydrate transport and metabolism than the large intestine. Thus, this study produced the first functional analyses of the porcine GIT biology, discussing the findings in relation to expected bacterial and host functions.

Benefits of procyanidins on gut microbiota in Bama minipigs and implications in replacing antibiotics

Several studies have reported the effect of absorption of procyanidins and their contribution to the small intestine. However, differences between dietary interventions of procyanidins and interventions via antibiotic feeding in pigs are rarely reported. Following 16S rRNA gene Illumina MiSeq sequencing, we observed that both procyanidin administration for 2 months (procyanidin-1 group) and continuous antibiotic feeding for 1 month followed by procyanidin for 1 month (procyanidin-2 group) increased the number of operational taxonomic units, as well as the Chao 1 and ACE indices, compared to those in pigs undergoing antibiotic administration for 2 months (antibiotic group). The genera Fibrobacter and Spirochaete were more abundant in the antibiotic group than in the procyanidin-1 and procyanidin-2 groups. Principal component analysis revealed clear separations among the three groups. Additionally, using the online Molecular Ecological Network Analyses pipeline, three co-occurrence networks were constructed; Lactobacillus was in a co-occurrence relationship with Trichococcus and Desulfovibrio and a co-exclusion relationship with Bacillus and Spharerochaeta. Furthermore, metabolic function analysis by phylogenetic investigation of communities by reconstruction of unobserved states demonstrated modulation of pathways involved in the metabolism of carbohydrates, amino acids, energy, and nucleotides. These data suggest that procyanidin influences the gut microbiota and the intestinal metabolic function to produce beneficial effects on metabolic homeostasis.

Effect of dietary fiber content on nutrient digestibility and fecal microbiota composition in growing-finishing pigs

Microbial population in the gastrointestinal tract plays a central role in health and nutrient digestion. The objective of the present study was to investigate the relationships between microbiota and apparent digestibility coefficients with respect to age and diet. Pigs from Large-White, Duroc or Pietrain breeds were raised under the same housing conditions and fed alternately a low-fiber (LF) and a high-fiber diet (HF) during 4 successive 3-week periods. Data collection for digestibility measurements was achieved during the last week of each period. At the end of each period, fecal microbiota was collected for 16S rRNA gene sequencing. The microbiota remained stable across periods whereas digestibility of energy, crude proteins and cell wall components increased. The microbiota was resilient to diet effect and pigs fed the LF diet were discriminated to those fed the HF diet using 31 predicting OTUs with a mean classification error-rate of 3.9%. Clostridiaceae and Turicibacter were negatively correlated whereas Lactobacillus was positively correlated with protein and energy digestibility coefficients in the LF group. In addition, Lachnospiraceae and Prevotella were negatively correlated with cell wall component digestibility. In contrast, no significant correlation was found between microbiota composition and digestibility coefficients when pigs were fed the HF diet. Interestingly, it was also no longer possible to distinguish animals from different breeds once the animals were fed a HF diet, so that the microbiota could only trace the breed origin in the first period and in the LF group. In our experimental conditions, 3 weeks of adaptation to a new diet seems to be sufficient to observe resilience in growing pigs’ microbiota. We demonstrated that fecal microbiota can be used to classify pigs according to their dietary treatment. Some bacteria are favorable or unfavorable to digestibility. This suggests that manipulations of bacterial populations can improve digestibility and feed efficiency.

Dietary L-Tryptophan Modulates the Structural and Functional Composition of the Intestinal Microbiome in Weaned Piglets

Background: Intestinal microbiota plays an important role in regulating metabolism, physiology, and immune response of the host. L-Tryptophan (Trp) are metabolized by several genera of bacteria. It remains largely unknown whether Trp can regulate the composition and diversity of the intestinal microbiota and contribute to intestinal homeostasis.

Methods: A total of 126 weaning piglets were fed a corn- and soybean meal-based diet supplemented with 0, 0.2, or 0.4% Trp for 4 weeks. The intestinal microbiota was measured by using bacterial 16S rRNA gene-based high-throughput sequencing methods. Metabolites of Trp and short-chain fatty acids (SCFAs) in the hindgut were determined by high-performance liquid chromatography and gas chromatography, respectively. The mRNA levels for aromatic hydrocarbon receptor (AhR), tumor necrotic factor-α (TNF-α), interleukin-8 (IL-8), and protein abundances of tight junction proteins were determined.

Results: Compared with the control group, Trp supplementation enhanced piglet growth performance and markedly altered the intestinal microbial composition as evidenced by enhanced alpha and beta diversity in the microbiome (P < 0.05). The abundances of Prevotella, Roseburia, and Succinivibrio genera were enriched, but those of Clostridium sensu stricto and Clostridium XI, opportunistic pathogens, were decreased with dietary Trp supplementation. Analysis of metabolic pathways indicated enhanced indole alkaloid biosynthesis and Trp metabolism, which was validated by elevated concentrations of 3-indoleacetic acid and indole in the intestinal contents of Trp-supplemented piglets (P < 0.05). These changes in Trp metabolites were correlated with activation of AhR and cytochrome p4501 A1 (CYP1A1) in cecum and colonic tissues, and with a decrease in the intestinal mucosal IL-8 mRNA level. Moreover, the protein abundances for zonula occluden (ZO)-1 and occludin were upregulated by Trp supplementation in colonic tissues.

Conclusion: Dietary Trp supplementation altered intestinal microbial composition and diversity, improved intestinal mucosal barrier function, activated AhR signaling, and downregulated expression of inflammatory cytokines in the large intestine of weaned piglets. These results indicate a crosstalk between dietary Trp and intestine in nutrition, microbial metabolism, and mucosal immunity.

Microbiota in fermented feed and swine gut

Development of alternatives to antibiotic growth promoters (AGP) used in swine production requires a better understanding of their impacts on the gut microbiota. Supplementing fermented feed (FF) in swine diets as a novel nutritional strategy to reduce the use of AGP and feed price, can positively affect the porcine gut microbiota, thereby improving pig productivities. Previous studies have noted the potential effects of FF on the shift in benefit of the swine microbiota in different regions of the gastrointestinal tract (GIT). The positive influences of FF on swine gut microbiota may be due to the beneficial effects of both pre- and probiotics. Necessarily, some methods should be adopted to properly ferment and evaluate the feed and avoid undesired problems. In this mini-review, we mainly discuss the microbiota in both fermented feed and swine gut and how FF influences swine gut microbiota.