Evolution of the Gut Microbiota and Its Fermentation Characteristics of Ningxiang Pigs at the Young Stage

Targeted Screening of Fiber Degrading Bacteria with Probiotic Function in Herbivore Feces

Cellulolytic bacteria with probiotic functions play a crucial role in promoting the intestinal health in herbivores. In this study, we aimed to correlate the 16S rRNA gene amplicon sequencing and fiber-degrading enzyme activity data from six different herbivore feces samples. By utilizing the separation and screening steps of probiotics, we targeted and screened high-efficiency fiber-degrading bacteria with probiotic functions. The animals included Maiwa Yak (MY), Holstein cow (CC), Tibetan sheep (TS), Southern Sichuan black goat (SG), Sichuan white rex rabbit (CR), and New Zealand white rabbit (ZR). The results showed that the enzymes associated with fiber degradation were higher in goat and sheep feces compared to cattle and rabbit's feces. Correlation analysis revealed that Bacillus and Fibrobacter were positively correlated with five types of fiber-degrading related enzymes. Notably, the relative abundance of Bacillus in the feces of Tibetan sheep was significantly higher than that of other five herbivores. A strain TS5 with good cellulose decomposition ability from the feces of Tibetan sheep by Congored staining, filter paper decomposition test, and enzyme activity determination was isolated. The strain was identified as Bacillus velezensis by biological characteristics, biochemical analysis, and 16S rRNA gene sequencing. To test the probiotic properties of Bacillus velezensis TS5, we evaluated its tolerance to acid and bile salt, production of digestive enzymes, antioxidants, antibacterial activity, and adhesion ability. The results showed that the strain had good tolerance to pH 2.0 and 0.3% bile salts, as well as good potential to produce cellulase, protease, amylase, and lipase. This strain also had good antioxidant capacity and the ability to antagonistic Staphylococcus aureus BJ216, Salmonella SC06, Enterotoxigenic Escherichia coli CVCC196, and Escherichia coli ATCC25922. More importantly, the strain had good self-aggregation and Caco-2 cell adhesion rate. In addition, we tested the safety of Bacillus velezensis TS5 by hemolysis test, antimicrobial susceptibility test, and acute toxicity test in mice. The results showed that the strain had no hemolytic phenotype, did not develop resistance to 19 commonly used antibiotics, had no cytotoxicity to Caco-2, and did not have acute toxic harm to mice. In summary, this study targeted isolated and screened a strain of Bacillus velezensis TS5 with high fiber-degrading ability and probiotic potency. This strain can be used as a potential probiotic for feeding microbial preparations for ruminants.

Comparative Analysis of Gut Microbiota Diversity Across Different Digestive Tract Sites in Ningxiang Pigs

BACKGROUND

Microbial communities in the gastrointestinal tract play a critical role in nutrient absorption, metabolism, and overall health of animals. Understanding the structure and function of tissue-specific microbial communities in Ningxiang pigs is essential for optimizing their growth, development, and nutritional efficiency. However, the diversity and functional roles of microbiota in different nutrient absorption tissues remain underexplored.

METHODS

We collected samples from four key nutrient absorption tissues (NFC: Cecal Content, NFI: Ileal Content, NFL: Colonic Content, NFG: Gastric Content, N = 6) of Ningxiang pigs and performed 16S rRNA gene sequencing to analyze microbial community composition. Bioinformatics analyses included alpha and beta diversity assessments, linear discriminant analysis effect size (LEfSe) for biomarker identification, and PICRUSt2-based functional prediction. Comparative metabolic abundance analysis was conducted to explore functional differences among tissues.

RESULTS

Alpha diversity indices (ACE, Chao1, Simpson, and Shannon) revealed significant differences in microbial richness and evenness among the four tissues. At the phylum level, Firmicutes dominated the microbiota, while Bacteroidota was prominent in NFC and NFL. LEfSe analysis identified tissue-specific dominant microbial groups, such as f_Prevotellaceae in NFC, o_Lactobacillales in NFG, f_Clostridiaceae in NFI, and f_Muribaculaceae in NFL. Functional profiling using PICRUSt2 showed that the microbiota was primarily involved in organismal systems (e.g., aging, digestion), cellular processes (e.g., cell growth, transport), environmental information processing (e.g., signaling), genetic information processing (e.g., transcription, translation), and metabolic regulation (e.g., amino acid and carbohydrate metabolism). Comparative metabolic abundance analysis highlighted distinct functional profiles across tissues, with significant differences observed in pathways related to the immune system, energy metabolism, lipid metabolism, transcriptional and translational regulation, and aging.

CONCLUSIONS

Our findings demonstrate that tissue-specific microbial communities in Ningxiang pigs exhibit distinct structural and functional characteristics, which are closely associated with nutrient absorption and metabolic regulation. These results provide valuable insights into the roles of microbiota in the growth and health of Ningxiang pigs and pave the way for future studies on microbe-mediated nutritional interventions.

Growth Performance, Apparent Digestibility, Serum Indices, and Fecal Bacterial Community Diversity in Yanbian Cattle Fed Diets With Fermented Spent Mushroom Substrate From Pleurotus Eryngii Instead of Brewers Spent Grain

This experiment was to evaluate the effect of fermented spent mushroom substrate from Pleurotus eryngii (FSMPE) instead of brewers spent grain (BSG) on growth performance, apparent digestibility, serum indices, and fecal bacterial community of Yanbian cattle. Thirty heifers were randomly divided into three groups: T0 group (control group, fed a diet without FSMPE); T1 group (fed a diet with FSMPE instead of 50% BSG); T2 group (fed a diet with FSMPE instead of 100% BSG). The results showed that replacing BSG with FSMPE increased nutrient intake (except ether extract), average daily gain and economic efficiency, among which T1 group had the best effect. The apparent digestibility of dry matter, organic matter, crude protein, and neutral detergent fiber in the T1 group was not affected by FSMPE, but decreased significantly in the T2 group. In addition, FSMPE instead of BSG improved the serum biochemical and antioxidant indices of cattle. Meanwhile, FSMPE not only had no adverse effects on the bacterial diversity, but also improved the abundance of certain cellulose-degrading bacteria and potentially probiotic bacteria in rectal feces. These findings showed that replacing 50% BSG with FSMPE had positive effects on growth performance, economic efficiency, and health status of Yanbian cattle.

Insights into the Gut Microbial Diversity of Wild Siberian Musk Deer (Moschus moschiferus) in Republic of Korea

The gut microbiota plays a crucial role in the health and well-being of wildlife. However, its composition and diversity remain unexplored, particularly in threatened species such as the Siberian musk deer (SMD). This study aimed to elucidate the gut microbiota composition within different wild SMD communities for assessing their health status. We conducted the first comprehensive fecal microbiome analysis of wild SMD inhabiting three distinct locations in Gangwon Province, Republic of Korea (Korea). Fecal samples were collected non-invasively and 16S rRNA gene sequencing was performed for gut microbiota characterization. Consistent with previous research, Firmicutes and Bacteroidetes were the dominant phyla in the gut microbiota of wild SMD. Planctomycetota was a prevalent phylum in wild SMD gut microbiota, warranting further investigation of its ecological significance. While significant differences were observed in the gut microbiota richness among the three groups, no significant disparities were detected in the beta diversity. Additionally, certain genera exhibited distinct relative abundances among the groups, suggesting potential associations with geographic factors, gut disorders, and dietary habits. Our findings provide valuable insights into the gut microbiome of wild SMD and offer a foundation for future microbiome-based conservation efforts for this vulnerable species.

The impact of Codonopsis Pilosulae and Astragalus Membranaceus extract on growth performance, immunity function, antioxidant capacity and intestinal development of weaned piglets

Introduction

The objective of this study was to examine the impact of Codonopsis pilosula and Astragalus membranaceus extract (CA) on the growth performance, diarrhea rate, immune function, antioxidant capacity, gut microbiota, and short-chain fatty acids (SCFAs) in weaned piglets.

Methods

A total of forty-eight 31-day-old weaned piglets, were divided into four groups randomly based on the treatment type: control group (CON), low dose group (LCA, 0.5% CA), medium dose group (MCA, 1.0% CA), and high dose group (HCA, 1.5% CA), and were fed for a duration of 28 days. On the morning of the 1st and 29th day, the piglets were assessed by weighing them on an empty stomach, recording their daily feed intake and diarrhea rate.

Results

CA increased the average daily weight gain and reduced F/G without significant differences, and the diarrhea rate was reduced in the LCA and MCA groups. Furthermore, the levels of T-AOC, SOD, GSH-Px, and MDA were increased. The levels of T-AOC in the LCA group and the MCA group, SOD in the MCA group, and GSH-Px in the HCA group were significantly higher compared with the CON group (p < 0.05). Additionally, CA significantly increased IgM, IgG, and IgA levels (p < 0.05). The results of gut microbiota analysis showed that the bacterial population and diversity of faeces were changed with the addition of CA to basal diets. CA increased the abundance of the beneficial bacterial Firmicutes and Lactobacillus. Additionally, Compared with the CON group, CA significantly increased the SCFAs content of weaned piglets (p < 0.05).

Discussion

CA can alleviate oxidative stress, improve immunity and antioxidant capacity, increase the abundance of beneficial bacteria, and the content of SCFAs for improving the intestinal barrier of piglets, thus promoting growth and reducing diarrhea rate in weaned piglets.

Effects of different ratios of soluble to insoluble dietary fiber on growth performance and intestinal health of piglets

This study investigated the impact of different ratios of soluble to insoluble dietary fiber (SDF:IDF) formulations by sugar beet pulp (SBP) supplementation on piglet growth performance, nutrient digestibility, immune function, intestinal morphology, intestinal microbiota and intestinal health. A total of 60 crossbred piglets (Duroc × [Landrace × Yorkshire]) at 40 d old with body weight of 10.0 ± 0.3 kg were randomly assigned to 5 treatments with 6 replicates per treatment and 2 piglets per replicate in a 21-d trial. The dietary treatments included a corn-soybean meal diet (0% SBP supplementation; CON), and diets supplemented with 2%, 4%, 6%, and 8% SBP, representing different SDF:IDF ratios at 10.16%, 13.53%, 16.79%, 19.86%, and 24.81%, respectively. The results indicated that the 8% SBP treatment had a negative effect on feed-to-gain ratio (linear, P = 0.009) compared with the CON treatment (P = 0.021). The apparent total tract digestibility (ATTD) of crude protein was lower in treatments supplemented with SBP (P = 0.002) and showed a linear decrease (P = 0.001), while the ATTD of IDF showed a linear increase (P = 0.037) in four SBP treatments compared to the CON treatment. The 4% SBP treatment increased serum concentrations of triglyceride (quadratic, P = 0.019) and K (linear, P < 0.0037), and decreased alanine transaminase concentration (quadratic, P = 0.015) compared with the CON treatment. The concentrations of Cit, Cys, Ile, Leu, Orn, Arg, taurine, urea, 1-methylhistidine, α-aminoadipic acid, α-aminobutyric acid and cystathionine in the 4% SBP treatment were highest among all treatments (P < 0.05). The serum concentrations of interleukin-6, interleukin-8, interleukin-10, transforming growth factor-β, and tumor necrosis factor-α in the 6% SBP treatment were higher than those in the CON treatment (P < 0.05), which also increased mucin-2 and G protein-coupled receptor 41 mRNA expression (P < 0.05) in colonic mucosa compared with the CON treatment and improved the intestinal barrier function. Diets containing more than 19.86% SDF:IDF could impair the intestinal health in piglets when SBP was used as the SDF source. Supplementing nursery piglet diets with 16.79% to 19.86% SDF:IDF is recommended for improving intestinal barrier function, increasing short-chain fatty acids concentrations, and improving intestinal microbiota composition.

Survey of the fecal microbiota of indigenous small ruminants living in different areas of Guizhou

Introduction

Gut microbiota are associated with the health and performance of ruminant species, and they are affected by altitude, host genetics, and sex. However, there has been little research on comparing the fecal microbiota of indigenous small ruminants such as sheep and goats in Guizhou province, China. In the present study, we revealed the effect of altitude, genetics, and sex on fecal microbiota profiles and enterotypes in indigenous small ruminants of Guizhou province, China.

Methods

Fecal samples were collected from Hei and Qianbei Ma goats and Weining sheep in the Chinese province of Guizhou. 16S rRNA gene sequencing targeting the V3-V4 region was performed using the Illumina MiSeq platform. Sequences were processed using QIIME2, and the qualified sequences were processed using the plugin DADA2 to generate amplicon sequence variants (ASVs). The statistical analysis was performed using R studio.

Results

The fecal microbial profile was found to vary by herd (influenced by genetics/altitude) and sex. All samples were categorized into two enterotypes. The first enterotype is dominated by UCG-005, and the second enterotype is dominated by the Christensenellaceae_R-7_group, which may be highly driven by the host's genetics (breed). The predicted functional profiles of the fecal microbiota were also assigned to two clusters that corresponded exactly to the enterotypes. Cluster 1 of the functional profiling was characterized by biosynthesis pathways, and cluster 2 was characterized by energy metabolism pathways.

Discussion

Our findings may provide new insights into the fecal microbial community and enterotypes in small ruminants by herds, offering clues for understanding the mechanisms by which the fecal microbiota contribute to divergent host phenotypes in indigenous small ruminants in Guizhou.

Ningxiang Pig-Derived Parabacteroides distasonis HNAU0205 Alleviates ETEC-Induced Intestinal Apoptosis, Oxidative Damage, and Inflammation in Piglets

Weaning is a critical stage in the growth and development of piglets, often inducing stress reactions. This study aims to investigate the effects of Parabacteroides distasonis (PBd) derived from Ningxiang pigs on growth performance, intestinal apoptosis, oxidative damage, and inflammation in ETEC-challenged weaned piglets. A total of 22 Duroc × Landrace × Yorkshire (DLY) piglets, 24 days old with similar body weights, were randomly divided into three groups: Control (n = 7), ETEC (n = 7), and PBd + ETEC (n = 8). The results show that, compared to the Control group, ETEC challenge led to decreased growth performance, reduced villus height in the duodenum and jejunum, increased crypt depth in the duodenum, a decreased villus-height-to-crypt-depth ratio, increased expression of apoptosis-related genes (Caspase-8 and Caspase-9), increased expression of oxidative damage-related genes (Nrf2, GSH-PX, mTOR, and Beclin1), increased expression of inflammation-related genes (Myd88, P65, TNF-α, and IL-6), and reduced the contents of SCFAs in the colonic chyme (acetate, propionate, butyrate, valerate, and total SCFAs). Compared to the ETEC group, the PBd + ETEC group alleviated the reduction in growth performance, mitigated intestinal morphological damage, and reduced the expression of the aforementioned apoptosis, oxidative damage, and inflammation-related genes with the increase in SCFAs. In conclusion, PBd derived from Ningxiang pigs effectively reduces ETEC-induced intestinal damage in weaned piglets, improves intestinal health, and increases the content of SCFAs in the colonic chyme, thereby enhancing growth performance.

Alteration of Fecal Microbiota, Fecal Metabolites, and Serum Metabolites in Dairy Cows with Pre-Retained Placenta

Retained placenta (RP) affects lactation and fertility in dairy cows and causes economic losses to the dairy industry. Therefore, screening for early warning of this disease is important. This study used multi omics techniques to reveal the metabolic differences of dairy cows before RP onset and to find potential warning markers. Fecal samples and serum samples of 90 healthy Holstein cows were collected 7 days pre-calving; 10 healthy and 10 RP cows were enrolled according to normal expulsion of fetal membranes after calving. Fecal samples were subjected to 16S rRNA sequencing and untargeted metabolomics analysis, while plasma was analyzed using targeted metabolomics. Pathogenic bacteria levels increased in the intestines of cows with RP compared to those in healthy cows. Lipid metabolites constituted the largest proportion of differential metabolites between feces and plasma. Six potential warning markers for RP in cows were identified, including two fecal microbiomics markers (Oscillospiraceae UCG-005 and Escherichia-Shigella), one fecal untargeted metabolomics marker (N-acetylmuramic acid), and three plasma targeted metabolomics markers (glycylcholic acid-3 sulfate, 7-ketolithocholic acid, and 12-ketolithocholic acid). These biomarkers can predict RP occurrence in the early perinatal period. These results lay a theoretical foundation for early nutritional intervention and pathogenesis research in dairy cows.

Maternal Malic Acid May Ameliorate Oxidative Stress and Inflammation in Sows through Modulating Gut Microbiota and Host Metabolic Profiles during Late Pregnancy

Sows suffer oxidative stress and inflammation induced by metabolic burden during late pregnancy, which negatively regulates reproductive and lactating performances. We previously found that L-malic acid (MA) alleviated oxidative stress and inflammation and improved reproductive performances in sows. However, the mechanism underlying the MA's positive effects remains unexplored. Here, twenty Large White × Landrace sows with similar parity were randomly divided into two groups and fed with a basal diet or a diet supplemented with 2% L-malic acid complex from day 85 of gestation to delivery. The gut microbiome, fecal short-chain fatty acids, and untargeted serum metabolome were determined. Results showed that Firmicutes, Bacteroidota, and Spirochaetota were the top abundant phyla identified in late pregnancy for sows. Maternal MA supplementation modulated the composition but not the richness and diversity of gut microbiota during late pregnancy. Correlation analysis between gut microbiota and antioxidant capacity (or inflammation indicators) revealed that unclassified_f_Ruminococcaceae, unclassified_f_Lachnospiraceae, UCG-002, norank_f_norank_o_RF3, and Lactobacillus might play a role in anti-oxidation, and Lachnospiraceae_XPB1014_group, Lachnospiraceae_NK4A136_group, UCG-002, unclassified_f_Ruminococcaceae, Candidatus_Soleaferrea, norank_f_UCG-010, norank_f_norank_o_RF39, and unclassified_f_Lachnospiraceae might be involved in the anti-inflammatory effect. The improved antioxidant and inflammation status induced by MA might be independent of short chain fatty acid changes. In addition, untargeted metabolomics analysis exhibited different metabolic landscapes of sows in the MA group from in the control group and revealed the contribution of modified amino acid and lipid metabolism to the improved antioxidant capacity and inflammation status. Notably, correlation results of gut microbiota and serum metabolites, as well as serum metabolites and antioxidant capacity (or inflammation indicators), demonstrated that differential metabolism was highly related to the fecal microorganisms and antioxidant or inflammation indicators. Collectively, these data demonstrated that a maternal dietary supply of MA can ameliorate oxidative stress and inflammation in sows through modulating gut microbiota and host metabolic profiles during late pregnancy.

Effects of Dietary Alfalfa Meal Supplementation on the Growth Performance, Nutrient Apparent Digestibility, Serum Parameters, and Intestinal Microbiota of Raccoon Dogs (Nyctereutes procyonoides)

The raccoon dog (Nyctereutes procyonoides) is a typical omnivore possessing wide dietary adaptability and tolerance to rough feeding, which may be attributed to its intestinal microbiota. The study aimed to investigate the effect of dietary alfalfa meal levels on the growth performance, nutrient apparent digestibility, serum parameters, and intestinal microbiota of raccoon dogs. Sixty raccoon dogs were randomly divided into four dietary treatments containing 0% (AM0), 5% (AM5), 10% (AM10), and 15% (AM15) alfalfa meal for a 60-day experiment. The results showed that compared to raccoon dogs fed the AM0 diet, those fed the AM5 and AM10 diets had no significant difference in growth performance, while those fed the AM15 diet experienced a significant decrease. Raccoon dogs fed the AM5 diet had no significant effect on the nutrient apparent digestibility. Dietary supplementation with alfalfa meal significantly decreased serum urea levels and increased the antioxidant capacity of raccoon dogs. The intestinal microbiome analysis showed that the richness and diversity of colonic microbiota significantly increased in the AM15 group. With the increase in dietary alfalfa meal levels, the relative abundance of fiber-degrading bacteria in the colon of raccoon dogs, such as Treponema, Phascolarctobacterium, and Christensenellaceae R-7 group, increased. However, the relative abundance of pathogenic bacteria, including Anaerobiospirillum, decreased. In conclusion, the inclusion of 5% alfalfa meal in the raccoon dogs' diet had no effect on growth performance, but it exhibited the potential to improve serum antioxidant capacity and intestinal microbiota. This indicates that raccoon dogs have a certain tolerance to the addition of alfalfa meal in their diet.

The Microbiota Architecture of the Chinchilla Gastrointestinal Tract

The gastrointestinal microbiota develop alongside the host and play a vital role in the health of cecal fermenters such as chinchillas. However, little is known about the microbiota architecture in healthy chinchillas. Illumine-based 16S rRNA gene amplicon sequencing was used to investigate the microbiota present in six different gastrointestinal tract regions of three healthy adult chinchillas. The findings revealed significantly more abundant microbiota in the large intestine compared with the proximal segments. In addition, the cecum exhibited better evenness compared to the colon. The core microbiota are Firmicutes, Bacteroidota, Actinobacteriota, and Proteobacteria at the phylum level. The signature microbiota of each segment were identified. The cecum had 10 signature microbiota, which had the widest coverage and overlapped with that of the cecum. The stomach had five signature microbiota, exhibiting the second widest coverage and overlapping with the duodenum. No signature microbiota were detected in the jejunum and ileum. While similarities exist with the microbiota of other cecal fermenters, chinchillas exhibit distinct microbiota closely related to their unique digestive mechanisms. This study is a preliminary study of the gastrointestinal microbiota architecture and distribution in healthy chinchillas. Further study is needed in order to better understand the effect of gastrointestinal microbiota on the health of the chinchilla.

Temporal and geographic distribution of gut microbial enterotypes associated with host thermogenesis characteristics in plateau pikas

IMPORTANCE

The gut microbiotas of small mammals play an important role in host energy homeostasis. However, it is still unknown whether small mammals with different enterotypes show differences in thermogenesis characteristics. Our study confirmed that plateau pikas with different bacterial enterotypes harbored distinct thermogenesis capabilities and employed various strategies against cold environments. Additionally, we also found that pikas with different fungal enterotypes may display differences in coprophagy.

Dietary supplementation with Acremonium terricola culture alters the gut microbial structure and improves the growth performance, antioxidant status, and immune function of weaning piglets

BACKGROUND

Acremonium terricola is used in the feed of dairy animals to promote growth and control diseases. However, the effects of dietary supplementation with A. terricola on the gut microbial structure of weaning piglets remain poorly understood. Therefore, in this study, we investigated the effects of dietary supplementation with A. terricola culture (ATC) on the growth performance, antioxidant status, immunity, and gut environment of weaning piglets. Sixty piglets were fed a basal diet supplemented with 1 g ATC/kg of basal diet (experimental group). Another 60 piglets did not receive ATC (control group). The intervention lasted for 20 days.

RESULTS

The experimental group had higher daily weight gain and feed efficiency than did the control group. Significant increases were noted in the levels of serum insulin (P = 0.0018), insulin-like growth factor (P = 0.0018), triiodothyronine (P = 0.0031), immunoglobulin A (P < 0.0001), immunoglobulin M (P = 0.001), immunoglobulin G (P = 0.0001), and interferon γ (P < 0.0001) in the experimental group compared with the levels in the control group. Furthermore, ATC supplementation significantly reduced (P < 0.05) the relative abundance of Shuttleworthia, Succinivibrio, Roseburia, Ruminococcus, and Paludibacter but increased that of Phascolarctobacterium, Megasphaera, Faecalibacterium, and Prevotella in the experimental group compared with that in the control group. Notably, ATC supplementation significantly increased the relative abundance of Faecalibacterium prausnitzii (P < 0.05), which is involved in anti-inflammatory activities, gut barrier enhancement, and butyrate production.

CONCLUSIONS

Dietary supplementation with ATC may improve the growth performance, antioxidant status, immunity, and fecal microflora of weaning pigs.

Modulation of Swine Gut Microbiota by Phytogenic Blends and High Concentrations of Casein in a Validated Swine Large Intestinal In Vitro Model

Phytogenic feed additives are gaining popularity in livestock as a replacement for antibiotic growth promotors. Some phytogenic blends (PB) positively affect the production performance, inhibit pathogens within the gut microbiota, and improve the overall health of farm animals. In this study, a swine large intestine in vitro model was used to evaluate the effect of two PBs, alone or in combination with casein, on swine gut microbiota. As a result, the combination of casein with PB1 had the most beneficial effects on swine gut microbiota, as it increased the relative abundance of some commensal bacteria and two genera (Lactobacillus and Oscillospiraceae UCG-002), which are associated with greater production performance in pigs. At the same time, supplementation with PBs did not lead to an increase in opportunistic pathogens, indicating their safety for pigs. Both PBs showed fewer changes in swine gut microbiota compared to interventions with added casein. In contrast, casein supplementation significantly increased beta diversity and the relative abundance of commensal as well as potentially beneficial bacteria. In conclusion, the combination of casein with PBs, in particular PB1, had the most beneficial effects among the studied supplements in vitro, with respect to microbiota modulation and metabolite production, although this data should be proven in further in vivo studies.

Morel (Morchella spp.) intake alters gut microbial community and short-chain fatty acid profiles in mice

Morels (Morchella spp.) are highly nutritious and consumed as both edible mushrooms and traditional Chinese medicine. This study aimed to investigate the effects of dietary supplementation with morel mushrooms on the gut bacterial microbiota and short-chain fatty acids (SCFAs) profiles in healthy mice. Healthy mice were randomly assigned to five groups: a control group (0% morel) and four intervention groups supplemented with different levels of morel mushrooms (5% for M5, 10% for M10, 15% for M15, and 20% for M20) over a period of 4 weeks. Fecal samples were collected at the end of the experiment to characterize the microbiota and assess the SCFAs levels. The morel intervention significantly altered the bacterial community composition, increasing Bacteroides, Lachnospiraceae NK4A136 group and Parabacteroides, while decreasing Staphylococcus and the Firmicutes to Bacteroidetes ratio (F/B ratio). Moreover, increased morel intake was associated with weight loss. All SCFAs content was upregulated in the morel-intervention groups. Potential SCFAs-producing taxa identified by regression analysis were distributed in the families Muribaculaceae, Lachnospiraceae, and in the genera Jeotgalicoccus, Gemella, Odoribacter, Tyzzerella 3 and Ruminococcaceae UCG-014. The functional categories involved with SCFAs-production or weight loss may contain enzymes such as beta-glucosidase (K05349), beta-galactosidase (K01190), and hexosaminidase (K12373) after morel intervention. The exploration of the impact of morel mushrooms on gut microbiota and metabolites contributes to the development of prebiotics for improving health and reducing obesity.

Comparative study of the gut microbiota in three captive Rhinopithecus species

BACKGROUND

Snub-nosed monkeys are highly endangered primates and their population continues to decline with the habitat fragmentation. Artificial feeding and breeding is an important auxiliary conservation strategy. Studies have shown that changes and imbalances in the gut microbiota often cause gastrointestinal problems in captive snub-nosed monkeys. Here, we compare the gut microbiota composition, diversity, and predicted metabolic function of three endangered species of snub-nosed monkeys (Rhinopithecus bieti, R. brelichi, and R. roxellana) under the same captive conditions to further our understanding of the microbiota of these endangered primates and inform captive conservation strategies. 16 S rRNA gene sequencing was performed on fecal samples from 15 individuals (R. bieti N = 5, R. brelichi N = 5, R. roxellana N = 5).

RESULTS

The results showed that the three Rhinopithecus species shared 24.70% of their amplicon sequence variants (ASVs), indicating that the composition of the gut microbiota varied among the three Rhinopithecus species. The phyla Firmicutes and Bacteroidetes represented 69.74% and 18.45% of the core microbiota. In particular, analysis of microbiota diversity and predicted metabolic function revealed a profound impact of host species on the gut microbiota. At the genus level, significant enrichment of cellulolytic genera including Rikenellaceae RC9 gut group, Ruminococcus, Christensenellaceae R7 group, UCG 004 from Erysipelatoclostridiaceae, and UCG 002 and UCG 005 from Oscillospiraceae, and carbohydrate metabolism including propionate and butyrate metabolic pathways in the gut of R. bieti indicated that R. bieti potentially has a stronger ability to use plant fibers as energy substances. Bacteroides, unclassified Muribaculaceae, Treponema, and unclassified Eubacterium coprostanoligenes group were significantly enriched in R. brelichi. Prevotella 9, unclassified Lachnospiraceae, and unclassified UCG 010 from Oscillospirales UCG 010 were significantly enriched in R. roxellana. Among the predicted secondary metabolic pathways, the glycan biosynthesis and metabolism had significantly higher relative abundance in the gut of R. brelichi and R. roxellana than in the gut of R. bieti. The above results suggest that different Rhinopithecus species may have different strategies for carbohydrate metabolism. The Principal coordinate analysis (PCoA) and Unweighted pair-group method with arithmetic mean (UPGMA) clustering tree revealed fewer differences between the gut microbiota of R. brelichi and R. roxellana. Correspondingly, no differences were detected in the relative abundances of functional genes between the two Rhinopithecus species.

CONCLUSION

Taken together, the study highlights that host species have an effect on the composition and function of the gut microbiota of snub-nosed monkeys. Therefore, the host species should be considered when developing nutritional strategies and investigating the effects of niche on the gut microbiota of snub-nosed monkeys.

Dietary Litsea cubeba essential oil supplementation improves growth performance and intestinal health of weaned piglets

This paper was to determine the effects of dietary Litsea cubeba essential oil (LEO) supplementation on growth performance, immune function, antioxidant level, intestinal morphology and microbial composition in weaned piglets. One hundred and ninety-two piglets (Duroc × [Large White × Landrace]) with 6.85 ± 0.22 kg mean body weight weaned at 21 d of age were randomly assigned to 4 treatment groups with 8 replicates and were fed with a basal diet (CON) or CON diet containing 100 (LLEO), 200 (MLEO) and 400 (HLEO) mg/kg LEO. The results revealed that HLEO supplementation (P < 0.05) increased the average daily gain on d 28 compared with CON. MLEO and HLEO supplementation decreased (P < 0.05) feed conversion ratio. LEO-containing diets had a lower (P < 0.05) diarrhea rate. Supplementation with HLEO increased (P < 0.05) total antioxidant capacity (T-AOC) both in the serum and liver. Meanwhile, the supplementation of MLEO and HLEO resulted in higher (P < 0.05) glutathione peroxidase (GPx) activities both in serum and liver. Supplementation of HLEO increased (P < 0.05) serum immunoglobulin A, immunoglobulin G and interleukin-10, whereas supplementation with MLEO and HLEO decreased (P < 0.05) tumor necrosis factor-α. Villus height in the duodenum or jejunum was increased (P < 0.05) in the HLEO group, and the villus height to crypt depth ratio in the jejunum was also improved (P < 0.05) in the MLEO group. The addition of LEO increased (P < 0.05) the richness and diversity of the microbial community in the cecum, which mainly increased the relative abundance of Oscillospiraceae _UCG-005, Faecalibacterium, Blautia and Coprococcus. Piglets supplemented with HLEO increased (P < 0.05) the concentration of short chain fatty acids (SCFA), including acetic acid in the cecum and propionic acid in the colon. In conclusion, these findings indicated that LEO supplementation improved growth performance and intestinal health in weaned piglets.

Potential of hydrochar/pyrochar derived from sawdust of oriental plane tree for stimulating methanization by mitigating propionic acid inhibition in mesophilic anaerobic digestion of swine manure

VFAs accumulation in anaerobic digestion systems can lead to disturbance of the acid base balance, which has brought major challenges for methane production. Meanwhile, less research explored the potential of biochar derived from wood wastes of oriental plane tree (Platanus orientalis L.) for stimulating methanization in mesophilic anaerobic digestion. In this study, the effects of pyrochar and hydrochar derived from sawdust of oriental plane tree on mesophilic anaerobic digestion of swine manure were compared for the first time. Fourier infrared transform analysis indicated that more functional groups existed on the surface of hydrochar, whereas higher ash content and BET specific surface area were found in pyrochar. The maximum methane production rate during anaerobic digestion was observed in the pyrochar treatment, which increased by 59.5% compared with the control without biochar. Although stimulative effects on dissolved organic carbon and volatile fatty acids production were both observed in the pyrochar and hydrochar treatments, the pyrochar treatment was much easier to trigger multipath methanogenesis and direct interspecific electron transport and subdue propionic acid accumulation compared to the hydrochar treatment. Moreover, redundancy analysis indicated that the variations in acetic acid and dissolved organic carbon were mostly associated with microbial succession. These results suggest that pyrochar has better promoting effects than HC in terms of methane generation and propionic acid inhibition alleviation owing to its special porous structures, functional groups (e.g., C=O, C-O and O-H), and physicochemical properties. These excellent properties play a greater role in recruiting functional archaea and bacteria to regulate the levels of volatile fatty acids and dissolved organic carbon to enhance the methane yield of anaerobic digestion. This study provides novel and valuable information for further engineering applications of pyrochar and hydrochar derived from sawdust of oriental plane tree in energy production and environmental waste treatment.

Alterations in gut microbiota improve SCFA production and fiber utilization in Tibetan pigs fed alfalfa diet

Tibetan pigs were thought to have good performances of rough feeding tolerance, which may be related to the gut microbiota. This study was conducted to investigate the changes of colonic microbiota contribute to fiber utilization in Tibetan pigs fed alfalfa supplementation diet compared with basal diet, and verified whether the microbial community in Tibetan pigs fed alfalfa diet was beneficial to utilize fiber using in vitro fermentation. A total of 40 Tibetan pigs were allocated into two groups and fed with a corn-soybean meal basal diet (CD) or a 50% alfalfa supplementation diet (AD) for 42d. Our results showed pigs fed CD diet improved carcass weight compared to pigs fed AD diet (p < 0.05), yet reduced the bacterial diversity (p < 0.05). Tibetan pigs fed CD diet increased certain pathogenic bacteria (Streptococcus) abundance (FDR < 0.05). Alfalfa consumption increased fiber-degrading bacteria abundance (UCG-005, Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG-003, Alloprevotella, Marvinbryantia, and Anaerovibrio) in the colonic digesta (FDR < 0.05) and improved concentrations of acetate, propionate, butyrate, and total SCFA in colonic content (p < 0.05). Higher fermentation capacity of fecal microbiota from pig fed AD diet was verified by in vitro fermentation. Collectively, our results indicated that alfalfa supplementation in diets improved the abundance of fiber-degrading bacteria and SCFA production in the hindgut of Tibetan pig, as well as enhanced the fermentation capacity of fecal microbiota.

Comparison of the Gut Microbiome between Atopic and Healthy Dogs—Preliminary Data

Simple Summary

Atopic dermatitis is a common inflammatory and itchy skin disease, constituting a global issue that affects up to 15% of the general human and dog population. The pathogenesis of this disease is known to be multifactorial and not only consisting of skin barrier dysfunction, but also with immunological dysregulation and skin microbiota changes having a central role. In humans, establishment of the gut microbiota in early life influences the development of allergies, among others also atopic dermatitis in children. To the author’s knowledge, there is currently no study comparing the gut microbiome between allergic and healthy dogs. We now present results demonstrating that allergic dogs have a significantly different gut microbiota when compared to healthy control dogs. Further investigations including a larger number of dogs are now required to confirm these results, in addition to studies utilizing novel interventions targeting the gut microbiota.

Abstract

Human studies show that in addition to skin barrier and immune cell dysfunction, both the cutaneous and the gut microbiota can influence the pathogenesis of atopic diseases. There is currently no data on the gut-skin axis in allergic canines. Therefore, the aim of this study was to assess the bacterial diversity and composition of the gut microbiome in dogs with atopic dermatitis (AD). Stool samples from adult beagle dogs (n = 3) with spontaneous AD and a healthy control group (n = 4) were collected at Days 0 and 30. After the first sampling, allergic dogs were orally dosed on a daily basis with oclacitinib for 30 days, and then re-sampled. Sequencing of the V3–V4 region of the 16S rRNA gene was performed on the Illumina MiSeq platform and the data were analyzed using QIIME2. The atopic dogs had a significantly lower gut microbiota alpha-diversity than healthy dogs (p = 0.033). In healthy dogs, a higher abundance of the families Lachnospiraceae (p = 0.0006), Anaerovoracaceae (p = 0.006) and Oscillospiraceae (p = 0.021) and genera Lachnospira (p = 0.022), Ruminococcustorques group (p = 0.0001), Fusobacterium (p = 0.022) and Fecalibacterium (p = 0.045) was seen, when compared to allergic dogs. The abundance of Conchiformibius (p = 0.01), Catenibacterium spp. (p = 0.007), Ruminococcus gnavus group (p = 0.0574) and Megamonas (p = 0.0102) were higher in allergic dogs. The differences in alpha-diversity and on the compositional level remained the same after 1 month, adding to the robustness of the data. Additionally, we could also show that a 4-week treatment course with oclacitinib was not associated with changes in the gut microbiota diversity and composition in atopic dogs. This study suggests that alterations in the gut microbiota diversity and composition may be associated with canine AD. Large-scale studies preferably associated to a multi-omics approach and interventions targeting the gut microbiota are needed to confirm these results.

Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes

Pigs are among the most numerous and intensively farmed food-producing animals in the world. The gut microbiome plays an important role in the health and performance of swine and changes rapidly after weaning. Here, fecal samples were collected from pigs at 7 different times points from 7 to 140 days of age. These swine fecal metagenomes were used to assemble 1,150 dereplicated metagenome-assembled genomes (MAGs) that were at least 90% complete and had less than 5% contamination. These MAGs represented 472 archaeal and bacterial species, and the most widely distributed MAGs were the uncultured species Collinsella sp002391315, Sodaliphilus sp004557565, and Prevotella sp000434975. Weaning was associated with a decrease in the relative abundance of 69 MAGs (e.g., Escherichia coli) and an increase in the relative abundance of 140 MAGs (e.g., Clostridium sp000435835, Oliverpabstia intestinalis). Genes encoding for the production of the short-chain fatty acids acetate, butyrate, and propionate were identified in 68.5%, 18.8%, and 8.3% of the MAGs, respectively. Carbohydrate-active enzymes associated with the degradation of arabinose oligosaccharides and mixed-linkage glucans were predicted to be most prevalent among the MAGs. Antimicrobial resistance genes were detected in 327 MAGs, including 59 MAGs with tetracycline resistance genes commonly associated with pigs, such as tet(44), tet(Q), and tet(W). Overall, 82% of the MAGs were assigned to species that lack cultured representatives indicating that a large portion of the swine gut microbiome is still poorly characterized. The results here also demonstrate the value of MAGs in adding genomic context to gut microbiomes. IMPORTANCE Many of the bacterial strains found in the mammalian gut are difficult to culture and isolate due to their various growth and nutrient requirements that are frequently unknown. Here, we assembled strain-level genomes from short metagenomic sequences, so-called metagenome-assembled genomes (MAGs), that were derived from fecal samples collected from pigs at multiple time points. The genomic context of a number of antimicrobial resistance genes commonly detected in swine was also determined. In addition, our study connected taxonomy with potential metabolic functions such as carbohydrate degradation and short-chain fatty acid production.

Superiority of Microencapsulated Essential Oils Compared With Common Essential Oils and Antibiotics: Effects on the Intestinal Health and Gut Microbiota of Weaning Piglet

Essential oils (EOs) have long been considered an alternative to antibiotics in the breeding industry. However, they are unstable and often present unpleasant odors, which hampers their application. Microencapsulation can protect the active gradients from oxidation and allow them to diffuse slowly in the gastrointestinal tract. The purpose of this study was to investigate the effect of microencapsulation technology on the biological function of EOs and the possibility of using microencapsulate EOs (MEEOs) as an alternative to antibiotics in weaning piglets. First, we prepared MEEOs and common EOs both containing 2% thymol, 5% carvacrol and 3% cinnamaldehyde (w/w/w). Then, a total of 48 weaning piglets were randomly allotted to six dietary treatments: (1) basal diet; (2) 75 mg/kg chlortetracycline; (3) 100 mg/kg common EOs; (4) 500 mg/kg common EOs; (5) 100 mg/kg MEEOs; and (6) 500 mg/kg MEEO. The trial lasted 28 days. The results showed that piglets in the 100 mg/kg MEEOs group had the lowest diarrhea index during days 15–28 (P < 0.05). In addition, 100 mg/kg MEEOs significantly alleviated intestinal oxidative stress and inflammation (P < 0.05), whereas 500 mg/kg common EOs caused intestinal oxidative stress (P < 0.05) and may lead to intestinal damage through activation of inflammatory cytokine response. MEEOs (100 mg/kg) significantly reduced the ratio of the relative abundance of potential pathogenic and beneficial bacteria in the cecum and colon (P < 0.05), thus contributing to the maintenance of intestinal health. On the other hand, chlortetracycline caused an increase in the ratio of the relative abundance of potential pathogenic and beneficial bacteria in the colon (P < 0.05), which could potentially have adverse effects on the intestine. The addition of a high dose of MEEOs may have adverse effects on the intestine and may lead to diarrhea by increasing the level of colonic acetic acid (P < 0.05). Collectively, the results suggest that microencapsulation technology significantly promotes the positive effect of EOs on the intestinal health of weaning piglets and reduces the adverse effect of EOs, and 100 mg/kg MEEOs are recommended as a health promoter in piglets during the weaning period.

Effects of Dietary Cereal and Protein Source on Fiber Digestibility, Composition, and Metabolic Activity of the Intestinal Microbiota in Weaner Piglets

Simple Summary

Rye and rapeseed meal can be alternative feed components for weaner piglets instead of wheat and soybean meal. Both components can help to meet current challenges in pig nutrition, such as increasingly dry weather conditions and the high amount of imported soybean. Since they contain more and differently composed fiber, effects on digestive physiology and intestinal microbiota might help to maintain gut health and prevent post-weaning diarrhea. This study shows that despite a similar composition of the large intestinal microbiota, the higher amount and solubility of complex carbohydrates from rye lead to a higher fermentative activity compared to wheat, which is considered a beneficial effect. The high amount of insoluble dietary fiber in rapeseed-based diets lowered bacterial metabolic activity and caused a shift toward insoluble fiber degrading bacteria.

Abstract

This study aimed to investigate the effect of fiber-rich rye and rapeseed meal (RSM) compared to wheat and soybean meal (SBM) on fiber digestibility and the composition and metabolic activity of intestinal microbiota. At weaning, 88 piglets were allocated to four feeding groups: wheat/SBM, wheat/RSM, rye/SBM, and rye/RSM. Dietary inclusion level was 48% for rye and wheat, 25% for SBM, and 30% for RSM. Piglets were euthanized after 33 days for collection of digesta and feces. Samples were analyzed for dry matter and non-starch-polysaccharide (NSP) digestibility, bacterial metabolites, and relative abundance of microbiota. Rye-based diets had higher concentrations of soluble NSP than wheat-based diets. RSM-diets were higher in insoluble NSP compared to SBM. Rye-fed piglets showed a higher colonic and fecal digestibility of NSP (p < 0.001, p = 0.001, respectively). RSM-fed piglets showed a lower colonic and fecal digestibility of NSP than SBM-fed piglets (p < 0.001). Rye increased jejunal and colonic concentration of short-chain fatty acids (SCFA) compared to wheat (p < 0.001, p = 0.016, respectively). RSM-fed pigs showed a lower jejunal concentration of SCFA (p = 0.001) than SBM-fed pigs. Relative abundance of Firmicutes was higher (p = 0.039) and of Proteobacteria lower (p = 0.002) in rye-fed pigs compared to wheat. RSM reduced Firmicutes and increased Actinobacteria (jejunum, colon, feces: p < 0.050), jejunal Proteobacteria (p = 0.019) and colonic Bacteroidetes (p = 0.014). Despite a similar composition of the colonic microbiota, the higher amount and solubility of NSP from rye resulted in an increased fermentative activity compared to wheat. The high amount of insoluble dietary fiber in RSM-based diets reduced bacterial metabolic activity and caused a shift toward insoluble fiber degrading bacteria. Further research should focus on host–microbiota interaction to improve feeding concepts with a targeted use of dietary fiber.