Microbiome analysis reveals the alterations in gut microbiota in different intestinal segments of Yimeng black goats

Spatial profiles of the bacterial microbiota throughout the gastrointestinal tract of dairy goats

The gastrointestinal tract (GIT) is stationed by a dynamic and complex microbial community with functions in digestion, metabolism, immunomodulation, and reproduction. However, there is relatively little research on the composition and function of microorganisms in different GIT segments in dairy goats. Herein, 80 chyme samples were taken from ten GIT sites of eight Xinong Saanen dairy goats and then analyzed and identified the microbial composition via 16S rRNA V1-V9 amplicon sequencing. A total of 6669 different operational taxonomic units (OTUs) were clustered, and 187 OTUs were shared by ten GIT segments. We observed 264 species belonging to 23 different phyla scattered across ten GITs, with Firmicutes (52.42%) and Bacteroidetes (22.88%) predominating. The results revealed obvious location differences in the composition, diversity, and function of the GIT microbiota. In LEfSe analysis, unidentified_Lachnospiraceae and unidentified_Succinniclassicum were significantly enriched in the four chambers of stomach, with functions in carbohydrate fermentation to compose short-chain fatty acids. Aeriscardovia, Candidatus_Saccharimonas, and Romboutsia were significantly higher in the foregut, playing an important role in synthesizing enzymes, amino acids, and vitamins and immunomodulation. Akkermansia, Bacteroides, and Alistipes were significantly abundant in the hindgut to degrade polysaccharides and oligosaccharides, etc. From rumen to rectum, α-diversity decreased first and then increased, while β-diversity showed the opposite trend. Metabolism was the major function of the GIT microbiome predicted by PICRUSt2, but with variation in target substrates along the regions. In summary, GIT segments play a decisive role in the composition and functions of microorganisms. KEY POINTS: • The jejunum and ileum were harsh for microorganisms to colonize due to the presence of bile acids, enzymes, faster chyme circulation, etc., exhibiting the lowest α-diversity and the highest β-diversity. • Variability in microbial profiles between the three foregut segments was greater than four chambers of stomach and hindgut, with a higher abundance of Firmicutes dominating than others. • Dairy goats dominated a higher abundance of Kiritimatiellaeota than cows, which was reported to be associated with fatty acid synthesis.

Metagenomic Analysis Reveals A Gut Microbiota Structure and Function Alteration between Healthy and Diarrheic Juvenile Yaks

Diarrhea-induced mortality among juvenile yaks is highly prevalent in the pastoral areas of the Qinghai-Tibet plateau. Although numerous diseases have been linked to the gut microbial community, little is known about how diarrhea affects the gut microbiota in yaks. In this work, we investigated and compared changes in the gut microbiota of juvenile yaks with diarrhea. The results demonstrated a considerable drop in the alpha diversity of the gut microbiota in diarrheic yaks, accompanied by Eysipelatoclostridium, Parabacteroides, and Escherichia-Shigella, which significantly increased during diarrhea. Furthermore, a PICRust analysis verified the elevation of the gut-microbial metabolic pathways in diarrhea groups, including glycine, serine, and threonine metabolism, alanine, aspartate, oxidative phosphorylation, glutamate metabolism, antibiotic biosynthesis, and secondary metabolite biosynthesis. Taken together, our study showed that the harmful bacteria increased, and beneficial bacteria decreased significantly in the gut microbiota of yaks with diarrhea. Moreover, these results also indicated that the dysbiosis of the gut microbiota may be a significant driving factor of diarrhea in yaks.

Effects of fermented feed of Pennisetum giganteum on growth performance, oxidative stress, immunity and gastrointestinal microflora of Boer goats under thermal stress

Introduction

This study was conducted to evaluate the effects of fermented feed of Pennisetum giganteum (P. giganteum) on growth performance, oxidative stress, immunity and gastrointestinal microflora of Boer goats under thermal stress.

Methods

The study was conducted during 45 days using twenty 2 months Boer goats. The goats were randomly allocated into two groups: NPG (n = 10; normal P. giganteum) and FPG (n = 10; fermented feed of P. giganteum), and the ratio of concentrates to roughage was 3:2. Both groups of animals were kept in sheds and exposed to summer thermal stress from 10:00 h to 18:00 h (temperature and humidity index, THI > 78). At the end of the study, the animals were slaughtered and assessed for various characteristics.

Results

The findings from the study revealed that FPG-feeding significantly increased (p < 0.05) average daily gain (ADG, 48.18 g) and carcass weight (4.38 kg), while decreased (p < 0.01) average daily feed intake (ADFI, 0.74 kg/d; p < 0.01) and the feed:gain (F/G, 15.36) ratio. The CAT, GSH-Px activities and GSH in serum, liver and spleen, and the levels of IgA, IgG, IgM, IL-2, IL-4 and IL-1β in serum of FPG-fed goats were significantly higher (p < 0.05) than those of NPG-feeding goats. Further, we found that FPG feed is rich in nutrients with Lactobacillus (65.83%) and Weissella (17.80%). Results for gastrointestinal microbiota composition showed that FPG-feeding significantly enhanced the abundance of Lactobacillus and unidentified Clostridiales, and reduced Anaerovibrio and Methanobrevibacter. Meanwhile, Spearman's correlation analysis showed that these microbiotas were closely related to the improvement of oxidative stress and immune indexes of goats.

Discussion

These results demonstrated that FPG-feeding not only reduces oxidative stress and improves ROS clearance to enhance antioxidant defense system, but also improves gastrointestinal microbiota to enhance immune function by overcoming the adverse effects of heat stress, and further improve growth performance of goats.

Radix paeoniae alba polysaccharide attenuates lipopolysaccharide-induced intestinal injury by regulating gut microbiota

Accumulating evidence indicated that oxidative stress is closely related to inflammation and the progression of multiple chronic diseases, which seriously threaten the host health. Currently, multiple plant-derived polysaccharides have been demonstrated to ameliorate the negative effects of oxidative stress on the host, but the potential protective effect of radix paeoniae alba polysaccharide (RPAP) on host have not been well characterized. Here, we investigated whether different doses of RPAP administration could alleviate lipopolysaccharide (LPS)-induced intestinal injury and gut microbial dysbiosis in mice. Results indicated that RPAP administration effectively alleviated LPS-induced intestinal damage in dose dependent. Additionally, amplicon sequencing showed that RPAP administration reversed the significant decrease in gut microbial diversity caused by LPS exposure and restored the alpha-diversity indices to normal levels. Microbial taxonomic investigation also indicated that LPS exposure resulted in significant changes in the gut microbial composition, characterized by a decrease in the abundances of beneficial bacteria (Lactobacillus, Alistipes, Bacillus, Rikenellaceae_RC9_gut_group, etc.) and an increase in the contents of pathogenic bacteria (Klebsiella, Helicobacter, Enterococcus, etc.). However, RPAP administration, especially in high doses, could improve the composition of the gut microbiota by altering the abundance of some bacteria. Taken together, this study demonstrated that RPAP administration could ameliorate LPS-induced intestinal injury by regulating gut microbiota. Meanwhile, this also provides the basis for the popularization and application of RPAP and alleviating oxidative stress from the perspective of gut microbiota.

Research on the Gut Microbiota of Hainan Black Goat

The intestine of animals is a complex micro-ecosystem containing a large number of microbiomes, which is essential for the host's health development. The Hainan black goat with good resistance and adaptability is a unique species in Hainan, China. These unique physiological characteristics are inseparable from their intestinal microbiota. In this study, high-throughput sequencing was used to investigate bacterial communities in different segments of the intestinal tract of Hainan black goat. The results showed that the indices of Chao1 and ACE in the cecum and colon were significantly greater than those in the ileum (p = 0.007, 0.018). According to PCoA, the intestinal flora composition of the cecum and colon is almost equivalent. In contexts of the phylum, Firmicutes, Bacteroidota, and Pseudomonadota were the dominant phyla in the gut of the Hainan black goat. While in context of the genus, the dominant groups in the gut of black goats mainly include Ruminococcaceae_UCG-005, Bacteroides, Paeniclostridium, Christensenellaceae_R-7_group, Rikenellaceae_RC9_gut_group, and Eubacterium coprostanoligenes _group, Prevotella_1, they have different proportions in different intestinal segments. The gut microbiota of Hainan black goat is mainly Firmicutes, Bacteroidota, and Pseudomonadota. Influenced by the intestinal location where they colonize, the large intestine has a more complex intestinal flora than the small intestine. In contrast, there are only minor differences between the caecum and the colon in the large intestine.

Comparative Analysis of Gut Microbiota Between Healthy and Diarrheic Horses

Increasing evidence reveals the importance of gut microbiota in animals for regulating intestinal homeostasis, metabolism, and host health. The gut microbial community has been reported to be closely related to many diseases, but information regarding diarrheic influence on gut microbiota in horses remains scarce. This study investigated and compared gut microbial changes in horses during diarrhea. The results showed that the alpha diversity of gut microbiota in diarrheic horses decreased observably, accompanied by obvious shifts in taxonomic compositions. The dominant bacterial phyla (Firmicutes, Bacteroidetes, Spirochaetes, and Kiritimatiellaeota) and genera (uncultured_bacterium_f_Lachnospiraceae, uncultured_bacterium_f_p-251-o5, Lachnospiraceae_AC2044_group, and Treponema_2) in the healthy and diarrheic horses were same regardless of health status but different in abundances. Compared with the healthy horses, the relative abundances of Planctomycetes, Tenericutes, Firmicutes, Patescibacteria, and Proteobacteria in the diarrheic horses were observably decreased, whereas Bacteroidetes, Verrucomicrobia, and Fibrobacteres were dramatically increased. Moreover, diarrhea also resulted in a significant reduction in the proportions of 31 genera and a significant increase in the proportions of 14 genera. Taken together, this study demonstrated that the gut bacterial diversity and abundance of horses changed significantly during diarrhea. Additionally, these findings also demonstrated that the dysbiosis of gut microbiota may be an important driving factor of diarrhea in horses.

Characteristics of Bacterial Microbiota in Different Intestinal Segments of Aohan Fine-Wool Sheep

The microbial community performs vital functions in the intestinal system of animals. Modulation of the gut microbiota structure can indirectly or directly affect gut health and host metabolism. Aohan fine-wool sheep grow in semi-desert grasslands in China and show excellent stress tolerance. In this study, we amplified 16S rRNA gene to investigate the dynamic distribution and adaptability of the gut microbiome in the duodenum, jejunum, ileum, cecum, colon, and rectum of seven Aohan fine-wool sheep at 12 months. The results showed that the microbial composition and diversity of the ileum and the large intestine (collectively termed the hindgut) were close together, and the genetic distance and functional projections between them were similar. Meanwhile, the diversity index results revealed that the bacterial richness and diversity of the hindgut were significantly higher than those of the foregut. We found that from the foregut to the hindgut, the dominant bacteria changed from Proteobacteria to Bacteroidetes. In LEfSe analysis, Succiniclasticum was found to be significantly abundant bacteria in the foregut and was involved in succinic acid metabolism. Ruminococcaceae and Caldicoprobacteraceae were significantly abundant in hindgut, which can degrade cellulose polysaccharides in the large intestine and produce beneficial metabolites. Moreover, Coriobacteriaceae and Eggthellaceae are involved in flavonoid metabolism and polyphenol production. Interestingly, these unique bacteria have not been reported in Mongolian sheep or other sheep breeds. Collectively, the gut microbiota of Aohan fine-wool sheep is one of the keys to adapting to the semi-desert grassland environment. Our results provide new insights into the role of gut microbiota in improving stress tolerance and gut health in sheep.

Preliminary Investigation of Mixed Orchard Hays on the Meat Quality, Fatty Acid Profile, and Gastrointestinal Microbiota in Goat Kids

This preliminary investigation was designed to study the effects of different mixed orchard hays on meat quality, fatty acids, amino acids, rumen intestinal microflora, and the relationship between rumen bacteria and fatty acids in the longissimus dorsi muscle of Saanen dairy goats. In this preliminary investigation, goats were separately fed crop straws (corn and wheat straws) and alfalfa (Medicago sativa L.) (CK group), alfalfa + oats (Avena sativa L.) (group I), alfalfa + perennial ryegrass (Lolium perenne L.) (group II), and hairy vetch (Vicia villosa Roth.) + perennial ryegrass (group III). There were differences in shear force and cooking loss between treatments. The contents of saturated fatty acids (SFAs) C14:0, C16:0, and C18:0 in the CK group were significantly higher than those in other three groups (p < 0.001). The 16S rDNA sequencing results showed that the relative abundance of Proteobacteria in group II were higher than those in other three groups (p < 0.05). Association analysis showed that Prevotella_1 was negatively correlated with C18:0 and significantly positively correlated with C16:1, while Clostridium and Romboutsia showed a positive correlation with monounsaturated fatty acids (MUFAs) and polyunsaturated fatty acids (PUFAs). Therefore, feeding mixed hays can increase beneficial fatty acids and the percentages of associated bacteria in rumen and intestines.

Analysis of Cow-Calf Microbiome Transfer Routes and Microbiome Diversity in the Newborn Holstein Dairy Calf Hindgut

Hindgut microorganisms in newborn calves play an important role in the development of immunity and metabolism, and optimization of performance. However, knowledge of the extent to which microbiome colonization of the calf intestine is dependent on maternal characteristics is limited. In this study, placenta, umbilical cord, amniotic fluid, colostrum, cow feces, and calf meconium samples were collected from 6 Holstein cow-calf pairs. Microbial composition was analyzed by 16S rRNA gene high-throughput sequencing, and maternal transfer characteristics assessed using SourceTracker based on Gibbs sampling to fit the joint distribution using the mean proportions of each sample with meconium as the "sink" and other sample types as different "sources." Alpha and beta diversity analyses revealed sample type-specific microbiome features: microbial composition of the placenta, umbilical cord, amniotic fluid, colostrum, and calf feces were similar, but differed from cow feces (p < 0.05). Compared with profiles of meconium vs. placenta, meconium vs. umbilical cord, and meconium vs. colostrum, differences between the meconium and amniotic fluid were most obvious. SourceTracker analysis revealed that 23.8 ± 2.21% of the meconium OTUs matched those of umbilical cord samples, followed by the meconium-placenta pair (15.57 ± 2.2%), meconium-colostrum pair (14.4 ± 1.9%), and meconium-amniotic fluid pair (11.2 ± 1.7%). The matching ratio between meconium and cow feces was the smallest (10.5 ± 1%). Overall, our data indicated that the composition of the meconium microflora was similar compared with multiple maternal sites including umbilical cord, placenta, colostrum, and amniotic fluid. The umbilical cord microflora seemed to contribute the most to colonization of the fecal microflora of calves. Bacteria with digestive functions such as cellulose decomposition and rumen fermentation were mainly transmitted during the maternal transfer process.

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

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