Evaluation of the nutrition and function of cow and goat milk based on intestinal microbiota by metagenomic analysis

Genomic Advancements in Assessing Growth Performance, Meat Quality, and Carcass Characteristics of Goats in Sub-Saharan Africa: A Systematic Review

Goats play a vital role in global livestock systems, particularly in developing regions, where they contribute significantly to meat production and smallholder livelihoods. Indigenous goats in sub-Saharan Africa are essential to low-input farming systems, valued for their adaptability to harsh environments and their provision of meat, milk, and income. However, genomic research on these goats remains limited despite their importance. Recent advancements in genomic technologies, such as next-generation sequencing (NGS), genome-wide association (GWAS) studies, and single nucleotide polymorphism (SNP) mapping, have identified key genes like MSTN, IGF1, and CAST. These genes influence muscle growth, fat deposition, and meat tenderness, which are critical for improving growth performance, carcass characteristics, and meat quality. Genomic selection offers a promising avenue for enhancing economically valuable traits, such as faster growth rates and adaptability to challenging climates. This review highlights the potential of integrating genomic tools with traditional breeding practices to optimise goat production systems, enhance meat quality, and improve economic outcomes for farmers. It also underscores the need for further research to fully characterise the genetic diversity of indigenous goat breeds in sub-Saharan Africa. Addressing these knowledge gaps could significantly contribute to the region's food security and sustainable farming practices.

Effects of Different Cow-Milk Beta-Caseins on the Gut-Brain Axis: A Narrative Review of Preclinical, Animal, and Human Studies

The gut and brain communicate through bidirectional neural, endocrine, and immune signals to coordinate central nervous system activity with gastrointestinal function. Dysregulated inflammation can promote immune cell activation and increase entero-endocrine signaling and intestinal permeability; hence, a functional gut-brain axis is necessary for a healthy digestive system. The consumption of milk products can lead to gut discomfort via effects on gastrointestinal tract function and the inflammatory state, which, in turn, affect the brain. A1 β-casein and A2 β-casein are major components of bovine-milk protein, and their digestion may result in different physiological effects following the consumption of milk products. Peptides derived from A1 β-casein, such as β-casomorphins, may increase gut dysfunction and inflammation, thereby modulating the availability of bioactive metabolites in the bloodstream and contribute to changes in cognitive function. This narrative review examines the functional interrelationships between the consumption of cow-milk-derived β-caseins and their effect on the brain, immune system, and the gut, which together comprise the gut-brain axis.

Functional properties and flavor characteristics of milk from cows supplemented with jujube powder

Jujube has various functional properties and is a promising source of bioactive compounds and flavors. This study investigated the functional properties and flavor characteristics of milk from cows supplemented with jujube powder (JP). Here, milk volatile profiles and taste properties were analyzed by using an electronic nose and headspace solid-phase microextraction GC-MS. Compared with the control group, the total antioxidant capacity, 2,2'-azino-bis-3-ethylbenzothiazoline-6-sulphonic free-radical-scavenging activity, lactoferrin, and IgG levels increased significantly in the JP group. Volatile flavor analysis indicated that ketone levels increased, acid abundance decreased, and toluene and dimethyl sulfone significantly increased in the JP group. Taste-profile analyses demonstrated that jujube supplementation altered the taste of the milk. In summary, dietary JP supplementation affects the volatile flavor composition and aroma of milk, as well as the bioactive components and antioxidant properties. These findings enhance our understanding of milk production using direct dietary supplementation to produce sustainable dairy products.

Association between the cashmere production performance, milk production performance, and body size traits and polymorphism of COL6A5 and LOC102181374 genes in Liaoning cashmere goats

The purpose of this study was to analyze the relationship between COL6A5 (collagen type VI alpha 5 chain) and LOC102181374 (alcohol dehydrogenase 1) genes and the production performance of Liaoning cashmere goats by single nucleotide polymorphism (SNP). We have searched for SNP loci of COL6A5 and LOC102181374 genes through sequence alignment and PCR experiments, and have used SPSS and SHEsis software to analyze production data. We obtained five SNP loci in total, including three SNP loci (G50985A, G51140T, G51175A) in COL6A5 gene and two SNP loci (A10067G, T10108C) in LOC102181374 gene. The genotypes G50985A (AG), G51140T (GT), G51175A (AA), A10067G (AA), and T10108C (CC) of these loci have certain advantages in improving the production performance of Liaoning cashmere goats. The haplotype combinations that can improve production performance in COL6A5 gene were H1H5:AGGGAG, H4H4:GGGGAA, and H4H4:GGGGAA. H3H3:GGCC and H2H4:AGTT were the dominant combinations in LOC102181374 gene. At G51175A and A10067G loci, we found that H1H2:AAAG and H1H3:AGAA have dominant effects. These results may provide some support for the molecular breeding of production traits in Liaoning cashmere goats.

Fermented Goat's Milk Contributes to the Recovery of Iron Deficiency Anemia via Modulation of the Gut Microbiome

Iron deficiency anemia (IDA) is a global public health concern affecting 1.6 billion people worldwide. The administration of iron supplements during the treatment of IDA adversely affects the intestinal barrier function and the composition and functionality of the intestinal microbiome, both of which are already altered during IDA. For this reason, it is of great interest to develop nutritional strategies aimed at alleviating these gut alterations associated with IDA and its treatment. In this sense, fermented goat's milk (FGM) was studied due to its nutritional quality. Our findings showed that in anemic animals the consumption of a FGM-based diet, compared to a standard diet, had positive modulatory effects on the intestinal microbiome. FGM-based diet restored intestinal dysbiosis, the intestinal barrier functionality, and bacterial translocation, contributing to a more efficient recovery of IDA. Therefore, FGM is a useful nutritional tool to ease intestinal alterations occurring during IDA and during its treatment.

Biological Relevance of Goat Milk Oligosaccharides to Infant Health

Milk is often regarded as the gold standard for the nourishment of all mammalian offspring. The World Health Organization (WHO) recommends exclusive breastfeeding for the first 6 months of the life of the infant, followed by a slow introduction of complementary foods to the breastfeeding routine for a period of approximately 2 years, whenever this is possible ( Global Strategy for Infant and Young Child Feeding; WHO, 2003). One of the most abundant components in all mammals' milk, which is associated with important health benefits, is the oligosaccharides. The milk oligosaccharides (MOS) of humans and other mammals differ in terms of their concentration and diversity. Among those, goat milk contains more oligosaccharides (gMOS) than other domesticated dairy animals, as well as a greater range of structures. This review summarizes the biological functions of MOS found in both human and goat milk to identify the possible biological relevance of gMOS in human health and development. Based on the existing literature, seven biological functions of gMOS were identified, namely, MOS action as prebiotics, immune modulators, and pathogen traps; their modulation of intestinal cells; protective effect against necrotizing enterocolitis; improved brain development; and positive effects on stressor exposure. Overall, goat milk is a viable alternate supply of functional MOS that could be employed in a newborn formula.

Milk protects against sarcopenic obesity due to increase in the genus Akkermansia in faeces of db/db mice

BACKGROUND

Sarcopenic obesity, a combination of sarcopenia and obesity, is a pathological feature of type 2 diabetes. Several human studies have shown that milk is useful in the prevention of sarcopenia. This study was aimed at clarifying the effect of milk on the prevention of sarcopenic obesity in db/db mice.

METHODS

A randomized and investigator-blinded study was conducted using male db/db mice. Eight-week-old db/db mice were housed for 8 weeks and fed milk (100 μL/day) using a sonde. The faecal microbiota transplantation (FMT) group received antibiotics for 2 weeks, starting at 6 weeks of age, followed by FMT twice a week until 16 weeks of age.

RESULTS

Milk administration to db/db mice increased grip strength (Milk-: 164.2 ± 4.7 g, Milk+: 230.2 ± 56.0 g, P = 0.017), muscle mass (soleus muscle, Milk-: 164.2 ± 4.7 mg, Milk+: 230.2 ± 56.0 mg, P < 0.001; plantaris muscle, Milk-: 13.3 ± 1.2 mg, Milk+: 16.0 ± 1.7 mg, P < 0.001) and decreased visceral fat mass (Milk-: 2.39 ± 0.08 g, Milk+: 1.98 ± 0.04 mg, P < 0.001), resulting in a significant increase in physical activity (light: P = 0.013, dark: P = 0.034). FMT from mice fed milk not only improved sarcopenic obesity but also significantly improved glucose intolerance. Microarray analysis of gene expression in the small intestine revealed that the expression of amino acid absorption transporter genes, namely, SIc7a5 (P = 0.010), SIc7a1 (P = 0.015), Ppp1r15a (P = 0.041) and SIc7a11 (P = 0.029), was elevated in mice fed milk. In 16S rRNA sequencing of gut microbiota, the genus Akkermansia was increased in both the mice fed milk and the FMT group from the mice fed milk.

CONCLUSIONS

The findings of this study suggest that besides increasing the intake of nutrients, such as amino acids, milk consumption also changes the intestinal environment, which might contribute to the mechanism of milk-induced improvement of sarcopenic obesity.

Effects of inoculation with active microorganisms derived from adult goats on growth performance, gut microbiota and serum metabolome in newborn lambs

This study evaluated the effects of inoculation with adult goat ruminal fluid on growth, health, gut microbiota and serum metabolism in lambs during the first 15 days of life. Twenty four Youzhou dark newborn lambs were selected and randomly distributed across 3 treatments (n = 8/group): autoclaved goat milk inoculated with 20 mL sterilized normal saline (CON), autoclaved goat milk inoculated with 20 mL fresh ruminal fluid (RF) and autoclaved goat milk inoculated with 20 mL autoclaved ruminal fluid (ARF). Results showed that RF inoculation was more effective at promoting recovery of body weight. Compared with CON, greater serum concentrations of ALP, CHOL, HDL and LAC in the RF group suggested a better health status in lambs. The relative abundance of Akkermansia and Escherichia-Shigella in gut was lower in the RF group, whereas the relative abundance of Rikenellaceae_RC9_gut_group tended to increase. Metabolomics analysis shown that RF stimulated the metabolism of bile acids, small peptides, fatty acids and Trimethylamine-N-Oxide, which were found the correlation relationship with gut microorganisms. Overall, our study demonstrated that ruminal fluid inoculation with active microorganisms had a beneficial impact on growth, health and overall metabolism partly through modulating the gut microbial community.

Identification markers of goat milk adulterated with bovine milk based on proteomics and metabolomics

This study investigated the differences in proteins and metabolites from goat and bovine milk, and their mixtures, using data-independent-acquisition-based proteomics and metabolomics methods. In the skim milk, relative abundances of secretoglobin family 1D member (SCGB1D), polymeric immunoglobulin receptor, and glycosylation-dependent cell adhesion molecule 1 were increased, with an increase in the amount of 1-100 % bovine milk and served as markers at the 1 % adulteration level. In whey samples, β-lactoglobulin and α-2-HS-glycoprotein could be used to detect adulteration at the 0.1 % adulteration level, and SCGB1D and zinc-alpha-2-glycoprotein at the 1 % level. The metabolites of uric acid and N-formylkynurenine could be used to detect bovine milk at adulteration levels as low as 1 % based on variable importance at a projection value of > 1.0 and P-value of < 0.05. Our findings suggest novel markers of SCGB1D, uric acid, and N-formylkynurenine that can help to facilitate assessments of goat milk authenticity.

Effect of Intramammary Dry Cow Antimicrobial Treatment on Fresh Cow's Milk Microbiota in California Commercial Dairies

This study used 16S rRNA sequencing to evaluate the effects of dry cow antimicrobial therapy on the udder milk microbiota by comparing the microbial populations in milk at dry-off (DRY) (~60 days before calving) and post-partum (FRESH) (4-11 days after calving) from cows receiving an intramammary antibiotic infusion prior to dry-off (IMT) and cows that did not receive treatment (CTL). Milk was collected from 23 cows from the IMT group and 27 cows from the CTL group. IMT and DRY samples had a greater correlation with the genera Brevibacterium and Amaricoccus, and the family Micrococcaceae, when compared to IMT and FRESH samples. CTL group samples collected at DRY had a greater correlation with the genera Akkermansia and Syntrophus, when compared to FRESH samples; no bacterial taxa were observed to have a significant correlation with FRESH samples in the CTL group. DRY samples collected from the CTL group had a greater correlation with the genus Mogibacterium when compared to IMT and CTL samples. For DRY samples collected from the IMT group, a greater correlation with the genus Alkalibacterium when compared to DRY and CTL samples, was observed. The lack of a correlation for FRESH samples between the CTL and IMT treatment groups indicated that intramammary antimicrobial dry cow therapy had no significant effect on the udder milk microbiota post-partum.

Comparison of whole goat milk and its major fractions regarding the modulation of gut microbiota

BACKGROUND

Goat milk can be important for human nutrition because of its nutritional value, which may be attributed to its richness in protein, lactose, fat, and other bioactive components. This study compared the diversity and composition of gut microbiota in response to whole goat milk and its major fractions (milk fat, casein, milk whey, whey protein, and whey supernatant). Goat milk, its major fractions, and sterile distilled water (for the control group) were administered to mice intragastrically, and gut microbiota were compared in these groups using metagenomic analysis.

RESULTS

We observed distinct patterns of gut microbiota from different diet groups. The sample distance heatmap showed that, compared with other goat milk fractions, gut microbiota in the casein group was more similar to that in the whole goat-milk group. The relative abundance of the genus Lactobacillus increased significantly after whole goat-milk treatment; the milk whey fraction increased the abundance of Blautia; milk fat and milk whey related fractions treatment promoted the population of Bacteroides. The network analysis showed that genera Lactobacillus and Lactococcus were negatively associated with Helicobacter and Acinetobacter, respectively.

CONCLUSION

Fractions of goat milk could contain different gut microbiota from whole goat milk. Consumption of certain goat milk fractions could increase the ingestion of beneficial bacteria and inhibit the growth of some pathogenic bacteria. Our results could provide the basis for the research into and development of goat-milk based functional foods. © 2021 Society of Chemical Industry.

Proliferation of Bifidobacterium L80 under different proportions of milk protein hydrolysate

The intestinal microecological environment is critical to an infant's growth. For those infants consuming milk power, it is very important to improve the intestinal microecological environment to promote the healthy growth of infants. In this paper, Milk protein hydrolysate (MPH), consisting of different proportions of proteins and small molecule peptides (5:5, 4:6, 3:7, 2:8, 1:9) were added to infant formula powder (IFP). The effects of MFP-enriched IFP addition on proliferation and metabolism of Bifidobacterium L80 were studied. Compared with MPH-free IFP, MFP-enriched IFP with 1:9 of proteins to small molecule peptides significantly enhanced the proliferation of Bifidobacterium L80, resulting in higher cell density, greater viable counts and higher titratable acidity. MFP-enriched IFP increased the content of seven organic acids and H₂O₂ in the system, and improved the antibacterial activity to E. coli BL21. This study suggested that MPH could be an effective addition to infant formula powder to promote the growth of Bifidobacterium, so to improve the intestinal health of infants.

Goat Milk Improves Glucose Homeostasis via Enhancement of Hepatic and Skeletal Muscle AMP-Activated Protein Kinase Activation and Modulation of Gut Microbiota in Streptozocin-Induced Diabetic Rats

SCOPE

Previously, the metabolic benefits of goat milk consumption in high-fat diet-fed rats are demonstrated. However, the effects are only reported in one animal model and the involvement of gut microbiota is not investigated. The aim of this study is to investigate the effects of goat milk consumption on glucose homeostasis and gut microbiota in streptozocin (STZ)-induced diabetic rats.

METHODS AND RESULTS

STZ-induced diabetic rats are fed with three dosages of goat milk: 2.5, 5, and 10 g kg-1 . Parameters related to glucose homeostasis, hepatic and skeletal muscle AMP-activated protein kinase (AMPK) activation, and gut microbiota are investigated. The dose of 10 g kg-1 exerts more metabolic benefits. Goat milk consumption improves fasting glucose levels, glucose tolerance, insulin sensitivity, and promotes hepatic and skeletal muscle AMPK activation in STZ-injected diabetic rats. Goat milk modulates gut microbiota, increases the relative abundance of Lactobacillus, and augments levels of propionic and butyric acids.

CONCLUSION

This study demonstrates the metabolic benefits of goat milk consumption in STZ-induced diabetic rats, which is consistent with the previous observations in high-fat diet-induced diabetic rats. Furthermore, this study elucidates the modulation of gut microbiota by goat milk, which likely mediates the metabolic effects of goat milk.

Characterization and association of bacterial communities and nonvolatile components in spontaneously fermented cow milk at different geographical distances

In the ecosystem of spontaneously fermented cow milk, the characteristics and relationship of bacterial communities and nonvolatile components at different scales of geographical distances (provincial, county, and village levels) are unclear. Here, 25 sampling sites from Xin Jiang and Tibet, 2 provinces of China, were selected based on the distribution of spontaneously fermented cow milk and used for metagenomic and metabolomic analysis. At the provincial geographical distance, the same predominant species, Lactobacillus delbrueckii ssp. bulgaricus and Streptococcus thermophilus, were detected in Xin Jiang and Tibet. Further, the richness of the bacterial composition of samples from Tibet was higher than those from Xin Jiang; specifically, at the species level, 28 species were identified in Tibet samples but only 7 species in Xin Jiang samples. At the provincial geographical level, we detected significant differences in bacterial structure, shown in principal coordinate analysis plots, and significant differences (Simpson index) in bacterial diversity were also detected. However, at the county and village levels, no significant differences were detected in bacterial communities and diversity, but a difference in bacterial compositions was detectable. This indicates that bacterial communities and diversity of spontaneously fermented milk dissimilarity significantly increased with geographic distance. For the nonvolatile component profiles, the partial least squares discriminant analysis plot (R²Y > 0.5 and Q² > 0.5 for the goodness-of-fit and predictive ability parameter, respectively) showed that samples from different geographical distances (provincial, county, and village) were all separated, which indicated that all the discriminations in nonvolatile components profiles were from different geographical distances. Investigating relationships between lactic acid bacteria and discriminatory nonvolatile components at the county level showed that 9 species were positively correlated with 16 discriminatory nonvolatile components, all species with low abundance rather than the predominant species L. delbrueckii ssp. bulgaricus and Strep. thermophilus, which indicates the importance of the selection of autochthonous nonpredominant bacteria.

Comparison of the Bifidogenic Effects of Goat and Cow Milk-Based Infant Formulas to Human Breast Milk in an in vitro Gut Model for 3-Month-Old Infants

Human milk contains prebiotic components, such as human milk oligosaccharides (HMOs), which stimulate the growth of specific members of the infant gut microbiota (e.g., Bifidobacteria). Plant-based or synthetic oligosaccharides are often added to infant formulas to simulate the bifidogenic effect of HMOs. Cow milk, the most common source of protein in infant formula, and goat milk, used increasingly in the manufacture of infant formula, contain naturally-occurring prebiotics. This study compared the upper gastrointestinal digestion and subsequent colonic fermentation of human milk vs. goat and cow milk-based infant formulas (goat IF and cow IF, respectively), without additional oligosaccharides using an in vitro model for 3-month-old infants based on the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). First, a dialysis approach using 3.5 kDa membranes was demonstrated to simulate small intestinal absorption of carbohydrates in conditions similar to those in vivo. During the in vitro digestion experiment, oligosaccharides were detected in human milk and goat IF but barely detected in the cow IF. Further, all three milk matrices decreased colonic pH by boosting acetate, lactate, and propionate production, which related to increased abundances of acetate/lactate-producing Bifidobacteriaceae for human milk (+25.7%) and especially goat IF (33.8%) and cow IF (37.7%). Only cow IF stimulated butyrate production which correlated with an increase in Lachnospiraceae and Clostridiaceae. Finally, Enterobacteriaceae and Acidaminococcaceae also increased with all three milk matrices, while production of proteolytic metabolites (branched-chain fatty acids) was only detected for the cow IF. Overall, goat and cow milk-based formulas without added oligosaccharides impacted gut microbial activity and composition similarly to human milk. This suggests that even without supplementation of formula with oligosaccharides, whole goat milk, whole cow milk and cow milk ingredients already supply compounds in formulas that exert beneficial bifidogenic effects. Further clinical research is warranted to elucidate the effect of whole goat milk-based formulas on the infant gut microbiome.

Differences in Gut Microbial Diversity are Driven by Drug Use and Drug Cessation by Either Compulsory Detention or Methadone Maintenance Treatment

In this work, we investigate differences in gut microbial diversity driven by drug use or by the widely used methods for drug cessation: methadone maintenance treatment (MMT) and compulsory detention (CD). Methods: 99 participants (28 CD participants, 16 MMT patients, 27 drug users, and 28 healthy controls) were selected using strict inclusion criteria. Nutritional intake and gut microbial diversity were analyzed with bioinformatics tools and SPSS 20.0. Results: Alpha diversity was not significantly different among groups, whereas beta diversity of gut microbiota and nutrient intake were significantly higher among MMT patients. Taxa were unevenly distributed between groups, with drug users having the highest proportion of Ruminococcus and MMT patients having the highest abundance of Bifidobacterium and Lactobacillus. Conclusion: Drug use, cessation method, and diet contribute to shaping human gut communities. High beta diversity among MMT patients is likely driven by methadone use and high nutrient intake, leading to increased orexin A and enrichment for beneficial bacteria, while diversity in CD participants is largely influenced by diet.

Effects of enrofloxacin treatment on the bacterial microbiota of milk from goats with persistent mastitis

Antibiotic resistance has become a major concern for human and animal health. As fluoroquinolones have been extensively used in human and veterinary medicine, there has also been the rapid emergence and spread of antimicrobial resistance around the world. Here, we analysed the microbiome of goat milk using samples from healthy goats and those diagnosed with persistent mastitis and treated using the antibiotic enrofloxacin with 16S rRNA amplicon sequencing. We selected a group of 11 goats and 22 samples of milk that did not respond clinically to enrofloxacin treatment. Milk samples were evaluated before and after treatment to verify changes of the microbiota; the three first lactating goats were selected from the healthy control group. The milk samples from the healthy control animals presented a larger abundance of different species of bacteria of the Staphylococcus genus, but a smaller number of different genera, which indicated a more specific niche of resident bacteria. The Firmicutes phylum was predominantly different between the studied groups. Samples from before-treatment animals had a higher number of new species than those from the control group, and after being treated again. These microbiota received new bacteria, increasing the differences in bacteria even more in relation to the control group. Genotypes such as Trueperella and Mannheimia, between other genera, had a high abundance in the samples from animals with persistent mastitis. The dysbiosis in this study, with marked evidence of a complex microbiota in activity in cases of the failure of antimicrobial treatment for persistent chronic mastitis, demonstrates a need to improve the accuracy of pathogen identification and increases concern regarding antibiotic treatments in milk production herds.

The distal intestinal microbiome of hybrids of Hainan black goats and Saanen goats

Intestinal microbiota performed numerous important functions during digestion. The first filial generation (F1) hybrids of Hainan black goats and Saanen goats had different traits, black goats (BG) and white goats (WG), which also brought different production performance. We explored the difference of gut microbiota between black goats and white goats that both belonged to the first filial generation (F1) hybrids. In general, the alpha diversity of the black goat group was significantly higher than the white goat group. The species richness had no significant difference, while the species evenness of BG was higher than WG. Bacteroides, Oscillospira, Alistipes, Ruminococcus, Clostridium and Oscillibacter, as the core gut microbial genera, all had high abundance in BG and WG group. Only the Bacteroides and Bacteroidaceae 5-7N15 were the different genera between the BG and WG group, of which Bacteroides overlapped with the core genera and enriched in the WG group. Besides, PICRUSt analysis showed that there was a high abundance in the secondary metabolic pathways including membrane transport, replication and repair, carbohydrate metabolism and amino acid metabolism. We found the intestinal microbial species of black goats and white goats were very similar for living in the identical growing environment and feeding conditions, but there was still a slight difference in the content. On the one hand, it was proved that the small effect of genotype and the great effect of diet affected the intestinal microbiota together. On the other hand, it was also proved that these different traits of first filial generation (F1) hybrids may not related to gut microbiota and only because of different genotype. Moreover, characterization of the gut microbiota in BG and WG will be useful in goats gut microbiota research.

Goat milk increases gastric emptying and alters caecal short chain fatty acid profile compared with cow milk in healthy rats

Goat and cow milk share similar protein and lipid content, yet goat milk forms softer curds during stomach digestion.

Characterization of the microbial community structure in intestinal segments of yak (Bos grunniens)

Yak (Bos grunniens), a ruminant, has a complex gastrointestinal microbial ecosystem, which is essential for host nutrition and health. However, not much is known about gut microbial communities of yak. This study was conducted to characterize the gut microbial diversity and composition of small intestinal and cecal contents of yaks through high-throughput sequencing targeting V3-V4 hypervariable region of 16S rRNA gene. A total of 916,934 high-quality sequences were obtained and 224 core operational taxonomic units (OTUs) shared all samples. The result showed that the microbial community in the small intestine was different from cecum sample. In all samples, the majority of bacterial phyla were Firmicutes, Bacteroidetes and Proteobacteria. A large proportion of anaerobes in the families Peptostreptococcaceae, Prevotellaceae, Flavobacteriaceae, Lachnospiraceae, and Succinivibrionaceae were present in the various intestinal segments. The relative abundance of Ruminococcaceae, Bacteroidaceae and Muribaculaceae were significantly higher in cecum than in other segments of intestines. At the genus level, Bacteroides was the most predominant genus in cecum. The results indicated that yak have abundant and diverse gut microbial community. In conclusion, this study characterized the profiles of microbial communities across intestinal segments and provide better insight into microbial population structure and diversity of yak.

Microbial Profile and Genetic Polymorphism of Predominant Species in Some Traditional Fermented Seafoods of the Hainan Area in China

Fermented fish, fermented shrimp and fermented crab are traditionally prepared seafoods that are commonly consumed in the Hainan area in China. We studied the microbial diversity and metabolic pathways in traditional fermented seafoods using high-throughput sequencing technology, and based on our previous research, we also compared the differences between fermented seafood and fermented vegetables. The alpha diversity of fermented seafood was higher than that of fermented vegetables and attained the highest level in fermented shrimp. The dominant genera in fermented seafood were different from those of fermented vegetables. Furthermore, we analyzed the 16S rDNA gene polymorphisms (SNPs) of the same dominant species (Lactobacillus plantarum and Lactobacillus fermentum) in two fermented environments, which showed that most of the mutations occurred in fermented vegetables and that fermenting environment might be the major factor for these mutations. This research provides us with new insights into beneficial microbial resources in regard to microbial diversity and genetic polymorphisms and lays a foundation for the subsequent development and utilization of beneficial microorganisms.

Metagenomic analysis revealed the effects of goat milk feeding and breast feeding on the gut microbiome of Amur tiger cubs

BACKGROUND

Ingredients in breast milk can help establish a healthy community of microorganisms in the infant gut, but no research exists regarding the effects of goat milk feeding and breast feeding on the gut microbiome of the Amur tiger, which is one of the most endangered species in the world.

METHODS

In this study, we used whole-metagenome shotgun sequencing to analyze the effects of two different feeding patterns, goat milk feeding and breast feeding, on the composition and functional structures of gut microbiota in Amur tiger cubs.

RESULTS

Goat milk-fed cubs have fewer beneficial bacteria and more pathogenic bacteria and a higher microbial diversity in their gut than breastfed cubs. A total of 15 genera showed statistically significant differences; the relative abundances of Streptomyces scabiei, Streptomyces avermitilis and Streptomyces davawensis were significantly decreased, whereas those of Niabella soli, Aeromonas media and Brochothrix thermosphacta were significantly increased in the goat milk-fed group compared with those in the breastfed group. At the functional level, carbohydrate metabolism, translation and replication and repair decreased, and amino acid metabolism, membrane transport and metabolism of cofactors and vitamins increased in the gut microbiota of goat milk-fed cubs compared with breastfed cubs.

CONCLUSION

Our results indicate for the first time that the different milk feeding patterns of goat milk feeding and breast feeding can change the composition and functional structures of gut microbiota in Amur tiger cubs and that breastfed tiger cubs and goat milk-fed tiger cubs have distinct microbiotas in their guts.