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Frontiers in Microbiology 2020The rumen microbiota is strongly associated with host health, nutrient absorption, and adaptability. However, the composition, functioning and adaptability of rumen...
The rumen microbiota is strongly associated with host health, nutrient absorption, and adaptability. However, the composition, functioning and adaptability of rumen microbiota in Tibetan sheep (TS) across different phenological periods are unclear. In this study we used sequencing of the V4-V5 region of 16S rRNA, qPCR technology and metagenomics to investigate the adaption of rumen microbiota to forage in different stages of phenology. In a grassy period, due to the high nutritional quality of the forage, TS can produce high concentrations of NH-N and short fatty acids by increasing the content of key bacteria in the rumen, such as Bacteroidetes, , , , , , , , and to aid in growth. In the withering period, there was a positive correlation between microorganisms which indicated the closely cooperation between microorganisms, and metagenomic analysis showed that the high genes (GHs and CBMs) and subtribe (GH8, GH12, GH45, GH6, GH9, GH5, GH10, GH3, GH52, GH11, GH57, CBM1, CBM4, CBM6, CBM16, CBM37, CBM13, CBM35, CBM42, CBM32, and CBM62) that encode cellulolytic enzymes were significantly increased when the host faced low quantity and quality of forage. Genes involved in metabolic pathways, fatty acid biosynthesis and biosynthesis of antibiotics were significantly enriched, which indicated that rumen microbiota could improve plant biomass deconstruction and energy maintenance in the face of nutritional deficiencies. In the regreen period, both the composition and function of rumen microbiota had obvious disadvantages, therefore, to improve the competitiveness of microorganisms, we suggest TS should be supplemented with high-protein feed. This study is of great significance for exploring the high altitude adaptability of TS.
PubMed: 33193243
DOI: 10.3389/fmicb.2020.587558 -
Veterinary World Jul 2018A critical prerequisite for studying rumen microbial community by high throughput molecular biology methods is good quality community DNA. Current methods of extraction...
BACKGROUND AND AIM
A critical prerequisite for studying rumen microbial community by high throughput molecular biology methods is good quality community DNA. Current methods of extraction use kits designed for samples from the different origin for rumen. This puts stress on the development of a relevant manual method for DNA extraction. The objective of this study was to modify the existing methods of community DNA extraction and thereby systematic comparison of their efficiency based on DNA yield, purity, 16S rRNA gene sequencing, and identification to determine the optimal DNA extraction methods whose DNA products reflect targeted bacterial communities special to rumen.
MATERIALS AND METHODS
Enzymatic method, Chemical method, Enzymatic + Chemical method, and Enzymatic + Chemical + Physical method were modified toward evaluation of community DNA extraction from solid, squeezed, and liquid fractions of goat rumen digesta. Each method was assessed critically for nucleic acid yield and its quality. The methods resulting in high nucleic acid yield, optimal purity ratios with intact band on agarose gel electrophoresis were optimized further. Optimized methods were studied using standard polymerase chain reaction (PCR) with universal bacterial primers and 16S rRNA primers of targeted rumen bacteria. Methods denoting the presence of targeted rumen bacteria were assessed further with 16S rRNA gene sequencing and identification studies. It led toward methods efficacy estimation for molecular biology applications. Effect of rumen sample preservation on community DNA extraction was also studied. Their mean standard deviation values were calculated to understand sampling criticality.
RESULTS
Modified Chemical method (Cetrimonium bromide) and Enzymatic+Chemical+Physical (ECP) method (Lysozyme-Cetrimonium bromide-Sodium Dodecyl Sulfate-freeze-thaw) could extract 835 ng/µl and 161 ng/µl community DNA from 1.5 g solid and 2 ml squeezed rumen digesta with purity ratios of 1.8 (A/A) and 2.3 (A/A) respectively. Comparative analysis showed the better efficiency of ECP method and chemical method toward freshly squeezed rumen digesta and solid rumen digesta. However, sample preservation at -80°C for 1.5 months drastically affected the yield and purity ratios of community DNA. New protocol revealed targeted microbial community having Gram-positive as well as Gram-negative bacteria such as , , , and .
CONCLUSION
To date, this is the first report of modified methods wherein least chemicals and steps lead toward PCR and 16S rRNA gene sequencing quality community DNA extraction from goat rumen digesta. Detection of targeted rumen bacteria in solid and squeezed rumen digesta proves their strongest association with rumen fiber mat. It also marks the presence of distinct microbial communities in solid and squeezed rumen fractions that in turn differs the performance of each different method employed and yield of nucleic acid obtained. It also leaves a possibility of the presence of complex microbial consortia in squeezed rumen digesta whose DNA extraction methods need more attention. Finally, manual protocols of community DNA extraction may vary in different ruminant which suggests undertaking rigorous research in their establishment.
PubMed: 30147271
DOI: 10.14202/vetworld.2018.990-1000 -
Microbiome Jan 2024The gut microbiome of domestic animals carries antibiotic resistance genes (ARGs) which can be transmitted to the environment and humans, resulting in challenges of...
BACKGROUND
The gut microbiome of domestic animals carries antibiotic resistance genes (ARGs) which can be transmitted to the environment and humans, resulting in challenges of antibiotic resistance. Although it has been reported that the rumen microbiome of ruminants may be a reservoir of ARGs, the factors affecting the temporal dynamics of the rumen resistome are still unclear. Here, we collected rumen content samples of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days of age, analyzed their microbiome and resistome profiles using metagenomics, and assessed the temporal dynamics of the rumen resistome in goats at the early stage of life under a conventional feeding system.
RESULTS
In our results, the rumen resistome of goat kids contained ARGs to 41 classes, and the richness of ARGs decreased with age. Four antibiotic compound types of ARGs, including drugs, biocides, metals, and multi-compounds, were found during milk feeding, while only drug types of ARGs were observed after supplementation with starter feed. The specific ARGs for each age and their temporal dynamics were characterized, and the network inference model revealed that the interactions among ARGs were related to age. A strong correlation between the profiles of rumen resistome and microbiome was found using Procrustes analysis. Ruminal Escherichia coli within Proteobacteria phylum was the main carrier of ARGs in goats consuming colostrum, while Prevotella ruminicola and Fibrobacter succinogenes associated with cellulose degradation were the carriers of ARGs after starter supplementation. Milk consumption was likely a source of rumen ARGs, and the changes in the rumen resistome with age were correlated with the microbiome modulation by starter supplementation.
CONCLUSIONS
Our data revealed that the temporal dynamics of the rumen resistome are associated with the microbiome, and the reservoir of ARGs in the rumen during early life is likely related to age and diet. It may be a feasible strategy to reduce the rumen and its downstream dissemination of ARGs in ruminants through early-life dietary intervention. Video Abstract.
Topics: Animals; Humans; Goats; Rumen; Microbiota; Animals, Domestic; Gastrointestinal Microbiome; Anti-Bacterial Agents
PubMed: 38254181
DOI: 10.1186/s40168-023-01733-5 -
FEMS Microbiology Letters Jul 2016This study aimed to investigate the effects of dietary fibre sources on the gut microbiota in suckling piglets, and to test the hypothesis that a moderate increase of...
This study aimed to investigate the effects of dietary fibre sources on the gut microbiota in suckling piglets, and to test the hypothesis that a moderate increase of dietary fibre may affect the gut microbiota during the suckling period. Suckling piglets were fed different fibre-containing diets or a control diet from postnatal day 7 to 22. Digesta samples from cecum, proximal colon and distal colon were used for Pig Intestinal Tract Chip analysis. The data showed that the effects of fibre-containing diet on the gut microbiota differed in the fibre source and gut location. The alfalfa diet increased Clostridium cluster XIVb and Sporobacter termitidis in the cecum compared to the pure cellulose diet. Compared to the control diet, the alfalfa diet also increased Coprococcus eutactus in the distal colon, while the pure cellulose diet decreased Eubacterium pyruvativorans in the cecum. The pure cellulose diet increased Prevotella ruminicola compared to the wheat bran diet. Interestingly, the alfalfa group had the lowest abundance of the potential pathogen Streptococcus suis in the cecum and distal colon. These results indicated that a moderate increase in dietary fibres affected the microbial composition in suckling piglets, and that the alfalfa inclusion produced some beneficial effects on the microbial communities.
Topics: Animal Feed; Animals; Animals, Newborn; Biodiversity; Cluster Analysis; Dietary Fiber; Gastrointestinal Microbiome; Intestine, Large; Metagenome; Metagenomics; Swine
PubMed: 27231242
DOI: 10.1093/femsle/fnw138 -
Journal of Animal Physiology and Animal... Nov 2019Researches on sodium selenite (SS) mainly focus on production performance and rumen fermentation in ruminants, and the influence of dietary Se addition on ruminal...
Researches on sodium selenite (SS) mainly focus on production performance and rumen fermentation in ruminants, and the influence of dietary Se addition on ruminal microbial population and enzyme activity in dairy bulls is scarce. This study mainly evaluated the effects of SS on ruminal fermentation, microflora and urinary excretion of purine derivatives (PD) in dairy bulls. Eight ruminally cannulated dairy bulls were used in a replicated 4 × 4 Latin square design. Treatments were control, low SS (LSS), medium SS (MSS) and high SS (HSS) with 0, 0.1, 0.3 and 0.5 mg/kg of selenium (Se) from SS in dietary dry matter (DM), respectively. The supplement of SS (1.0 g/kg of Se) was mixed into the first third of the daily ration. Bulls were fed a total mixed ration with corn silage to concentrate ratio of 50:50 on a DM basis. Dry matter intake was not affected, average daily gain linearly increased, while feed conversion ratio quadratically decreased with increasing Se addition. The linearly increased digestibility of DM, organic matter, crude protein, ether extract, neutral detergent fibre and acid detergent fibre was observed. Both ruminal pH and ammonia-N concentration linearly decreased, whereas total volatile fatty acid concentration linearly increased. A lower acetate to propionate ratio was observed due to the unchanged acetate proportion and increased propionate proportion. Activity of cellobiase, xylanase, pectinase, α-amylase and protease, populations of total bacteria, fungi, protozoa, Ruminococcus (R.) albus, R. flavefaciens, Fibrobacter succinogenes, Butyrivibrio fibrisolvens and Ruminobacter amylophilus as well as urinary total PD excretion linearly increased, whereas populations of total methanogens and Prevotella ruminicola linearly decreased. The data indicated that dietary Se addition stimulated ruminal microbial growth and enzyme activity, and resulting in the increased nutrient digestion and growth performance, and the optimum supplementary dose of Se was 0.3 mg/kg dietary DM from SS in dairy bulls.
Topics: Animal Feed; Animals; Bacteria; Cattle; Dietary Supplements; Fermentation; Male; Purines; Rumen; Sodium Selenite
PubMed: 31441137
DOI: 10.1111/jpn.13193 -
Frontiers in Microbiology 2024Niacin is one of the essential vitamins for mammals. It plays important roles in maintaining rumen microecological homeostasis. Our previous study indicated that dietary...
Metagenomic sequencing identified microbial species in the rumen and cecum microbiome responsible for niacin treatment and related to intramuscular fat content in finishing cattle.
INTRODUCTION
Niacin is one of the essential vitamins for mammals. It plays important roles in maintaining rumen microecological homeostasis. Our previous study indicated that dietary niacin significantly elevated intramuscular fat content (IMF) in castrated finishing steers. Whether niacin affects fat deposition by regulating the microbial composition and functional capacities of gastrointestinal microbiome has been unknown yet.
METHODS
In this study, 16 castrated Xiangzhong Black cattle were randomly assigned into either control group fed with a basal concentrate diet ( = 8) or niacin group fed with a basal concentrate diet added 1000 mg/kg niacin ( = 8). Seven rumen samples and five cecum content samples were randomly collected from each of control and niacin groups for metagenomic sequencing analysis.
RESULTS
A total of 2,981,786 non-redundant microbial genes were obtained from all tested samples. Based on this, the phylogenetic compositions of the rumen and cecum microbiome were characterized. We found that bacteria dominated the rumen and cecum microbiome. and were the most abundant bacterial species in the rumen microbiome, while and were predominant bacterial species in the cecum microbiome. Rumen microbiome had significantly higher abundances of GHs, GTs, and PLs, while cecum microbiome was enriched by CBMs and AAs. We found a significant effect of dietary niacin on rumen microbiome, but not on cecum microbiome. Dietary niacin up-regulated the abundances of bacterial species producing lactic acid and butyrate, fermenting lactic acid, and participating in lipid hydrolysis, and degradation and assimilation of nitrogen-containing compounds, but down-regulated the abundances of several pathogens and bacterial species involved in the metabolism of proteins and peptides, and methane emissions. From the correlation analysis, we suggested that niacin improved nutrient digestion and absorption, but reduced energy loss, and Valine, leucine and isoleucine degradation of rumen microbiome, which resulted in the increased host IMF.
CONCLUSION
The results suggested that dietary manipulation, such as the supplementation of niacin, should be regarded as the effective and convenient way to improve IMF of castrated finishing steers by regulating rumen microbiome.
PubMed: 38529181
DOI: 10.3389/fmicb.2024.1334068 -
Animal Bioscience May 2024This study investigated the impact of Aspergillus niger lysing polysaccharide monooxygenase (AnLPMO) on in vitro rumen microbial fermentation of rice straw.
OBJECTIVE
This study investigated the impact of Aspergillus niger lysing polysaccharide monooxygenase (AnLPMO) on in vitro rumen microbial fermentation of rice straw.
METHODS
AnLPMO was heterologously expressed in Escherichia coli. Fourier transform infrared spectrometry and X-ray photoelectron spectroscopy analyzed the surface structure of rice straw after AnLPMO treatment. Two in vitro experiments, coupled with 16S high-throughput sequencing and qRT-PCR techniques, assessed the influence of AnLPMO on rumen microbial fermentation of rice straw.
RESULTS
AnLPMO exhibited peak activity at 40 °C and pH 6.5, with a preference for rice straw xylan hydrolysis, followed by Avicel. AnLPMO application led to the fractional removal of cellulose and hemicelluloses and a notable reduction in the levels of carbon elements and C-C groups present on the surface of rice straw. Compared to the control (no AnLPMO), supplementing AnLPMO at 1.1 U-2.0 U significantly enhanced in vitro digestibility of dry matter (IVDMD, P < 0.01), total gas production (P < 0.01), and concentrations of total volatile fatty acids (VFA, P < 0.01), acetate (P < 0.01), and ammonia-N (P < 0.01). Particularly, the 1.4 U AnLPMO group showed a 14.8% increase in IVDMD. In the second experiment, compared to deactivated AnLPMO (1.4 U), supplementing bioactive AnLPMO at 1.4 U increased IVDMD (P = 0.01), total gas production (P = 0.04), and concentrations of total VFA (P < 0.01), propionate (P < 0.01), and ammonia-N (P < 0.01), with a limited 9.6% increase in IVDMD. Supplementing AnLPMO stimulated the growth of ruminal bacterial taxa facilitating fiber degradation, including Proteobacteria, Spirochaetes, Succinivibrio, Rikenellaceae_RC9_Gut_Group, Prevotelaceae_UCG-003, Desulfovibrio, Fibrobacter succinogenes, Ruminococcus albus, R. flavefaciens, Prevotella bryantii, P. ruminicola, and Treponema bryantii.
CONCLUSION
These findings highlight AnLPMO's potential as a feed additive for improving rice straw utilization in ruminant production.
PubMed: 38754847
DOI: 10.5713/ab.24.0026 -
Archives of Animal Nutrition Feb 2019This study evaluated the effects of folic acid (FA) supplementation on growth performance, ruminal fermentation, nutrient digestibility and urinary purine derivatives...
This study evaluated the effects of folic acid (FA) supplementation on growth performance, ruminal fermentation, nutrient digestibility and urinary purine derivatives (PD) excretion in dairy calves. Forty-eight Chinese Holstein male dairy calves at 60 ± 3.2 d of age and 89 ± 5.9 kg body weight (mean ± standard error) were assigned to one of four groups in a randomised block design. Calves in control group were fed basal diet, calves in low FA, medium FA and high FA groups with 3.6, 7.2 and 10.8 mg FA per kg basal diet, respectively. The dietary corn silage to concentrate ratio was 50:50 (dry matter [DM] basis). DM intake and average daily gain (ADG) quadratically increased, and feed conversion ratio quadratically decreased with increasing FA supplementation. Ruminal pH linearly decreased, whereas total volatile fatty acids quadratically increased. The unchanged acetate-to-propionate ratio was due to the similar change in acetate and propionate concentration. Ammonia N content quadratically decreased. Digestibility of DM, organic matter, crude protein, ether extract, neutral detergent fibre and acid detergent fibre linearly increased. Activities of carboxymethyl cellulase, cellobiase, xylanase and pectinase linearly increased, but -amylase and protease quadratically increased. Abundance of and linearly increased, but and quadratically increased. Urinary total PD excretion quadratically increased. The results indicated that FA supplementation increased ADG, ruminal fermentation and nutrient digestibility with promoted ruminal microbial growth and enzyme activity, and the optimum dose was 7.2 mg FA per kg basal diet for calves.
Topics: Animal Feed; Animal Nutritional Physiological Phenomena; Animals; Bacteria; Cattle; Diet; Dietary Supplements; Digestion; Dose-Response Relationship, Drug; Fermentation; Folic Acid; Gastrointestinal Microbiome; Male; Nutrients; Purines; Random Allocation; Renal Elimination; Rumen; Weaning
PubMed: 30475059
DOI: 10.1080/1745039X.2018.1547028 -
Animals : An Open Access Journal From... Apr 2023This experiment was conducted to investigate growth performance, ruminal fermentation, rumen microbial protein synthesis, and serum antioxidant capacity with different...
This experiment was conducted to investigate growth performance, ruminal fermentation, rumen microbial protein synthesis, and serum antioxidant capacity with different doses of curcumin (CUR) included in the diet of housed growing lambs. Forty-eight four-month-old Dorper × Thin-tailed Han F crossbred male lambs (body weight = 20.89 ± 1.15 kg, age = 120 ± 10 days; mean ± SD) were randomly divided into four groups for a single-factor, completely randomized experiment. Treatments comprised the following: the basal diet supplemented with 0 (Control), 300 mg/kg (300 CUR), 600 mg/kg (600 CUR), or 900 mg/kg (900 CUR) CUR, respectively. The results showed that dietary CUR increased average daily gain (ADG), and the 300 CUR group evidenced the highest value. There were no significant effects on dry matter intake (DMI) and DMI/ADG. Lambs in the 300 CUR group showed higher totals of volatile fatty acids (VFA) and acetate than other groups, while decreased valerate was observed with supplementary CUR. The ruminal pH and ammonia N (NH-N) concentration decreased with increasing CUR, with the greatest effect in the 300 CUR group. The quadratic effects were found in pectinase, carboxymethyl cellulose, and protease, with the greatest value in the 300 CUR group. The microbial populations of total bacteria and also responded quadratically, and the methanogens, protozoan, and populations decreased linearly with increasing CUR. Lambs receiving additional CUR showed increased population. Microbial protein (MCP) synthesis was promoted by supplementary CUR. As supplementation with CUR increased, the serum activity of total antioxidant capacity (T-AOC), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) was enhanced, with the greatest value in the 300 CUR group. In conclusion, dietary CUR improved ruminal fermentation, promoted rumen microbial protein (MCP) synthesis, and enhanced serum antioxidant activity, as well as promoting growth performance in housed growing lambs.
PubMed: 37174476
DOI: 10.3390/ani13091439 -
Nature Communications Mar 2019The abilities of certain microorganisms to be transferred across the food production chain, persist in the final product and, potentially, colonize the human gut are...
The abilities of certain microorganisms to be transferred across the food production chain, persist in the final product and, potentially, colonize the human gut are poorly understood. Here, we provide strain-level evidence supporting that dairy cattle-associated bacteria can be transferred to the human gut via consumption of Parmesan cheese. We characterize the microbial communities in samples taken from five different locations across the Parmesan cheese production chain, confirming that the final product contains microorganisms derived from cattle gut, milk, and the nearby environment. In addition, we carry out a human pilot study showing that Bifidobacterium mongoliense strains from cheese can transiently colonize the human gut, a process that can be enhanced by cow milk consumption.
Topics: Animals; Bifidobacterium; Cattle; Cheese; Corynebacterium; DNA Barcoding, Taxonomic; DNA, Bacterial; Feces; Gastrointestinal Microbiome; Humans; Lactobacillus delbrueckii; Milk; Phylogeny; Pilot Projects; Prevotella ruminicola; RNA, Ribosomal, 16S; Streptococcus thermophilus
PubMed: 30894548
DOI: 10.1038/s41467-019-09303-w