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Frontiers in Microbiology 2020Rumen microbiome composition and functionality is linked to animal feed efficiency, particularly for bovine ruminants. To investigate this in sheep, we compared rumen...
Rumen microbiome composition and functionality is linked to animal feed efficiency, particularly for bovine ruminants. To investigate this in sheep, we compared rumen bacterial and archaeal populations (and predicted metabolic processes) of sheep divergent for the feed efficiency trait feed conversion ratio (FCR). In our study 50 Texel cross Scottish Blackface (TXSB) ram lambs were selected from an original cohort of 200 lambs. From these, 26 were further selected for experimentation based on their extreme FCR (High Feed Efficiency, HFE = 13; Low Feed Efficiency, LFE = 13). Animals were fed a 95% concentrate diet over 36 days. 16S rRNA amplicon sequencing was used to investigate the rumen bacterial and archaeal communities in the liquid and solid rumen fractions of sheep divergent for FCR. Weighted UniFrac distances separated HFE and LFE archaea communities from the liquid rumen fraction (Permanova, < 0.05), with greater variation observed for the LFE cohort (Permdisp, < 0.05). LFE animals exhibited greater Shannon and Simpson diversity indices, which was significant for the liquid rumen fraction ( < 0.05). (in liquid and solid fractions) and (liquid fraction) were differentially abundant, and increased in the LFE cohort ( < 0.05), while (liquid fraction) was increased in the HFE cohort ( < 0.05). This suggests that methanogenic archaea may be responsible for a potential loss of energy for the LFE cohort. Bacterial community composition (Permanova, 0.1) and diversity ( > 0.1) was not affected by the FCR phenotype. Only the genus was differentially abundant between HFE and LFE cohorts. Although no major compositional shifts of bacterial populations were identified amongst the feed efficient cohorts ( > 0.05), correlation analysis identified putative drivers of feed efficiency with (liquid, = -0.53; solid, = -0.56) and (solid, = -0.40) exhibiting significant negative association with FCR ( < 0.05). and showed significant positive correlations with ADG. Major cellulolytic bacteria (liquid, = 0.43) and (liquid, = 0.41; solid, = 41) correlated positively with FCR ( < 0.05). Our study provides evidence that feed efficiency in sheep is likely influenced by compositional changes to the archaeal community, and abundance changes of specific bacteria, rather than major overall shifts within the rumen microbiome.
PubMed: 32983009
DOI: 10.3389/fmicb.2020.01981 -
Frontiers in Microbiology 2021Genetically selected chickens with better growth and early maturation show an incidental increase in abdominal fat deposition (AFD). Accumulating evidence reveals a...
Genetically selected chickens with better growth and early maturation show an incidental increase in abdominal fat deposition (AFD). Accumulating evidence reveals a strong association between gut microbiota and adiposity. However, studies focusing on the role of gut microbiota in chicken obesity in conventional breeds are limited. Therefore, 400 random broilers with different levels of AFD were used to investigate the gut microbial taxa related to AFD by 16S rRNA gene sequencing of 76 representative samples, and to identify the specific microbial taxa contributing to fat-related metabolism using shotgun metagenomic analyses of eight high and low AFD chickens. The results demonstrated that the richness and diversity of the gut microbiota decrease as the accumulation of chicken abdominal fat increases. The decrease of Bacteroidetes and the increase of Firmicutes were correlated with the accumulation of chicken AFD. The Bacteroidetes phylum, including the genera , , and the species, , , and , were correlated to alleviate obesity by producing secondary metabolites. Several genera of Firmicutes phylum with circulating lipoprotein lipase activity were linked to the accumulation of chicken body fat. Moreover, the genera, and , might positively contribute to fat and energy metabolism, whereas the genus, , was possible to enhance energy capture, and associated to accumulate chicken AFD. These findings provide insights into the roles of the gut microbiota in complex traits and contribute to the development of effective therapies for the reduction of chicken fat accumulation.
PubMed: 33815329
DOI: 10.3389/fmicb.2021.643025 -
Journal of Dairy Science Nov 2023The aim of this study was to assess the potential consequences on calf intake, performance, behavior, ruminal microbiome, and ruminal epithelium development of combining...
The aim of this study was to assess the potential consequences on calf intake, performance, behavior, ruminal microbiome, and ruminal epithelium development of combining the inclusion of chopped barley straw and alfalfa hay during the pre- and postweaning periods keeping concentrate to forage ratio constant among dietary treatments. Forty-five Holstein calves (44 ± 5.7 kg of body weight [BW] and 3 ± 1.5 d of age) individually penned were blocked by BW and randomly assigned to a common pellet concentrate fed ad libitum along with one of following forage feeding strategies: barley straw before and after weaning (S-S), barley straw before and alfalfa hay after weaning (S-A), or alfalfa hay before and after weaning (A-A). All calves received the same milk replacer regimen. Forage was supplied in a separated bucket at the rate of 7.5% (preweaning) and 15% (postweaning) of total solid feed intake of the previous day. Feed intake and BW were recorded daily and weekly, respectively. Rumen samples were obtained via a stomach tube at 53, 66, and 87 d and were composite in 3 samples of 5 animals each for subsequent rumen microbiome analysis. A rumen epithelium sample was taken by endoscopy at 90 d to assess gene expression of OCLN, CLDN4, SLC9A1, SLC9A3, SLC16A1, SLC16A4, IL6, and TGFB1. Data were analyzed with a mixed-effects model accounting for the fixed effects of block, forage, week of study, and their interaction, and calf as a random effect. The type of forage fed did not affect concentrate feed, forage, or total DM intake before weaning. However, S-A and A-A calves consumed less concentrate feed and S-A calves grew at a lower rate after weaning than S-S calves. Expression of the gene coding for SLC16A1 in the rumen epithelium was greatest in S-S among treatments. Rumen microbiome did not differ among treatments, while the relative abundance of Acidaminococcus and Selenomas genera increased, while Alloprevotella, Bifidobaterium, Olsenella, and Succiclasticum genera decreased with age. In conclusion, feeding barley straw before and after weaning was more effective than feeding alfalfa hay in promoting concentrate feed intake after weaning and fostering an increase in the expression of SLC16A1 in the rumen epithelium.
PubMed: 37558048
DOI: 10.3168/jds.2023-23401 -
Frontiers in Cellular and Infection... 2022The prevalence of dental caries in the Mexican adult population aged 20 to 85 years is around 93.3%, and 50% in Mexican children and adolescents. Worldwide, it is the...
The prevalence of dental caries in the Mexican adult population aged 20 to 85 years is around 93.3%, and 50% in Mexican children and adolescents. Worldwide, it is the most common non-communicable disease. One of the main etiological factors for dental caries is the oral microbiome and changes in its structure and function, with an expansion of pathogenic bacteria like . The exposed dental pulp tissue triggers an innate immune response to counteract this bacterial invasion. The relation between oral dysbiosis and innate immune responses remains unclear. We aimed to understand the relationship between innate immune response and the oral microbiota by quantifying the expression of Toll-like receptors (TLRs) and proinflammatory markers (cytokines and a chemokine) in dental pulp tissue, either exposed or not to carious dentin, and to correlate this information with the oral microbiome found in healthy teeth and those with moderate caries. RNA was purified from pulp tissue, subjected to RT-qPCR and analysed with the method. Supragingival dental plaque of non-carious teeth and dentin of carious teeth were subjected to 16S targeted sequencing. Principal coordinate analysis, permutational multivariate ANOVA, and linear discriminant analysis were used to assess differences between non-carious and carious teeth. Correlations were assessed with Spearman´s test and corrected for multiple comparisons using the FDR method. The relative abundance (RA) of , and was increased in carious teeth; while the RA of and decreased. and were only detected in carious teeth. Significant overexpression of interleukin 1 beta (IL1 β), IL6, and CXCL8 was detected in pulp tissue exposed to carious dentin. IL1β correlated positively with TLR2 and ; yet negatively with These findings suggest that immune response of pulp tissue chronically exposed to cariogenic microbiome is triggered by proinflammatory cytokines IL1β and IL6 and the chemokine CXCL8.
Topics: Adolescent; Adult; Child; Humans; Actinobacteria; Actinomyces; Cytokines; Dental Caries; Dental Pulp; Dentin; Interleukin-6; Microbiota; Streptococcus mutans
PubMed: 36569197
DOI: 10.3389/fcimb.2022.958722 -
MicrobiologyOpen Feb 2018An animal feeding trial was conducted on 18 seven-day-old Holstein dairy bull calves weighing 42 ± 3 kg each. Calves were randomly assigned into three groups...
An animal feeding trial was conducted on 18 seven-day-old Holstein dairy bull calves weighing 42 ± 3 kg each. Calves were randomly assigned into three groups (n = 6 each). The dietary treatments were as follows: (1) milk and starter for the control group (MS), (2) supplementation of oat hay from week 2 on the basis of milk and starter (MSO2), and (3) supplementation of oat hay from week 6 on the basis of milk and starter (MSO6). All animals were fed starter and oat hay ad libitum. The major phyla in the different groups of rumen fluid included Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, and Euryarchaeota. The major genera were identified, and major genera proportions in the three groups were as follows: Methanobrevibacter (Euryarchaeota), 2.1%, 1.7%, and 2.1%; Olsenella (Actinobacteria), 23.9%, 17.7%, and 12.8%; Prevotella (Bacteroidetes), 10.5%, 16.5%, and 19.2%; Dialister (Firmicutes), 3.3%, 4.1%, and 2.8%; Succiniclasticum (Firmicutes), 3.8%, 4.7%, and 9.2%; and Sharpea (Firmicutes), 0.4%, 2.5%, and 0.2%, respectively. There were no significant differences in the various phyla among the three groups (p > .05). The results showed that calves hay supplementation time did not affect the diversity of the rumen microbiota in the suckling calves. However, the hay supplementation altered the proportion of the various microbial populations, supplementation of oat hay from week 2 on the basis of milk and starter could improve calves rumen pH.
Topics: Animal Feed; Animals; Animals, Newborn; Archaea; Bacteria; Cattle; Diet; Microbiota; Rumen
PubMed: 29280327
DOI: 10.1002/mbo3.430 -
Nutrients May 2024Recurrent oral ulcer (ROU) is a prevalent and painful oral disorder with implications beyond physical symptoms, impacting quality of life and necessitating comprehensive...
Recurrent oral ulcer (ROU) is a prevalent and painful oral disorder with implications beyond physical symptoms, impacting quality of life and necessitating comprehensive management. Understanding the interplays between dietary factors, oral microbiota, and ROU is crucial for developing targeted interventions to improve oral and systemic health. Dietary behaviors and plant-based diet indices including the healthful plant-based diet index (hPDI) were measured based on a validated food frequency questionnaire. Saliva microbial features were profiled using 16S rRNA gene amplicon sequencing. In this cross-sectional study of 579 community-based participants (aged 22-74 years, 66.5% females), 337 participants had ROU. Participants in the highest tertile of hPDI exhibited a 43% lower prevalence of ROU (odds ratio [OR] = 0.57, 95%CI: 0.34-0.94), compared to the lowest tertile, independent of demographics, lifestyle, and major chronic diseases. Participants with ROU tended to have lower oral bacterial richness (Observed ASVs, < 0.05) and distinct bacterial structure compared to those without ROU (PERMANOVA, = 0.02). The relative abundances of 16 bacterial genera were associated with ROU (-FDR < 0.20). Of these, , , and unclassified Muribaculaceae were identified as potential mediators in the association between hPDI and ROU (all -mediations < 0.05). This study provides evidence of the intricate interplays among dietary factors, oral microbiota, and ROU, offering insights that may inform preventive and therapeutic strategies targeting diets and oral microbiomes.
Topics: Humans; Female; Middle Aged; Male; Adult; Aged; Oral Ulcer; Microbiota; Cross-Sectional Studies; Saliva; Mouth; Young Adult; RNA, Ribosomal, 16S; Recurrence; Diet; Diet, Vegetarian; Bacteria; Diet, Healthy
PubMed: 38794756
DOI: 10.3390/nu16101519 -
BMC Women's Health Feb 2024An increasing body of observational studies have indicated an association between gut microbiota and endometriosis. However, the causal relationship between them is not...
BACKGROUND
An increasing body of observational studies have indicated an association between gut microbiota and endometriosis. However, the causal relationship between them is not yet clear. In this study, we employed Mendelian randomization method to investigate the causal relationship between 211 gut microbiota taxa and endometriosis.
METHODS
Independent genetic loci significantly associated with the relative abundance of 211 gut microbiota taxa, based on predefined thresholds, were extracted as instrumental variables. The primary analytical approach employed was the IVW method. Effect estimates were assessed primarily using the odds ratio and 95% confidence intervals. Supplementary analyses were conducted using MR-Egger regression, the weighted median method, the simple mode and the weighted mode method to complement the IVW results. In addition, we conducted tests for heterogeneity, horizontal pleiotropy, sensitivity analysis, and MR Steiger to assess the robustness of the results and the strength of the causal relationships.
RESULTS
Based on the IVW method, we found that the family Prevotellaceae, genus Anaerotruncus, genus Olsenella, genus Oscillospira, and order Bacillales were identified as risk factors for endometriosis, while class Melainabacteria and genus Eubacterium ruminantium group were protective factors. Additionally, no causal relationship was observed between endometriosis and gut microbiota. Heterogeneity tests, pleiotropy tests, and leave-one-out sensitivity analyses did not detect any significant heterogeneity or pleiotropic effects.
CONCLUSIONS
Our MR study has provided evidence supporting a potential causal relationship between gut microbiota and endometriosis, and it suggests the absence of bidirectional causal effects. These findings could potentially offer new insights for the development of novel strategies for the prevention and treatment of endometriosis.
Topics: Female; Humans; Endometriosis; Mendelian Randomization Analysis; Gastrointestinal Microbiome; Risk Factors; Odds Ratio
PubMed: 38365715
DOI: 10.1186/s12905-024-02945-z -
Frontiers in Neurology 2023It has emerged that disturbances of the gut microbiota (GM) are linked to insomnia. However, the causality of the observed associations remains uncertain.
BACKGROUND
It has emerged that disturbances of the gut microbiota (GM) are linked to insomnia. However, the causality of the observed associations remains uncertain.
METHODS
We conducted a two-sample Mendelian randomization analysis based on genome-wide association study data to explore the possible causal link between GM and insomnia. The GM data were from the MiBioGen consortium, while the summary statistics of insomnia were obtained from the FinnGen consortium R9 release data. Cochran's Q statistics were used to analyze instrumental variable heterogeneity.
RESULTS
According to the inverse variance weighted estimates, the family Ruminococcaceae (odds ratio = 1.494, 95% confidence interval:1.004-2.223, = 0.047) and the genus Lachnospiraceae (odds ratio = 1.726, 95% confidence interval: 1.191-2.501, = 0.004) play a role in insomnia risk. In contrast, the genus Flavonifractor (odds ratio = 0.596, 95% confidence interval: 0.374-0.952, = 0.030) and the genus Olsenella (odds ratio = 0.808, 95% confidence interval: 0.666-0.980, = 0.031) tended to protect against insomnia. According to the reverse MR analysis, insomnia can also alter GM composition. Instrumental variables were neither heterogeneous nor horizontal pleiotropic.
CONCLUSION
In conclusion, our Mendelian randomization study provides evidence of a causal relationship between GM and insomnia. The identified GM may be promising gut biomarkers and new therapeutic targets for insomnia. This investigation also provides a foundation for future studies examining the influence of GM on sleep disorders beyond insomnia, with potential implications for redefining the mechanisms governing sleep regulation.
PubMed: 38145126
DOI: 10.3389/fneur.2023.1277996 -
Antioxidants (Basel, Switzerland) Sep 2022This study aims to explore the effects of modified montmorillonite (MMT, copper loading) on the growth performance, gut microbiota, intestinal barrier, antioxidative...
Modified Montmorillonite Improved Growth Performance of Broilers by Modulating Intestinal Microbiota and Enhancing Intestinal Barriers, Anti-Inflammatory Response, and Antioxidative Capacity.
This study aims to explore the effects of modified montmorillonite (MMT, copper loading) on the growth performance, gut microbiota, intestinal barrier, antioxidative capacity and immune function of broilers. Yellow-feathered broilers were randomly divided into control (CTR), modified montmorillonite (MMT), and antibiotic (ANTI) groups. Results revealed that MMT supplementation increased the BW and ADG and decreased the F/R during the 63-day experiment period. 16S rRNA sequencing showed that MMT modulated the cecal microbiota composition of broilers by increasing the relative abundance of two phyla (Firmicutes and Bacteroidetes) and two genera ( and ) and decreasing the abundance of genus . MMT also improved the intestinal epithelial barrier indicated by the up-regulated mRNA expression of , , and and the increased length of microvilli in jejunum and the decreased levels of DAO and D-LA in serum. In addition, MMT enhanced the immune function indicated by the increased levels of immunoglobulins, the decreased levels of MPO and NO, the down-regulated mRNA expression of , , and , and the up-regulated mRNA expression of and . Moreover, MMT down-regulated the expression of jejunal TLRs/MAPK/NF-κB signaling pathway-related genes (, , , , , and ) and related proteins (TRAF6, p38, ERK, NF-κB, and iNOS). In addition, MMT increased the antioxidant enzyme activities and the expression of Nrf2/HO-1 signaling pathway-related genes and thereby decreased the apoptosis-related genes expression. Spearman's correlation analysis revealed that , , and were related to the inflammatory index (MPO and NO), oxidative stress (T-AOC, T-SOD, and CAT) and intestinal integrity (D-LA and DAO). Taken together, MMT supplementation improved the growth performance of broilers by modulating intestinal microbiota, enhancing the intestinal barrier function, and improving inflammatory response, which might be mediated by inhibiting the TLRs/MAPK/NF-κB signaling pathway, and antioxidative capacity mediated by the Nrf2/HO-1 signaling pathway.
PubMed: 36139873
DOI: 10.3390/antiox11091799 -
Frontiers in Microbiology 2022With the advent of high throughput technology, it is now feasible to study the complex relationship of the rumen microbiota with methanogenesis in large populations of...
With the advent of high throughput technology, it is now feasible to study the complex relationship of the rumen microbiota with methanogenesis in large populations of ruminant livestock divergently ranked for enteric emissions. Recently, the residual methane emissions (RME) concept has been identified as the optimal phenotype for assessing the methanogenic potential of ruminant livestock due to the trait's independence from animal productivity but strong correlation with daily methane emissions. However, there is currently a dearth of data available on the bacterial and archaeal microbial communities residing in the rumens of animals divergently ranked for RME. Therefore, the objective of this study was to investigate the relationship between the rumen microbiota and RME in a population of finishing beef cattle. Methane emissions were estimated from individual animals using the GreenFeed Emissions Monitoring system for 21 days over a mean feed intake measurement period of 91 days. Residual methane emissions were calculated for 282 crossbred finishing beef cattle, following which a ∼30% difference in all expressions of methane emissions was observed between high and low RME ranked animals. Rumen fluid samples were successfully obtained from 268 animals during the final week of the methane measurement period using a trans-oesophageal sampling device. Rumen microbial DNA was extracted and subjected to 16S rRNA amplicon sequencing. Animals ranked as low RME had the highest relative abundances ( < 0.05) of lactic-acid-producing bacteria (, , and ) and , and the lowest ( < 0.05) proportions of , , and . Within the rumen methanogen community, an increased abundance ( < 0.05) of the genus and RO clade was observed in low RME animals. The relative abundances of both and were negatively correlated ( < 0.05) with RME and positively correlated with ruminal propionate. A similar relationship was observed for the abundance of and the RO clade. Findings from this study highlight the ruminal abundance of bacterial genera associated with the synthesis of propionate the acrylate pathway, as well as the methanogens and members of the RO clade as potential microbial biomarkers of the methanogenic potential of beef cattle.
PubMed: 35572638
DOI: 10.3389/fmicb.2022.855565