-
Translational Animal Science 2023Our objective was to evaluate the effects of combinations of and as direct-fed microbials (DFM) on ruminal microbiome during an acute acidosis challenge in a...
Our objective was to evaluate the effects of combinations of and as direct-fed microbials (DFM) on ruminal microbiome during an acute acidosis challenge in a continuous culture system. Treatments provided a DFM dose of 1 × 10 colony-forming unit (CFU)/mL, as follows: control (no DFM), YM1 ( and strain 1), YM2 ( and strain 2), and YMM ( and half of the doses of strains 1 and 2). We conducted four experimental periods of 11 d, which consisted of non-acidotic days (1 to 8) and acidotic challenge days (9 to 11) to establish acute ruminal acidosis conditions with a common basal diet containing 12% neutral detergent fiber and 58% starch. Treatments were applied from days 8 to 11, and samples of liquid and solid-associated bacteria were collected on days 9 to 11. Overall, 128 samples were analyzed by amplification of the V4 region of bacterial 16S rRNA, and data were analyzed with R and SAS for alpha and beta diversity, taxa relative abundance, and correlation of taxa abundance with propionate molar proportion. We observed a lower bacterial diversity (Shannon index, = 0.02) when YM1 was added to the diet in comparison to the three other treatments. Moreover, compared to control, addition of YM1 to the diet increased relative abundance of phylum ( = 0.05) and family ( = 0.05) in the solid fraction and tended to increase abundance of family ( = 0.10) and genus ( = 0.09) in the liquid fraction. Correlation analysis indicated a positive association between propionate molar proportion and relative abundance of ( = 0.36, = 0.04) and ( = 0.36, = 0.05) in the solid fraction. The inclusion of YM1 in high-grain diets with a high starch content resulted in greater abundance of bacteria involved in succinate synthesis which may have provided the substrate for the greater propionate synthesis observed.
PubMed: 38023425
DOI: 10.1093/tas/txad123 -
EBioMedicine May 2021The relationship between tuberculosis (TB), one of the leading infectious causes of death worldwide, and the microbiome, which is critical for health, is poorly...
BACKGROUND
The relationship between tuberculosis (TB), one of the leading infectious causes of death worldwide, and the microbiome, which is critical for health, is poorly understood.
METHODS
To identify potential microbiome-host interactions, profiling of the oral, sputum and stool microbiota [n = 58 cases, n = 47 culture-negative symptomatic controls (SCs)] and whole blood transcriptome were done in pre-treatment presumptive pulmonary TB patients. This was a cross-sectional study. Microbiota were also characterised in close contacts of cases (CCCs, n = 73) and close contacts of SCs (CCSCs, n = 82) without active TB.
FINDINGS
Cases and SCs each had similar α- and β-diversities in oral washes and sputum, however, β-diversity differed in stool (PERMANOVA p = 0•035). Cases were enriched with anaerobes in oral washes, sputum (Paludibacter, Lautropia in both) and stool (Erysipelotrichaceae, Blautia, Anaerostipes) and their stools enriched in microbial genes annotated as amino acid and carbohydrate metabolic pathways. In pairwise comparisons with their CCCs, cases had Megasphaera-enriched oral and sputum microbiota and Bifidobacterium-, Roseburia-, and Dorea-depleted stools. Compared to their CCSCs, SCs had reduced α-diversities and many differential taxa per specimen type. Cases differed transcriptionally from SCs in peripheral blood (PERMANOVA p = 0•001). A co-occurrence network analysis showed stool taxa, Erysipelotrichaceae and Blautia, to negatively co-correlate with enriched "death receptor" and "EIF2 signalling" pathways whereas Anaerostipes positively correlated with enriched "interferon signalling", "Nur77 signalling" and "inflammasome" pathways; all of which are host pathways associated with disease severity. In contrast, none of the taxa enriched in SCs correlated with host pathways.
INTERPRETATION
TB-specific microbial relationships were identified in oral washes, induced sputum, and stool from cases before the confounding effects of antibiotics. Specific anaerobes in cases' stool predict upregulation of pro-inflammatory immunological pathways, supporting the gut microbiota's role in TB.
FUNDING
European & Developing Countries Clinical Trials Partnership, South African-Medical Research Council, National Institute of Allergy and Infectious Diseases.
Topics: Adult; Bacteria, Anaerobic; Female; Gastrointestinal Microbiome; Humans; Inflammasomes; Interferons; Male; Signal Transduction; Transcriptome; Tuberculosis, Pulmonary; Up-Regulation
PubMed: 33975252
DOI: 10.1016/j.ebiom.2021.103374 -
Tropical Animal Health and Production Mar 2023This study aimed to investigate the effect of rumen pH-adjusting additives in the high-concentrated diet on functional traits, nutrient digestion, some meat parameters,...
Comparison of the effect of Saccharomyces cerevisiae-Megasphaera elsdenii and buffer on growth performance, digestibility, ruminal histomorphometry, and carcass characteristics of fattening lambs in high concentrate diet.
This study aimed to investigate the effect of rumen pH-adjusting additives in the high-concentrated diet on functional traits, nutrient digestion, some meat parameters, and histomorphometry, and rumen histopathology. Twenty-four Arabia male lambs with 3 to 4 months old and initial body weight of 23.9 ± 3.15 kg were used in a completely randomized design with three treatments and eight replicates. The study was 77 days, including 14 days of the adaptation period and 63 days of the record taking and sampling period. The experimental treatments consisted of a control diet, control diet + sodium bicarbonate buffer, control diet + Megasphaera elsdenii, and Saccharomyces cerevisiae (bacterial-yeast). Rumen fluid was taken by stomach tube at 3 h after morning feeding to measure pH. The lambs were weighed every 3 weeks during the period, and the body weight changes, average daily gain, and total weight gain were measured, and the feed conversion ratio was calculated. At the end of the experiment, the lambs were slaughtered, and the longissimus dorsi muscle was prepared to determine the meat parameters. For histological studies, the abdominal rumen sac was sampled. There were no differences among treatments in dry matter intake (DMI), daily weight gain (ADG), and feed conversion ratio (P > 0.05). Propionate concentration was higher in the bacteria-yeast treatment than other treatments (P < 0.05). Protein digestibility was higher in control and bacteria-yeast treatments than buffer treatment (P < 0.05). The percentage of meat protein, carcass weight, and dressing percentage in bacterial-yeast treatment was higher than other treatments (P < 0.05). Rumen wall thickness in the buffer and bacterial-yeast receiving treatments was greater than the control treatment and was significant in the buffer treatment compared to the control treatment (P < 0.05). The thickness of rumen epithelial tissue in the buffer and bacterial-yeast recipient treatments was less than the control treatment (P < 0.05). Rumen papillae thickness was higher in the control treatment than other treatments (P < 0.05). Hydropic degeneration and parakeratosis were less in pH-regulating treatments than in control. The results showed that the use of Megasphaera elsdenii could be an effective way to modulate the ruminal fermentation conditions of lambs fed with high concentrate diets. In addition, to increaseing dressing percentage and meat protein, it can also reduce tissue damage and improve ruminal tissue structure.
Topics: Sheep; Animals; Male; Saccharomyces cerevisiae; Megasphaera elsdenii; Rumen; Diet; Sheep, Domestic; Fermentation; Meat Proteins; Body Weight; Animal Feed; Digestion
PubMed: 36977895
DOI: 10.1007/s11250-023-03532-4 -
Translational Animal Science Apr 2020Simmental-Angus calves [ = 135; 72 steers and 63 heifers; body weight (BW) = 212.4 kg ± 36.1] were early weaned (~5 mo) to evaluate multiple feeding regimens...
Simmental-Angus calves [ = 135; 72 steers and 63 heifers; body weight (BW) = 212.4 kg ± 36.1] were early weaned (~5 mo) to evaluate multiple feeding regimens (conventional vs. aggressive energy diets ± NCIMB 41125 ( culture (MEC); Lactipro Advance; MS Biotec Inc., Wamego, KS) in order to elucidate the optimal development strategy. Objectives were measured by tracking the effects of caloric density and oral drenching of growing phase performance and subsequent carcass traits. The 72-d experiment featured three groups: 1) control (CON), fed exclusively a 35% roughage diet; 2) aggressive (AGR), fed a blend of a 10% and 35% roughage diets; 3) MEC, fed the same diet as AGR and drenched with 50 mL of NCIMB 41125 on day 1. A subset of calves ( = 45) was equipped with wireless rumination tags (Allflex Flex Tag; SCR Engineers, Ltd; Netanya, Israel), which logged daily rumination and general activity. Skeletal growth variables were assessed by measuring wither and hip height pretrial and posttrial. Ultrasonography provided additional resolution concerning growing phase compositional gain, which was later verified by carcass data collection. Data were analyzed as a nested analysis of variance with BW and gender serving as blocking factors. The increased caloric density of the diets administered to MEC and AGR calves resulted in greater average daily gain and gain:feed values compared with CON even during the first 21 d of diet acclimation ( ≤ 0.05). Additional fiber concentration of CON diets led to increased rumination times in 9 of the 10 wk of trial ( ≤ 0.10). No differences amongst treatments were detected for skeletal variables or ultrasound 12th rib fat. Cattle fed CON diets posted 3.4% inferior BW at the end of the growing period trial and a 3.8% reduction in hot carcass weight (HCW), reinforcing the theory that intensifying caloric intake during the growing phase does not compromise future feedlot performance. Ultrasound marbling scores for MEC-treated cattle were 19° greater than AGR treated cattle ( ≤ 0.05) at the end of the growing phase trial. Nearly the exact same advantage (22°) was observed in the cooler 5 mo later ( = 0.42). Implying MEC metabolically imprinted cattle to favor marbling development. It appears that maximizing dietary caloric density in light-weight calves does not adversely affect the growth curve, while oral dosing of MEC during the growing period may be a precursor for enhanced quality grade.
PubMed: 32705029
DOI: 10.1093/tas/txaa031 -
Journal of Investigative Medicine : the... Mar 2022Recurrent aphthous stomatitis (RAS) is a common recurrent ulcerative disease of the oral mucosa which is closely related to oral microbial composition. However, the...
Recurrent aphthous stomatitis (RAS) is a common recurrent ulcerative disease of the oral mucosa which is closely related to oral microbial composition. However, the specific effect and the mechanism of smoking in RAS are unclear. In this study, 16S rRNA sequencing technology was used to compare the differences in saliva microbial community between 28 non-smoking healthy controls (NSctrl), 31 non-smoking RAS patients (NSras), and 19 smoking RAS patients (Sras). The results showed that the bacterial community diversity in patients with RAS (NSras and Sras) was lower than that of NSctrl. The microbial community in smoking-associated RAS is less diverse and distinct from that of non-smokers. The RAS groups have higher abundance of , , and and lower abundance of , , , , , and at the genera level. A significantly different abundance of , , , , , and was observed between the Sras and the NSras group. Notably, there was a significant difference in many species from the genus and between the NSras and the Sras group. Further, the relative abundance of several taxa is correlated with smoking age or frequency, including , , , and at the genera level, and , , , , , , , and at the species level. Among patients with RAS, smoking aggravated the pathways of respiration and human pathogens. Our results suggest that smoking is closely related to changes in the oral microbiota, which may contribute an opposite effect to the pathogenesis of RAS. This study provides new insight and theoretical basis for the cause and pathogenesis of RAS and better prevention and treatment.
Topics: Bacteria; Cigarette Smoking; Humans; Microbiota; RNA, Ribosomal, 16S; Stomatitis, Aphthous
PubMed: 34824153
DOI: 10.1136/jim-2021-002119 -
Frontiers in Cellular and Infection... 2021The incidence of preterm birth (PTB) in India is around 13%. Specific bacterial communities or individual taxon living in the vaginal milieu of pregnant women is a...
BACKGROUND
The incidence of preterm birth (PTB) in India is around 13%. Specific bacterial communities or individual taxon living in the vaginal milieu of pregnant women is a potential risk factor for PTB and may play an important role in its pathophysiology. Besides, bacterial taxa associated with PTB vary across populations.
OBJECTIVE
Conduct a comparative analysis of vaginal microbiome composition and microbial genomic repertoires of women who enrolled in the Interdisciplinary Group for Advanced Research on Birth Outcomes - A DBT India Initiative (GARBH-Ini) pregnancy cohort to identify bacterial taxa associated with term birth (TB) and PTB in Indian women.
METHODS
Vaginal swabs were collected during all three trimesters from 38 pregnant Indian women who delivered spontaneous term (n=20) and preterm (n=18) neonates. Paired-end sequencing of V3-V4 region of 16S rRNA gene was performed using the metagenomic DNA isolated from vaginal swabs (n=115). Whole genome sequencing of bacterial species associated with birth outcomes was carried out by shotgun method. species were grown anaerobically in the De Man, Rogosa and Sharpe (MRS) agar culture medium for isolation of genomic DNA and whole genome sequencing.
RESULTS
Vaginal microbiome of both term and preterm samples reveals similar alpha diversity indices. However, significantly higher abundance of (p-value <0.02), sp (p-value0.05), (p-value= 0.01) and (p-value0.0001) were identified in preterm samples whereas higher abundance of (p-value =0.010) was observed in term samples by Wilcoxon rank-sum test. The relative abundance of , and sp. were found to be significantly different over time between term and preterm mothers. Analyses of the representative genomes of and indicate presence of secretory transcriptional regulator and several ribosomally synthesized antimicrobial peptides correlated with anti-inflammatory condition in the vagina. These findings indicate protective role of and in reducing the risk of PTB.
CONCLUSION
Our findings indicate that the dominance of specific species and few other facultative anaerobes are associated with birth outcomes.
Topics: Female; Fusobacteria; Humans; India; Infant, Newborn; Lactobacillus; Pregnancy; Premature Birth; RNA, Ribosomal, 16S; Vagina
PubMed: 34094994
DOI: 10.3389/fcimb.2021.622474 -
Clinical and Experimental Dental... Feb 2022It has been suggested that smoking affects the oral microbiome, but its effects on sites other than the subgingival microbiome remain unclear. This study investigated...
OBJECTIVES
It has been suggested that smoking affects the oral microbiome, but its effects on sites other than the subgingival microbiome remain unclear. This study investigated the composition of the salivary and tongue bacterial communities of smokers and nonsmokers in periodontally healthy adults.
METHODS
The study population included 50 healthy adults. The bacterial composition of resting saliva and the tongue coating was identified through barcoded pyrosequencing analysis of the 16S rRNA gene. The Brinkman index (BI) was used to calculate lifetime exposure to smoking. The richness and diversity of the microbiome were evaluated using the t-test. Differences in the proportions of bacterial genera between smokers and nonsmokers were evaluated using the Mann-Whitney U test. The quantitative relationship between the proportions of genera and the BI was evaluated using Pearson's correlation analysis.
RESULTS
The richness and diversity of the oral microbiome differed significantly between saliva and the tongue but not between smokers and nonsmokers. The saliva samples from smokers were enriched with the genera Treponema and Selenomonas. The tongue samples from smokers were enriched with the genera Dialister and Atopobium. The genus Cardiobacterium in saliva, and the genus Granulicatella on the tongue, were negatively correlated with BI values. On the other hand, the genera Treponema, Oribacterium, Dialister, Filifactor, Veillonella, and Selenomonas in saliva and Dialister, Bifidobacterium, Megasphaera, Mitsuokella, and Cryptobacterium on the tongue were positively correlated with BI values.
CONCLUSIONS
The saliva and tongue microbial profiles of smokers and nonsmokers differed in periodontally healthy adults. The genera associated with periodontitis and oral malodor accounted for high proportions in saliva and on the tongue of smokers without periodontitis and were positively correlated with lifetime exposure to smoking. The tongue might be a reservoir of pathogens associated with oral disease in smokers.
Topics: Adult; Bacteria; Cigarette Smoking; Humans; Microbiota; Periodontitis; RNA, Ribosomal, 16S; Tongue
PubMed: 34505401
DOI: 10.1002/cre2.489 -
Microbial Pathogenesis Oct 2023The etiology remains to be understood for endometriosis (EMS) which affected health negatively for 10% of reproductive-age women globally. Emerging studies found the...
The etiology remains to be understood for endometriosis (EMS) which affected health negatively for 10% of reproductive-age women globally. Emerging studies found the associations of EMS with genital microbiota dysbiosis. However, the role of vaginal and cervical microbiota is not fully understood for Chinese women. This study recruited forty Chinese women (21 healthy women and 19 EMS patients) to analyze vaginal and cervical microbiota using 16S rRNA amplicon sequencing method. For both sites, there were no significant differences for distribution of microbial samples between control and EMS group, which was concordant with dominated Lactobacillus in both groups. In contrast, we observed accumulation of several low-abundance genera in vaginal and cervical microbiota of EMS patients, such as Fannyhessea, Prevotella, Streptococcus, Bifidobacterium, Veillonella, Megasphaera and Sneathia. Random forest analysis found that translocation of these genera had the significant importance in differentiating EMS patients from controls. In addition, cervix/vagina ratio of these genera also associated with EMS severity. And these genera had notable associations with ascending infection-related functional pathways, including flagellar assembly, bacterial motility proteins, bacterial toxins and epithelial cell signaling in Helicobacter pylori infection. These findings suggest that translocation of specific genera between vaginal and cervical sites play a role in EMS.
Topics: Humans; Female; Cervix Uteri; Pilot Projects; Endometriosis; Lactobacillus; RNA, Ribosomal, 16S; Helicobacter Infections; Helicobacter pylori; Vagina; Bacterial Proteins
PubMed: 37586463
DOI: 10.1016/j.micpath.2023.106309 -
Bioengineering (Basel, Switzerland) Aug 2022Recent studies have revealed that LuxS/AI-2 quorum sensing (QS) is the most universal cell-to-cell communication in rumen bacteria; however, it remains unknown how they...
Recent studies have revealed that LuxS/AI-2 quorum sensing (QS) is the most universal cell-to-cell communication in rumen bacteria; however, it remains unknown how they respond to nutritional stress from a diet shift. This study aimed to explore whether a diet shift could trigger rumen bacterial LuxS/AI-2 QS and its influences on rumen fermentation characteristics and bacterial community diversity and composition. A total of fifteen Hu sheep were selected to undergo a pre-shift diet (Pre, concentrate to forage ratio 75:25) for one month and then abruptly switch to a post-shift diet (Post, concentrate to forage ratio 49:51). Results showed that the serum cortisol and immunoglobulin G concentrations were higher in Post than in Pre (p < 0.05). The microbial density, AI-2 concentration, biofilm formation, and the gene expression of ftsH were higher in Post when compared with Pre (p < 0.05), whilst the gene expression of luxS tended to be lower in Post (p = 0.054). The molar concentration of valerate and fermentation efficiency decreased after the diet shift, while the acetate to propionate ratio and the molar proportion of butyrate were higher in Post compared to Pre (p < 0.05). Moreover, the diet shift increased the richness of ruminal bacteria and the relative abundances of Roseburia, Prevotellaceae UCG-001, and Lachnospira, and decreased the relative abundances of Prevotella, Megasphaera, and Dialister (p < 0.05). A difference in trends was also observed in an analysis of similarity (R = 0.1208 and p = 0.064). This study suggests that a diet shift could trigger rumen bacterial LuxS/AI-2 QS by altering microbial density, AI-2 concentration, biofilm formation, and related gene expression, as well as affect the rumen fermentation pattern and bacterial community diversity and composition. This study may provide insight into a potential strategy for relieving nutritional stress via regulating bacterial communication.
PubMed: 36004904
DOI: 10.3390/bioengineering9080379 -
Gut-microbiome-based predictive model for ST-elevation myocardial infarction in young male patients.Frontiers in Microbiology 2022ST-segment elevation myocardial infarction (STEMI) in young male patients accounts for a significant proportion of total heart attack events. Therefore, clinical...
BACKGROUND
ST-segment elevation myocardial infarction (STEMI) in young male patients accounts for a significant proportion of total heart attack events. Therefore, clinical awareness and screening for acute myocardial infarction (AMI) in asymptomatic patients at a young age is required. The gut microbiome is potentially involved in the pathogenesis of STEMI. The aim of the current study is to develop an early risk prediction model based on the gut microbiome and clinical parameters for this population.
METHODS
A total of 81 young males (age < 44 years) were enrolled in this study. Forty-one young males with STEMI were included in the case group, and the control group included 40 young non-coronary artery disease (CAD) males. To identify the differences in gut microbiome markers between these two groups, 16S rRNA-based gut microbiome sequencing was performed using the Illumina MiSeq platform. Further, a nomogram and corresponding web page were constructed. The diagnostic efficacy and practicability of the model were analyzed using K-fold cross-validation, calibration curves, and decision curve analysis (DCA).
RESULTS
Compared to the control group, a significant decrease in tendency regarding α and β diversity was observed in patients in the case group and identified as a significantly altered gut microbiome represented by and . Regarding clinical parameters, compared to the control group, the patients in the case group had a higher body mass index (BMI), systolic blood pressure (SBP), triglyceride (TG), alanine aminotransferase (ALT), and aspartate aminotransferase (AST) and low blood urea nitrogen (BUN). Additionally, BMI and SBP were significantly (p<0.05) positively correlated with and . Further, BMI and SBP were significantly (p<0.05) negatively correlated with and . A significant negative correlation was only observed between and AST ( < 0.05). Finally, an early predictive nomogram and corresponding web page were constructed based on the gut microbiome and clinical parameters with an area under the receiver-operating characteristic (ROC) curve (AUC) of 0.877 and a C-index of 0.911. For the internal validation, the stratified -fold cross-validation ( = 3) was as follows: AUC value of 0.934. The calibration curves of the model showed good consistency between the actual and predicted probabilities. The DCA results showed that the model had a high net clinical benefit for use in the clinical setting.
CONCLUSION
In this study, we combined the gut microbiome and common clinical parameters to construct a prediction model. Our analysis shows that the constructed model is a non-invasive tool with potential clinical application in predicting STEMI in the young males.
PubMed: 36532426
DOI: 10.3389/fmicb.2022.1031878