scholarly journals PSXII-24 Effects of supplementing ruminally protected and non-protected active dried yeast on fecal bacterial community of finishing beef steers

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 425-426
Author(s):  
Tao Ran ◽  
Peixin Jiao ◽  
Ousama AlZahal ◽  
Xiaolai Xie ◽  
Karen A Beauchemin ◽  
...  

Abstract The objective of this study was to evaluate the effects of supplementing ruminally protected and non-protected active dried yeast (ADY; AB Vista, UK) on fecal bacterial diversity of finishing beef steers. Seventy-five Angus steers (initial BW 448 kg) were randomly assigned to one of five treatments: control, antibiotics (ANT, 330 mg monensin + 110 mg tylosin/d), ADY (1.5 g/d), encapsulated ADY (EDY; 3 g/d), and mixture of ADY and EDY (MDY). The ADY (1.7×1010 cfu/g) was encapsulated with equal amount of ADY and capsule material. Steers were fed a diet containing 10% barley silage and 90% barley concentrate (DM basis), ANT, ADY, EDY and MDY were top-dressed at feeding. Fecal samples were rectally collected from 10 steers of each treatment on d 56 to determine fecal bacterial diversity using high throughput MiSeq sequencing. Alpha diversity indices were not different among treatments. Principal coordinate analysis revealed that samples were not clustered by treatments. Bacteroidetes and Firmicutes were dominant phyla in the fecal bacterial community for all treatments, with a tendency (P < 0.10) of ANT, EDY and MDY to have greater relative abundance of Bacteroidetes (averaged 51.3 vs 46.8%) but lesser Firmicutes (averaged 39.5 vs 47.9%) than control steers. About 50 to 61% of sequences remained unclassified and identified 32 genus, with Prevotella ranging from 15.8 to 25.5% as the dominant genus in all treatments. Notably, steers with ANT, EDY, MDY vs. control had greater (P < 0.05) relative abundance of Prevotella (averaged 23.5 vs 16.8%) but lesser (P < 0.03) Oscillospira (averaged 1.7 vs 2.8%). No differences between ADY and control were observed for aforementioned variables. The results indicate that supplementing ruminally protected or non-protected ADY have limited effect on diversity of fecal bacteria, whereas feeding protected ADY and ANT to finishing beef steers altered dominant fecal bacteria at phylum and genus level.

2020 ◽  
Vol 98 (4) ◽  
Author(s):  
Tao Ran ◽  
Peixin Jiao ◽  
Ousama AlZahal ◽  
Xiaolai Xie ◽  
Karen A Beauchemin ◽  
...  

Abstract Our previous study suggested that supplementation of high-grain diets with ruminally protected and non-protected active dried yeast (ADY) may potentially reduce manure pathogen excretion by feedlot cattle. We hypothesized that feeding ruminally protected ADY might change the fecal bacterial community of finishing cattle. The objective of this study was to investigate the effects of feeding ruminally protected and non-protected ADY to finishing beef steers on their fecal bacterial community. Fresh fecal samples were collected on day 56 from 50 steers fed one of five treatments: 1) control (no monensin, tylosin, or ADY), 2) antibiotics (ANT, 330 mg monensin + 110 mg tylosin·steer−1d−1), 3) ADY (1.5 g·steer−1d−1), 4) encapsulated ADY (EDY; 3 g·steer−1d−1), and 5) a mixture of ADY and EDY (MDY; 1.5 g ADY + 3 g EDY·steer−1d−1). Bacterial DNA was extracted from fecal samples and sequenced using a MiSeq high-throughput sequencing platform. A total number of 2,128,772 high-quality V4 16S rRNA sequences from 50 fecal samples were analyzed, and 1,424 operational taxonomic units (OTU) were detected based on 97% nucleotide sequence identity among reads, with 769 OTU shared across the five treatments. Alpha diversity indices, including species observed, Chao estimate, abundance-based coverage estimator, Shannon, Simpson, and coverage, did not differ among treatments, and principal coordinate analysis revealed a high similarity among treatments without independent distribution. Bacteroidetes and Firmicutes were dominant phyla in the fecal bacterial community for all treatments, with a tendency (P < 0.10) for greater relative abundance of Bacteroidetes but lesser Firmicutes with ANT, EDY, and MDY compared with control steers. Prevotella was the dominant genus in all treatments and steers supplemented with ANT, EDY, and MDY had greater (P < 0.05) relative abundance of Prevotella than control steers, but lesser (P < 0.03) relative abundance of Oscillospira. No differences between ADY and control were observed for the aforementioned variables. Fecal starch contents were not different among treatments, but the relative abundance of Bacteroidetes, as well as Prevotella at genera level, tended (P < 0.06) to be positively correlated to fecal starch content. We conclude that supplementing ruminally protected or non-protected ADY or ANT had no effect on diversity and richness of fecal bacteria of finishing beef cattle, whereas feeding protected ADY or ANT to finishing beef steers altered the dominant fecal bacteria at phylum and genus levels. Therefore, supplementation of ruminally protected ADY may potentially improve intestinal health by stimulating the relative abundance of Prevotella.


2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 430-430
Author(s):  
Ibukun M Ogunade ◽  
Devan M Compart ◽  
Andres A Pech-Cervantes

Abstract We examined the effects of dietary supplementation of a Saccharomyces cerevisiae-based direct-fed microbial on plasma carbonyl-metabolome and fecal bacterial community of beef steers during a 42-d receiving period. Forty newly-weaned beef steers were used in this study. The steers were stratified by BW and randomly assigned to receive a basal diet with no additive (CON; n = 20) or a basal diet supplemented with 19 g of CommenceTM (PROB; n = 20). CommenceTM (PMI, Arden Hills, MN) contains a blend of 6.2 × 1011 cfu/g of S. cerevisiae, 3.5 × 1010 cfu/g of a mixture of Enterococcus lactis, Bacillus subtilis, Enterococcus faecium, and L. casei. On d 0 and 40, rectal fecal samples were collected for bacterial community analysis via sequencing of the V3-V4 region of 16S rRNA gene. On d 42, blood was collected for analysis of carbonyl-containing metabolites in plasma using a chemical isotope labeling/liquid chromatography mass spectrometry-based untargeted metabolomics. The data were analyzed using the GLIMMIX procedure of SAS with treatment as a fixed effect) and (random effect). A total number of 812 unique plasma metabolites were detected. Up to 305 metabolites [fold change (FC) ≥ 1.5, FDR ≤ 0.01] including glucose, hippuric acid, glycoaldehyde, and 5-hydroxykynurenamine were increased by PROB supplementation, whereas 199 metabolites (FC ≤ 0.63, FDR ≤ 0.01) including acetoacetate were reduced. Correlation analysis showed that plasma concentrations of 5-oxopentanoate, 2-aceto-2-hydroxybutanoate, and 3-methyl-2-oxopentanoic acid were positively correlated (P ≤ 0.10) with average daily gain. Supplemental PROB increased (P ≤ 0.05) the relative abundance of Prevotellaceae, Megasphaera, Dorea, Acetitomaculum, and Blautia. In contrast, the relative abundance of Elusimicrobium, Moheibacter, and Stenotrophomonas were reduced (P ≤ 0.05). This study demonstrated that PROB altered the plasma carbonyl-metabolome and fecal bacterial community of the beef steers.


Author(s):  
Kreete Lüll ◽  
Riikka K Arffman ◽  
Alberto Sola-Leyva ◽  
Nerea M Molina ◽  
Oliver Aasmets ◽  
...  

Abstract Context Despite the gut microbiome being widely studied in metabolic diseases, its role in polycystic ovary syndrome (PCOS) has been scarcely investigated. Objective Compare the gut microbiome in late fertile age women with and without PCOS and investigate whether changes in the gut microbiome correlate with PCOS-related metabolic parameters. Design Prospective, case–control study using the Northern Finland Birth Cohort 1966. Setting General community. Participants A total of 102 PCOS women and 201 age- and body mass index (BMI)-matched non-PCOS control women. Clinical and biochemical characteristics of the participants were assessed at ages 31 and 46 and analyzed in the context of gut microbiome data at the age of 46. Intervention (s): None Main outcome measure(s) Bacterial diversity, relative abundance, and correlations with PCOS-related metabolic measures. Results Bacterial diversity indices did not differ significantly between PCOS and controls (Shannon diversity P = .979, unweighted UniFrac P = .175). Four genera whose balance helps to differentiate between PCOS and non-PCOS were identified. In the whole cohort, the abundance of 2 genera from Clostridiales, Ruminococcaceae UCG-002, and Clostridiales Family XIII AD3011 group, were correlated with several PCOS-related markers. Prediabetic PCOS women had significantly lower alpha diversity (Shannon diversity P = .018) and markedly increased abundance of genus Dorea (false discovery rate = 0.03) compared with women with normal glucose tolerance. Conclusion PCOS and non-PCOS women at late fertile age with similar BMI do not significantly differ in their gut microbial profiles. However, there are significant microbial changes in PCOS individuals depending on their metabolic health.


2020 ◽  
Vol 2020 ◽  
pp. 1-8 ◽  
Author(s):  
Cheng-Xing Long ◽  
Hao-Qing Shao ◽  
Cheng-Yu Luo ◽  
Rong Yu ◽  
Zhou-Jin Tan

The current research tried to explore the effect of Qiweibaizhu powder (QWBZP) on the bacterial diversity and community structure of the intestinal mucosa of dysbiosis diarrhea mice and provide a scientific basis for the efficacy of QWBZP on antibiotic-induced diarrhea. A dysbiosis diarrhea mouse model was constructed with broad-spectrum antibiotics through a mixture of cephradine capsules and gentamicin sulfate (23.33 mL·kg-1·d-1). Intestinal mucosa was collected, and DNA was extracted from each group. The bacterial characteristics in intestinal mucosa were analyzed by MiSeq sequencing based on the 16S rRNA sequencing platform. There were no significant differences in alpha diversity indices among the three groups. The sample distributions in both the normal and QWBZP groups were relatively concentrated, and the distance among individuals was close. However, an opposite result was obtained in the model group. Furthermore, the composition and abundance of species were similar between the normal group and the QWBZP group at both the phylum and genus levels. After treatment with QWBZP, the abundance of Lactobacillus increased, and Proteobacteria decreased, and the Firmicutes/Bacteroidetes ratio decreased to a normal level. Our results indicate that QWBZP can help repair mucosal bacterial structure and recover mucosal microbiota. Specifically, QWBZP increased the abundance of Lactobacillus and Bacteroidales S24-7 group norank.


2019 ◽  
Author(s):  
Jiaxin Wang ◽  
Xuening Lu ◽  
Jiaen Zhang ◽  
Guangchang Wei ◽  
Yue Xiong

AbstractGolden apple snails (GAS) have become a serious pest for agricultural production in Asia. A sustainable method for managing GAS is urgently needed, including potentially using them to produce commercial products. In this study, we evaluate the effects of GAS residues (shell and meat) on soil pH, bacterial diversity, enzyme activities, and other soil characteristics. Results showed that the amendment of GAS residues significantly elevated soil pH (to near-neutral), total organic carbon (TOC) (by 10-134%), NO3-N (by 46-912%), NH4-N (by 18-168%) and total nitrogen (TN) (by 12-132%). Bacterial diversity increased 13% at low levels of amendment and decreased 5% at high levels, because low-levels of GAS residues increased soil pH to near-neutral, while high-levels of amendment substantially increased soil nutrients and subsequently suppressed bacterial diversity. The dominant phyla of bacteria were: Proteobacteria (about 22%), Firmicutes (15-35%), Chloroflexi (12%-22%), Actinobacteria (8%-20%) Acidobacteria, Gemmatimonadetes, Cyanobacteria and Bacterioidetes. The amendment of GAS residues significantly increased the relative abundance of Firmicutes, Gemmatimonadetes, Bacterioidetes and Deinococcus-Thermus, but significantly decreased the relative abundance of Chloroflexi, Actinobacteria, Acidobacteria, Cyanobacteria and Planctomycetes. Our results suggest that GAS residues treatment induces a near-neutral and nutrient-rich soil. In this soil, soil pH may not be the best predictor of bacterial community composition or diversity; rather soil nutrients (ie., NH4-N and NO3-N) and soil TOC showed stronger correlations with bacterial community composition. Overall, GAS residues could replace lime for remediation of acidic and degraded soils, not only to remediate physical soil properties, but also microbial communities.ImportanceThe wide spreading golden apple snail (GAS) is a harmful pest to crop productions and could result in soil and air pollutions after death. In the previous study, we developed a biocontrol method: adding GAS residues to acidic soil to mitigate the living GAS invasion and spread, improve soil quality, and reduce soil and air pollution. However, the effects of GAS residues amendment on bacterial diversity and community still remain unclear. This study provided insights into bacterial diversity and community compositions to facilitate the evaluation of GAS residues application.


PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0244341
Author(s):  
Christine Niemeier-Walsh ◽  
Patrick H. Ryan ◽  
Jaroslaw Meller ◽  
Nicholas J. Ollberding ◽  
Atin Adhikari ◽  
...  

Background Exposure to particulate matter has been shown to increase the adhesion of bacteria to human airway epithelial cells. However, the impact of traffic-related air pollution (TRAP) on the respiratory microbiome is unknown. Methods Forty children were recruited through the Cincinnati Childhood Allergy and Air Pollution Study, a longitudinal cohort followed from birth through early adolescence. Saliva and induced sputum were collected at age 14 years. Exposure to TRAP was characterized from birth through the time of sample collection using a previously validated land-use regression model. Sequencing of the bacterial 16S and ITS fungal rRNA genes was performed on sputum and saliva samples. The relative abundance of bacterial taxa and diversity indices were compared in children with exposure to high and low TRAP. We also used multiple linear regression to assess the effect of TRAP exposure, gender, asthma status, and socioeconomic status on the alpha diversity of bacteria in sputum. Results We observed higher bacterial alpha diversity indices in sputum than in saliva. The diversity indices for bacteria were greater in the high TRAP exposure group than the low exposure group. These differences remained after adjusting for asthma status, gender, and mother’s education. No differences were observed in the fungal microbiome between TRAP exposure groups. Conclusion Our findings indicate that exposure to TRAP in early childhood and adolescence may be associated with greater bacterial diversity in the lower respiratory tract. Asthma status does not appear to confound the observed differences in diversity. These results demonstrate that there may be a TRAP-exposure related change in the lower respiratory microbiota that is independent of asthma status.


Archaea ◽  
2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
Shaoping Kuang ◽  
Yaqing Su ◽  
Huihui Wang ◽  
Wenjuan Yu ◽  
Qiaolin Lang ◽  
...  

Microorganisms are sensitive indicators of edaphic environmental variation. The Illumina MiSeq sequencing technology was used to analyze soil bacterial community diversity around an aging oil sludge in the Yellow River Delta. The alpha diversity index of soil bacterial community results (Ace, Chao, Shannon, and Simpson) determined that bacterial community diversity sampling within the scope of a 20 cm radius from the center of an aging oil sludge spot showed the most abundant diversity. The level of diversity distributed symmetrically with radial direction from the center of the aging oil sludge spot. Over the distance of 100 m from the center, bacterial community diversity tends to be monotonous, with small differences especially in the horizontal direction underground. The alpha-diversity indicators also showed that the bacterial diversity of samples were close under the aging oil sludge. In addition, the aging oil sludge inhibited the growth of bacteria compared with the referenced unpolluted soil sample and also increased the diversities of soil bacteria. At the phylum level, the Proteobacteria, Chloroflexi, and Actinobacteria existing in the aging oil sludge-contaminated wetland soil constituted a larger proportion of the community, while the proportion of Firmicute was relatively less. On the contrary, Firmicute showed the highest content of 63.8% in the referenced soil. Under the genus level and family level, the corresponding strains that resisted the aging oil sludge were selected. According to the bacterial diversity analysis, the basic structure of the bacterial community which could be used for remediation of aging oil sludge-contaminated soil was also developed.


2021 ◽  
Vol 8 ◽  
Author(s):  
Hee-Young Yoon ◽  
Su-Jin Moon ◽  
Jin Woo Song

Background: Several studies using bronchoalveolar lavage fluid (BALF) reported that lung microbial communities were associated with the development and clinical outcome of idiopathic pulmonary fibrosis (IPF). However, the microbial communities in IPF lung tissues are not well known. This study is aimed to investigate bacterial microbial communities in lung tissues and determine their impact on the clinical outcomes of patients with IPF.Methods: Genomic DNA extracted from lung tissues of patients with IPF (n = 20; 10 non-survivors) and age- and sex-matched controls (n = 20) was amplified using fusion primers targeting the V3 and V4 regions of the 16S RNA genes with indexing barcodes.Results: Mean age of IPF subjects was 63.3 yr, and 65% were male. Alpha diversity indices did not significantly differ between IPF patients and controls, or between IPF non-survivors and survivors. The relative abundance of Lactobacillus, Paracoccus, and Akkermansia was increased, whereas that of Caulobacter, Azonexus, and Undibacterium decreased in patients with IPF compared with that in the controls. A decreased relative abundance of Pelomonas (odds ratio [OR], 0.352, p = 0.027) and Azonexus (OR, 0.013, p = 0.046) was associated with a diagnosis of IPF in the multivariable logistic analysis adjusted by age and gender. Multivariable Cox analysis adjusted for age and forced vital capacity (FVC) revealed that higher relative abundance of Streptococcus (hazard ratio [HR], 1.993, p = 0.044), Sphingomonas (HR, 57.590, p = 0.024), and Clostridium (HR, 37.189, p = 0.038) was independently associated with IPF mortality. The relative abundance of Curvibacter (r = 0.590) and Thioprofundum (r = 0.373) was correlated positively, whereas that of Anoxybacillus (r = −0.509) and Enterococcus (r = −0.593) was correlated inversely with FVC. In addition, the relative abundance of the Aquabacterium (r = 0.616) and Peptoniphilus (r = 0.606) genera was positively correlated, whereas that of the Fusobacterium (r = −0.464) and Phycicoccus (r = −0.495) genera was inversely correlated with distance during the 6-min walking test.Conclusions: The composition of the microbiome in lung tissues differed between patients with IPF and controls and was associated with the diagnosis, mortality, and disease severity of IPF.


2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 251-251
Author(s):  
Madison T Henniger ◽  
Phillip R Myer ◽  
Timothy P L Smith ◽  
Tara G McDaneld ◽  
Larry A Kuehn ◽  
...  

Abstract Bovine respiratory disease complex (BRDC) is caused by a variety of complex factors that involves host elements, environmental elements, inadequate management and housing, as well as viral and bacterial pathogens, such as Mannheimia haemolytica and Mycoplasma bovis. The objective of the study was to develop and evaluate a deep-nasopharyngeal bacterial community database to provide greater assignment of taxa within the bovine nasopharynx and as a site-specific tool for examining microbiome dysbioses involved in BRDC. A total of 180 cattle with an overall BW ranging from 164-269 kg were obtained from Athens, Tennessee (n = 60), Maryville, Missouri (n = 60), and Richmond, Kentucky (n = 60). Cattle were transported to a feeding facility in Kansas and housed in open air, dirt floor, group housing pens. At the first diagnosis of BRD, deep nasopharyngeal samples were collected. DNA library preparation of the bacterial 16S rRNA V1–V8 hypervariable regions was performed and sequenced on the Pacific Biosciences RSII instrument. Database construction and all sequencing data were curated using mothur (v1.39.5). For validation analyses using, a subset of cattle was sampled as described above, and three samples sequenced using the V1–V3 hypervariable 16SrRNA regions and the Illumina MiSeq. In the database, Mycoplasma accounted for over 57% of the reads and Mannheimia was present at 0.7%. When validating the database using short-reads, unassigned taxa in the Greengenes analysis was 4.22% contrasted to the 0.91% of the closed reference database analysis. The two taxonomic compositions were not correlated and the correlation was statistically significant (r = -0127; P = 0.001). All alpha diversity indices between the two analysis methods differed (P < 0.05). Development of this reference database provides researchers a tool with considerable improvements in performance for the analysis of bacterial communities in the nasopharynx relating to cattle diagnosed with BRDC.


2020 ◽  
Vol 98 (9) ◽  
Author(s):  
Ibukun M Ogunade ◽  
Megan McCoun ◽  
Modoluwamu D Idowu ◽  
Sunday O Peters

Abstract We examined the effects of two direct-fed microbials (DFM) containing multiple microbial species and their fermentation products on energy status, nutrient digestibility, and ruminal fermentation, bacterial community, and metabolome of beef steers. Nine ruminally cannulated Holstein steers (mean ± SD body weight: 243 ± 12.4 kg) were assigned to three treatments arranged in a triplicated 3 × 3 Latin square design with three 21-d periods. Dietary treatments were 1) control (CON; basal diet), 2) Commence (PROB; basal diet plus 19 g/d of Commence), and 3) RX3 (SYNB; basal diet plus 28 g/d of RX3). Commence and RX3 are both multispecies DFM products. From day 16 to 20 of each period, feed and fecal samples were collected daily to determine the apparent total tract digestibilities of nutrients using indigestible neutral detergent fiber method. On day 21 of each period, blood samples were collected for analysis of plasma glucose and nonesterified fatty acid. Ruminal contents were collected at approximately 1, 3, 6, 9, 12, and 18 h after feeding on day 21 for analysis of volatile fatty acids (VFA), lactate, ammonia-N concentrations, bacterial community, and metabolome profile. Total tract digestibilities of nutrients did not differ (P &gt; 0.05) among treatments. Compared with CON, steers fed either supplemental PROB or SYNB had greater (P = 0.04) plasma glucose concentrations. Compared with CON, total ruminal VFA, propionate, isovalerate, and valerate concentrations increased (P ≤ 0.05) or tended to increase (P ≤ 0.10) with either supplemental PROB or SYNB, but were not different (P &gt; 0.05) between PROB and SYNB. Compared with CON, PROB reduced (P ≤ 0.05) the relative abundance of Prevotella 1 and Prevotellaceae UCG-001 but increased (P ≤ 0.05) the relative abundance of Rikenellaceae RC9, Succinivibrionaceae UCG-001, Succiniclasticum, and Ruminococcaceae UCG-002. Supplemental SYNB decreased (P ≤ 0.05) the relative abundance of Prevotella 1 and Prevotellaceae UCG-001 but increased (P ≤ 0.05) the relative abundance of Prevotella 7, Succinivibrio, Succiniclasticum, and Ruminococcaceae UCG-014. Compared with CON, metabolome analysis revealed that some amino acids were increased (P ≤ 0.05) in steers fed PROB. This study demonstrated that, compared with CON, supplementation of either PROB or SYNB altered the ruminal bacterial community and metabolome differently; however, their effects on the ruminal VFA profile and energy status of the steers were not different from each other.


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