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2022 ◽  
Vol 12 ◽  
Author(s):  
Chao Yang ◽  
Tianxi Zhang ◽  
Quanhua Tian ◽  
Yan Cheng ◽  
Kefyalew Gebeyew ◽  
...  

Successful establishment of passive immunity (PIT) and regulation of intestinal microbiota are crucial for ruminants to maintain body health and reduce the risk of disease during the neonatal period. Thus, the objective of this study was to investigate the effects of mannan oligosaccharide (MOS) supplementation on passive transfer of immunoglobulin G (IgG), serum inflammatory cytokines and antioxidant levels as well as bacteria composition in the ileal digesta. A total of 14 healthy neonatal Ganxi black goats with similar birth weight (BW: 2.35 ± 0.55 kg) were selected and allocated into two groups, only fed colostrum and milk replacer (CON, n = 7) and supplemented MOS (0.06% of birth BW) in the colostrum and milk replacer (MOS, n = 7). The results indicated that MOS supplementation significantly reduced (p < 0.05) serum IgG level at 3 and 6 h after colostrum feeding. Serum GLP-1 level of goats in the MOS group was significantly lower (p = 0.001) than that in the CON group. Goats in the MOS group had higher serum CAT and lower MDA level than those in the CON group (p < 0.05). Serum anti-inflammatory cytokine level of interleukin 4 (IL-4) was increased (p < 0.05), while pro-inflammatory cytokine IL-6 level was reduced (p < 0.05) in the MOS group when compared with the CON group. In addition, MOS supplementation remarkably increased (p < 0.05) the level of secretory IgA (sIgA) in the ileal digesta. Principal coordinate analysis of 16S rRNA sequence based on Brinary jaccard, Bray curtis, and weighted UniFrac distance of ileal microbiota showed a distinct microbial differentiation between the CON and MOS groups (p < 0.05). The relative abundance of Firmicutes in the MOS group was higher than that in the CON group, while the abundance of Verrucomicrobia was lower in the MOS group than that in the CON group at the phylum level (p < 0.05). The relative abundance of Proteobacteria tended to decrease (p = 0.078) in the MOS group at the phylum level. The results of LEfSe analysis showed that MOS group was characterized by a higher relative abundance of Lactobacillus, while the CON group was represented by a higher relative abundance of Akkermansia and Ruminiclostridium_5. Our findings demonstrated that MOS supplementation during the neonatal period increases antioxidant capacity and reduces the inflammatory response, and promotes IgA secretion and Lactobacillus colonization in the ileum. Thus, MOS induced positive effects are more pronounced in neonatal goats that might be an effective approach to maintain intestinal health and improve the surviving rate of neonatal ruminants.


2021 ◽  
Author(s):  
Han-Ki Park ◽  
Sang Jin Lee

Abstract Introduction: Although factors initiating the inflammatory response to monosodium urate crystals have been identified, the role of the gut microbiota and their metabolites on gout remain unknown. This study aimed to investigate changes in both gut microbiota and short chain fatty acids (SCFAs) according to inflammatory states of gout in the same patients.Methods: This study enrolled 20 patients with gout in the acute state who had active joints and were followed-up until the recovery state with no active joints. Blood and fecal samples were simultaneously collected within 3 days for each disease state. The stool microbiome was analyzed using 16S rRNA sequencing, and serum SCFAs were measured by gas chromatography-mass spectrometry. Differences in gut microbiome and serum SCFAs were compared between the acute and recovery states.Results: Beta diversity of the microbiome was significantly different between the acute and recovery states in terms of weighted UniFrac distance. In the recovery state, Prevotellaceae (p = 0.006) and the genus Prevotella (p = 0.009) were significantly enriched, whereas Enterobacteriaceae (p = 0.019) and its derivative genus Shigella (p = 0.023) were significantly decreased compared to the acute state. Similarly, the levels of acetate was dramatically increased in the recovery state compared to the acute state (p < 0.010). Levels of propionate and butyrate tended to increase but without statistical significance.Conclusion: Substantial alterations of bacterial composition with promotion of SCFA formation (especially acetate) were found after treatment in patients with gouty arthritis.


2021 ◽  
Author(s):  
Deepthi M ◽  
Kumar Arvind ◽  
Rituja Saxena ◽  
Joby Pulikkan ◽  
Vineet K Sharma ◽  
...  

Abstract The indigenous cattle are efficient in converting low quality feeds and forage into animal products. Kasaragod Dwarf cattle, a unique non-descriptive native cattle of Kerala, India, are noted for their unique qualities, such as low feed intake, thermotolerance, greater resistance to diseases and A2 allelic variant milk. However, owing to the higher milk yield, Holstein crossbred cattle are given more importance over Kasaragod Dwarf. The hindgut microbiota plays a major role in various biological processes such as the digestion, vitamins synthesis, and immunity in cattle. In this study, we compared the hindgut microbiota of the Kasaragod Dwarf with the highly found, Holstein crossbred utilizing 16S rRNA high-throughput sequencing for a better understanding of the relationship between the host and microbial community. Four replicates of each 20 samples comprising two cattle type (n=10) were sequenced and analyzed. Marker gene-based taxonomic analysis affirmed variations in their microbial composition. Principle Coordinate Analysis (PCoA) using weighted and unweighted UniFrac distance matrices showed the distinct microbial architecture of the two cattle type. Random Forest analysis further confirmed the distinctness and revealed the signature taxa in K-Dwarf. The study observed the predominance of feed efficiency associated genera viz., Anaerovibrio, Succinivibrio, Roseburia, Coprococcus, Anaerostipes, Paludibacter, Elusimicrobium, Sutterella, Oribacterium, Coprobacillus, and Ruminobacter in Kasaragod Dwarf cattle. The study highlights the abundance of unique and beneficial hindgut microflora found in Kasaragod Dwarf, which may attest its importance over exotic cattle breeds viz., Holstein. To our knowledge, this is the first report of Kasaragod Dwarf cattle gut microbiome profiling. This study is pivotal towards developing genetic resources for the microbial population in K-Dwarf and how it could be differentiated from Holstein crossbred cattle.


Author(s):  
Kelsey L Batson ◽  
Alison C Neujahr ◽  
Thomas Burkey ◽  
Samodha C Fernando ◽  
Mike D Tokach ◽  
...  

Abstract Reduction in dietary crude protein and addition of fiber could mitigate the incidence and severity of post-weaning diarrhea, a common gastrointestinal condition in newly weaned pigs. Therefore, 360 weanling pigs, initially 5.0 ± 0.10 kg, were used to evaluate the effects of crude protein (CP) level and fiber source on growth performance and fecal microbial communities. At weaning, pigs were randomly assigned to pens and allotted to 1 of 8 dietary treatments in a 2 × 4 factorial with main effects of CP (21 or 18%) and fiber source (none, coarse wheat bran, oat hulls, or cellulose). There were 5 pigs per pen and 9 pens per treatment. Experimental diets were formulated in two dietary phases from d 0 to 10 and 10 to 24, with a common post-treatment diet fed from 24 to 45. The 21% CP diets contained 1.40% standardized ileal digestible (SID) Lys in phase 1 and 1.35% SID Lys in phase 2. By using a maximum SID Lys:digestible CP ratio of 6.35%, the 18% CP diets contained 1.25% SID Lys in both phases. Diets containing a fiber source were formulated to the level of insoluble fiber provided by 4% coarse wheat bran, resulting in the addition of 1.85% oat hulls and 1.55% cellulose. No fiber source × CP level interactions (P &gt; 0.05) were observed. Decreasing CP (and subsequently SID lysine) decreased (P = 0.05) ADG and G:F during the experimental period. From d 0 to 45, ADG decreased (P = 0.05) for pigs fed 18% CP diets compared to pigs fed 21% CP. No effect of fiber source was observed for growth performance. Fecal DM on d 17 increased (P &lt; 0.001) for pigs fed 18% CP diets compared to pigs fed 21% CP diets. Pigs fed diets with added cellulose had increased (P &lt; 0.05) fecal dry matter during the experimental period compared to pigs fed no fiber source or wheat bran. Bacterial community structure was investigated by sequencing the V4 region of the 16S rRNA gene. Analysis indicated a significant difference between CP content at d 24 (P = 0.023) using a Weighted UniFrac distance matrix. Further investigation identified five differential Amplicon Sequence Variants associated with CP content at d 24. In conclusion, reducing crude protein (and subsequently SID Lys) decreased growth performance but increased fecal dry matter content. The source of dietary fiber in nursery diets had no impact on growth performance; but pigs fed added cellulose had increased fecal DM compared with other treatments. Microbial analysis identified differential taxa associated with CP content.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Karina A. Chavarria ◽  
Kristin Saltonstall ◽  
Jorge Vinda ◽  
Jorge Batista ◽  
Megan Lindmark ◽  
...  

AbstractLand use is known to affect water quality yet the impact it has on aquatic microbial communities in tropical systems is poorly understood. We used 16S metabarcoding to assess the impact of land use on bacterial communities in the water column of four streams in central Panama. Each stream was influenced by a common Neotropical land use: mature forest, secondary forest, silvopasture and traditional cattle pasture. Bacterial community diversity and composition were significantly influenced by nearby land uses. Streams bordered by forests had higher phylogenetic diversity (Faith’s PD) and similar community structure (based on weighted UniFrac distance), whereas the stream surrounded by traditional cattle pasture had lower diversity and unique bacterial communities. The silvopasture stream showed strong seasonal shifts, with communities similar to forested catchments during the wet seasons and cattle pasture during dry seasons. We demonstrate that natural forest regrowth and targeted management, such as maintaining and restoring riparian corridors, benefit stream-water microbiomes in tropical landscapes and can provide a rapid and efficient approach to balancing agricultural activities and water quality protection.


2021 ◽  
Vol 12 ◽  
Author(s):  
Juejie Long ◽  
Wei Luo ◽  
Jianmei Xie ◽  
Yuan Yuan ◽  
Jia Wang ◽  
...  

The giant panda has developed a series of evolutionary strategies to adapt to a bamboo diet. The abundance and diversity of the phyllosphere microbiome change dramatically depending on the season, host species, location, etc., which may, in turn, affect the growth and health of host plants. However, few studies have investigated the factors that influence phyllosphere bacteria in bamboo, a staple food source of the giant panda. Amplicon sequencing of the 16S rRNA gene was used to explore the abundance and diversity of phyllosphere bacteria in three bamboo species (Arundinaria spanostachya, Yushania lineolate, and Fargesia ferax) over different seasons (spring vs. autumn), elevation, distance from water, etc., in Liziping National Nature Reserve (Liziping NR), China. And whole-genome shotgun sequencing uncovered the differences in biological functions (KEGG and Carbohydrate-Active enzymes functions) of A. spanostachya phyllosphere bacteria between spring and autumn. The results showed that the abundance and diversity of F. ferax phyllosphere bacteria were greater than that of the other two bamboo species in both seasons. And three kinds of bamboo phyllosphere bacteria in autumn were significantly higher than in spring. The season was a more important factor than host bamboo species in determining the community structure of phyllosphere bacteria based on the (un)weighted UniFrac distance matrix. The composition, diversity, and community structure of phyllosphere bacteria in bamboo were primarily affected by the season, species, altitude, tree layer, and shrub layer. Different bacterial communities perform different functions in different bamboo species, and long-term low temperatures may shape more varied and complex KEGG and Carbohydrate-Active enzymes functions in spring. Our study presented a deeper understanding of factors influencing the bacterial community in the bamboo phyllosphere. These integrated results offer an original insight into bamboo, which can provide a reference for the restoration and management of giant panda bamboo food resources in the Xiaoxiangling mountains.


2021 ◽  
Vol 22 (11) ◽  
Author(s):  
Samat Kozhakhmetov ◽  
Yermek Aitenov ◽  
Bakhyt Ramazanova ◽  
Yekaterina Koloskova ◽  
Tatyana Burkutbayeva ◽  
...  

Abstract. Kozhakhmetov S, Aitenov Y, Ramazanova B, Koloskova Y, Burkutbayeva T, Yeraliyeva L, Mustafina K, Beglarova G, Yergazina M, Kushugulova A. 2021. Influence of pneumococcal conjugate vaccine 13 on upper respiratory tract microbial biodiversity in infants. Biodiversitas 22: 5055-5060. Pneumococcal disease and its associated mortality are burdens on the healthcare system. The intensive introduction of pneumococcal vaccines has provided robust control and infection management worldwide. The Pneumococcal Conjugate Vaccine (PCV) has been successfully employed in the national programs of many countries. However, no studies have yet analyzed the effect of pneumococcal vaccines on Central Asian populations. We investigated the effect of the pneumococcal vaccine on the nasopharyngeal microbiome of infants under the age of two years. Samples were collected from healthy patients as part of routine hospital check-ups, then subjected to high-throughput sequencing of the V1–V3 region of 16S rRNA for bioinformatics analysis. The obtained data were combined with the results of a previously published study (with matching criteria) to increase statistical power. No significant differences were found in vaccination status, sex or age. Nevertheless, the results demonstrated structural changes in the microbiome of the upper respiratory tract under the influence of the PCV13 vaccine. The results of beta-diversity unweighted UniFrac distance measuring showed that the experimental groups differed in their qualitative (taxonomic) structure (p < 0.1). In the vaccinated group, the abundance of several symbiotic taxa was significantly decreased, including Streptococcus pneumonia.


2021 ◽  
Author(s):  
Yushu Shi ◽  
Liangliang Zhang ◽  
Christine Peterson ◽  
Kim-Anh Do ◽  
Robert Jenq

Abstract Background: In microbiome data analysis, unsupervised clustering is often used to identify naturally occurring clusters, which can then be assessed for associations with characteristics of interest. In this work, we systematically compared beta diversity and clustering methods commonly used in microbiome analyses. We applied these to four published datasets where highly distinct microbiome profiles could be seen between sample groups, as well a clinical dataset with less clear separation between groups. Results: Although no single method outperformed the others consistently, we did identify key scenarios where certain methods can underperform. Specifically, the Bray Curtis (BC) metric resulted in poor clustering in a dataset where high-abundance OTUs were relatively rare. In contrast, the unweighted UniFrac (UU) metric clustered poorly on dataset with a high prevalence of low-abundance OTUs. To explore these hypotheses about BC and UU, we systematically modified properties of the poorly performing datasets and found that this approach resulted in improved BC and UU performance. Based on these observations, we rationally combined BC and UU to generate a novel metric. We tested its performance while varying the relative contributions of each metric and also compared it with another combined metric, the generalized UniFrac distance. The proposed metric showed high performance across all datasets. Conclusions Our systematic evaluation of clustering performance in these five datasets demonstrates that there is no existing clustering method that universally performs best across all datasets. We propose a combined metric of BC and UU that capitalizes on the complementary strengths of the two metrics.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Quang P. Nguyen ◽  
Margaret R. Karagas ◽  
Juliette C. Madan ◽  
Erika Dade ◽  
Thomas J. Palys ◽  
...  

Abstract Background The infant intestinal microbiome plays an important role in metabolism and immune development with impacts on lifelong health. The linkage between the taxonomic composition of the microbiome and its metabolic phenotype is undefined and complicated by redundancies in the taxon-function relationship within microbial communities. To inform a more mechanistic understanding of the relationship between the microbiome and health, we performed an integrative statistical and machine learning-based analysis of microbe taxonomic structure and metabolic function in order to characterize the taxa-function relationship in early life. Results Stool samples collected from infants enrolled in the New Hampshire Birth Cohort Study (NHBCS) at approximately 6-weeks (n = 158) and 12-months (n = 282) of age were profiled using targeted and untargeted nuclear magnetic resonance (NMR) spectroscopy as well as DNA sequencing of the V4-V5 hypervariable region from the bacterial 16S rRNA gene. There was significant inter-omic concordance based on Procrustes analysis (6 weeks: p = 0.056; 12 months: p = 0.001), however this association was no longer significant when accounting for phylogenetic relationships using generalized UniFrac distance metric (6 weeks: p = 0.376; 12 months: p = 0.069). Sparse canonical correlation analysis showed significant correlation, as well as identifying sets of microbe/metabolites driving microbiome-metabolome relatedness. Performance of machine learning models varied across different metabolites, with support vector machines (radial basis function kernel) being the consistently top ranked model. However, predictive R2 values demonstrated poor predictive performance across all models assessed (avg: − 5.06% -- 6 weeks; − 3.7% -- 12 months). Conversely, the Spearman correlation metric was higher (avg: 0.344–6 weeks; 0.265–12 months). This demonstrated that taxonomic relative abundance was not predictive of metabolite concentrations. Conclusions Our results suggest a degree of overall association between taxonomic profiles and metabolite concentrations. However, lack of predictive capacity for stool metabolic signatures reflects, in part, the possible role of functional redundancy in defining the taxa-function relationship in early life as well as the bidirectional nature of the microbiome-metabolome association. Our results provide evidence in favor of a multi-omic approach for microbiome studies, especially those focused on health outcomes.


2021 ◽  
Author(s):  
Deepthi M ◽  
Kumar Arvind ◽  
Rituja Saxena ◽  
Joby Pulikkan ◽  
Shamjana U ◽  
...  

Abstract The indigenous cattle are efficient in converting low quality feeds and forage into animal products. Kasaragod Dwarf (K-Dwarf) cattle, a non-descriptive native cattle variety of Kerala, are noted for their unique qualities, like short stature, low feed intake, thermotolerance, greater resistance to diseases and A2 allelic variant milk. This study hypothesizes that K-Dwarf cow relies on their unique hindgut microbes to ferment the low quality feeds into the efficient animal product. To compare and contrast this unique microbiota and their relationship between the host, we performed microbial profiling of the two genetically distinct cattle-type viz., K-Dwarf, and Holstein utilizing 16S rRNA high-throughput sequencing. Principle Coordinate Analysis using weighted and unweighted UniFrac distance matrices showed significantly distinct clustering of K-Dwarf microbial community compared to Holstein, implying the distinct microbial architecture that K-Dwarf harbors. The dissimilarities observed between the two cattle types were further revealed from the signature taxa identified in each cattle type following Random Forest analysis. In addition, the study observed the predominance of feed efficiency associated genera viz., Anaerovibrio, Succinivibrio, Roseburia, Coprococcus, Anaerostipes, Paludibacter, Elusimicrobium, Sutterella, Oribacterium, Coprobacillus, and Ruminobacter in K-Dwarf cattle. The study highlights the abundance of unique and beneficial hindgut microflora found in K-Dwarf, which may attest its importance over exotic cattle breeds viz., Holstein. To our knowledge, this is the first report of K-Dwarf cattle gut microbiome profiling. Further molecular characterization is solicited to better understand the microbial role in the conversion of low-quality feeds into more efficient animal products, a well-defined characteristic of indigenous cattle.


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