PSVII-9 Influence of lactose and milk oligosaccharides in whey permeate on jejunal mucosa-associated microbiota in nursery pigs during 7 to 11 kg BW

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 407-407
Author(s):  
Ki Beom Jang ◽  
Sung Woo Kim
Keyword(s):  
Alpha Diversity ◽  
Jejunal Mucosa ◽  
16S Rdna Sequencing ◽  
Sequencing Data ◽  
Milk Oligosaccharides ◽  
Whey Permeate ◽  
Nursery Pigs ◽  
Rdna Sequencing ◽  
Acid Producing Bacteria ◽  
Diversity Estimates

Abstract This study aimed to evaluate supplemental effects of milk carbohydrates in whey permeate on jejunal mucosa-associated microbiota in nursery pigs during 7 to 11 kg BW. A total of 720 pigs at 7.5 kg BW were allotted to 6 treatments (6 pens/treatment and 20 pigs/pen). Treatments were 6 levels of whey permeate supplementation (0, 3.75, 7.50, 11.25, 15.00, and 18.75%) and fed to pigs for 11 d. On d 11, 36 pigs representing median BW of each pen were euthanized to collect the jejunal mucosa to evaluate microbiota in the jejunum by 16S rDNA sequencing. Data were analyzed using contrasts in MIXED procedure of SAS. Whey permeate contained 76.3% lactose and 0.4% milk oligosaccharides. Increasing whey permeate supplementation from 0 to 18.75% did not affect the alpha-diversity estimates of microbiota. Whey permeate supplementation tended to decrease (P = 0.073, 1.59 to 1.22) Firmicutes:Bacteroidetes compared with no addition of whey permeate. Increasing whey permeate supplementation tended to linearly increase Bifidobacteriaceae (P = 0.089, 0.73 to 1.11), decrease Enterobacteriaceae (P = 0.091, 1.04 to 0.52), decrease Stretococcaceae (P = 0.094, 1.50 to 0.71), and caused quadratic changes (P < 0.05) on Lactobacillaceae (maximum: 9.14% at 12.91% whey permeate). Increasing whey permeate supplementation caused a quadratic change (P < 0.05) on Lactobacillus_Salivarius (maximum: 0.92% at 7.35% whey permeate) and tended to cause quadratic changes on Lactobacillus_Rogosae (P = 0.083; maximum: 0.53% at 8.45% whey permeate) and Lactobacillus_Mucosae (P = 0.092; maximum: 0.70% at 6.98% whey permeate). In conclusion, supplementation of whey permeate as sources of lactose and milk oligosaccharides at a range from 7 to 13% seems to be beneficial to nursery pigs by increasing the abundance of lactic acid-producing bacteria in the jejunal mucosa.

scholarly journals 2-Way k-Means as a Model for Microbiome Samples

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Weston J. Jackson ◽  
Ipsita Agarwal ◽  
Itsik Pe’er
Keyword(s):  
Unsupervised Learning ◽  
16S Rdna ◽  
Mixture Model ◽  
Vaginal Microbiome ◽  
16S Rdna Sequencing ◽  
Sequencing Data ◽  
Cluster Assignment ◽  
Rdna Sequencing

Motivation. Microbiome sequencing allows defining clusters of samples with shared composition. However, this paradigm poorly accounts for samples whose composition is a mixture of cluster-characterizing ones and which therefore lie in between them in the cluster space. This paper addresses unsupervised learning of 2-way clusters. It defines a mixture model that allows 2-way cluster assignment and describes a variant of generalized k-means for learning such a model. We demonstrate applicability to microbial 16S rDNA sequencing data from the Human Vaginal Microbiome Project.

scholarly journals 2-Way k-Means as a Model for Microbiome Samples

2017 ◽  
Author(s):  
Weston J. Jackson ◽  
Ipsita Agarwal ◽  
Itsik Pe’er
Keyword(s):  
Unsupervised Learning ◽  
16S Rdna ◽  
Mixture Model ◽  
Vaginal Microbiome ◽  
16S Rdna Sequencing ◽  
Sequencing Data ◽  
Cluster Assignment ◽  
Rdna Sequencing

ABSTRACTMotivationMicrobiome sequencing allows defining clusters of samples with shared composition. However, this paradigm poorly accounts for samples whose composition is a mixture of cluster-characterizing ones, and therefore lie in-between them in cluster space. This paper addresses unsupervised learning of 2-way clusters. It defines a mixture model that allows 2-way cluster assignment and describes a variant of generalized k-means for learning such a model. We demonstrate applicability to microbial 16S rDNA sequencing data from the Human Vaginal Microbiome [email protected]

scholarly journals Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling

2017 ◽  
Author(s):  
Sajan C. Raju ◽  
Sonja Lagström ◽  
Pekka Ellonen ◽  
Willem M. de Vos ◽  
Johan G. Eriksson ◽  
...  
Keyword(s):  
Large Scale ◽  
Alpha Diversity ◽  
Epidemiological Studies ◽  
Molecular Techniques ◽  
16S Rdna Sequencing ◽  
High Reproducibility ◽  
Rdna Sequencing ◽  
Culture Independent ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractCulture-independent molecular techniques and advances in next generation sequencing (NGS) technologies make large-scale epidemiological studies on microbiota feasible. A challenge using NGS is to obtain high reproducibility and repeatability, which is mostly attained through robust amplification. We aimed to assess the reproducibility of saliva microbiota by comparing triplicate samples. The microbiota was produced with simplified in-house 16S amplicon assays taking advantage of large number of barcodes. The assays included primers with Truseq (TS-tailed) or Nextera (NX-tailed) adapters and either with dual index or dual index plus a 6-nt internal index. All amplification protocols produced consistent microbial profiles for the same samples. Although, in our study, reproducibility was highest for the TS-tailed method. Five replicates of a single sample, prepared with the TS-tailed 1-step protocol without internal index sequenced on the HiSeq platform provided high alpha-diversity and low standard deviation (mean Shannon and Inverse Simpson diversity was 3.19 ± 0.097 and 13.56 ± 1.634 respectively). Large-scale profiling of microbiota can consistently be produced by all 16S amplicon assays. The TS-tailed-1S dual index protocol is preferred since it provides repeatable profiles on the HiSeq platform and are less labour intensive.

93 Effects of a Functional Oils Blend on Intestinal Health and Growth Performance of Nursery Pigs

2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 47-47
Author(s):  
Vitor Hugo C Moita ◽  
Marcos Elias Duarte ◽  
Sung Woo Kim
Keyword(s):  
Growth Performance ◽  
Relative Abundance ◽  
Alpha Diversity ◽  
Protein Carbonyl ◽  
Jejunal Mucosa ◽  
Intestinal Health ◽  
Nursery Pigs ◽  
Oxidative Damages ◽  
Potential Benefits ◽  
Oil Blend

Abstract This study was to investigate the role of castor oil and cashew nutshell liquid (functional oil blend, FOB) on intestinal health and growth performance of nursery pigs and to determine an optimal supplemental level. Newly weaned pigs (20 barrows and 20 gilts at 25 d of age, 7.02 ± 0.58 kg BW) were randomly allotted to 5 treatments in a RCBD and fed in 2 phases (13 and 21 d respectively) with increasing levels (0, 0.050, 0.075, 0.100, and 0.150%) of FOB. Growth performance was measured by each phase. Titanium dioxide (0.4%) was added to phase 2 diets as an indigestible marker to measure AID. On d 34, all pigs were euthanized to collect jejunum to measure immune status, oxidative stress status, microbiota, morphology, and crypt cell proliferation. Data were analyzed using Proc Mixed of SAS. Supplementation of FOB did not affect the overall growth performance. Supplementation of FOB tended to decrease (P = 0.064) the concentration of jejunal protein carbonyl (3.11 to 2.45 nmol/protein) and tended to increase villus height (P = 0.098, 401 to 453 μm) and crypt depth (P = 0.070, 86 to 99 μm). Increasing FOB reduced (P < 0.05) relative abundance of Helicobacteraceae (46.8 to 21.0%) and increased (P < 0.05) relative abundance of Prevotellaceae (7.9 to 13.1%), Burkholderiaceae (6.3 to 10.8%) and Pseudomonadaceae (0.1 to 1.0%), and increased (P < 0.05) alpha diversity of the jejunal mucosa-associated microbiota at the family level (Chao1 index 42.8 to 56.8%). In conclusion, FOB showed potential benefits on intestinal health of nursery pigs by increasing beneficial and reducing harmful bacteria reducing oxidative damages in the jejunal mucosa, and by enhancing villus structure, whereas without affecting the growth performance. The FOB at a range of 0.050% to 0.150% provided the most benefit for nursery pigs.

scholarly journals Foes or Friends? Bacteria Enriched in the Tumor Microenvironment of Colorectal Cancer

Cancers ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 372 ◽  
Author(s):  
Xu ◽  
Yin ◽  
Zhang ◽  
Lv ◽  
Yang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Tumor Microenvironment ◽  
Human Health ◽  
16S Rdna ◽  
Intestinal Microbiota ◽  
Intestinal Bacteria ◽  
16S Rdna Sequencing ◽  
Sequencing Data ◽  
Rdna Sequencing ◽  
Prevention And Treatment

Colorectal cancer (CRC) is the second most commonly diagnosed cancer and the third cause of cancer death in the world, while intestinal microbiota is a community of microbes living in human intestine that can potentially impact human health in many ways. Accumulating evidence suggests that intestinal microbiota, especially that from the intestinal bacteria, play a key role in the CRC development; therefore, identification of bacteria involved in CRC development can provide new targets for the CRC diagnosis, prevention, and treatment. Over the past decade, there have been considerable advances in applying 16S rDNA sequencing data to verify associated intestinal bacteria in CRC patients; however, due to variations of individual and environment factors, these results seem to be inconsistent. In this review, we scrutinized the previous 16S rDNA sequencing data of intestinal bacteria from CRC patients, and identified twelve genera that are specifically enriched in the tumor microenvironment. We have focused on their relationship with the CRC development, and shown that some bacteria could promote CRC development, acting as foes, while others could inhibit CRC development, serving as friends, for human health. Finally, we highlighted their potential applications for the CRC diagnosis, prevention, and treatment.

scholarly journals Dose–response and functional role of whey permeate as a source of lactose and milk oligosaccharides on intestinal health and growth of nursery pigs

2021 ◽  
Vol 99 (1) ◽  
Author(s):  
Ki Beom Jang ◽  
Jerry M Purvis ◽  
Sung W Kim
Keyword(s):  
Cell Proliferation ◽  
Growth Performance ◽  
Dose Response ◽  
Feed Intake ◽  
Phase 1 ◽  
Jejunal Mucosa ◽  
Whey Permeate ◽  
Nursery Pigs ◽  
Crypt Cell Proliferation ◽  
Line Analysis

Abstract Two experiments were conducted to evaluate dose–response and supplemental effects of whey permeate on growth performance and intestinal health of nursery pigs. In experiment (exp.) 1, 1,080 pigs weaned at 6.24 kg body weight (BW) were allotted to five treatments (eight pens/treatment) with increasing levels of whey permeate in three phases (from 10% to 30%, 3% to 23%, and 0% to 9% for phase 1, 2, and 3, respectively) fed until 11 kg BW and then fed a common phase 4 diet (0% whey permeate) until 25 kg BW in a 48-d feeding trial. Feed intake and BW were measured at the end of each phase. In exp. 2, 1,200 nursery pigs at 7.50 kg BW were allotted to six treatments (10 pens/treatment) with increasing levels of whey permeate from 0% to 18.75% fed until 11 kg BW. Feed intake and BW were measured during 11 d. Six pigs per treatment (1 per pens) were euthanized to collect the jejunum to evaluate tumor necrosis factor-alpha, interleukin-8 (IL-8), transforming growth factor-beta 1, mucin 2, histomorphology, digestive enzyme activity, crypt cell proliferation rate, and jejunal mucosa-associated microbiota. Data were analyzed using contrasts in the MIXED procedure and a broken-line analysis using the NLIN procedure of SAS. In exp. 1, increasing whey permeate had a quadratic effect (P < 0.05) on feed efficiency (G:F; maximum: 1.35 at 18.3%) in phase 1. Increasing whey permeate linearly increased (P < 0.05) average daily gain (ADG; 292 to 327 g/d) and G:F (0.96 to 1.04) of pigs in phase 2. In exp. 2, increasing whey permeate linearly increased (P < 0.05) ADG (349 to 414 g/d) and G:F (0.78 to 0.85) and linearly increased (P < 0.05) crypt cell proliferation rate (27.8% to 37.0%). The breakpoint from a broken-line analysis was obtained at 13.6% whey permeate for maximal G:F. Increasing whey permeate tended to change IL-8 (quadratic, P = 0.052; maximum: 223 pg/mg at 10.9%), to decrease Firmicutes:Bacteroidetes (P = 0.073, 1.59 to 1.13), to increase (P = 0.089) Bifidobacteriaceae (0.73% to 1.11%), and to decrease Enterobacteriaceae (P = 0.091, 1.04% to 0.52%) and Streptococcaceae (P = 0.094, 1.50% to 0.71%) in the jejunal mucosa. In conclusion, dietary inclusion of whey permeate increased the growth of nursery pigs from 7 to 11 kg BW. Pigs grew most efficiently with 13.6% whey permeate. Improvement in growth performance is partly attributed to stimulating intestinal immune response and enterocyte proliferation with positive changes in jejunal mucosa-associated microbiota in nursery pigs.

Metabolite fingerprinting of novel Streptomyces UK-238 from the Himalayan forest

2020 ◽  
Vol 16 ◽  
Author(s):  
Nidhi Srivastava ◽  
Indira P. Sarethy
Keyword(s):  
Ethyl Acetate ◽  
16S Rdna ◽  
Retention Index ◽  
Ethyl Acetate Extract ◽  
Similarity Index ◽  
Antimicrobial Drug ◽  
16S Rdna Sequencing ◽  
Metabolite Fingerprinting ◽  
Streptomyces Sp ◽  
Rdna Sequencing

Aims: Characterization of antimicrobial metabolites of novel Streptomyces sp. UK-238. Background: Novel antimicrobial drug discovery is urgently needed due to emerging multi antimicrobial drug resistance among pathogens. Since many years, natural products have provided the basic skeletons for many therapeutic compounds including antibiotics. Bioprospection of un/under explored habitats and focussing on selective isolation of actinobacteria as major reservoir of bio and chemodiversity has yielded good results. Objective: The main objectives of the study were the identification of UK-238 by 16S rDNA sequencing and antimicrobial metabolite fingerprinting of culture extracts. Method: In the present study, a promising isolate, UK-238, has been screened for antimicrobial activity and metabolite fingerprinting from the Himalayan Thano Reserve forest. It was identified by 16S rDNA sequencing. Ethyl acetate extract was partially purified by column chromatography. The pooled active fractions were fingerprinted by GC-MS and compounds were tentatively identified by collated data analysis based on Similarity Index, observed Retention Index from Databases and calculated Retention Index. Results: UK-238 was identified as Streptomyces sp. with 98.4% similarity to S. niveiscabiei. It exhibited broad-spectrum antibacterial and antifungal activity. GC-MS analysis of active fractions of ethyl acetate extract showed the presence of eighteen novel antimicrobial compounds belonging to four major categories- alcohols, alkaloid, esters and peptide. Conclusion: The study confirms that bioprospection of underexplored habitats can elaborate novel bio and chemodiversity.

scholarly journals The plant secondary compound swainsonine reshapes gut microbiota in plateau pikas (Ochotona curzoniae)

2021 ◽  
Author(s):  
Shien Ren ◽  
Chao Fan ◽  
Liangzhi Zhang ◽  
Xianjiang Tang ◽  
Haibo Fu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Artificial Diet ◽  
Alpha Diversity ◽  
Term Treatment ◽  
Short Term Treatment ◽  
Ochotona Curzoniae ◽  
Rdna Sequencing ◽  
Long Term Treatment ◽  
Significant Difference ◽  
Herbivorous Mammals

Abstract Plants produce various plant secondary compounds (PSCs) to deter the foraging of herbivorous mammals. However, little is known about whether PSCs can reshape gut microbiota and promote gut homeostasis of hosts. Using 16S rDNA sequencing to investigate the effects of PSCs on the gut microbiota of small herbivorous mammals, we studied plateau pikas (Ochotona curzoniae) fed diets containing swainsonine (SW) extracted from Oxytropis ochrocephala. Our results showed that both long- and short-term treatment of a single artificial diet in the laboratory significantly reduced alpha diversity and significantly affected beta diversity, core bacteria abundance, and bacterial functions in pikas. After SW was added to the artificial diet, the alpha diversity significantly increased in the long-term treatment, and core bacteria (e.g., Akkermansiaceae) with altered relative abundances in the two treatments showed no significant difference compared with pikas in the wild. The complexity of the co-occurrence network structure was reduced in the artificial diet, but it increased after SW was added in both treatments. Further, the abundances of bacteria related to altered alanine, aspartate, and glutamate metabolism in the artificial diet were restored in response to SW. SW further decreased the concentration of short-chain fatty acids (SCFAs) in both treatments. Our results suggest that PSCs play a key role in regulating gut microbiota community and intestinal homeostasis, thereby maintaining host health. Key points • Swainsonine improves the intestinal bacterial diversity of plateau pikas. • Swainsonine promotes the recovery of core bacterial abundances in the gut of plateau pikas. • Swainsonine promotes the restoration of intestinal bacterial functions of plateau pikas.

scholarly journals 367 Combinational use of sodium butyrate and phytogenics on intestinal health of nursery pigs

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 132-133
Author(s):  
S Bloomer ◽  
Y C Cheng ◽  
H M Yakout ◽  
S W Kim
Keyword(s):  
Sodium Butyrate ◽  
Fixed Effects ◽  
Protein Carbonyl ◽  
Jejunal Mucosa ◽  
Gut Health ◽  
Intestinal Health ◽  
Necrosis Factor Alpha ◽  
Nursery Pigs ◽  
Enterocyte Proliferation ◽  
Tnf Α

Abstract The effects of encapsulated sodium butyrate (SB), phytogenics (PH), or a combination were studied on intestinal health of nursery pigs. Phytogenics were blends of dry herbs and essential oil components. Forty-eight weaned pigs (21-d-old; 6.9 ± 0.6 kg BW) were individually housed, blocked by initial BW and sex, allotted to 4 dietary treatments (n = 12) in a RCBD, and fed for 33-d (P1: 0–7; P2: 7–19; and P3: 19–33). Treatments were arranged by 2 factors: SB (P1: 0.2% and P2: 0.1%) and PH (P3: 0.033%). Diets were formulated to meet or exceed NRC (2012) nutrient requirements and pigs were fed ad libitum. For each phase, ADG, ADFI, and G:F were measured. Fecal scores were assessed during d 3–19 and d 26–33. Blood samples were drawn in P2 and P3 to measure tumor necrosis factor alpha (TNF-α), IL-6, and immunoglobulin G (IgG). Four pigs at P2 and 8 pigs in P3 from each treatment were euthanized to collect jejunal tissue, jejunal mucosa, and ileal digesta to measure gut histology, TNF-α, IL-6, myeloperoxidase (MPO), malondialdehyde (MDA), and protein carbonyl. Data were analyzed using PROC MIXED of SAS. Fixed effects were treatments and random effects were blocks. In P2 and P1-2, SB decreased (P < 0.05) ADFI whereas no effect on ADG and G:F. In P2, SB tended to decrease (P = 0.063) villus height to crypt depth ratio (VH:CD) whereas increased (P < 0.05) enterocyte proliferation in P3. In P3 and overall, PH increased (P < 0.05) G:F. No changes were found in TNF-α, IL-6, MPO, MDA, IgG, and protein carbonyl. Conclusively, SB and a combinational use of SB and PH showed minimal effects on growth performance and gut health when added to the diets of nursery pigs. However, PH supplementation increased feed efficiency of nursery pigs during 19–33 d post-weaning.

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