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      Effects of Maternal Low-Protein Diet on Microbiota Structure and Function in the Jejunum of Huzhu Bamei Suckling Piglets

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          Abstract

          Simple Summary

          In mammals, the intestine is the main organ where nutrients are digested and absorbed, thus serving a central role in the growth and health of animals. Low-protein diets are based on the “ideal amino acid” theory, where AA crystals are added to ensure the amino acid balance of the diet. As a result, the amino acid nutritional needs of piglets are reduced along with the total protein level of the diet as well as the metabolic burden of piglets. This typically results in reduced diarrhea and improved gut health. In this study, the microbial composition and function of jejunum chyme samples were analyzed from 30 Huzhu Bamei suckling piglets from sows fed diets with different protein levels via16S rRNA sequencing and bioinformatics. This work provides a theoretical basis for the production of low-protein diets for use in the production of Bamei pigs.

          Abstract

          The jejunum is the primary organ for digestion and nutrient absorption in mammals. The development of the jejunum in suckling piglets directly affects their growth performance post-weaning. The jejunum microbiome plays an important role in proliferation, metabolism, apoptosis, immune, and homeostasis of the epithelial cells within the organ. The composition and diversity of the gut microbiome is susceptible to the protein composition of the diet. Therefore, the effects of maternal low-protein diets on piglets’ intestinal microbial structure and function have become a hot topic of study. Herein, a maternal low-protein diet was formulated to explore the effects on jejunum microbiome composition and metabolic profiles in Bamei suckling piglets. Using 16S ribosomal RNA (16S rRNA) sequencing in conjunction with bioinformatics analysis, 21 phyla and 297 genera were identified within the gut microflora. The top 10 phyla and 10 genera are within the gut bacteria. Next, KEGG analysis showed that the low-protein diet significantly increased the gut microbial composition, transport and catabolism, immune system, global and overview maps, amino acid metabolism, metabolism of cofactors and vitamins, endocrine system, biosynthesis of other secondary metabolites, signal transduction, environmental adaptation, and cell motility. Taken together, low-protein diets do not appear to affect the reproductive performance of Bamei sows but improved the gut microbiome of the suckling piglets as well as reduced the probability of diarrhea. The data presented here provide new insights on the dietary protein requirements to support the Huzhu Bamei pig industry.

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          FLASH: fast length adjustment of short reads to improve genome assemblies.

          Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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            Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome

            Development of the preterm infant gut microbiota is emerging as a critical research priority(1). Since preterm infants almost universally receive early and often extended antibiotic therapy(2), it is important to understand how these interventions alter gut microbiota development(3-6). Analysis of 401 stools from 84 longitudinally sampled preterm infants demonstrates that meropenem, cefotaxime and ticarcillin-clavulanate are associated with significantly reduced species richness. In contrast, vancomycin and gentamicin, the antibiotics most commonly administered to preterm infants, have non-uniform effects on species richness, but these can be predicted with 85% accuracy based on the relative abundance of only two bacterial species and two antibiotic resistance (AR) genes at treatment initiation. To investigate resistome development, we functionally selected resistance to 16 antibiotics from 21 faecal metagenomic expression libraries. Of the 794 AR genes identified, 79% had not previously been classified as AR genes. Combined with deep shotgun sequencing of all stools, we find that multidrug-resistant members of the genera Escherichia, Klebsiella and Enterobacter, genera commonly associated with nosocomial infections, dominate the preterm infant gut microbiota. AR genes that are enriched following specific antibiotic treatments are generally unique to the specific treatment and are highly correlated with the abundance of a single species. The most notable exceptions include ticarcillin-clavulanate and ampicillin, both of which enrich for a large number of overlapping AR genes, and are correlated with Klebsiella pneumoniae. We find that all antibiotic treatments are associated with widespread collateral microbiome impact by enrichment of AR genes that have no known activity against the specific antibiotic driver.
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              Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations.

              Disturbance of the beneficial gut microbial community is a potential collateral effect of antibiotics, which have many uses in animal agriculture (disease treatment or prevention and feed efficiency improvement). Understanding antibiotic effects on bacterial communities at different intestinal locations is essential to realize the full benefits and consequences of in-feed antibiotics. In this study, we defined the lumenal and mucosal bacterial communities from the small intestine (ileum) and large intestine (cecum and colon) plus feces, and characterized the effects of in-feed antibiotics (chlortetracycline, sulfamethazine and penicillin (ASP250)) on these communities. 16S rRNA gene sequence and metagenomic analyses of bacterial membership and functions revealed dramatic differences between small and large intestinal locations, including enrichment of Firmicutes and phage-encoding genes in the ileum. The large intestinal microbiota encoded numerous genes to degrade plant cell wall components, and these genes were lacking in the ileum. The mucosa-associated ileal microbiota harbored greater bacterial diversity than the lumen but similar membership to the mucosa of the large intestine, suggesting that most gut microbes can associate with the mucosa and might serve as an inoculum for the lumen. The collateral effects on the microbiota of antibiotic-fed animals caused divergence from that of control animals, with notable changes being increases in Escherichia coli populations in the ileum, Lachnobacterium spp. in all gut locations, and resistance genes to antibiotics not administered. Characterizing the differential metabolic capacities and response to perturbation at distinct intestinal locations will inform strategies to improve gut health and food safety.
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                Author and article information

                Journal
                Animals (Basel)
                Animals (Basel)
                animals
                Animals : an Open Access Journal from MDPI
                MDPI
                2076-2615
                23 September 2019
                October 2019
                : 9
                : 10
                : 713
                Affiliations
                [1 ]College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China 18219613915@ 123456163.com (X.Z.); swb887246@ 123456126.com (W.S.)
                [2 ]Key of Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
                [3 ]College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China; a18740958061@ 123456163.com (Q.C.); YuanZan13897405406@ 123456163.com (Z.Y.)
                [4 ]Qinghai Province Huzhu County Bamei Pig Seed Breeding Farm, Huzhu, Qinghai 810500, China zsj632126@ 123456163.com (S.Z.); mmm_258369@ 123456yeah.net (L.M.); mmm_147258@ 123456126.com (G.Z.)
                Author notes
                [* ]Correspondence: zhanglp512@ 123456163.com (L.Z.); jiajianlei870620@ 123456163.com (J.J.); Tel.: +86-15002638216 (L.Z.); +86-18797328237 (J.J.)
                Article
                animals-09-00713
                10.3390/ani9100713
                6826398
                31547553
                55a655d0-67e6-472a-83fb-9b9dede8a627
                © 2019 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 28 June 2019
                : 16 September 2019
                Categories
                Article

                maternal low-protein diet,16s rrna,jejunum microbiota,suckling piglets,bioinformatics

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