J Am Assoc Lab Anim Sci. 2016;55(5):582-587.
Evaluation of Fecal Microbiota Transfer as Treatment for Postweaning Diarrhea in Research-Colony Puppies.
Burton EN1, O'Connor E1, Ericsson AC2, Franklin CL3.
Frequently just prior to or at weaning (approximate age, 6 to 8 wk), puppies in research settings often develop diarrheal disease, which may be due, in part, to an immature and unstable intestinal microbiota that is permissive to opportunistic pathogens. The overall objective of this study was to assess whether fecal microbiota transfer (FMT) increased the transmission of a stable maternal microbiota to pups and decreased the incidence of postweaning diarrhea. Puppies were designated by litter as treated (FMT) or sham-treated. The FMT group received fecal inoculum orally for 5 consecutive days during weaning (at 6 to 8 wk of age). Diarrhea was evaluated according to a published scoring system for 11 d during the weaning period. Fresh feces were collected from dams and puppies at 3 d before weaning and 3, 10, and 24 d after weaning for analysis of the fecal microbiota by using 16S rRNA amplicon sequencing. The composition of fecal inoculum refrigerated at 3 to 5 °C was stable for at least 5 d. No diarrhea was reported in either group during the study period, making comparison of treated and control groups problematic. However, 16S rRNA gene analysis revealed microbial variability across time in both groups. Therefore, although the fecal microbiota of neither group of puppies mirrored the dam at any of the designated time points, the data provided fundamental and novel information regarding the dynamic maturation process of the fecal microbiota of puppies after weaning.
[PubMed - as supplied by publisher]
Select item 27656165
Front Microbiol. 2016 Sep 5;7:1364. doi: 10.3389/fmicb.2016.01364. eCollection 2016.
Composition of Ileal Bacterial Community in Grazing Goats Varies across Non-rumination, Transition and Rumination Stages of Life.
Jiao J1, Wu J2, Zhou C1, Tang S1, Wang M1, Tan Z1.
The establishment of gut microbiota is increasingly recognized as a crucial action in neonatal development, host health and productivity. We hypothesized that the ileal microbiome shifted as goats matured, and this colonization process would be associated with host fermentation capacity. To this end, 18 Liuyang black grazing goats were randomly slaughtered at d 0, 7, 28, 42, and 70. Ileal microbiota was profiled by Miseq sequencing of 16S rRNA gene of bacteria, and fermentation capacity [volatile fatty acid, activities of amylase, carboxymethylcellulase (CMCase) and xylanase] was determined using digesta sample. Principal coordinate analysis revealed that each age group harbored its distinct bacteria. Total bacteria copy number and most alpha diversity indexes increased (P < 0.01) from d 0 to 70. At the phylum level, abundances of Cyanobacteria (P = 0.018) and TM7 (P = 0.010) increased linearly, abundances of Bacteroidetes (P = 0.075) and Fibrobacteres (P = 0.076) tended to increase linearly, whist Proteobacteria abundance tended to decline quadratically (P = 0.052) with age. At the genus level, Enterococcus (30.9%), Lactobacillus (32.8%), and Escherichia (2.0%) dominated at d 0, while Prevotella, Butyrivibrio, Ruminococcus, SMB53, and Fibrobacter surged in abundance after day 20. The highest amylase activity was observed at day 42, while xylanase activity increased quadratically (P = 0.002) from days 28 to 70. Correlation analysis indicated that abundances of Bacteroides, Clostridium, Lactobacillus, Propionibacterium, Enterococcus, and p-75-a5 positively correlated with enzyme activity. Collectively, ileal bacteria in grazing goats assemble into distinct communities throughout development, and might participate in the improvement of host fermentation capacity.
age; bacterial colonization; fermentation capacity; goats; ileum
PMID: 27656165 DOI: 10.3389/fmicb.2016.01364
Select item 27655399
PLoS One. 2016 Sep 21;11(9):e0161836. doi: 10.1371/journal.pone.0161836.
Microbial Characterization of Qatari Barchan Sand Dunes.
Abdul Majid S1, Graw MF2, Chatziefthimiou AD1, Nguyen H2, Richer R1, Louge M3, Sultan AA1, Schloss P4, Hay AG2.
This study represents the first characterization of sand microbiota in migrating barchan sand dunes. Bacterial communities were studied through direct counts and cultivation, as well as 16S rRNA gene and metagenomic sequence analysis to gain an understanding of microbial abundance, diversity, and potential metabolic capabilities. Direct on-grain cell counts gave an average of 5.3 ± 0.4 x 105 cells g-1 of sand. Cultured isolates (N = 64) selected for 16S rRNA gene sequencing belonged to the phyla Actinobacteria (58%), Firmicutes (27%) and Proteobacteria (15%). Deep-sequencing of 16S rRNA gene amplicons from 18 dunes demonstrated a high relative abundance of Proteobacteria, particularly enteric bacteria, and a dune-specific-pattern of bacterial community composition that correlated with dune size. Shotgun metagenome sequences of two representative dunes were analyzed and found to have similar relative bacterial abundance, though the relative abundances of eukaryotic, viral and enterobacterial sequences were greater in sand from the dune closer to a camel-pen. Functional analysis revealed patterns similar to those observed in desert soils; however, the increased relative abundance of genes encoding sporulation and dormancy are consistent with the dune microbiome being well-adapted to the exceptionally hyper-arid Qatari desert.
PMID: 27655399 DOI: 10.1371/journal.pone.0161836
[PubMed - as supplied by publisher]
Select item 27654339
Int J Syst Evol Microbiol. 2016 Sep 18. doi: 10.1099/ijsem.0.001493. [Epub ahead of print]
High intraspecies heterogeneity within Staphylococcus sciuri and rejection of its classification into S. sciuri subsp. sciuri, S. sciuri subsp. carnaticus and S. sciuri subsp. rodentium.
Švec P1, Petráš P2, Pantůček R3, Doškař J4, Sedláček I5.
A polyphasic taxonomic approach was applied to strains of the species Staphylococcus sciuri in order to clarify the taxonomic legitimacy of the delineation of S. sciuri into S. sciuri subsp. sciuri, S. sciuri subsp. carnaticus and S. sciuri subsp. rodentium. A group of 81 S. sciuri isolates obtained from human (n = 62) and veterinary (n = 17) clinical materials, foods (n = 2) and ten reference and type strains obtained from the Czech Collection of Microorganisms were characterized by extensive biotyping using conventional tests and commercial identification kits (ID 32 Staph, STAPHYtest, Biolog Microbial ID System), matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry, automated ribotyping with EcoRI restriction enzyme, 16S-23S rRNA gene intergenic transcribed spacer PCR fingerprinting and repetitive sequence-based PCR fingerprinting with the (GTG)5 primer. Selected strains representing different ribotypes were further characterized using the β-subunit of RNA polymerase (rpoB) gene sequencing. Individual techniques revealed high heterogeneity within the analysed S. sciuri strains but differentiation of the investigated strains into groups corresponding to the aforementioned S. sciuri subspecies and supported by these techniques was not clearly revealed. Based on obtained results and data retrieved from literature we propose rejecting the separation of S. sciuri species into S. sciuri subsp. sciuri, S. sciuri subsp. carnaticus and S. sciuri subsp. rodentium and we suggest reclassification these subspecies as S. sciuri with the type strain W.E. Kloos SC 116T (=ATCC 29062T = BCRC 12927T = CCM 3473T = CCUG 15598T = CNCTC 5683T = DSM 20345T = JCM 2425T = NCTC 12103T).
PMID: 27654339 DOI: 10.1099/ijsem.0.001493
[PubMed - as supplied by publisher]
Select item 27650624
Ann Clin Lab Sci. 2016 Sep;46(5):549-51.
Rapid Diagnosis of Mycobacterium genavense Disseminated Infection by the Microseq 500: A Case Report in A Two Year Old HIV-Negative Child.
Arosio M1, Ruggeri M2, Buoro S3, Locatelli A2, Ortalli G4, D'Antiga L2, Farina C4.
This paper evaluates the capability of MicroSeq 500 instrument to improve the diagnosis of Mycobacterium genavense The strain was isolated from a two year old child admitted to our hospital for hepatosplenomegaly and massive abdominal lymphadenopathies. DNA was extracted from a lymph node and examined by amplifying 500 bp at the 5' end of 16S rRNA gene using MicroSeq 500 16S rDNA Bacterial Identification PCR kit. Sequencing reactions were performed with MicroSeq 500 16S rDNA Bacterial Identification Sequencing kit (Applied Biosystems, USA). Afterwards, sequences were analyzed by GenBank database and identified as Mycobacterium genavense, a slow-growing nontuberculous mycobacterium. The use of 16S rRNA gene sequencing for the identification of bacteria allows the recognition of new clinically relevant agents, eliminating the culture result waiting times.
© 2016 by the Association of Clinical Scientists, Inc.
HIV-negative; MICROSEQ 500 16S rDNA sequencing; Mycobacterium genavense; disseminated infection; pediatrics
[PubMed - in process]
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Select item 27650378
Mar Genomics. 2016 Sep 16. pii: S1874-7787(16)30091-5. doi: 10.1016/j.margen.2016.09.001. [Epub ahead of print]
Choice of molecular barcode will affect species prevalence but not bacterial community composition.
Lebret K1, Schroeder J2, Balestreri C2, Highfield A2, Cummings D3, Smyth T3, Schroeder D4.
The rapid advancement of next generation sequencing protocols in recent years has led to the diversification in the methods used to study microbial communities; however, how comparable the data generated from these different methods are, remains unclear. In this study we compared the taxonomic composition and seasonal dynamics of the bacterial community determined by two distinct 16s amplicon sequencing protocols: sequencing of the V6 region of the 16s rRNA gene using 454 pyrosequencing vs the V4 region of the 16s rRNA gene using the Illumina Hiseq 2500 platform. Significant differences between relative abundances at all taxonomic levels were observed; however, their seasonal dynamics between phyla were largely consistent between methods. This study highlights that care must be taken when comparing datasets generated from different methods.
Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.