scholarly journals Intestinal Microbiota of Fattening Pigs Offered Non-Fermented and Fermented Liquid Feed with and without the Supplementation of Non-Fermented Coarse Cereals

2020 ◽  
Vol 8 (5) ◽  
pp. 638 ◽  
Author(s):  
Sebastian Bunte ◽  
Richard Grone ◽  
Birgit Keller ◽  
Christoph Keller ◽  
Eric Galvez ◽  
...  
Keyword(s):  
Hypervariable Region ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Liquid Feed ◽  
Faecal Samples ◽  
Genus Lactobacillus ◽  
Miseq Platform ◽  
Small And Large Intestine

Introducing high numbers of lactic acid bacteria into the gastrointestinal tract of pigs via fermented liquid feed (FLF) could have an impact on intestinal bacterial ecosystems. Twenty piglets were allocated into four groups and fed a botanically identical liquid diet that was offered either non-fermented (twice), fully fermented or partially fermented but supplemented with 40% of non-fermented coarse cereals. Microbiota studies were performed on the small and large intestine digesta and faecal samples. A 16S rRNA gene amplification was performed within the hypervariable region V4 and sequenced with the Illumina MiSeq platform. R (version 3.5.2) was used for the statistical analyses. The digesta of the small intestines of pigs fed FLF were dominated by Lactobacillaceae (relative abundance up to 95%). In the colonic contents, the abundance of Lactobacillaceae was significantly higher only in the pigs fed the FLF supplemented with non-fermented coarse cereals. Additionally, the digesta of the small and large intestines as well as in the faeces of the pigs fed the FLF supplemented with non-fermented coarse cereals were significantly enriched for two operational taxonomic units (OTUs) belonging to the genus Lactobacillus and Bifidobacterium. The FLF supplemented with non-fermented coarse cereals had probiotic and prebiotic-like impacts on the intestinal and faecal bacterial composition of pigs.

scholarly journals Faecal Microbiota of Dogs Offered a Vegetarian Diet with or without the Supplementation of Feather Meal and either Cornmeal, Rye or Fermented Rye: A Preliminary Study

2020 ◽  
Vol 8 (9) ◽  
pp. 1363
Author(s):  
Julia Hankel ◽  
Amr Abd El-Wahab ◽  
Richard Grone ◽  
Birgit Keller ◽  
Eric Galvez ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Hypervariable Region ◽  
Illumina Miseq ◽  
Vegetarian Diet ◽  
Rrna Gene ◽  
Feather Meal ◽  
Illumina Miseq Platform ◽  
Faecal Samples ◽  
Miseq Platform ◽  
Preliminary Study

Anthropomorphism of dogs has affected feeding and the choice of components present in diets for dogs. Conflicting trends are present: raw or vegetarian appear more prevalent. Animal-derived proteins seem to have unfavourable impacts on intestinal microflora by decreasing the presence of Bacteroidetes. This preliminary study evaluates whether effects of diets with animal proteins on intestinal microbiota can be compensated by the addition of certain carbohydrates to dog diet. Eight female beagles were included in a cross-over study and fed a vegetarian diet or the same diet supplemented with feather meal (2.7%) and either 20% of cornmeal, fermented or non-fermented rye (moisture content of the diets about 42%). A 16S rRNA gene amplification was performed within the hypervariable region V4 on faecal samples and sequenced with the Illumina MiSeq platform. The Firmicutes/Bacteroidetes ratio tended to shift to the advantage of Firmicutes when feather meal and cornmeal were added (Firmicutes/Bacteroidetes ratio of 5.12 compared to 2.47 when offered the vegetarian diet) and tended to switch back to the advantage of Bacteroidetes if rye: fermented (2.17) or not (1.03) was added. The addition of rye might have the potential to compensate possible unfavourable effects of diets with animal proteins on intestinal microbiota of dogs.

scholarly journals Comparing Approaches for Capturing Bacterial Assemblages Associated with Symptomatic (Bacterial Blotch) and Asymptomatic Mushroom (Agaricus bisporus) Caps

2020 ◽  
Vol 4 (1) ◽  
pp. 90-99
Author(s):  
Samuel J. Martins ◽  
Ryan V. Trexler ◽  
Fabricio R. Vieira ◽  
John A. Pecchia ◽  
Prem P. Kandel ◽  
...  
Keyword(s):  
Health Status ◽  
Hypervariable Region ◽  
Target Surface ◽  
Operational Taxonomic Unit ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Associated Bacteria ◽  
Pseudomonas Spp ◽  
Shannon Diversity

Bacterial blotch is a complex of diseases, caused by Pseudomonas tolaasii and other Pseudomonas spp., whose growth may be influenced by other microorganisms associated with mushroom caps. The objectives of this work were to (i) compare methods for extracting DNA from mushroom caps to assess bacterial composition, and (ii) describe and quantify the composition of bacteria in and on symptomatic and asymptomatic mushroom caps. Symptomatic and asymptomatic mushrooms were collected at an organic farm in Pennsylvania and processed. Bacteria were removed from mushrooms by sonication to target surface-associated bacteria (washate), from whole mushrooms postsonication to target bacteria within or tightly adhering to the mushrooms (post-washate), or from whole macerated mushrooms to target all mushroom-associated bacteria in one sample (whole). Bacterial composition was determined through sequencing the V4 hypervariable region of the 16S rRNA gene on an Illumina MiSeq. Bacterial composition differed significantly based on mushroom health status and community removal method. Regardless of sampling approach, Proteobacteria and Bacteroidetes appeared as the most dominant phyla. In comparing the three extraction methods, higher Shannon diversity and Pielou’s evenness were observed for the washate and post-washate methods compared with whole mushroom sampling. Additionally, higher Shannon diversity, operational taxonomic unit richness, and Pielou’s evenness were found for the asymptomatic mushrooms when compared with symptomatic mushrooms. Pseudomonas spp. were overrepresented on mushroom surfaces (washate method), regardless of health status. This research made strides in describing the mushroom cap microbiome and established sampling methods that will allow researchers to target studies and isolation of specific bacterial taxa.

scholarly journals PSIX-6 Gastrointestinal microbiome of calves fed solid diets containing different levels and sources of NDF

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 418-419
Author(s):  
Gercino F Virgínio Júnior ◽  
Milaine Poczynek ◽  
Ana Paula Silva ◽  
Ariany Toledo ◽  
Amanda Cezar ◽  
...  
Keyword(s):  
Illumina Miseq ◽  
Diversity Indices ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Gastrointestinal Microbiome ◽  
Fecal Microbiome ◽  
Miseq Platform ◽  
Holstein Calves ◽  
Ad Libitum ◽  
Different Levels

Abstract Different levels and sources of NDF can modify the gastrointestinal microbiome. This study evaluated 18 Holstein calves housed in not-bedded suspended individual cages and fed one of three treatments: 22NDF - conventional starter containing 22% NDF (n = 7); 31NDF - starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22NDF+H - conventional starter with 22% NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily (24% CP; 18.5% fat; diluted to 12.5% solids), divided into two meals, being weaned at 8th week of age. After weaning, animals were housed in tropical shelters, fed with the respective solid diet and coast-cross hay ad libitum for all treatments. To evaluate the microbiome, ruminal fluid samples were collected using a modified Geishauser oral probe at weeks 2, 4, 6, 8 and 10, two hours after the morning feeding, and fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. Ruminal microbiome had no differences in diversity for the effects of weeks, treatments or interaction of both factors (Table 1). In feces, the diversity indices and evenness were higher for 22NDF+H when compared to 22NDF, with no difference for 31NDF. All indices were significantly affected by calves age. At birth, calves had the greatest diversity and richness. Week 1 and 2 had less evenness and diversity. Bacteroidota, Firmicutes_A and Firmicutes_C were the most abundant phylum in rumen and feces. The supply of hay was only effective in modifying the fecal microbiome of dairy calves, suggesting a resilience in the ruminal microbiome.

scholarly journals Transition of Bacterial Diversity and Composition in Tongue Microbiota during the First Two Years of Life

mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Shinya Kageyama ◽  
Mikari Asakawa ◽  
Toru Takeshita ◽  
Yukari Ihara ◽  
Shunsuke Kanno ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Bacterial Diversity ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Bacterial Composition ◽  
Content Type ◽  
Operational Taxonomic Units ◽  
Rrna Gene Sequencing

ABSTRACTNewborns are constantly exposed to various microbes from birth; hence, diverse commensal bacteria colonize the oral cavity. However, how or when these bacteria construct a complex and stable ecosystem remains unclear. This prospective cohort study examined the temporal changes in bacterial diversity and composition in tongue microbiota during infancy. We longitudinally collected a total of 464 tongue swab samples from 8 infants (age of <6 months at baseline) for approximately 2 years. We also collected samples from 32 children (aged 0 to 2 years) and 73 adults (aged 20 to 29 years) cross-sectionally as control groups. Bacterial diversities and compositions were determined by 16S rRNA gene sequencing. The tongue bacterial diversity in infancy, measured as the number of observed operational taxonomic units (OTUs), rapidly increased and nearly reached the same level as that in adults by around 80 weeks. The overall tongue bacterial composition in the transitional phase, 80 to 120 weeks, was more similar to that of adults than to that of the early exponential phase (EEP), 10 to 29 weeks, according to analysis of similarities. Dominant OTUs in the EEP corresponding toStreptococcus perorisandStreptococcus lactariusexponentially decreased immediately after EEP, around 30 to 49 weeks, whereas several OTUs corresponding toGranulicatella adiacens,Actinomyces odontolyticus, andFusobacterium periodonticumreciprocally increased during the same period. These results suggest that a drastic compositional shift of tongue microbiota occurs before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years.IMPORTANCEEvaluating the development of oral microbiota during infancy is important for understanding the subsequent colonization of bacterial species and the process of formation of mature microbiota in the oral cavity. We examined tongue microbiota longitudinally collected from 8 infants and found that drastic compositional shifts in tongue microbiota occur before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years. These results may be helpful for preventing the development of various diseases associated with oral microbiota throughout life.

scholarly journals 4425 Anibiotic-Resistant Organism Acquisition in Nursing Facility Patients

2020 ◽  
Vol 4 (s1) ◽  
pp. 2-3
Author(s):  
Joyce Wang ◽  
Marco Cassone ◽  
Kristen Gibson ◽  
Bonnie Lansing ◽  
Lona Mody ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Hypervariable Region ◽  
Resistant Organism ◽  
Rrna Gene ◽  
Bioinformatics Pipeline ◽  
Nursing Facility ◽  
Included Patient ◽  
Study Population ◽  
Miseq Platform

OBJECTIVES/GOALS: We investigated the association between gut microbiota features in newly admitted nursing facility (NF) patients and the acquisition of vancomycin-resistant Enterococcus (VRE) and/or resistant Gram-negative bacteria (rGNB) within 14 days. METHODS/STUDY POPULATION: Patients were recruited at 6 Michigan NFs from 09/16-08/18. VRE or rGNB colonization status was determined by culture swabs collected from multiple body sites at enrolment, day 7, and day 14. Our analysis focused on patients with no colonization at baseline, a perirectal swab collected at baseline, and at least one follow-up visit. The V4 hypervariable region of the 16S rRNA gene from bacterial DNA in each sample was PCR-amplified and sequenced on the MiSeq platform. Sequencing results were then processed with the mothur bioinformatics pipeline to classify bacterial taxa present in each sample. Taxa typically associated with the skin microbiota were removed. The primary outcome was acquisition of VRE and/or rGNB within 14 days. Exposures of interest included patient and microbiota characteristics. RESULTS/ANTICIPATED RESULTS: Among 61 patients, 18 (30%) acquired AROs within 14 days of enrolment (3 VRE, 13 rGNB, 2 both) (Table 1). The baseline microbiota features differed significantly in those who acquired a new ARO. Of the major 8 phyla found across samples, patients who acquired an ARO were depleted in the number of phyla present (5.74 ± 1.20 vs 5.06 ± 1.43; p = 0.037) (Fig. 1). The log10-transformed relative abundance of Enterococcus was enriched in patients who acquired an ARO (−0.32 ± 1.47) compared to those who did not (−1.68 ± 1.76; p = 0.021) (Fig. 2). Patients who did not acquire an ARO tended to harbour more butyrate-producing bacterial taxa and strict anaerobes, although the differences were not statistically significant (relative abundance of butyrate producer: 29.49 ± 22.09 vs 22.05 ± 17.76; anaerobes: 64.78 ± 23.54 vs 53.68 ± 27.61). DISCUSSION/SIGNIFICANCE OF IMPACT: Microbiota metrics calculated from perirectal samples are predictive of ARO acquisition. The clinical utility of perirectal samples thus warrants further assessment.

scholarly journals Metabarcoding Analyses of Gut Microbiota of Nile Tilapia (Oreochromis niloticus) from Lake Awassa and Lake Chamo, Ethiopia

2020 ◽  
Vol 8 (7) ◽  
pp. 1040
Author(s):  
Negash Kabtimer Bereded ◽  
Manuel Curto ◽  
Konrad J. Domig ◽  
Getachew Beneberu Abebe ◽  
Solomon Workneh Fanta ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Large Scale ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Operational Taxonomic Units ◽  
Nile Tilapia Oreochromis Niloticus ◽  
Miseq Platform ◽  
Ethiopian Lakes

The Nile tilapia (Oreochromis niloticus) gut harbors a diverse microbial community; however, their variation across gut regions, lumen and mucosa is not fully elucidated. In this study, gut microbiota of all samples across gut regions and sample types (luminal content and mucosa) were analyzed and compared from two Ethiopian lakes. Microbiota were characterized using 16S rRNA Illumina MiSeq platform sequencing. A total of 2061 operational taxonomic units (OTUs) were obtained and the results indicated that Nile tilapia from Lake Chamo harbored a much more diversified gut microbiota than Lake Awassa. In addition, the gut microbiota diversity varied significantly across the gut region based on the Chao1, Shannon and Simpson index. The microbiome analyses of all samples in the midgut region showed significantly higher values for alpha diversity (Chao 1, Shannon and Simpson). Beta diversity analysis revealed a clear separation of samples according to sampling areas and gut regions. The most abundant genera were Clostridium_sensu_stricto and Clostridium_XI genera across all samples. Between the two sampling lakes, two phyla, Phylum Fusobacteria and Cyanobacteria, were found to be significantly different. On the other hand, six phyla (Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria and Cyanobacteria) were significantly different across gut regions. In this study, we found that all samples shared a large core microbiota, comprising a relatively large number of OTUs, which was dominated by Proteobacteria, Firmicutes, Cyanobacteria, Fusobacteria and Actinobacteria. This study has established the bases for future large-scale investigations of gut microbiota of fishes in Ethiopian lakes.

scholarly journals PSXIII-29 Farm of origin has a major influence on the colonic microbiome but alterations due to selection for feed efficiency are also evident

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 475-475
Author(s):  
Stafford Vigors ◽  
Torres Sweeney
Keyword(s):  
Feed Efficiency ◽  
Hypervariable Region ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Nutrient Digestibility ◽  
Major Influence ◽  
Rrna Gene ◽  
Diversity Analysis ◽  
Selection For

Abstract While the intestinal microbiota is functionally important in nutrient digestibility and animal performance, the role of the microbiome in influencing feed efficiency is not well characterised. The objective of this experiment was to determine the relative influence of feed efficiency and farm of origin on the pig colonic microbiome. Animals were sourced from two geographically distinct locations in Ireland (farm A + B) and evaluated to identify pigs divergent in feed efficiency. The 8 most efficient (LRFI) & 8 least efficient (HRFI) pigs from farm A and 12 LRFI & 12 HRFI pigs from farm B were slaughtered. Colonic digesta was collected for sequencing of the V3-V4 hypervariable region of the bacterial 16S rRNA gene was performed on the Illumina MiSeq. Alpha diversity differed between the farms in this study with pigs from farm A having greater diversity based on Shannon and InvSimpson measures compared to pigs from farm B (P &lt; 0.05). In agreement with this observation, pigs grouped by farm of origin rather than RFI in the beta diversity analysis. However, despite variation between farms, interesting taxonomic differences were identified between RFI groups. Within the phylum Bacteroidetes, the LRFI pigs had increased abundance of two families BS11 (P &lt; 0.05) and a tendency towards increased Bacteroidaceae (P &lt; 0.10) relative to the HRFI group. At genus level, the LRFI pigs had a tendency towards increased Bacteroides and CF231 (P &lt; 0.10). In conclusion, while farm of origin has a substantial influence on microbial diversity in the pig colon, a microbial signature indicative of feed efficiency status was evident.

scholarly journals A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Siwen Deng ◽  
Heidi M.-L. Wipf ◽  
Grady Pierroz ◽  
Ted K. Raab ◽  
Rajnish Khanna ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Amendment ◽  
Bacterial Community Composition ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Microbiome ◽  
Plant Growth Promoting ◽  
Miseq Platform ◽  
Soil Rhizosphere

AbstractDespite growing interest in utilizing microbial-based methods for improving crop growth, much work still remains in elucidating how beneficial plant-microbe associations are established, and what role soil amendments play in shaping these interactions. Here, we describe a set of experiments that test the effect of a commercially available soil amendment, VESTA, on the soil and strawberry (Fragaria x ananassa Monterey) root bacterial microbiome. The bacterial communities of the soil, rhizosphere, and root from amendment-treated and untreated fields were profiled at four time points across the strawberry growing season using 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform. In all sample types, bacterial community composition and relative abundance were significantly altered with amendment application. Importantly, time point effects on composition are more pronounced in the root and rhizosphere, suggesting an interaction between plant development and treatment effect. Surprisingly, there was slight overlap between the taxa within the amendment and those enriched in plant and soil following treatment, suggesting that VESTA may act to rewire existing networks of organisms through an, as of yet, uncharacterized mechanism. These findings demonstrate that a commercial microbial soil amendment can impact the bacterial community structure of both roots and the surrounding environment.

scholarly journals Early Methanogenic Colonisation in the Faeces of Meishan and Yorkshire Piglets as Determined by Pyrosequencing Analysis

Archaea ◽  
2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Yong Su ◽  
Gaorui Bian ◽  
Zhigang Zhu ◽  
Hauke Smidt ◽  
Weiyun Zhu
Keyword(s):  
Energy Metabolism ◽  
Methanogenic Archaea ◽  
Rrna Gene ◽  
Methanogenic Community ◽  
Neonatal Piglets ◽  
Operational Taxonomic Units ◽  
Faecal Samples ◽  
16S Rrna Gene Pyrosequencing ◽  
Pyrosequencing Analysis ◽  
Early Establishment

Gut methanogenic archaea of monogastric animals are considered to be related to energy metabolism and adipose deposition of the host; however, information on their development in young piglets is limited. Thus, to investigate early methanogenic colonisation in the faeces of Meishan and Yorkshire piglets, faecal samples were collected from piglets at 1, 3, 7, and 14 days after birth and used to analyse the methanogenic community with 16S rRNA gene pyrosequencing. Results showed that the diversity of the methanogenic community in the faeces of neonatal piglets decreased from one to 14 days of age, as the total methanogen populations increased. The age of piglets, but not the breed, significantly affected the diversity of the methanogenic community which was dominated by the genusMethanobrevibacter. From the ages of one to 14 days, the abundance ofM. smithii-related operational taxonomic units (OTUs) increased significantly, while the abundances ofM. thaueri- andM. millerae-related OTUs decreased significantly. The substitution ofM. smithiiforM. thaueri/M. milleraewas faster in Yorkshire piglets than in Meishan piglets. These results suggest that the early establishment of microbiota in neonatal piglets is accompanied by dramatic changes in the methanogenic community, and that the changes vary among pigs of different genotypes.

scholarly journals Faecal bacterial composition in dairy cows shedding Mycobacterium avium subsp. paratuberculosis in faeces in comparison with nonshedding cows

2016 ◽  
Vol 62 (6) ◽  
pp. 538-541 ◽  
Author(s):  
Marija Kaevska ◽  
Petra Videnska ◽  
Karel Sedlar ◽  
Iva Bartejsova ◽  
Alena Kralova ◽  
...  
Keyword(s):  
Dairy Cows ◽  
Mycobacterium Avium ◽  
Mycobacterium Avium Subsp ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Bacterial Composition ◽  
Bacterial Populations ◽  
Faecal Samples ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
The 16S Rrna Gene

The aim of this study was to determine possible differences in the faecal microbiota of dairy cows infected with Mycobacterium avium subsp. paratuberculosis (Johne’s disease) in comparison with noninfected cows from the same herds. Faecal samples from cows in 4 herds were tested for M. avium subsp. paratuberculosis by real-time PCR, and faecal bacterial populations were analysed by 454 pyrosequencing of the 16S rRNA gene. The most notable differences between shedding and nonshedding cows were an increase in the genus Psychrobacter and a decrease in the genera Oscillospira, Ruminococcus, and Bifidobacterium in cows infected with M. avium subsp. paratuberculosis. The present study is the first to report the faecal microbial composition in dairy cows infected with M. avium subsp. paratuberculosis.

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