Insights into the Oral Bacterial Microbiota of Sows

The investigation of bacterial microbiota represents a developing research field in veterinary medicine intended to look for correlations between animal health and the balance within bacterial populations. The aim of the present work was to define the bacterial microbiota of the oral cavity of healthy sows, which had not been thoroughly described so far. In total, 22 samples of oral fluid were collected and analyzed by 16S-rRNA gene sequencing. CLC Genomics Workbench 20.0 (QIAGEN Digital Insights, Aarhus, Denmark) was then used to examine the results. The predominant orders were Lactobacillales, Clostridiales, and Corynebacteriales. Lactobacillaceae, Corynebacteriaceae, Moraxellaceae, Aerococcaceae, and Staphylococcaceae were the most represented families. As regards the most abundant genera, Lactobacillus, Corynebacterium, Acinetobacter, Staphylococcus, Rothia, Aerococcus, and Clostridium can be pointed out as the bacterial core microbiota. Sows were also divided into “gestating” and “lactating” groups, and mild differences were found between pregnant and lactating sows. The data herein described represent an original contribution to the knowledge of the porcine bacterial microbiota. Moreover, the choice of sows as experimental animals was strategic for identifying the adult microbial community. These data provide a basis for further studies on the oral bacterial microbiota of pigs.

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Characterization of Bacterial Microbiota Composition along the Gastrointestinal Tract in Rabbits

Animals ◽

10.3390/ani11010031 ◽

2020 ◽

Vol 11 (1) ◽

pp. 31

Author(s):

Elisa Cotozzolo ◽

Paola Cremonesi ◽

Giulio Curone ◽

Laura Menchetti ◽

Federica Riva ◽

...

Keyword(s):

Digestive Tract ◽

Large Intestine ◽

Bacterial Species ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Productive Performance ◽

Bacterial Populations ◽

Bacterial Microbiota ◽

Rrna Gene Sequencing

The microbiota is extremely important for the animal’s health, but, to date, knowledge on the intestinal microbiota of the rabbit is very limited. This study aimed to describe bacterial populations that inhabit the different gastrointestinal compartments of the rabbit: stomach, duodenum, jejunum, ileum, caecum, and colon. Samples of the luminal content from all compartments of 14 healthy New White Zealand rabbits were collected at slaughter and analyzed using next generation 16S rRNA Gene Sequencing. The findings uncovered considerable differences in the taxonomic levels among the regions of the digestive tract. Firmicutes were the most abundant phylum in all of the sections (45.9%), followed by Bacteroidetes in the large intestine (38.9%) and Euryarchaeota in the foregut (25.9%). Four clusters of bacterial populations were observed along the digestive system: (i) stomach, (ii) duodenum and jejunum, (iii) ileum, and (iv) large intestine. Caecum and colon showed the highest richness and diversity in bacterial species, while the highest variability was found in the upper digestive tract. Knowledge of the physiological microbiota of healthy rabbits could be important for preserving the health and welfare of the host as well as for finding strategies to manipulate the gut microbiota in order to also promote productive performance.

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Adaptation of Microbial Communities to Environmental Arsenic and Selection of Arsenite-Oxidizing Bacteria From Contaminated Groundwaters

Frontiers in Microbiology ◽

10.3389/fmicb.2021.634025 ◽

2021 ◽

Vol 12 ◽

Author(s):

Sarah Zecchin ◽

Simona Crognale ◽

Patrizia Zaccheo ◽

Stefano Fazi ◽

Stefano Amalfitano ◽

...

Keyword(s):

Microbial Communities ◽

Inorganic Arsenic ◽

16S Rrna Gene Sequencing ◽

Northern Italy ◽

Rrna Gene ◽

Bacterial Populations ◽

Main Driver ◽

Rrna Gene Sequencing ◽

Arsenite Oxidizing Bacteria ◽

Card Fish

Arsenic mobilization in groundwater systems is driven by a variety of functionally diverse microorganisms and complex interconnections between different physicochemical factors. In order to unravel this great ecosystem complexity, groundwaters with varying background concentrations and speciation of arsenic were considered in the Po Plain (Northern Italy), one of the most populated areas in Europe affected by metalloid contamination. High-throughput Illumina 16S rRNA gene sequencing, CARD-FISH and enrichment of arsenic-transforming consortia showed that among the analyzed groundwaters, diverse microbial communities were present, both in terms of diversity and functionality. Oxidized inorganic arsenic [arsenite, As(III)] was the main driver that shaped each community. Several uncharacterized members of the genus Pseudomonas, putatively involved in metalloid transformation, were revealed in situ in the most contaminated samples. With a cultivation approach, arsenic metabolisms potentially active at the site were evidenced. In chemolithoautotrophic conditions, As(III) oxidation rate linearly correlated to As(III) concentration measured at the parental sites, suggesting that local As(III) concentration was a relevant factor that selected for As(III)-oxidizing bacterial populations. In view of the exploitation of these As(III)-oxidizing consortia in biotechnology-based arsenic bioremediation actions, these results suggest that contaminated aquifers in Northern Italy host unexplored microbial populations that provide essential ecosystem services.

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Early-Life Intake of an Isotonic Protein Drink Improves the Gut Microbial Profile of Piglets

Animals ◽

10.3390/ani10050879 ◽

2020 ◽

Vol 10 (5) ◽

pp. 879

Author(s):

Stefan G. Buzoianu ◽

Ava M. Firth ◽

CallaBria Putrino ◽

Fabio Vannucci

Keyword(s):

Environmental Changes ◽

16S Rrna Gene Sequencing ◽

Control Group ◽

Rrna Gene ◽

Bacterial Populations ◽

E Coli ◽

Microbial Profile ◽

Before And After ◽

Potential Alternative ◽

Rrna Gene Sequencing

A healthy microbial community in the gut of piglets is critical to minimize the negative performance consequences associated with dietary and environmental changes that occur at weaning. Tonisity Px, an isotonic protein drink, is a potential alternative to balance the gut microbiota as it contains key ingredients for nourishing the small intestine. In the present study, 16 litters comprising 161 piglets were randomly allocated to a group to which Tonisity Px was provided from days 2 to 8 of age (TPX group) or to a control group, to which no Tonisity Px was provided. The TPX group also received Tonisity Px in the 3 days before and after weaning. At days 9, 17, and 30 of age, fecal and ileum samples were collected from piglets belonging to both groups and analyzed using 16S rRNA gene sequencing, semiquantitative PCR of Rotavirus serogroups, and semiquantitative Escherichia coli culture. Overall, Tonisity Px increased the abundance of beneficial bacterial populations (Lactobacillus and Bacteroides species) and reduced potentially pathogenic bacterial populations (E. coli and Prevotellaceae), in both the pre-weaning and post-weaning periods.

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Characterization of Cutaneous Bacterial Microbiota from Superficial Pyoderma Forms in Atopic Dogs

Pathogens ◽

10.3390/pathogens9080638 ◽

2020 ◽

Vol 9 (8) ◽

pp. 638

Author(s):

Caitlin E. Older ◽

Aline Rodrigues Hoffmann ◽

Kathleen Hoover ◽

Frane Banovic

Keyword(s):

Quantitative Polymerase Chain Reaction ◽

16S Rrna Gene Sequencing ◽

Molecular Techniques ◽

Rrna Gene ◽

Bacterial Microbiota ◽

Starting Point ◽

Rrna Gene Sequencing ◽

Antimicrobial Treatments ◽

Staphylococcus Spp

Although Staphylococcus pseudintermedius is considered the major pathogen associated with superficial canine pyoderma, no study has investigated the entire bacterial community in these lesions with molecular techniques. The objectives of this study were to characterize the bacterial microbiota in two forms of superficial canine pyoderma lesions, superficial bacterial folliculitis (SBF) and epidermal collarette (EC), especially in terms of the staphylococcal community. Swabs from 12 SBF and 9 EC lesions were obtained from eight and six atopic dogs, respectively. Eight samples from the axilla and groin of four healthy dogs served as controls. DNA was extracted for 16S rRNA gene sequencing and quantitative polymerase chain reaction of Staphylococcus spp. and S. pseudintermedius. Healthy skin samples harbored significantly more diverse bacterial communities than pyoderma samples. Healthy samples had communities that were more similar to each other, and were distinct from pyoderma samples. Staphylococcus spp. abundance was increased in pyoderma samples, especially those from EC samples. Although determining species-level identities of staphylococcal sequences revealed many species, S. pseudintermedius was the primary staphylococcal species found in all sample types. As expected, there are many differences in the microbiota when comparing healthy and canine pyoderma lesions samples. These lesions do not seem to be associated with a change in the relative abundance of specific Staphylococcus species, but simply an overall increase in Staphylococcus spp. abundance. The results of this study provide a starting point for future studies investigating how antimicrobial treatments may further change the microbiota associated with these lesions.

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Strain Diversity of Pseudomonas fluorescens Group with Potential Blue Pigment Phenotype Isolated from Dairy Products

Journal of Food Protection ◽

10.4315/0362-028x.jfp-15-589 ◽

2016 ◽

Vol 79 (8) ◽

pp. 1430-1435 ◽

Cited By ~ 13

Author(s):

MARGHERITA CHIERICI ◽

CLAUDIA PICOZZI ◽

MARISA GRAZIA LA SPINA ◽

CARLA ORSI ◽

ILEANA VIGENTINI ◽

...

Keyword(s):

Pseudomonas Fluorescens ◽

Sodium Succinate ◽

16S Rrna Gene Sequencing ◽

Pigment Production ◽

Blue Pigment ◽

Rrna Gene ◽

Bacterial Populations ◽

Strain Diversity ◽

Blue Discoloration ◽

Rrna Gene Sequencing

ABSTRACT The blue discoloration in Mozzarella cheese comes from bacterial spoilage due to contamination with Pseudomonas. Fourteen Pseudomonas fluorescens strains from international collections and 55 new isolates of dominant bacterial populations from spoiled fresh cheese samples were examined to assess genotypic and phenotypic strain diversity. Isolates were identified by 16S rRNA gene sequencing and tested for the production of the blue pigment at various temperatures on Mascarpone agar and in Mozzarella preserving fluid (the salty water in which the cheese is conserved, which becomes enriched by cheese minerals and peptides during storage). Pulsed-field gel electrophoresis analysis after treatment with the endonuclease SpeI separated the isolates into 42 genotypes at a similarity level of 80%. Based on the pulsotype clustering, 12 representative strains producing the blue discoloration were chosen for the multilocus sequence typing targeting the gyrB, glnS, ileS, nuoD, recA, rpoB, and rpoD genes. Four new sequence typing profiles were discovered, and the concatenated sequences of the investigated loci grouped the tested strains into the so-called “blue branch” of the P. fluorescens phylogenetic tree, confirming the linkage between pigment production and a specific genomic cluster. Growth temperature affected pigment production; the blue discoloration appeared at 4 and 14°C but not at 30°C. Similarly, the carbon source influenced the phenomenon; the blue phenotype was generated in the presence of glucose but not in the presence of galactose, sodium succinate, sodium citrate, or sodium lactate.

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Nitrogen Fertilisers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants

10.1101/672162 ◽

2019 ◽

Author(s):

Federica Caradonia ◽

Domenico Ronga ◽

Marcello Catellani ◽

Cleber Vinícius Giaretta Azevedo ◽

Rodrigo Alegria Terrazas ◽

...

Keyword(s):

Crop Production ◽

Developmental Stages ◽

Agricultural Practices ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Two Component System ◽

Tomato Root ◽

Bacterial Microbiota ◽

Rrna Gene Sequencing ◽

Soil Interface

ABSTRACTThe microbial communities thriving at the root-soil interface have the potential to improve plant growth and sustainable crop production. Yet, how agricultural practices, such as the application of either mineral or organic nitrogen fertilisers, impact on the composition and functions of these communities remains to be fully elucidated. By deploying a two-pronged 16S rRNA gene sequencing and predictive metagenomics approach we demonstrated that the bacterial microbiota of field-grown tomato (Solanum lycopersicum) plants is the product of a selective process that progressively differentiates between rhizosphere and root microhabitats. This process initiates as early as plants are in a nursery stage and it is then more marked at late developmental stages, in particular at harvest. This selection acts on both the bacterial relative abundances and phylogenetic assignments, with a bias for the enrichment of members of the phylum Actinobacteria in the root compartment. Digestate-based and mineral-based nitrogen fertilisers trigger a distinct bacterial enrichment in both rhizosphere and root microhabitats. This compositional diversification mirrors a predicted functional diversification of the root-inhabiting communities, manifested predominantly by the differential enrichment of genes associated to ABC transporters and the two-component system. Together, our data suggest that the microbiota thriving at the tomato root-soil interface is modulated by and in responses to the type of nitrogen fertiliser applied to the field.

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Nitrogen Fertilizers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants

Phytobiomes Journal ◽

10.1094/pbiomes-06-19-0028-r ◽

2019 ◽

Vol 3 (4) ◽

pp. 315-325 ◽

Cited By ~ 7

Author(s):

Federica Caradonia ◽

Domenico Ronga ◽

Marcello Catellani ◽

Cleber Vinícius Giaretta Azevedo ◽

Rodrigo Alegria Terrazas ◽

...

Keyword(s):

Crop Production ◽

Developmental Stages ◽

Agricultural Practices ◽

16S Rrna Gene Sequencing ◽

Nitrogen Fertilizers ◽

Rrna Gene ◽

Tomato Root ◽

Bacterial Microbiota ◽

Rrna Gene Sequencing ◽

Soil Interface

The microbial communities thriving at the root−soil interface have the potential to improve plant growth and sustainable crop production. Yet, how agricultural practices, such as the application of either mineral or organic nitrogen fertilizers, impact on the composition and functions of these communities remains to be fully elucidated. By deploying a two-pronged 16S rRNA gene sequencing and predictive metagenomics approach, we demonstrated that the bacterial microbiota of field-grown tomato (Solanum lycopersicum) plants is the product of a selective process that progressively differentiates between rhizosphere and root microhabitats. This process initiates as early as plants are in a nursery stage and it is then more marked at late developmental stages, in particular at harvest. This selection acts on both the bacterial relative abundances and phylogenetic assignments, with a bias for the enrichment of members of the phylum Actinobacteria in the root compartment. Digestate-based and mineral-based nitrogen fertilizers trigger a distinct bacterial enrichment in both rhizosphere and root microhabitats. This compositional diversification mirrors a predicted functional diversification of the root-inhabiting communities, manifested predominantly by the differential enrichment of genes associated to ABC transporters and the two-component system. Together, our data suggest that the microbiota thriving at the tomato root−soil interface is modulated by and in responses to the type of nitrogen fertilizer applied to the field. [Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

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Assessment of Oral Vancomycin-Induced Alterations in Gut Bacterial Microbiota and Metabolome of Healthy Men

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.629438 ◽

2021 ◽

Vol 11 ◽

Author(s):

Andrew HyoungJin Kim ◽

Yujin Lee ◽

Eunwoo Kim ◽

Sang Chun Ji ◽

Jae-Yong Chung ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Oral Vancomycin ◽

Healthy Men ◽

Bacterial Microbiota ◽

Rrna Gene Sequencing ◽

Metabolomics Analysis

Several classes of antibiotics have reduced the mortality caused by infectious diseases; however, orally administered antibiotics alter the composition of gut microbiota, leading to dysbiosis-related disease. Therefore, in this study, we used 16S rRNA gene sequencing- and metabolomics-based approaches to investigate the effects of oral vancomycin on gut bacterial microbiota and the metabolome in biospecimens collected from healthy men. Samples collected from 11 healthy men were analyzed using 16S rRNA gene sequencing and metabolomics. 16S rRNA gene sequencing was performed to analyze the gut bacterial microbiota, and GC-TOFMS-based untargeted metabolomics was performed to analyze fecal, urine, and plasma metabolomics. Spearman’s rank correlation was utilized to explore the associations between gut bacterial microbiota and metabolome. Fecal 16S rRNA gene sequencing analysis showed decreased relative abundance of genera belonging to the phyla Bacteroidetes and Firmicutes, and increased relative abundance of genera of the phyla Proteobacteria and Fusobacteria. Fecal metabolomics analysis showed that levels of uracil, L-aspartic acid, lithocholic acid, and deoxycholic acid were significantly higher at baseline, whereas that of dihydrouracil was significantly higher after vancomycin administration. No significant metabolic markers were selected from urine and plasma metabolomics analysis. This study demonstrates that oral vancomycin administration induces alterations in gut bacterial microbiota and metabolome. Correlation analysis between our two datasets shows that alteration of the gut bacterial microbiota, induced by oral vancomycin, potentially affected the systemic activity of dihydropyrimidine dehydrogenase. This correlation should be further examined in future studies to define the effects of gut bacterial microbiota on drug-metabolizing enzymes, thereby contributing to the development of personalized therapy.

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Analysis of the Microbial Intestinal Tract in Broiler Chickens during the Rearing Period

Biology ◽

10.3390/biology10090942 ◽

2021 ◽

Vol 10 (9) ◽

pp. 942

Author(s):

Alessandro Stamilla ◽

Susana Ruiz-Ruiz ◽

Alejandro Artacho ◽

Javier Pons ◽

Antonino Messina ◽

...

Keyword(s):

Broiler Chickens ◽

Animal Health ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Microbial Composition ◽

Commercial Diet ◽

Associated Functions ◽

Rrna Gene Sequencing ◽

Proximal Intestine

Gut microbiota contributes to animal health. However, identifying which microorganisms or associated functions are involved remains, still, difficult to assess. In the present study, the microbiota of healthy broiler chickens, under controlled diet and farm conditions, was investigated by 16S rRNA gene sequencing in four intestine segments and at four ages. In detail, 210 Ross-308 male chickens were raised according to the EU guidelines and fed on a commercial diet. The duodenum, jejunum, ileum, and caecum microbiota were analyzed at 11, 24, 35, and 46 days of life. Although the microbial composition was revealed as homogeneous 11 days after chicks hatched, it was found to be similar in the proximal intestine segments and different in ileum and caecum, where almost the same genera and species were detected with different relative abundances. Although changes during the later growth stage were revealed, each genus remained relatively unchanged. Lactobacillus mostly colonized the upper tract of the intestine, whereas the Escherichia/Shigella genus the ileum. Clostridium and Bacteroides genera were predominant in the caecum, where the highest richness of bacterial taxa was observed. We also analyze and discuss the predicted role of the microbiota for each intestine segment and its potential involvement in nutrient digestion and absorption.

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Estructura de la comunidad bacteriana en diferentes tejidos de Lobatus gigas silvestres (Linnaeus, 1758) de la Reserva de Biosfera Seaflower del Caribe

Bulletin of Marine and Coastal Research ◽

10.25268/bimc.invemar.2018.47.2.746 ◽

2018 ◽

Vol 47 (2) ◽

Author(s):

Mónica Marcela Higuita-Valencia ◽

Olga Inés Montoya Campuzano ◽

Edna Judith Márquez Fernández ◽

Claudia Ximena Moreno Herrera

Keyword(s):

Biosphere Reserve ◽

16S Rrna Gene Sequencing ◽

Reproductive Rate ◽

Rrna Gene ◽

Bacterial Populations ◽

Microbiological Methods ◽

Culture Independent ◽

Total Dna ◽

Rrna Gene Sequencing ◽

Genetic Profiles

The microbial diversity of Lobatus gigas has not been thoroughly studied despite of them is a specie endangered. Knowledge of microbiota may help to improve the conservation and cultivation of this species. The objective of this study was to evaluate the bacterial populationsassociated with the gonad and the gut compartments of the wild endangered L. gigas from the Caribbean Seaflower Biosphere Reserve, using microbiological methods and culture-independent molecular tools. The genetic profiles of the bacterial populations were generated and Temporal Temperature Gradient Electrophoresis (TTGE) was used to compare them with total DNA. A genetic and statistical analysis of the bacterial communities revealed a low level of diversity in gonad tissue based on the number of bands detected using TTGE. In addition, statistical differences in bacterial community structure were found between the foregut and hindgut tissue of L. gigas. The dominant phylogenetic affiliations of the gonad bacteria, as determined using 16S rRNA gene sequencing, belong to Ralstonia (50%). The possible involvement of this genus in the reproduction and development of the conch is discussed. On the other hand, the bacterial phylotypes from foregut and hindgut included members of Alphaproteobactera (12.5%), Betaproteobacteria (12.5%), Gammaproteobacteria (12.5%), Bacilli (31.25%), Clostridia (6.25%), Actinobacteria (6.25%), Mollicutes (6.25%) and Deinococci (6.25%) classes. Knowing the composition of the gonad and foregut and hindgut bacteria of L. gigas is the first step toward exploring the proper management of this species, as well as provides useful information to future researches that allow a better understanding of the role of these bacterial populations in the health and reproductive rate of L. gigas.

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