scholarly journals Fast and slow-growing breeds: characterisation of broiler caecal microbiota development throughout the growing period

2020 ◽  
Author(s):  
Laura Montoro Dasí ◽  
Arantxa Villagra ◽  
Maria de Toro ◽  
María Teresa Pérez-Gracia ◽  
Santiago Vega ◽  
...  
Keyword(s):  
16S Rrna ◽  
Animal Health ◽  
Resistant Bacteria ◽  
Production Cycle ◽  
Sequencing Analysis ◽  
Poultry Production ◽  
Growing Period ◽  
Rrna Sequencing ◽  
Slow Growing ◽  
Caecal Microbiota

Abstract Background: The caecal microbiota and its modulation play an important role in animal health, productivity and disease control in poultry production. In this sense, it could be considered as a biomarker of poultry health. Furthermore, due to the emergence of resistant bacteria and the increasing social pressure to establish animal-friendly management on farms, producers are motivated to select more extensive and antibiotic-free breeds. It is therefore necessary to gain better knowledge on the development of major bacteria in healthy broilers, both in commercial fast-growing and in new slow-growing breeds. Hence, the aim of this study was to characterise caecal microbiota in two genetic poultry breeds throughout the growing period using 16S rRNA sequencing analysis. Results: A total of 50 caecal pools (25 per breed) were sequenced by the 16S rRNA method. The complexity of caecal microbiota composition increased significantly as animals grew. Furthermore, there were statistical differences between breeds at the end of the growing period. The dominant phyla throughout the production cycle were Firmicutes, Bacteroidetes and Proteobacteria. The predominantly identified genera were Ruminococcus spp., Lactobacillus spp. and Bacteroides spp.Conclusion: The results showed that the main caecal bacteria for both breeds were similar. Thus, these phyla or genera should be considered as biomarkers of poultry health in the evaluation of different treatments applied to animals.

scholarly journals Fast and Slow-Growing Management Systems: Characterisation of Broiler Caecal Microbiota Development throughout the Growing Period

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1401
Author(s):  
Laura Montoro-Dasi ◽  
Arantxa Villagra ◽  
María de Toro ◽  
María Teresa Pérez-Gracia ◽  
Santiago Vega ◽  
...  
Keyword(s):  
Production Systems ◽  
Management Systems ◽  
Resistant Bacteria ◽  
Production Cycle ◽  
Antibiotic Administration ◽  
Sequencing Analysis ◽  
Growing Period ◽  
Slow Growing ◽  
Lactobacillus Spp ◽  
Caecal Microbiota

Caecal microbiota and its modulation play an important role in poultry health, productivity and disease control. Moreover, due to the emergence of antimicrobial-resistant bacteria, society is pressing for a reduction in antibiotic administration by finding effective alternatives at farm level, such as less intensified production systems. Hence, the aim of this study was to characterise the caecal microbiota in two different broiler management systems, fast and slow-growing, using 16S rRNA sequencing analysis. To this end 576 broilers were reared in two different management systems (fast and slow-growing). Results showed that Firmicutes represented the dominant phylum for both systems. At the onset, Proteobacteria was the second prevalent phylum for fast and slow-growing breeds, outnumbering the Bacteroidetes. However, during the rest of the production cycle, Bacteroidetes was more abundant than Proteobacteria in both groups. Finally, regardless of the management system, the most predominant genera identified were Oscillospira spp., Ruminococcus spp., Coprococcus spp., Lactobacillus spp. and Bacteroides spp. In conclusion, fast and slow-growing broiler microbiota are in constant development throughout rearing, being relatively stable at 21 days of age. Regarding the genus, it should be noted that the three most abundant groups for both systems, Ruminococcus spp., Lactobacillus spp. and Bacteroides spp., are related to better productive performance and intestinal health.

scholarly journals Assessment of Microbiota Modulation in Poultry to Combat Infectious Diseases

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 615
Author(s):  
Laura Montoro-Dasi ◽  
Arantxa Villagra ◽  
María de Toro ◽  
María Teresa Pérez-Gracia ◽  
Santiago Vega ◽  
...  
Keyword(s):  
Management Practices ◽  
Animal Health ◽  
Farm Management ◽  
Sequencing Analysis ◽  
Microbiota Composition ◽  
Public Concern ◽  
Infectious Disease Control ◽  
Growing Period ◽  
Rrna Sequencing ◽  
Microbiota Diversity

Poultry is one of the main agricultural sub-sectors worldwide. However, public concern regarding animal welfare and antimicrobial resistance has risen in recent years. Due to the influence of management practices on microbiota, it might be considered to evaluate poultry welfare and health. Therefore, the objective of this research was to analyse the influence on microbiota balance of broilers under commercial and optimal farm conditions, using 16S rRNA sequencing analysis. The research was performed in two identical poultry houses (commercial vs. optimal). Results showed a higher level of microbiota complexity in the group reared under optimal farm conditions at the end of rearing. Regarding microbiota composition, Firmicutes was the dominant phylum during the entire growing period. However, the second most prevalent phylum was Proteobacteria at the arrival day, and Bacteroidetes from the mid-period onward in both groups. Moreover, the most predominant genera identified were Oscillospira, Ruminococcus, Bacteroides, and Coprococcus. In conclusion, it is necessary to optimize farm management as much as possible. Using gut microbiota diversity and composition as biomarkers of animal health could be an important tool for infectious disease control, with the aim of reducing the administration of antibiotics at field level.

scholarly journals Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 40
Author(s):  
Liang Cui ◽  
Bitong Zhu ◽  
Xiaobo Zhang ◽  
Zhuhua Chan ◽  
Chungui Zhao ◽  
...  
Keyword(s):  
Water Quality ◽  
16S Rrna ◽  
Relative Abundance ◽  
Animal Health ◽  
Denitrifying Bacteria ◽  
Nitrite Reduction ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Analysis ◽  
Shrimp Culture

The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

scholarly journals First Detection of Carbapenem-Resistant Escherichia fergusonii Strains Harbouring Beta-Lactamase Genes from Clinical Samples

Pathogens ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 164 ◽  
Author(s):  
Tomilola Adesina ◽  
Obinna Nwinyi ◽  
Nandita De ◽  
Olayemi Akinnola ◽  
Emmanuel Omonigbehin
Keyword(s):  
16S Rrna ◽  
16S Rrna Sequencing ◽  
Clinical Samples ◽  
Sequencing Analysis ◽  
Beta Lactamase ◽  
Extended Spectrum Beta Lactamase ◽  
Carbapenem Resistant ◽  
Evolutionary Relatedness ◽  
Rrna Sequencing ◽  
Physiological Tests

Recently discovered extraintestinal Escherichia fergusonii obtained from non-clinical samples has exhibited the potential for acquiring multiple beta-lactamase genes, just like many extraintestinal Escherichia coli strains. Albeit, they are often omitted or classified as E. coli. This study aimed to, therefore, identify carbapenem-resistant extended-spectrum beta-lactamase (ESBL) producing E. fergusonii isolates from clinical samples, determine their evolutionary relatedness using 16S rRNA sequencing analysis and screen for beta-lactamase genes. A total of 135 septic wound samples were obtained from patients on referral at a General Hospital in Lagos, Nigeria. For the phenotypic identification of isolates from culture-positive samples, morphological, and physiological tests were carried out. Identities of the isolates harbouring beta-lactamase genes were assigned to their genus strains using the 16S rRNA sequencing. The Kirby Bauer disc diffusion technique and double-disc synergy test were used to screen isolates for multidrug resistance and ESBL production. Carbapenem-resistant ESBL producing isolates were screened for beta-lactamase genes in a polymerase chain reaction. Three E. fergusonii isolates (CR11, CR35 and CR49) were obtained during this study. E. fergusonii strains were motile, non-lactose and non-sorbitol fermenting but positive for cellobiose and adonitol fermentation. The I6S rRNA assigned the phenotypically identified isolates to E. fergusonii species. All three isolates were multidrug-resistant, carbapenem-resistant and ESBL producers. Isolates CR11 and CR35 harboured cefotaximase (CTX-M) and temoniera (TEM) beta-lactamase genes while CR49 harboured sulfhydryl variable (SHV) beta-lactamase gene. We herein report the detection of multiple beta-lactamase genes in carbapenem-resistant ESBL producing E. fergusonii from clinical samples.

scholarly journals Eggshell and Feed Microbiota Do Not Represent Major Sources of Gut Anaerobes for Chickens in Commercial Production

2021 ◽  
Vol 9 (7) ◽  
pp. 1480
Author(s):  
Jiri Volf ◽  
Magdalena Crhanova ◽  
Daniela Karasova ◽  
Marcela Faldynova ◽  
Tereza Kubasova ◽  
...  
Keyword(s):  
Drinking Water ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Commercial Production ◽  
Neonatal Development ◽  
Egg Incubation ◽  
Hatching Process ◽  
Rrna Sequencing ◽  
Chicken Gut Microbiota ◽  
Caecal Microbiota

In this study, we addressed the origin of chicken gut microbiota in commercial production by a comparison of eggshell and feed microbiota with caecal microbiota of 7-day-old chickens, using microbiota analysis by 16S rRNA sequencing. In addition, we tested at which timepoint during prenatal or neonatal development it is possible to successfully administer probiotics. We found that eggshell microbiota was a combination of environmental and adult hen gut microbiota but was completely different from caecal microbiota of 7-day-old chicks. Similarly, we observed that the composition of feed microbiota was different from caecal microbiota. Neither eggshell nor feed acted as an important source of gut microbiota for the chickens in commercial production. Following the experimental administration of potential probiotics, we found that chickens can be colonised only when already hatched and active. Spraying of eggs with gut anaerobes during egg incubation or hatching itself did not result in effective chicken colonisation. Such conclusions should be considered when selecting and administering probiotics to chickens in hatcheries. Eggshells, feed or drinking water do not act as major sources of gut microbiota. Newly hatched chickens must be colonised from additional sources, such as air dust with spores of Clostridiales. The natural colonisation starts only when chickens are already hatched, as spraying of eggs or even chickens at the very beginning of the hatching process did not result in efficient colonisation.

scholarly journals Isolation of actinomycetes from Nile tilapia (Oreochromis niloticus) cultivated in semi-intensive systems from Morelos, Mexico central zone

2020 ◽  
Vol 48 (5) ◽  
pp. 758-767
Author(s):  
Rocio Parra-Laca ◽  
Laura Hernández-Andrade ◽  
Gary García-Espinosa ◽  
Elizabeth Loza-Rubio
Keyword(s):  
16S Rrna ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Central Zone ◽  
16S Rrna Sequencing ◽  
Sequencing Analysis ◽  
Nile Tilapia Oreochromis Niloticus ◽  
Rrna Sequencing ◽  
16S Rrna Sequencing Analysis

The production of Nile tilapia (Oreochromis niloticus) has good technological development; however, today, it is still necessary to make it more efficient. One way to increase efficiency is to prevent disease and improve the food conversion factor. Since previous investigations of tilapia microbiota detected a high proportion of organisms belonging to the order Actinomycetes, this study was to isolate, identify, and describe the species of bacteria microbiota belonging to the cultured Nile tilapia. These were done with Nile tilapia grown in a warm sub-humid climate during spring and summer seasons. The biopsy of different organs was performed for bacteriological culture and 16S rRNA sequencing analysis. From the 180 tissue samples, 49 isolates of the order Actinomycetes were obtained, representing ten species from seven genera: Microbacterium, Brevibacterium, Cellulomonas, Corynebacterium, Kocuria, Actinomyces, and Micrococcus. In spring, Microbacterium dominated, accounting for 74% of the total population. In the summer, lower diversity was observed, with 39% represented by Microbacterium. 16S rRNA sequencing analysis enabled the classification of Actinomyces neuii and Microbacterium lacticum as Kocuria varians and Agromyces indicus; the classification of Microbacterium imperiale as Rhodococcus and Micrococcus luteus was confirmed. No sequences of K. varians have been reported in fish. Microbacterium dextranoliticum showed high similarity to environmental samples. Here is the first study that analyzes the bacteria population in tilapia at the genetic level with an ecosystem approach, present in healthy cultured tilapia, indicating their beneficial associations with the host, making them candidates as probiotics, among other possible functions, applicable in tilapia cultivation.

scholarly journals Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Chhedi Lal Gupta ◽  
Shlomo E. Blum ◽  
Karuppasamy Kattusamy ◽  
Tali Daniel ◽  
Shelly Druyan ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Resistant Bacteria ◽  
Production Cycle ◽  
Antibiotic Administration ◽  
Poultry Production ◽  
Antibiotic Resistant Bacteria ◽  
Antibiotic Resistant ◽  
E Coli ◽  
Vancomycin Resistant ◽  
Growth Promoting

Abstract Background Therapeutic and growth-promoting antibiotics are frequently used in broiler production. Indirect evidence indicates that these practices are linked to the proliferation of antimicrobial resistance (AMR), the spread of antibiotic-resistant bacteria from food animals to humans, and the environment, but there is a lack of comprehensive experimental data supporting this. We investigated the effects of growth promotor (bacitracin) and therapeutic (enrofloxacin) antibiotic administration on AMR in broilers for the duration of a production cycle, using a holistic approach that integrated both culture-dependent and culture-independent methods. We specifically focused on pathogen-harboring families (Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae). Results Antibiotic-resistant bacteria and antibiotic resistance genes were ubiquitous in chicken cloaca and litter regardless of antibiotic administration. Environment (cloaca vs. litter) and growth stage were the primary drivers of variation in the microbiomes and resistomes, with increased bacterial diversity and a general decrease in abundance of the pathogen-harboring families with age. Bacitracin-fed groups had higher levels of bacitracin resistance genes and of vancomycin-resistant Enterococcaceae (total Enterococcaceae counts were not higher). Although metagenomic analyses classified 28–76% of the Enterococcaceae as the commensal human pathogens E. faecalis and E. faecium, culture-based analysis suggested that approximately 98% of the vancomycin-resistant Enterococcaceae were avian and not human-associated, suggesting differences in the taxonomic profiles of the resistant and non-resistant strains. Enrofloxacin treatments had varying effects, but generally facilitated increased relative abundance of multidrug-resistant Enterobacteriaceae strains, which were primarily E. coli. Metagenomic approaches revealed a diverse array of Staphylococcus spp., but the opportunistic pathogen S. aureus and methicillin resistance genes were not detected in culture-based or metagenomic analyses. Camphylobacteriaceae were significantly more abundant in the cloacal samples, especially in enrofloxacin-treated chickens, where a metagenome-assembled C. jejuni genome harboring fluoroquinolone and β-lactam resistance genes was identified. Conclusions Within a “farm-to-fork, one health” perspective, considering the evidence that bacitracin and enrofloxacin used in poultry production can select for resistance, we recommend their use be regulated. Furthermore, we suggest routine surveillance of ESBL E. coli, vancomycin-resistant E. faecalis and E. faecium, and fluoroquinolone-resistant C. jejuni strains considering their pathogenic nature and capacity to disseminate AMR to the environment.

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