Microbiome and antimicrobial resistance genes in microbiota of cloacal samples from European herring gulls (<i>Larus argentatus</i>)

Merkevičienė, Lina; Ruzauskaite, Neda; Klimienė, Irena; Šiugždinienė, Rita; Dailidavičienė, Jurgita; Virgailis, Marius; Mockeliūnas, Raimundas; Ružauskas, Modestas

doi:10.1515/jvetres-2017-0004

Cited by 23 publications

(21 citation statements)

References 21 publications

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“…Then sample was purified using a DNA Clean & Concentrator‐25 kit (Zymo Research, Irvine, USA) and used as template DNA in PCR with specific oligonucleotide primers. A variety of genes encoding resistance in Gram‐negative bacteria were investigate as described previously (Kaase, Szabados, Wassill, & Gatermann, ; Merkeviciene et al, ). Briefly, a PCR using specific primers for genes encoding antimicrobial resistance was performed using Dream Taq Green PCR Master Mix (Thermo Fisher Scientific Baltics, Lithuania).…”

Section: Methodsmentioning

confidence: 99%

Composition and antimicrobial resistance profile of Gram‐negative microbiota prevalent in aquacultured fish

Ružauskas

Klimienė

Armalytė

et al. 2018

Journal of Food Safety

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Aquatic environments are one of the most favorable settings for acquisition and dissemination of antimicrobial resistance. The aims of this study were twofold: (1) to isolate and identify antimicrobial resistant Gram-negative bacteria that are prevalent in fish kept in open aquaculture ponds and(2) to analyse their antimicrobial resistance profiles. One hundred and nineteen isolates from fish resistant to at least one antimicrobial were investigated. The most predominant genera were Pseudomonas, Chryseobacterium, Enterobacteriaceae, and Aeromonas. The highest numbers of multiresistant isolates were found within Pseudomonas spp., and the lowest, in Aeromonas spp.Resistance to beta-lactams was the most common among all of the bacterial genera. The absence or very low rates of resistance to fluoroquinolones, the small number of clinically important resistance genes, and bacterial taxonomic composition suggest that the most widespread resistant bacteria in aquacultured fish are autochthonous microbiota. Practical applicationsThe majority of antimicrobial resistant bacteria that are prevalent in aquacultured fish from open ponds can be treated as natural (autochthonous microbiota). In this study, only a minority of resistant bacteria detected in fish could be associated with polluted waters originating from animal farms or human healthcare facilities. Some strains, particularly the family Enterobacteriaceae that is found in fish, contain clinically important resistance determinants that potentially can be transmitted to human microbiota in cases of inappropriate processing of fish intended for food. With regard to antimicrobial resistant bacteria, measures for control of inflowing waters to aquaculture ponds should be taken in addition to monitoring fish microbiota and its' resistance should be investigated on a regular basis.

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Section: Methodsmentioning

confidence: 99%

Composition and antimicrobial resistance profile of Gram‐negative microbiota prevalent in aquacultured fish

Ružauskas

Klimienė

Armalytė

et al. 2018

Journal of Food Safety

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“…A large number of studies investigating the gut microbiome of birds and reptiles have sampled bacteria from the cloaca (Allegretti et al., ; Barbosa et al., ; Bowman & Jacobson, ; Charruau, Pérez‐Flores, Pérez‐Juárez, Cedeño‐Vázquez, & Rosas‐Carmona, ; Cooper, Needham, & Lawrence, ; D'Aloia, Bailey, Samour, Naldo, & Howlett, ; Dewar, Arnould, Krause, Dann, & Smith, ; Dewar et al., ; Dickinson, Duck, Schwalbe, Jarchow, & Trueblood, ; van Dongen et al., ; Ganz et al., ; Hoar, Whiteside, Ward, Inglis, & Morck, ; Klomp et al., ; Kreisinger, Čížková, Kropáčková, & Albrecht, ; Lamberski, Hull, Fish, Beckmen, & Morishita, ; Lobato, Geraldes, Melo, Doutrelant, & Covas, ; Lombardo et al., ; Lucas & Heeb, ; Martin, Gilman, & Weiss, ; Matson, Versteegh, van der Velde, & Tieleman, ; Maul, Gandhi, & Farris, ; Merkeviciene et al., ; Mills, Lombardo, & Thorpe, ; Moreno et al., ; Ruiz‐Rodríguez, Lucas, Heeb, & Soler, ; Ruiz‐Rodríguez, Soler, et al., ; Santoro, Hernández, & Caballero, ; Santos et al., ; Stanley, Geier, Chen, Hughes, & Moore, ; Stenkat, Krautwald‐Junghanns, Schmitz Ornés, Eilers, & Schmidt, ; Xenoulis et al., ). Cloacal sampling is widely used because it is straightforward to perform, allows repeated sampling of individuals and affords the possibility of reliably obtaining samples from all individuals at the same time.…”

Section: Introductionmentioning

confidence: 99%

Measuring the gut microbiome in birds: Comparison of faecal and cloacal sampling

Videvall

Strandh

Engelbrecht³

et al. 2017

Molecular Ecology Resources

132

162

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The gut microbiomes of birds and other animals are increasingly being studied in ecological and evolutionary contexts. Numerous studies on birds and reptiles have made inferences about gut microbiota using cloacal sampling; however, it is not known whether the bacterial community of the cloaca provides an accurate representation of the gut microbiome. We examined the accuracy with which cloacal swabs and faecal samples measure the microbiota in three different parts of the gastrointestinal tract (ileum, caecum, and colon) using a case study on juvenile ostriches, Struthio camelus, and high-throughput 16S rRNA sequencing. We found that faeces were significantly better than cloacal swabs in representing the bacterial community of the colon. Cloacal samples had a higher abundance of Gammaproteobacteria and fewer Clostridia relative to the gut and faecal samples. However, both faecal and cloacal samples were poor representatives of the microbial communities in the caecum and ileum. Furthermore, the accuracy of each sampling method in measuring the abundance of different bacterial taxa was highly variable: Bacteroidetes was the most highly correlated phylum between all three gut sections and both methods, whereas Actinobacteria, for example, was only strongly correlated between faecal and colon samples. Based on our results, we recommend sampling faeces, whenever possible, as this sample type provides the most accurate assessment of the colon microbiome. The fact that neither sampling technique accurately portrayed the bacterial community of the ileum nor the caecum illustrates the difficulty in noninvasively monitoring gut bacteria located further up in the gastrointestinal tract. These results have important implications for the interpretation of avian gut microbiome studies.

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“…DNA was extracted with a fecal DNA MiniPrep kit (D6010, Zymo Research, USA). Library preparation, metagenomic sequencing, and taxonomic characterization of reads was performed as described previously (21). ZymoBIOMICS Microbial Community Standard (D6300, Zymo Research, USA) was used as a microbiome profiling quality control.…”

Section: Metagenomics and Microbial Profiling Analysismentioning

confidence: 99%

Combination of Antimicrobial Starters for Feed Fermentation: Influence on Piglet Feces Microbiota and Health and Growth Performance, Including Mycotoxin Biotransformation in vivo

et al. 2020

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The aim of this study was to apply a combination of the microbial starters Lactobacillus uvarum LUHS245, Lactobacillus casei LUHS210, Pediococcus acidilactici LUHS29, and Pediococcus pentosaceus LUHS183 for feed fermentation and to evaluate the influence of fermentation on feed acidity and microbiological characteristics, as well as on the piglet feces microbiota, health, and growth performance. Additionally, mycotoxin biotransformation was analyzed, including masked mycotoxins, in feed and piglet feces samples. The 36-day experiment was conducted using 25-day-old Large White/Norwegian Landrace (LW/NL) piglets with an initial body weight of 6.9-7.0 kg, which were randomly distributed into two groups (in each 100 piglets): control group, fed with basal diet (based on barley, wheat, potato protein, soybean protein concentrate, and whey powder), and treated group, fed with fermented feed at 500 g kg −1 of total feed. Compared to a commercially available lactic acid bacteria (LAB) combination, the novel LAB mixture effectively reduced feed pH (on average pH 3.65), produced a 2-fold higher content of L(+) lactic acid, increased viable LAB count [on average 8.8 log 10 colony-forming units (CFU) g −1 ], and led to stable feed fermentation during the entire test period (36 days). Fecal microbiota analysis showed an increased number of probiotic bacteria in the treated group, particularly Lactobacillus, when compared with the control group at the end of experiment. This finding indicates that fermented feed can modify microbial profile change in the gut of pigs. In treated piglets' blood (at day 61), the serum high-density lipoprotein (HDL) cholesterol and triglycerides (TG) were significantly higher, but the levels of T4, glucose, K, alkaline phosphatase (AP), and urea were significantly decreased (p ≤ 0.05) compared with the control group. Mycotoxin analysis showed that alternariol monomethyl ether (AME) and altenuene were found in 61-day-old control piglets' feces and in fermented feed samples. However, AME was not found in treated Vadopalas et al. Biomodification of Piglet Microbiota With Feed piglets' feces. Feed fermentation with the novel LAB combination is a promising means to modulate piglets' microbiota, which is essential to improve nutrient absorption, growth performance, and health parameters. The new LAB composition suggests a novel dietary strategy to positively manipulate fermented feed chemicals and bio-safety and the piglet gut microbial ecology to reduce antimicrobials use in pig production and increase local feed stock uses and economical effectiveness of the process.

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Microbiome and antimicrobial resistance genes in microbiota of cloacal samples from European herring gulls (Larus argentatus)

Cited by 23 publications

References 21 publications

Composition and antimicrobial resistance profile of Gram‐negative microbiota prevalent in aquacultured fish

Composition and antimicrobial resistance profile of Gram‐negative microbiota prevalent in aquacultured fish

Measuring the gut microbiome in birds: Comparison of faecal and cloacal sampling

Combination of Antimicrobial Starters for Feed Fermentation: Influence on Piglet Feces Microbiota and Health and Growth Performance, Including Mycotoxin Biotransformation in vivo

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