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Comparative analysis of two nonlethal methods for the study of the gut bacterial communities in wild lizards

Integrative Zoology 2023年第6期18卷 1056-1071页

作者： Mauricio HERNÁNDEZ Sergio ANCONA Stephanie HEREIRA-PACHECO Aníbal HDÍAZ DE LA VEGA-PÉREZ Yendi E.NAVARRO-NOYA Doctorado en Ciencias Biológicas Centro de Tlaxcala de Biología de la ConductaUniversidad Autónoma de TlaxcalaTlaxcalaMexico Departamento de Ecología Evolutiva Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico Estación Científica la Malinche Centro de Tlaxcala de Biología de la ConductaUniversidad Autónoma de TlaxcalaTlaxcalaMexico Consejo Nacional de Ciencia y Tecnología—Centro Tlaxcala de Biología de la Conducta Universidad Autónoma de TlaxcalaTlaxcalaMexico Laboratorio de Interacciones Bióticas Centro de Investigación en Ciencias BiológicasUniversidad Autónoma de TlaxcalaTlaxcalaMexico

Fecal samples or cloacal swabs are preferred over lethal dissections to study vertebrate gut microbiota for ethical reasons,but it remains unclear which nonlethal methods provide more accurate information about gut microbiota.We compared the bacterial communities of three gastrointestinal tract(GIT)segments,that is,stomach,small intestine(midgut),and rectum(hindgut)with the bacterial communities of the cloaca and feces in the mesquite lizard Sceloporus grammicus.The hindgut had the highest taxonomic and functional alpha diversity,followed by midgut and feces,whereas the stomach and cloaca showed the lowest diversities.The taxonomic assemblages of the GIT segments at the phylum level were strongly correlated with those retrieved from feces and cloacal swabs(rs>0.84 in all cases).The turnover ratio of Amplicon Sequence Variants(ASVs)between midgut and hindgut and the feces was lower than the ratio between these segments and the cloaca.More than half of the core-ASVs in the midgut(24 of 32)and hindgut(58 of 97)were also found in feces,while less than 5 were found in the cloaca.At the ASVs level,however,the structure of the bacterial communities of the midgut and hindgut were similar to those detected in feces and cloaca.Our findings suggest that fecal samples and cloacal swabs of spiny lizards provide a good approximation of the taxonomic assemblages and beta diversity of midgut and hindgut microbiota,while feces better represent the bacterial communities of the intestinal segments at a single nucleotide variation level than cloacal swabs.

关键词： animal microbiome cloacal swabs fecal samples intestinal tract reptile gut microbiome

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A network meta-analysis on comparison of invasive and non-invasive sampling methods to characterize intestinal microbiota of birds

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Avian Research 2023年第2期14卷 281-290页

作者： Tianlong Zhou Kasun H.Bodawatta Aiwu Jiang Guangxi Key Laboratory of Forest Ecology and Conservation College of ForestryGuangxi UniversityNanning530004China Natural History Museum of Denmark University of CopenhagenCopenhagenDenmark

Birds maintain complex and intimate associations with a diverse community of microbes in their intestine.Multiple invasive and non-invasive sampling methods are used to characterize these communities to answer a multitude of eco-evolutionary questions related to host-gut microbiome symbioses.However,the comparability of these invasive and non-invasive sampling methods is sparse with contradicting findings.Through performing a network meta-analysis for 13 published bird gut microbiome studies,here we attempt to investigate the comparability of these invasive and non-invasive sampling methods.The two most used non-invasive sampling methods(cloacal swabs and fecal samples)showed significantly different results in alpha diversity and taxonomic relative abundances compared to invasive samples.Overall,non-invasive samples showed decreased alpha diversity compared to intestinal samples,but the alpha diversities of fecal samples were more comparable to the intestinal samples.On the contrary,the cloacal swabs characterized significantly lower alpha diversities than in intestinal samples,but the taxonomic relative abundances acquired from cloacal swabs were similar to the intestinal samples.Phylogenetic status,diet,and domestication degree of host birds also influenced the differences in microbiota characterization between invasive and non-invasive samples.Our results indicate a general pattern in microbiota differences among intestinal mucosal and non-invasive samples across multiple bird taxa,while highlighting the importance of evaluating the appropriateness of the microbiome sampling methods used to answer specific research questions.The overall results also suggest the potential importance of using both fecal and cloacal swab sampling together to properly characterize bird microbiomes.

关键词： Avian microbiomes cloacal swabs Fecal samples Intestinal samples Meta regressions

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Antibiotic resistance assessment in bacteria isolated in migratory Passeriformes transiting through the Metaponto territory(Basilicata,Italy)

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Avian Research 2017年第4期8卷 255-265页

作者： Maria Foti Antonietta Mascetti Vittorio Fisichella Egidio Fulco Bianca Maria Orlandella Francesco Lo Piccolo Department of Veterinary Sciences University of MessinaPolo Universitario dell’Annunziata98168 MessinaItaly Naturalistic Study Milvus Pantano Street 13485010 PignolaPZItaly

Background: Wild birds are considered to be reservoirs of human enteric pathogens and vectors of antimicrobial resistance dissemination in the environment.During their annual migration,they play a potential role in the epidemiology of human associated zoonoses.The aim of this study was to investigate the frequency of isolation and antimicrobial susceptibility profiles of microorganisms found in the cloaca of common European passerines.Methods: One hundred and twenty-one cloacal swabs were collected during a monitoring program of migratory birds in the Forest Reserve for Protection "Metaponto"(Basilicata,Italy).All samples were cultured using standard bacteriological methods and antibiotic susceptibility testing(agar disk diffusion test) of isolated strains was performed.Results: The bacteriological analysis produced 122 strains belonging to 18 different species.The most commonly isolated species were Enterobacter cloacae and Providencia rettgeri(21 strains,17.2%).Potentially pathogenic species including Klebsiella pneumoniae,Serratia marcescens and Pseudomonas spp.have also been identified.Isolates showed significant frequencies of antimicrobial resistance.The highest frequency of resistance was observed against amoxicillin(n = 79,64.8%);ampicillin(n = 77,63.1%);rifampicin(n Thirty-one strains(25.4%) showed resistance to imipenem a= 75,61.5%);amoxicillin–clavulanic acid(n nd 8(6.6%) to meropenem.= 66,54.1%).Conclusions: Migratory birds play an important role in the ecology,circulation and dissemination of potentially pathogenic antimicrobial resistant organisms.They can therefore be considered sentinel species and environmental health indicators.Our results suggest that the integration of epidemiological surveillance networks during ringing campaigns of wild species can be an effective tool to study this phenomenon.

关键词： Passeriformes cloacal swabs Bacteriological test Antimicrobial resistance

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