FN Archimer Export Format
PT J
TI Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach
BT 
AF BOUKERB, Mohamed
   Noël, Cyril
   Quenot, Emmanuelle
   Cadiou, Bernard
   Chevé, Julien
   Quintric, Laure
   Cormier, Alexandre
   Dantan, Luc
   Gourmelon, Michele
AS 1:1;2:2;3:1;4:3;5:4;6:2;7:2;8:1;9:1;
FF 1:PDG-RBE-SGMM-LSEM;2:PDG-IRSI-SEBIMER;3:PDG-DCB;4:;5:PDG-ODE-LITTORAL-LERBN;6:PDG-IRSI-SEBIMER;7:PDG-IRSI-SEBIMER;8:;9:PDG-RBE-SGMM-LSEM;
C1 IFREMER, RBE-SGMM-LSEM, Laboratoire Santé Environnement Microbiologie, Plouzané, France
   IFREMER, PDG-IRSI-SEBIMER, Plouzané, France
   Bretagne Vivante , SEPNB, Brest, France
   IFREMER, ODE-UL-LERBN, Laboratoire Environnement Ressource Bretagne Nord, Dinard, France
C2 IFREMER, FRANCE
   IFREMER, FRANCE
   BRETAGNE VIVANTE, FRANCE
   IFREMER, FRANCE
SI BREST
   DINARD
SE PDG-RBE-SGMM-LSEM
   PDG-IRSI-SEBIMER
   PDG-DCB
   PDG-ODE-LITTORAL-LERBN
IN WOS Ifremer UPR
   DOAJ
   copubli-france
IF 6.064
TC 20
UR https://archimer.ifremer.fr/doc/00705/81692/86250.pdf
   https://archimer.ifremer.fr/doc/00705/81692/86251.pdf
   https://archimer.ifremer.fr/doc/00705/81692/86252.pdf
   https://archimer.ifremer.fr/doc/00705/81692/86253.xlsx
LA English
DT Article
DE ;microbiome;wild waterbird;fecal pollution;microbial source tracking;enteric pathogens;environmental pathogens;NGS;qPCR
AB Fecal pollution in coastal areas is of a high concern since it affects bathing and shellfish harvesting activities. Wild waterbirds are non-negligible in the overall signal of the detectable pollution. Yet, studies on wild waterbirds’ gut microbiota focus on migratory trajectories and feeding impact on their shape, rare studies address their comparison to other sources and develop quantitative PCR (qPCR)-based Microbial Source Tracking (MST) markers to detect such pollution. Thus, by using 16S rRNA amplicon high-throughput sequencing, the aims of this study were (i) to explore and compare fecal bacterial communities from wild waterbirds (i.e., six families and 15 species, n = 275 samples) to that of poultry, cattle, pigs, and influent/effluent of wastewater treatment plants (n = 150 samples) and (ii) to develop new MST markers for waterbirds. Significant differences were observed between wild waterbirds and the four other groups. We identified 7,349 Amplicon Sequence Variants (ASVs) from the hypervariable V3–V4 region. Firmicutes and Proteobacteria and, in a lesser extent, Actinobacteria and Bacteroidetes were ubiquitous while Fusobacteria and Epsilonbacteraeota were mainly present in wild waterbirds. The clustering of samples in non-metric multidimensional scaling (NMDS) ordination indicated a by-group clustering shape, with a high diversity within wild waterbirds. In addition, the structure of the bacterial communities was distinct according to bird and/or animal species and families (Adonis R2 = 0.13, p = 10–4, Adonis R2 = 0.11, p = 10–4, respectively). The Analysis of Composition of Microbiomes (ANCOM) showed that the wild waterbird group differed from the others by the significant presence of sequences from Fusobacteriaceae (W = 566) and Enterococcaceae (W = 565) families, corresponding to the Cetobacterium (W = 1427) and Catellicoccus (W = 1427) genera, respectively. Altogether, our results suggest that some waterbird members present distinct fecal microbiomes allowing the design of qPCR MST markers. For instance, a swan- and an oystercatcher-associated markers (named Swan_2 and Oyscab, respectively) have been developed. Moreover, bacterial genera harboring potential human pathogens associated to bird droppings were detected in our dataset, including enteric pathogens, i.e., Arcobacter, Clostridium, Helicobacter, and Campylobacter, and environmental pathogens, i.e., Burkholderia and Pseudomonas. Future studies involving other wildlife hosts may improve gut microbiome studies and MST marker development, helping mitigation of yet unknown fecal pollution sources. 
PY 2021
PD JUN
SO Frontiers In Microbiology
SN 1664-302X
PU Frontiers Media SA
VL 12
UT 000679362000001
DI 10.3389/fmicb.2021.697553
ID 81692
ER

EF