Comparative Analysis of Fecal Microbiomes From Wild Waterbirds to Poultry, Cattle, Pigs, and Wastewater Treatment Plants for a Microbial Source Tracking Approach

Abstract

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.

Zengye Decoction Attenuated Severe Acute Pancreatitis Complicated with Acute Kidney Injury by Modulating the Gut Microbiome and Serum Amino Acid Metabolome

“…The β -diversity analysis (NMDS based on Bray-Curtis distance) displays the similarity of the overall bacterial structure [ 34 ]. Although the cluster of samples in MG could not be separated from the C, ZYD dramatically shifted microbial structure from SAP-AKI status (ANOSIM R = 0.14, P =0.025) ( Figure 2(a) ).…”

“…Linear discriminant analysis (LDA) of effect size (LEfSe) was performed according to Zhu et al [ 32 ]. Nonmetric multidimensional scaling (NMDS) based on Bray-Curtis distance, analysis of similarities (ANOSIM), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was described in the research implemented by Lei et al [ 33 , 34 ]. Ribosomal Database Project (RDP) classifier was utilized to annotate all typical reads against the SILVA database (version 123) with a 70% confidence threshold [ 35 ].…”

Host Species Affects Bacterial Evenness, but Not Diversity: Comparison of Fecal Bacteria of Cows and Goats Offered the Same Diet

“…This is in good agreement with the findings of Andrade et al, who examined the fecal microbial populations in Nelore cattle and found that 16% of the sequences belonged to Ruminococcaceae UCG-005 and UCG-010 [ 54 ]. These two genera were also described for cattle, goat kids, and musk deer fecal microbiomes [ 55 , 56 , 57 ]. Less abundant genera were Alistipes , Romboutsia , Rikenellaceae RC9 gut group, Eubacterium coprostanoligenes group, Family XIII AD3011 group, Ruminococcaceae UCG-013, Ruminococcaceae UCG-014, Ruminococcaceae UCG-009, Treponema 2, Solibacillus , Prevotellaceae UCG-003, Paeniclostridium , Prevotellaceae UCG-004, and Ruminococcaceae NK4A214 group.…”

“…The influence of the host animal on the fecal microbiome has been investigated in a few studies [ 43 , 55 , 63 ]. Shabana et al [ 63 ] compared the bacterial composition in the feces of sheep and goats of the same age, located on the same farm and offered the same diet (pellet feed and alfalfa hay).…”

Fish gut-associated bacterial communities in a tropical lagoon (Aghien lagoon, Ivory Coast)

“…Clostridium sensu stricto 1 and Romboutsia are reportedly abundant genera in tilapia fish, for example in both wild and aquaculture-reared Nile tilapia specimens (genus Oreochromis ; Bereded et al, 2021 , 2022 ). They are also abundant in the gut of many vertebrates and often reported in wastewater ( Boukerb et al, 2021 ). Clostridium sensu stricto was for example reported to be primarily transported to surface waters by runoff events after manure application ( Rieke et al, 2018 ).…”