Intestinal Microbiota and Species Diversity of Campylobacter and Helicobacter spp. in Migrating Shorebirds in Delaware Bay

Abstract

dUsing 16S rRNA gene sequencing analysis, we examined the bacterial diversity and the presence of opportunistic bacterial pathogens (i.e., Campylobacter and Helicobacter) in red knot (Calidris canutus; n ‫؍‬ 40), ruddy turnstone (Arenaria interpres; n ‫؍‬ 35), and semipalmated sandpiper (Calidris pusilla; n ‫؍‬ 22) fecal samples collected during a migratory stopover in Delaware Bay. Additionally, we studied the occurrence of Campylobacter spp., enterococci, and waterfowl fecal source markers using quantitative PCR (qPCR) assays. Of 3,889 16S rRNA clone sequences analyzed, the bacterial community was mostly composed of Bacilli (63.5%), Fusobacteria (12.7%), Epsilonproteobacteria (6.5%), and Clostridia (5.8%). When epsilonproteobacterium-specific 23S rRNA gene clone libraries (i.e., 1,414 sequences) were analyzed, the sequences were identified as Campylobacter (82.3%) or Helicobacter (17.7%) spp. Specifically, 38.4%, 10.1%, and 26.0% of clone sequences were identified as C. lari (>99% sequence identity) in ruddy turnstone, red knot, and semipalmated sandpiper clone libraries, respectively. Other pathogenic species of Campylobacter, such as C. jejuni and C. coli, were not detected in excreta of any of the three bird species. Most Helicobacter-like sequences identified were closely related to H. pametensis (>99% sequence identity) and H. anseris (92% sequence identity). qPCR results showed that the occurrence and abundance of Campylobacter spp. was relatively high compared to those of fecal indicator bacteria, such as Enterococcus spp., E. faecalis, and Catellicoccus marimammalium. Overall, the results provide insights into the complexity of the shorebird gut microbial community and suggest that these migratory birds are important reservoirs of pathogenic Campylobacter species.

Identifying avian sources of faecal contamination using sterol analysis

“…The public health risk from avian sources of pollution has been less certain, and risk assessment has suggested a lower pathogen potential compared with human sources (Soller et al 2010). A number of potential pathogens, however, have been found in avian faecal droppings including Campylobacter (Broman et al 2004;Waldenstrom et al 2002;Ryu et al 2014;Lu et al 2013), pathogenic E. coli (Wallace et al 1997), Salmonella serovars (Refsum et al 2002), microsporidian spp. (Slodkowicz-Kowalska et al 2006), avian influenza viruses (Gilbert et al 2006;Brown et al 2006), and clinically relevant antibiotic resistant bacteria (Bonnedahl et al 2014).…”

Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species

“…However, DNA sequencing launched the new field of culture-independent analysis of the microbial community. The affordable cost nowadays of performing tests such as clonal libraries [7,8], qPCR [9], microarrays [10], terminal restriction fragment length polymorphism [11–14] and next-generation sequencing technologies [11,14–17] opened access to new approaches in characterizing microbial communities in the gastrointestinal tract of various animal species.…”

Gastric and Enterohepatic Helicobacters other than Helicobacter pylori

“…Of 3889 16S rRNA sequences analyzed from the feces of migrating birds (migratory stopover, Delaware Bay, USA), 6.5% corresponded to Epsilonproteobacteria, that is, Campylobacter (82.3%) and Helicobacter (17.7%) species. Most Helicobacter ‐like sequences were closely related to H. pametensis and H. anseris , while the low percentage of sequence identity (92%) with H. anseris suggests a different Helicobacter species . Helicobacters were detected at low frequence in feces and intestinal tissues of tropical terrestrial wild birds (Venezuela) by molecular methods , suggesting that these bacteria may be uncommon in the populations studied.…”