Table 1.
Bacterial species detected in the faeces of blue tits in Lancaster, UK, and the frequency with which they occurred. Homologues were identified by analysis of partial 16S rRNA gene sequences using the BLASTn program
| TCbt clone no. | Sequence length obtained (bp) | Presence (+) or absence (−) by year | Frequency in present population (%; n = 142) | Closest 16S rRNA gene homologue(s) in Genbank [accession no.] (% nucleotide identity) | Origin of homologous sequences (reference) | |
|---|---|---|---|---|---|---|
| 2007 | 2008 | |||||
| TCbt1 | 434 | + | − | 30.3 | TCbt7 & TCbt18 (100%) | Present study |
| TCbt2 | 413 | + | + | 40.1 | Campylobacter lari spp. [e.g. HM007571] (99%) | Various human gastroenteritis patients (UDS) |
| TCbt3 | + | + | − | 2.1 | No homology >95% | – |
| TCbt4 | 419 | + | + | 49.3 | No homology >96% | – |
| TCbt5 | 437 | + | + | 50.0 | No homology >96% | – |
| TCbt6 | 410 | + | + | 8.5 | Lactobacillus sp. [NR104979.1] and uncultured bacterium [HM335530] (99%) | Lactobacillus aviarius subsp. araffinosus (UDS); Skin microbiome (Kong et al. 2012) |
| TCbt7 | 417 | + | + | 14.1 | TCbt1 & TCbt18 (100%) | Present study |
| TCbt8 | 412 | − | + | 0.7 | Serratia spp. [KJ095676] & Rahnella spp. [JN656281] (100%) | Unknown source (2014 UDS); Ips sexdentatus; Coleoptera (Sevim et al. 2012) |
| TCbt9 | 411 | − | + | 4.2 | Uncultured bacterium [JF168221] (100%) & TCbt14 (99%) | Skin microbiome (Kong et al. 2012); present study |
| TCbt10 | 411 | − | + | 1.4 | Uncultured bacterium clone [EU777815] (100%) | Polar bear faeces (Ley et al. 2008) |
| TCbt11 | 412 | − | + | 19.0 | Rickettsiella spp. [HQ640943] (99%) | Agroites sp. wireworm pathogen (Leclerque et al. 2011) |
| TCbt12 | 436 | + | − | 1.4 | Pseudomonas spp. [KM058081.1] (99%) | Unknown source (UDS) |
| TCbt13 | 407 | + | − | 4.9 | Uncultured rumen bacterium clone [GU304476.1] (98%); Atopobium parvulum [KC999391] (97%) | Uncultured rumen bacterium (UDS); Atopobium parvulum (UDS) |
| TCbt14 | 411 | − | + | 0.7 | TCbt9 and uncultured bacterium [JF168221] (99%) | Present study; skin microbiome (Kong et al. 2012) |
| TCbt15 | 411 | + | + | 72.5 | Bacillus licheniformis strains [KJ495982; KJ126941; KJ126938] (99%) | Unknown source (2014 UDS) |
| TCbt16 | 434 | − | + | 15.5 | Uncultured bacterium clone [HM341167] (99%) | Skin microbiome (Kong et al. 2012) |
| TCbt17 | 419 | + | − | 37.3 | Staphylococcus spp. [KC213932] (99%) | Freshwater roach (2013 UDS) |
| TCbt18 | 383 | + | + | 29.6 | TCbt1 & TCbt7 (100%) | Present study |
| TCbt19 | 412 | − | + | 0.7 | Uncultured Moraxella spp. [JN792320] (99%) | Finless porpoise faeces (McLaughlin et al. 2012) |
| TCbt20 | 412 | + | − | 2.8 | Pseudomonas spp. [DQ904607] (99%) | Wireworm gut (2006 UDS) |
| TCbt21 | 409 | + | + | 11.3 | Uncultured bacterium clone [JQ451662] (99%) | Environmental samples (2012 UDS) |
| TCbt22 | 439 | − | + | 1.4 | Uncultured bacteria [EU540256; DQ264573] (99%) | Human skin (Grice et al. 2008); subsurface groundwater (DeSantis et al. 2007) |
| TCbt23 | 410 | − | + | 1.4 | Uncultured Lactobacillus sp. (99%) | Silkworm midgut (Yuan et al. 2005, UDS) fasted chicks (UDS) |
| TCbt24 | 412 | − | + | 2.8 | Erwinia persicina. [AB934973] (100%) | Beer brewing process (2014 UDS) |
| TCbt25 | 376 | + | − | 2.8 | Pseudomonas veronii [KJ726603] (100%) | 2014 UDS |
| TCbt26 | 412 | + | − | 2.8 | Pseudomonas spp. [KF263621] (97%) | Antarctic soil bacteria (Goh and Tan 2012) |
| TCbt27 | 414 | + | + | 4.2 | Campylobacter lari [KF703982] (99%) | American crows (Weis et al. 2014) |
| TCbt28 | 436 | + | + | 4.9 | Uncultured Pseudomonas [DQ144425] (100%) | Soil (Hjort et al. 2007) |
| TCbt29 | 411 | + | − | 3.5 | Salmonella enterica subsp. enterica [CP003836] (99%) | Unknown source (2014 UDS) |
| TCbt30 | 435 | + | + | 13.4 | Uncultured and cultured Erwinia spp. [JN793861; CU468135] (99%) | Environmental sources (UDS and Kube et al. 2008) |
| TCbt31 | 412 | − | + | 4.2 | Uncultured bacteria [HM557599] [JX559723] (99%) | Leaf cutting ants (Suen et al. 2010); green tea (UDS) |
| TCbt32 | 418 | − | + | 2.8 | Salmonella spp. [CP003416] (98%) | Faeces (Le Bars et al. 2012) |
| TCbt33 | 403 | + | + | 4.2 | Uncultured bacterium [EU136788] (98%) | Environmental samples (Jones et al. 2008) |
| TCbt34 | 436 | + | + | 4.2 | Uncultured [JF829474] and Microlunatus spp. [NR_116819] (98%) | Soil (Kampfer et al. 2010; Talia et al. 2012) |
| TCbt35 | 381 | + | + | 28.2 | Uncultured bacterium [FM872481] (99%) | House floor dust (Taubel et al. 2009) |
| TCbt36 | 437 | + | + | 4.2 | Uncultured bacterium [JF729045] (99%) | 2011 UDS |
| TCbt37 | 433 | + | − | 1.4 | Uncultured Microbacterium spp. [KC922070] (99%) | Rabbit (2014 UDS) |
| TCbt38 | 433 | + | − | 2.1 | Arthrobacter spp. [KJ870017] (99%) | Picrorhiza rhizosphere (2014 UDS) |
UDS = Unpublished direct submission of DNA sequence.