New insights into the biodiversity of coliphages in the intestine of poultry

Abstract

Despite phages’ ubiquitous presence and great importance in shaping microbial communities, little is known about the diversity of specific phages in different ecological niches. Here, we isolated, sequenced, and characterized 38 Escherichia coli-infecting phages (coliphages) from poultry faeces to gain a better understanding of the coliphage diversity in the poultry intestine. All phages belonged to either the Siphoviridae or Myoviridae family and their genomes ranged between 44,324 and 173,384 bp, with a G+C content between 35.5 and 46.4%. Phylogenetic analysis was performed based on single “marker” genes; the terminase large subunit, portal protein, and exonucleases, as well as the full draft genomes. Single gene analysis resulted in six distinct clusters. Only minor differences were observed between the different phylogenetic analyses, including branch lengths and additional duplicate or triplicate subclustering. Cluster formation was according to genome size, G+C content and phage subfamily. Phylogenetic analysis based on the full genomes supported these clusters. Moreover, several of our Siphoviridae phages might represent a novel unclassified phage genus. This study allowed for identification of several novel coliphages and provides new insights to the coliphage diversity in the intestine of poultry. Great diversity was observed amongst the phages, while they were isolated from an otherwise similar ecosystem.

Systematic exploration ofEscherichia coliphage-host interactions with the BASEL phage collection

“…In marine environments, the coexistence of a few specialized, highly successful phage groups was proposed to be stable in space and time because extinction of individual phages would usually result in their replacement by relatives from the same, highly adapted group [110]. This "royal family model" could also explain why the same groups of E. coli phages sampled in our work have already been found again and again in previous studies that sampled diverse other environments [23][24][25][26][27][28][29] (Fig 2).…”

“…This strain, E. coli K-12 MG1655 ΔRM, therefore lacks the O-antigen glycan barrier (see below), all restriction systems, as well as the RexAB and PifA Abi systems (see Materials and Methods as well as S1 Text). E. coli K-12 ΔRM was subsequently used to isolate hundreds of phages from environmental samples such as river water or compost, but mostly from the inflow of different sewage treatment facilities (Fig 2A and Previous bacteriophage isolation studies had already provided deep insight into the diversity of tailed, lytic E. coli phages in samples ranging from sewage over diverse natural environments to infant guts or blood and urine of patients in tertiary care [23][24][25][26][27][28][29]. Despite the wide diversity of known E. coli phages [30], nearly all phage isolates reported in these studies belonged to five major groups and were either myoviruses of 1) Tevenvirinae or 2) Vequintavirinae subfamilies and close relatives, 3) large siphoviruses of the Markadamsvirinae subfamily within Demerecviridae, or small siphoviruses of 4) diverse Drexlerviridae subfamilies or 5) the genera Dhillonvirus, Nonagvirus, and Seuratvirus of the Siphoviridae family.…”

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“…In marine environments, the coexistence of a few specialized, highly successful phage groups was proposed to be stable in space and time because extinction of individual phages would usually result in their replacement by relatives from the same, highly adapted group [111]. This "royal family model" could elegantly explain why the same groups of E. coli phages sampled in our work for the BASEL collection have also been found again and again in previous studies that sampled in distant geographic locations and specific other environments [21][22][23][24][25][26][27] (Fig 1). Notably, the molecular mechanisms underlying a possible divergent adaptation of phage groups into "functional types" with different ecological strategies have largely remained elusive so far [112].…”

“…Previous bacteriophage isolation studies had already provided deep insight into the diversity of tailed, lytic E. coli phages in samples ranging from sewage over diverse natural environments to infant guts or blood and urine of patients in tertiary care [21][22][23][24][25][26][27]. Despite the wide diversity of known E. coli phages [28], nearly all phage isolates reported in these studies belonged to 5 major groups: Among myoviruses, the so-called "T-even" phages (relatives of T2, T4, and T6; Myoviridae subfamily Tevenvirinae) dominated together with relatives of E. coli O157:H7 typing phage rV5 (Myoviridae subfamily Vequintavirinae and related phages).…”

Classification of In Vitro Phage–Host Population Growth Dynamics

“…Bacteriophages (phages) are viruses that specifically infect bacteria. They are estimated to be the most abundant organisms on Earth (~10 31 entities) and play a major role in shaping the microbial communities [1,2]. Phages are unable to replicate independently of a susceptible bacterial host, and their host range is determined by a combination of various factors, including host-binding protein specificity and bacterial phage-resistance mechanisms [3,4].…”