Data_Sheet_2_Impact of a phage cocktail targeting Escherichia coli and Enterococcus faecalis as members of a gut bacterial consortium in vitro and in vivo.xls

Escherichia coli and Enterococcus faecalis have been implicated as important players in human gut health that have been associated with the onset of inflammatory bowel disease (IBD). Bacteriophage (phage) therapy has been used for decades to target pathogens as an alternative to antibiotics, but the ability of phage to shape complex bacterial consortia in the lower gastrointestinal tract is not clearly understood. We administered a cocktail of six phages (either viable or heat-inactivated) targeting pro-inflammatory Escherichia coli LF82 and Enterococcus faecalis OG1RF as members of a defined community in both a continuous fermenter and a murine colitis model. The two target strains were members of a six species simplified human microbiome consortium (SIHUMI-6). In a 72-h continuous fermentation, the phage cocktail caused a 1.1 and 1.5 log (log10 genome copies/mL) reduction in E. faecalis and E. coli numbers, respectively. This interaction was accompanied by changes in the numbers of other SIHUMI-6 members, with an increase of Lactiplantibacillus plantarum (1.7 log) and Faecalibacterium prausnitzii (1.8 log). However, in germ-free mice colonized by the same bacterial consortium, the same phage cocktail administered twice a week over nine weeks did not cause a significant reduction of the target strains. Mice treated with active or inactive phage had similar levels of pro-inflammatory cytokines (IFN-y/IL12p40) in unstimulated colorectal colonic strip cultures. However, histology scores of the murine lower GIT (cecum and distal colon) were lower in the viable phage-treated mice, suggesting that the phage cocktail did influence the functionality of the SIHUMI-6 consortium. For this study, we conclude that the observed potential of phages to reduce host populations in in vitro models did not translate to a similar outcome in an in vivo setting, with this effect likely brought about by the reduction of phage numbers during transit of the mouse GIT.

大肠杆菌（Escherichia coli）和屎肠球菌（Enterococcus faecalis）已被证实为影响人类肠道健康的关键角色，并与炎症性肠病（IBD）的发病密切相关。噬菌体疗法（bacteriophage therapy）作为抗生素的替代疗法，已使用数十年，用以针对病原体，但其对下消化道中复杂细菌群落的塑造能力尚不明确。本研究中，我们向连续发酵器和小鼠结肠炎模型中，以六种噬菌体混合液（其中部分为活性或经热灭活处理）为目标，针对具有促炎特性的大肠杆菌LF82和屎肠球菌OG1RF这两种界定群落中的成员。这两种目标菌株属于六种物种简化的人类微生物组联合体（SIHUMI-6）。在72小时的连续发酵过程中，噬菌体混合液导致屎肠球菌和大肠杆菌数量分别降低了1.1和1.5个对数单位（以每毫升基因组拷贝数计，log10）。此作用伴随其他SIHUMI-6成员数量的变化，其中植物乳杆菌（Lactiplantibacillus plantarum）增加1.7个对数单位，普拉氏菌（Faecalibacterium prausnitzii）增加1.8个对数单位。然而，在由相同细菌群落定植的无菌小鼠中，每周两次，持续九周给予相同的噬菌体混合液，并未引起目标菌株数量的显著减少。接受活性或非活性噬菌体治疗的小鼠，在未刺激的结肠直肠黏膜片培养中，其促炎细胞因子（IFN-y/IL12p40）水平相似。然而，接受活性噬菌体治疗的小鼠的鼠类下消化道（盲肠和远端结肠）的组织学评分较低，这表明噬菌体混合液确实影响了SIHUMI-6联合体的功能。对于本研究，我们得出结论，噬菌体在体外模型中降低宿主种群数量的潜在能力并未在体内环境中产生类似效果，这种影响可能是由噬菌体在鼠标肠道中传输过程中数量的减少所引起的。