Data_Sheet_1_Impact of a phage cocktail targeting Escherichia coli and Enterococcus faecalis as members of a gut bacterial consortium in vitro and in vivo.docx

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）与粪肠球菌（Enterococcus faecalis）被证实为影响人类肠道健康的关键菌群，且与炎症性肠病（IBD）的发病相关。噬菌体（Bacteriophage，简称phage）疗法作为抗生素的替代方案，已被用于靶向病原体数十年，但噬菌体塑造下胃肠道复杂细菌群落的机制仍未明确。本研究针对促炎性大肠杆菌LF82与粪肠球菌OG1RF，配制了包含六种噬菌体的混合制剂（分为活性组与热灭活组），并将其作用于由两种目标菌组成的限定菌群，分别在连续发酵罐与小鼠结肠炎模型中开展实验。这两种目标菌均属于六物种简化人类微生物组联合体（SIHUMI-6）。在72小时的连续发酵实验中，噬菌体混合制剂分别使粪肠球菌与大肠杆菌的数量降低了1.1与1.5 log₁₀基因组拷贝/毫升。该菌群互作伴随SIHUMI-6其他成员的丰度变化：植物乳杆菌（Lactiplantibacillus plantarum）与普拉梭菌（Faecalibacterium prausnitzii）的丰度分别提升了1.7 log与1.8 log。然而，在定植了相同细菌联合体的无菌小鼠中，每周两次、持续九周施用相同的噬菌体混合制剂，并未显著降低目标菌株的数量。经活性或灭活噬菌体处理的小鼠，其未受刺激的结直肠组织培养物中促炎细胞因子（IFN-γ/IL12p40）水平无明显差异。但活性噬菌体处理组小鼠的下胃肠道（盲肠与远端结肠）组织学评分更低，提示噬菌体混合制剂确实能够影响SIHUMI-6联合体的功能。综上，本研究得出结论：体外模型中观察到的噬菌体降低宿主菌群丰度的潜力，并未在体内环境中重现，该现象可能源于噬菌体在小鼠胃肠道转运过程中数量减少所致。