肠道菌群对宿主生理功能的维持具有重要贡献，细菌和宿主的共生关系已经有比较多的研究，但是真核生物也可以感染病毒，而且在正常肠道内，不仅存在大量细菌，病毒的数量也不含糊。这些肠道内病毒是否对维持宿主的生理功能有贡献，是否应该有肠道病毒群这个概念。最新纽约大学医学院科学家在《自然》在线发表研究论文，明确了肠道病毒确实具有十分重要的功能，甚至能代替肠道菌群，维持宿主生理功能，该发现被学者称赞为病毒是肠道菌群的备份。

a, Schematic of MNV mono-association procedure (see Methods for additional details). GF breeder pairs (F₀) within a gnotobiotic isolator were infected with 3 × 10⁶ p.f.u. of MNV.CR6, which was allowed to transmit naturally to offspring (F₁). Weaned offspring were maintained in isolators until adulthood, and then either used for analysis or as breeders to generate additional experimental animals (F₂). b, Successful transmission to offspring and the persistent presence of the virus in mono-associated GF mice (GF+MNV) was confirmed by performing a plaque assay using stool harvested from 8-week-old offspring (~1 month after weaning). The amount of virus in stool from GF mice, antibiotic (ABX)-treated wild-type (WT) and Ifnar1^−/− mice, and conventional (Conv) mice infected with 3 × 10⁶ p.f.u. of the indicated strains of MNV for 10 days are also shown, n = 5 mice per group. c–f, Mice receiving the indicated treatments did not display marked histopathology in the small intestine (c, e) and colon (d, f) based on blind quantification of H&E-stained sections using a previously described scoring system³⁷. Mice receiving a pathology score of 1 displayed mild blunting of villi (additional details in Methods). No histopathology was detected in spleens, and no other signs of disease were noted. Note that a previous publication in which mice were reported to display pathologies after MNV infection used a different strain of MNV, an early time point (24 h after infection), and mice on a different background (129/Sv)³⁸. The lack of pathology in C57BL/6 mice persistently infected with MNV.CR6 is consistent with our previous publication¹⁵. n = 5–7 mice per group. All graphs show means ± s.e.m.

从研究的角度，这一新思路完全没有问题。但现实是，细菌和病毒都存在，可能是两者相互协作共同维持宿主健康，另外细菌本身也可以感染病毒，例如各种噬菌体，这些噬菌体作为制约细菌过度增生显然十分重要，也是肠道内菌群平衡的一个重要因素。总之，肠道环境是一个多元的生态系统，应该吸收系统论和复杂系统的研究手段，不能简单地用一种物种和单一因素来认识这个复杂系统，否则可能会误入歧途。

最新研究为确定一种普通的肠RNA病毒是否能取代肠道共生菌的功能，研究将诺沃克病毒感染给无菌动物或经过抗生素处理的小鼠，观察对肠道形态和淋巴功能的影响，以及在炎症方面的表现。结果发现，无菌动物组2先天淋巴样细胞增生，感染了诺沃克病毒的动物能抑制这种变化，也能诱导肠道免疫系统的发育相关的基因转录和I 型干扰素信号系统的变化。进一步研究发现，干扰素α受体是产生上述效应的重要条件。诺沃克病毒感染能对抗抗生素治疗或致病菌感染导致的肠道损伤，不可思议！病毒感染能对抗细菌感染！结果就是这样。这些研究结果说明，真核细胞的病毒具有维持肠道稳态的功能，能启动黏膜免疫功能，这非常类似肠道菌群的功能。

a, Representative images of H&E-stained colonic small intestinal sections of GF, GF+MNV (mono-association with MNV.CR6) and conventional (Conv) mice. Scale bar, 100 μm. b, In these mice the crypt height was measured, showing a significant difference between GF and conventional mice. c, Percentages of NK T cells (CD1d⁺, TCR-β⁺) in colonic lamina propria of GF, GF+MNV and conventional mice. d–g, Percentages of CD4⁺TCR-β⁺ (d) and CD8⁺TCR-β⁺ cells (f), and percentages of IFN-γ-producing CD4⁺ (e) and CD8⁺ T cells (g) in the colonic lamina propria of GF, GF+MNV and conventional mice. n = 5 mice per group. NS, not significant. *P < 0.05, **P < 0.01. ANOVA with Holm–Sidak correction. All graphs show means ± s.e.m. from at least two independent experiments.

肠道内应该有更多这类病毒，是否应该提出肠道病毒群这个概念，为什么不应该？

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13960.html