Rice sheath rot has been mainly associated with the bacterial pathogen Pseudomonas fuscovaginae and in some cases to the fungal pathogen Sarocladium oryzae; it is yet unclear if they are part of a complex disease. The bacterial and fungal community associated with rice sheath rot symptomatic and asymptomatic rice plants was determined/studied with the main aim to shed light on the pathogen(s) causing rice sheath rot. Plant samples were collected from different rice varieties in two locations (highland and lowland) in two rice-growing seasons (wet and dry season) in Burundi. Our results showed that the bacterial Pseudomonas genus was prevalent in highland in both rice-growing seasons and was not affected by rice plant varieties. Pseudomonas sequence reads displayed a significant high similarity to Pseudomonas fuscovaginae indicating that it is the causal agent of rice sheath rot as previously reported. The fungal Sarocladium genus was on the other hand prevalent in lowland only in the wet season; the sequence reads were most significantly similar to Sarocladium oryzae. These studies showed that plant microbiome analysis is very useful in determining the microorganisms involved in a plant disease. P. fuscovaginae and S. oryzae were prevalent in symptomatic samples in highland and lowland respectively being present independently and hence are not part of a complex disease. The significant presence of other bacterial and fungal taxa in symptomatic samples is also discussed possibly making this disease more complex. Finally, we also report the microbial communities that are associated with the plant sheath in symptomatic and asymptomatic plants from the same rice fields.

水稻皮腐烂主要与细菌病原假单胞菌假单胞菌有关，在某些情况下与真菌病原稻米假单胞菌（Sarocladium oryzae）有关; 尚不清楚它们是否是复杂疾病的一部分。确定/研究了有症状和无症状水稻鞘腐病相关植物的细菌和真菌群落，其主要目的是阐明引起水稻鞘腐病的病原体。在布隆迪的两个水稻生长季节（湿季和干旱季），在两个地点（高地和低地）的不同水稻品种中收集了植物样本。我们的结果表明，细菌假单胞菌属在两个水稻生长季节均在高原地区盛行，不受水稻品种的影响。假单胞菌序列读数显示与褐藻假单胞菌（Pseudomonas fuscovaginae）有很高的相似性，表明它是水稻鞘腐病的病原。另一方面，真菌沙门氏菌属仅在雨季时才在低地盛行。该序列的读数与米线腊肠杆菌最相似。这些研究表明，植物微生物组分析对于确定涉及植物病害的微生物非常有用。P. fuscovaginae和米曲霉在高地和低地的有症状样品中普遍存在，分别独立存在，因此不是复杂疾病的一部分。还讨论了有症状样品中其他细菌和真菌类群的显着存在，可能使这种疾病更加复杂。最后，我们还报告了同一稻田有症状和无症状植物中与植物鞘相关的微生物群落。