Identifying Potential Polymicrobial Pathogens: Moving Beyond Differential Abundance to Driver Taxa

Lü, Jiaqi; Zhang, Xuechen; Qiu, Qiongfen; Chen, Jiong; Xiong, Jinbo

doi:10.1007/s00248-020-01511-y

Cited by 28 publications

(5 citation statements)

References 53 publications

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“…Notably, several taxa were affiliated with the order Vibrionales (Fig. S4), which includes some opportunistic pathogens in shrimp aquaculture (Lu et al ., 2020; Shen et al ., 2021). In this context, it is reasonable that the specific disease‐discriminatory taxa are pathogenically related to different diseases.…”

Section: Discussionmentioning

confidence: 99%

A meta‐analysis study of the robustness and universality of gut microbiota–shrimp diseases relationship

Sha

Lü

Chen

et al. 2022

Environmental Microbiology

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Intensive case study has established dysbiosis in the gut microbiota-shrimp disease relationship; however, variability in experimental design and the diversity of diseases arise the question of whether some gut indicators are robust and universal in response to shrimp health status, irrespective of causal agents. Through an unbiased subject-level meta-analysis framework, we re-analysed 10 studies, including 261 samples, four lifestages and six different diseases (the causal agents are virus, bacterial, eukaryotic pathogens, or unknown). Results showed that shrimp diseases reproducibly altered the structure of gut bacterial community, but not diversity. After ruling out the lifestage-and disease specific-discriminatory taxa (different diseases dependent indicators), we identify 18 common disease-discriminatory taxa (indicative of health status, irrespective of causal agents) that accurately diagnosed (90.0% accuracy) shrimp health status, regardless of different diseases. These optimizations substantially improved the performance (62.6% vs. 90.0%) diagnosing model. The robustness and universality of model were validated for effectiveness via leave-onedataset-out validation and independent cohorts. Interspecies interaction and stability of the gut microbiotas were consistently compromised in diseased shrimp compared with corresponding healthy cohorts, while stochasticity and beta-dispersion exhibited the opposite trend. Collectively, our findings exemplify the utility of microbiome metaanalyses in identifying robust and reproducible features for quantitatively diagnosing disease incidence, and the downstream consequences for shrimp pathogenesis from an ecological prospective.

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Section: Discussionmentioning

confidence: 99%

A meta‐analysis study of the robustness and universality of gut microbiota–shrimp diseases relationship

Sha

Lü

Chen

et al. 2022

Environmental Microbiology

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“…In addition, pathogens invasion induces host inflammatory response, thereby converging the spatial niche along host gut. Consistent with this assertion, diseased shrimp exhibit a disease‐like gut microbiota as indicated by the relative stable gut microbiota along the severe disease stages (Lu et al, 2020; Wang et al, 2019). As a result, the relative importance of variable selection also decreased in diseased cohorts compared with health shrimp.…”

Section: Discussionmentioning

confidence: 73%

“…Owing to the economic value and high nutrition, shrimp ( Litopenaeus vannamei , Penaeidae) is the most widely cultivated shrimp species globally (Dong et al, 2021). As the results of high density and stressed conditions, shrimp aquaculture is threatened by diverse diseases such as acute hepatopancreatic necrosis disease (AHPND; Kumar et al, 2020), white faeces syndrome (WFS; Lu et al, 2020), and Enterocytozoon hepatopenaei (Shen et al, 2022). Shrimp lack an adaptive immune system for natural protection, thus hampering the conventional vaccination against pathogens (Johnson et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

“…Some studies have uncovered that dysbiosis in the shrimp gut microbiota is closely associated with the occurrence of diverse diseases (Holt et al, 2021; Sha et al, 2022; Yu et al, 2018). The magnitude of microbiome departure to healthy gut microbiome is linearly associated with the severity of shrimp disease (Chen et al, 2017; Lu et al, 2020). Furthermore, dysbiosis in the gut microbiota precedes the onset of shrimp disease (Garibay‐Valdez et al, 2021; Xiong, Zhu, et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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Consistent features of the gut microbiota in response to diverse shrimp Litopenaeus vannamei diseases: A meta‐analysis

Mao,

Lu,

Chen

et al. 2023

Fish and Fisheries

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Dysbiosis in the gut microbiota has been intimately implicated in shrimp (Litopenaeus vannamei, Penaeidae) diseases. However, considering the variety of shrimp diseases and the variability in experimental conditions, studies addressing common features of the gut microbiota−shrimp disease relationship are limited. Through an unbiased subject‐level meta‐analysis framework, 463 shrimp gut bacterial communities from 27 studies were re‐analysed, including six lifestages and eight diseases of shrimp, with the causal agents of viral, bacterial, eukaryotic, and unknown pathogens. Shrimp lifestages and diseases were the predominant factors governing the gut microbiota. After ruling out the top lifestage‐ and disease‐specific discriminatory amplicon sequence variants (ASVs) from the gut microbiota, the top 27 disease common‐discriminatory ASVs were identified, contributing to an overall accuracy of 95.9% in diagnosing shrimp health status. By using these optimisation procedures, the accuracy of our diagnosis model was unbiased by shrimp lifestage, specific disease, sampling size, hypervariable region and sequencing platform. The shrimp eight diseases consistently and significantly increased the relative importance of stochasticity, the relative abundance of pathogenic potentials and diversified core ASVs, whereas decreased the diversity and stability of gut microbiota. Collectively, these findings illustrate the effectiveness of meta‐analysis in determining the robust and common features of the shrimp gut microbiota in response to diverse diseases. In particular, disease common‐discriminatory ASVs could accurately diagnose shrimp health status, although the data are divergent in biotic and technical variances.

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“…In addition, the function of infectious diseases was significantly higher in the epimicrobiome of the Ht group in August. Lu et al [ 62 ] found that the metabolic function of infectious diseases was associated with white feces syndrome in shrimp, and the increase in this function might lead to promote the invasiveness of other opportunistic pathogens. As this function was enriched in the Ht group, we speculate that an increase in temperature might affect the health status of the invasive G. vermiculophylla .…”

Section: Discussionmentioning

confidence: 99%

Elevated Temperature-Induced Epimicrobiome Shifts in an Invasive Seaweed Gracilaria vermiculophylla

et al. 2023

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Epibacterial communities on seaweeds are affected by several abiotic factors such as temperature and acidification. Due to global warming, surface seawater temperatures are expected to increase by 0.5–5 °C in the next century. However, how epibacterial communities associated with seaweeds will respond to global warming remains unknown. In this study, we investigated the response of epibacterial communities associated with the invasive Gracilaria vermiculophylla exposed to 3 °C above ambient temperature for 4 months using a benthocosm system in Kiel, Germany, and 16S rRNA gene amplicon sequencing. The results showed that elevated temperature affected the beta-diversity of the epibacterial communities. Some potential seaweed pathogens such as Pseudoalteromonas, Vibrio, Thalassotalea, and Acinetobacter were identified as indicator genera at the elevated temperature level. Thirteen core raw amplicon sequence variants in the elevated temperature group were the same as the populations distributed over a wide geographical range, indicating that these core ASVs may play an important role in the invasive G. vermicullophylla. Overall, this study not only contributes to a better understanding of how epibacterial communities associated with G. vermiculophylla may adapt to ocean warming, but also lays the foundation for further exploration of the interactions between G. vermiculophylla and its epimicrobiota.

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Identifying Potential Polymicrobial Pathogens: Moving Beyond Differential Abundance to Driver Taxa

Cited by 28 publications

References 53 publications

A meta‐analysis study of the robustness and universality of gut microbiota–shrimp diseases relationship

A meta‐analysis study of the robustness and universality of gut microbiota–shrimp diseases relationship

Consistent features of the gut microbiota in response to diverse shrimp Litopenaeus vannamei diseases: A meta‐analysis

Elevated Temperature-Induced Epimicrobiome Shifts in an Invasive Seaweed Gracilaria vermiculophylla

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