Statistical Methods for Microbiome Compositional Data Network Inference: A Survey

Chen, Liang; Wan, Hui; He, Qiuyan; He, Songnian; Deng, Minghua

doi:10.1089/cmb.2021.0406

Cited by 6 publications

(6 citation statements)

References 62 publications

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“…However, the driving force behind this remodeling remains unknown, and it may be due to the relative abundance changes in individual species or the disturbed balance of the whole gut flora. Additionally, the interpretation of the network analysis result is not always direct and straightforward; no gold standard comparison methodology has existed yet [ 79 , 80 , 81 ]. Nonetheless, it does not undermine the observed distinction of a co-occurrence network between psoriasis and the apparent normal group and partial restoration of gut dysbiosis in psoriasis after taking 8 weeks of oral probiotics [ 79 ].…”

Section: Discussionmentioning

confidence: 99%

A Novel E3 Probiotics Formula Restored Gut Dysbiosis and Remodelled Gut Microbial Network and Microbiome Dysbiosis Index (MDI) in Southern Chinese Adult Psoriasis Patients

Choy¹,

Chan²,

Siu³

et al. 2023

IJMS

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Psoriasis is a common chronic immune-mediated inflammatory skin disease with the association of various comorbidities. Despite the introduction of highly effective biologic therapies over the past few decades, the exact trigger for an immune reaction in psoriasis is unclear. With the majority of immune cells residing in the gut, the effect of gut microbiome dysbiosis goes beyond the gastrointestinal site and may exacerbate inflammation and regulate the immune system elsewhere, including but not limited to the skin via the gut-skin axis. In order to delineate the role of the gut microbiome in Southern Chinese psoriasis patients, we performed targeted 16S rRNA sequencing and comprehensive bioinformatic analysis to compare the gut microbiome profile of 58 psoriasis patients against 49 healthy local subjects presumably with similar lifestyles. Blautia wexlerae and Parabacteroides distasonis were found to be enriched in psoriasis patients and in some of the healthy subjects, respectively. Metabolic functional pathways were predicted to be differentially abundant, with a clear shift toward SCFA synthesis in healthy subjects. The alteration of the co-occurrence network was also evident in the psoriasis group. In addition, we also profiled the gut microbiome in 52 of the 58 recruited psoriasis patients after taking 8 weeks of an orally administrated novel E3 probiotics formula (with prebiotics, probiotics and postbiotics). The Dermatological Life Quality Index (p = 0.009) and Psoriasis Area and Severity Index (p < 0.001) were significantly improved after taking 8 weeks of probiotics with no adverse effect observed. We showed that probiotics could at least partly restore gut dysbiosis via the modulation of the gut microbiome. Here, we also report the potential application of a machine learning-derived gut dysbiosis index based on a quantitative PCR panel (AUC = 0.88) to monitor gut dysbiosis in psoriasis patients. To sum up, our study suggests the gut microbial landscape differed in psoriasis patients at the genera, species, functional and network levels. Additionally, the dysbiosis index could be a cost-effective and rapid tool to monitor probiotics use in psoriasis patients.

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Section: Discussionmentioning

confidence: 99%

A Novel E3 Probiotics Formula Restored Gut Dysbiosis and Remodelled Gut Microbial Network and Microbiome Dysbiosis Index (MDI) in Southern Chinese Adult Psoriasis Patients

Choy¹,

Chan²,

Siu³

et al. 2023

IJMS

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“…Microbiota data are compositional [i.e., describe relationships between components that are not independent and have an arbitrary sum (Quinn et al, 2018)], sparse [i.e., having excessive zero counts (Hu et al, 2018)], and high dimensional [(i.e., with a larger number of features per sample (Hernańdez Medina et al, 2022)], and, as such, require special treatment. For specifics on how to deal with microbiota data, the reader is referred to other publications (e.g., Chen et al, 2022;Lin and Peddada, 2020;Galloway-Peña and Hanson, 2020). Although a detailed discussion of this issue is out of the scope of the present editorial, we will refer to two examples in which methodological choice has a big impact on data interpretation.…”

Section: The Epistemological Challengementioning

confidence: 99%

Grand challenges in arachnid microbiota and diseases

Cabezas-Cruz

2023

Front. Arachn. Sci.

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“…In addition, a longitudinal approach may help detect correlations across data types that are influenced by a delay of time (Chen et al, 2022). Signal transduction and decoding among host and microorganisms may be time-consuming (Pan, 2021;Xiao et al, 2022) as can the delay between transcriptional shifts and downstream changes affecting the biosynthesis of proteins and metabolites in the host (Jamil et al, 2020).…”

Section: Experimental Setups Of Holo-omics Studies In Microbial Horti...mentioning

confidence: 99%

“…This procedure is not simple since metabarcoding data are always compositional and can be skewed by amplification and sequencing abnormalities (Arribas et al, 2022). SparCC (Chen et al, 2022) was one of the methods used for estimating interaction networks from relative sequence counts. SparCC avoided the compositional effect by obtaining correlation using log-transformed components.…”

Section: Big Data Integration and Computational Tools Used In Holo-omicsmentioning

confidence: 99%

Holo-omic applications to unveil microbiome shaping sustainable horticultural production

Ait-El-Mokhtar

Baslam

2023

Front. Sustain. Food Syst.

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Plant-associated microorganisms play a key role in the future sustainability of terrestrial ecosystems. In nature, plants and their associated microbiome can form an assemblage of species, considered interacting metaorganisms or holobionts. Horticultural plants, including vegetables, fruit and berries, and ornamentals live in intimate association with complex and diverse microbial communities that have evolved a myriad of cooperative and competitive interaction mechanisms that shape the holobiont fitness. Nonetheless, our understanding of these interactions in shaping more complex microbial horticulture communities, along with their relevance for host growth, fitness, stress resilience, and health in a more natural context remains sparse. In this perspective, the holo-omic landscape that requires careful consideration of study design and integrates multi-omic data from both host and microbiota domains is a promising approach to unveil the interplay between the two to advance horticultural production. The analysis of horticulture (meta)-omics and phenotyping, along with mechanistic experiments in model systems, is revolutionizing research by enhancing our ability to understand the structure and core function of the plant-associated microbiome. These advancements are complemented by improvements in the throughput and accuracy of DNA sequencing, enabling us to delve deeper into the genomes of microbial communities. Yet, many challenges remain. We focus this review on the potential for holo-omics to generate a more holistic perspective of molecular networks, and we further discuss the implementation and current limitations of the holo-omic approach within microbial horticulture. We argue that holo-omics will pave the way to improve, from a horticultural perspective, food security and safety, sustainability, breeding practices, development of microbiota- and host-tailored horticultural crops’ health treatments and increasing production efficiency.

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Statistical Methods for Microbiome Compositional Data Network Inference: A Survey

Cited by 6 publications

References 62 publications

A Novel E3 Probiotics Formula Restored Gut Dysbiosis and Remodelled Gut Microbial Network and Microbiome Dysbiosis Index (MDI) in Southern Chinese Adult Psoriasis Patients

A Novel E3 Probiotics Formula Restored Gut Dysbiosis and Remodelled Gut Microbial Network and Microbiome Dysbiosis Index (MDI) in Southern Chinese Adult Psoriasis Patients

Grand challenges in arachnid microbiota and diseases

Holo-omic applications to unveil microbiome shaping sustainable horticultural production

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