BugBase predicts organism-level microbiome phenotypes

Ward, Tonya; Larson, Jennifer Sue; Meulemans, Jeremy; Hillmann, Benjamin; Lynch, Joshua; Sidiropoulos, Dimitrios N.; Caporaso, Gregory J; Blekhman, Ran; Knight, Rob; Fink, Ryan C.; Knights, Dan

doi:10.1101/133462

Cited by 270 publications

(228 citation statements)

References 40 publications

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“…The functional differences between groups were determined with Linear Discriminant Analysis Effect Size (LEfSe). Organism level microbiome phenotypes were predicted and compared with BugBase . The proportions of six phenotypic categories, including Gram staining, oxygen tolerance, ability to form biofilms, mobile element content, pathogenicity, and oxidative stress tolerance, were compared among different groups of patients with gastritis.…”

Section: Methodsmentioning

confidence: 99%

Helicobacter pylori infection alters gastric and tongue coating microbial communities

et al. 2019

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Objective Infection with Helicobacter pylori ( H pylori ), especially cytotoxin‐associated gene A‐positive (CagA+) strains, has been associated with various gastrointestinal and extragastric diseases. The aim of this study was to characterize H pylori ‐induced alterations in the gastric and tongue coating microbiota and evaluate their potential impacts on human health. Design The gastric mucosa and tongue coating specimens were collected from 80 patients with chronic gastritis, and microbiota profiles were generated by 16S rRNA gene sequencing. Samples were grouped as H pylori negative (n = 32), CagA‐negative H pylori infection (n = 13), and CagA‐positive H pylori infection (n=35). The comparison of bacterial relative abundance was made using a generalized linear model. Functional profiling of microbial communities was predicted with PICRUSt and BugBase. Microbial correlation networks were produced by utilizing SparCC method. Results Significant alterations of the gastric microbiota were found in the H pylori +/CagA+ samples, represented by a decrease in bacterial diversity, a reduced abundance of Roseburia , and increased abundances of Helicobacter and Haemophilus genera. At the community level, functions involved in biofilm forming, mobile element content, and facultative anaerobiosis were significantly decreased in gastric microbiome of the H pylori + subjects. The presence of CagA gene was linked to an increased proportion of Gram‐negative bacteria in the stomach, thereby contributing to an upregulation of lipopolysaccharide (LPS) biosynthesis. The number of bacterial interactions was greatly reduced in networks of both tongue coating and gastric microbiota of the H pylori +/CagA+ subject, and the cooperative bacterial interactions dominated the tongue coating microbiome. Conclusions Infection with H pylori strains possessing CagA may increase the risk of various diseases, by upregulating LPS biosynthesis in the stomach and weakening the defense of oral microbiota against microorganisms with pathogenic potential.

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Section: Methodsmentioning

confidence: 99%

Helicobacter pylori infection alters gastric and tongue coating microbial communities

et al. 2019

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“…To obtain the phenotypic traits, OTU tables were introduced into the METAGENassist server . Before prediction of potentially pathogenic bacteria by the BugBase server, the OTU table was re‐picked against the Greengenes database (version 13.8) with a closed‐reference approach in QIIME …”

Section: Methodsmentioning

confidence: 99%

“…24,36 To obtain the phenotypic traits, OTU tables were introduced into the METAGENassist server. 37 Before prediction of potentially pathogenic bacteria by the BugBase server, 38 the OTU table was re-picked against the Greengenes database (version 13.8) with a closed-reference approach in QIIME. 39 For comparison, currently available 16S rRNA amplicon data sets based on Illumina sequencing (Lymantria dispar, SRP030624; Helicoverpa armigera and Ostrinia furnacalis, SRP152395; Plutella xylostella, SRP091798; Spodoptera frugiperda, SRP185622) were downloaded from the NCBI SRA (www.ncbi.nlm.nih.gov).…”

Section: Bacterial Community Analysis and Functional Predictionmentioning

confidence: 99%

Gut microbiota metabolic potential correlates with body size between mulberry‐feeding lepidopteran pest species

Chen

Xie

Zhang

et al. 2019

Pest Management Science

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BACKGROUND Many insect pests rely on microbial symbionts to obtain nutrients or for defence, thereby allowing them to exploit novel food sources and degrade environmental xenobiotics, including pesticides. Although Lepidoptera is one of the most diverse insect taxa and includes important agricultural pests, lepidopteran microbiotas, particularly functional traits, have not been studied widely. Here, we provide a comprehensive characterization of the gut microbiota across multiple mulberry‐feeding lepidopteran species, resolving both community structure and metabolic potential. RESULTS Our results indicate abundant bacteria inside the gut of larval Lepidoptera. However, even though they were fed the same diet, the structures of the bacterial communities differed in four major mulberry pest species, suggesting host‐specific effects on microbial associations. Community‐level metabolic reconstructions further showed that although taxonomic composition varied greatly, carbohydrate and amino acid metabolism and membrane transporter were key functional capabilities of the gut bacteria in all samples, which may play basic roles in the larval gut. In addition, principal coordinate analysis (PCoA) of gut bacterial‐predicted gene ontologies revealed specialized features of the microbiota associated with these mulberry pests, which were divided into two distinct clusters (macrolepidopterans and microlepidopterans). This pattern became even more prominent when further Lepidoptera species were involved. CONCLUSIONS A suite of gut microbiota metabolic functions significantly correlated with larval size; the metabolism of terpenoids and polyketides, xenobiotics biodegradation and metabolism were specifically enriched in large species, while small larvae had enhanced nucleotide metabolism. Our report paves the way for uncovering the correlation between host phenotype and microbial symbiosis in this notorious insect pest group. © 2019 Society of Chemical Industry

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“…For bacterial functional potential, we used the BugBase (Ward et al. ) tool that groups organisms into functional groups based on KEGG pathways (Ogata et al. ) compiled by PICRUSt (Langille et al.…”

Section: Methodsmentioning

confidence: 99%

“…We analyzed outputs at the trophic mode level to understand the proportion of the root communities composed of mutualists (symbiotrophs), pathogens (pathotrophs), and likely commensalists (saprotrophs). For bacterial functional potential, we used the BugBase (Ward et al 2017) tool that groups organisms into functional groups based on KEGG pathways (Ogata et al 1999) compiled by PICRUSt (Langille et al 2013). This tool allowed us to view bacterial communities by their oxygen requirements and potential for stress tolerance.…”

Section: Functional Assignmentmentioning

confidence: 99%

Root endophytes and invasiveness: no difference between native and non‐native Phragmites in the Great Lakes Region

et al. 2018

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Microbial interactions could play an important role in plant invasions. If invasive plants associate with relatively more mutualists or fewer pathogens than their native counterparts, then microbial communities could foster plant invasiveness. Studies examining the effects of microbes on invasive plants commonly focus on a single microbial group (e.g., bacteria) or measure only plant response to microbes, not documenting the specific taxa associating with invaders. We surveyed root microbial communities associated with co‐occurring native and non‐native lineages of Phragmites australis, across Michigan, USA. Our aim was to determine whether (1) plant lineage was a stronger predictor of root microbial community composition than environmental variables and (2) the non‐native lineage associated with more mutualistic and/or fewer pathogenic microbes than the native lineage. We used microscopy and culture‐independent molecular methods to examine fungal colonization rate and community composition in three major microbial groups (bacteria, fungi, and oomycetes) within roots. We also used microbial functional databases to assess putative functions of the observed microbial taxa. While fungal colonization of roots was significantly higher in non‐native Phragmites than the native lineage, we found no differences in root microbial community composition or potential function between the two Phragmites lineages. Community composition did differ significantly by site, with soil saturation playing a significant role in structuring communities in all three microbial groups. The relative abundance of some specific bacterial taxa did differ between Phragmites lineages at the phylum and genus level (e.g., Proteobacteria, Firmicutes). Purported function of root fungi and respiratory mode of root bacteria also did not differ between native and non‐native Phragmites. We found no evidence that native and non‐native Phragmites harbored distinct root microbial communities; nor did those communities differ functionally. Therefore, if the trends revealed at our sites are widespread, it is unlikely that total root microbial communities are driving invasion by non‐native Phragmites plants.

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BugBase predicts organism-level microbiome phenotypes

Cited by 270 publications

References 40 publications

Helicobacter pylori infection alters gastric and tongue coating microbial communities

Helicobacter pylori infection alters gastric and tongue coating microbial communities

Gut microbiota metabolic potential correlates with body size between mulberry‐feeding lepidopteran pest species

Root endophytes and invasiveness: no difference between native and non‐native Phragmites in the Great Lakes Region

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