RiteeshGrandhi/sciclaimeval-shared-task huggingface dataset:
Conclusions
In conclusion, NEMM medium was superior in yielding more biomass when used to cultivate dental plaque-derived biofilm. The 16S rRNA gene sequencing results strongly supported that NEMM was able to maintain an in vitro oral microbial community with high diversity. It also supported the growth of many oral species that have not been cultured so far, which may be helpful in capturing more pathogenic bacteria and will contribute to real strains for research via culturomics.
Supplemental Information
Different colors represent different groups. The core microbial community contains 14 bacteria at species level. C:clinical sample.

The predominant taxa (the top ten abundance levels) are shown.

Visualization is carried out to display genera in the form of evolutionary tree and pie chart, which reflects:(1) Evolutionary relationship between genera; (2) Information such as the relative abundance ratios of genera between different groups.

Blank controls are the PCR product generated from two liquid media as PCR templates, respectively. M:marker; NC: blank control.

Bacteria significantly higher in aNEMM compared to aSHI ( P < 0.05).

Bacteria significantly higher in nNEMM compared to nSHI ( P < 0.05).
Figure 1: Alpha diversity of bacterial communities among aerobic culture, anaerobic culture and clinical.
(A) Alpha diversity was measured with ACE index, Chao1 index, Shannon index and Simpson index between clinical samples and liquid media cultured bacteria. (B) Alpha diversity was measured with ACE index, Chao1 index, Shannon index and Simpson index between clinical sample group and liquid media cultured bacteria group among clinical sample group, two liquid media cultured bacteria under anaerobic condition group and under normoxia condition group.

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DOI: 10.7717/peerj.18312/fig-1
Figure 2: Venn diagram and NMDS based on the abundance of OTUs.
(A) Venn diagram displays the number of common and unique characteristics among the groups. Different colors represent different groups. The overlaps represent the common taxa between groups, and the non-overlapping portions represent unique taxa in each group. (B) NMDS was measured with weighted UniFrac. Each sample is represented by a dot.

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Figure 3: Bacterial community structure analysis.
(A) The distributions of the predominant bacteria at genus level. (B) The relative abundance of differential predominant bacteria among aerobic culture, anaerobic culture and clinical groups analyzed at genus level by ANOVA.

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Figure 4: BugBase analysis among different groups.
The three lines from the bottom up are the lower quartile, the mean and the upper quartile in BugBase analysis.

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Figure 5: General bacterial community structure analysis between NEMM and SHI media during aerobic (normoxia) and anaerobic culture.
(A) Alpha diversity was measured with ACE index and Chao1 index. P < 0.05 was considered statistically significant. (B) NMDS was measured with Unweighted UniFrac. Each sample is represented by a dot. (C) Venn diagram displays the number of common and unique characteristics among the groups.

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DOI: 10.7717/peerj.18312/fig-5
Figure 6: The relative abundance of differential predominant bacteria between NEMM and SHI analyzed at genus level by ANOVA.

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Figure 7: BugBase analysis among different groups.
Note: X-axis, group name; Y-axis, Relative abundance in percentage. The three lines from bottom to top are lines indicating lower quartile, average and upper quartile.

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Figure 8: Function prediction by PICRUSt2.
The differential analysis of COG function (A) and KEGG pathway (B) show the abundance ratio of different functions between groups, whose middle figures show the difference ratio of functional abundance within the 95% confidence interval.

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Figure 9: Bacterial genus change between NEMM and SHI medium over time under anaerobic condition (A) and normoxia condition (B).

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Figure 10: Cladogram and LDA score for taxonomic representation of significant differences among groups under anaerobic condition.
The colored nodes from the inner to the outer circles represent taxa from the phylum to genus level. The significantly different taxa are signified by different colors representing the four groups through cladogram (A) and LDA score (B).

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Figure 11: Cladogram and LDA score for taxonomic representation of significant differences among groups under normoxia condition.
The colored nodes from the inner to the outer circles represent taxa from the phylum to genus level. The significantly different taxa are signified by different colors representing the four groups through cladogram (A) and LDA score (B).

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Figure 12: Metastats statistical analysis at genus level under anaerobic condition (A) and normoxia condition (B).

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Statistical analysis of difference between NEMM and SHI media by analyzing genus, species and uncultured bacteria (at species level) captured at different time points.
NEMM and SHI media are suitable for culturing specific bacteria, respectively.