Type 2 diabetes and its risk factors such as dyslipidemia and/or obesity enhance severe periodontitis with a poorly understood microbiome. Hence, the purpose of the present study was to describe and compare the subgingival microbiomes of Type 2 diabetes subjects classified by periodontal diseases, to determine the association between periodontal severity and metabolic condition. 71 DNA subgingival samples of 36 subjects were evaluated by Human Oral Microbiome Identification Microarray using 16S rRNA gene-probe. Blood chemistries were obtained to test hemoglobin, and serum lipid profile. Obesity classification was obtained by Body-Mass-Index. Kruskal-Wallis, Mann-Whitney, Spearman’s correlation, and Multivariate ordinal logistic-regression (periodontal-severity) test were applied (IBM-SPSS-21/Stata 17). Our results suggest samples of subjects with Gingivitis (n=12) presented with higher Bacteroidetes proportion vs. Generalized Periodontitis grouped by severity Stage-I (n=17, NS), Stage-II (n=30, p<0.05), and Stage-III (n=12, p<0.05); and Generalized Periodontitis Stage-II presented higher Firmicutes proportion (p<0.05_MW_vs._Gingivitis). Human-Microbial-Taxon presented significant higher Score-levels (Levels), frequency (%), or Odds Ratio (OR) of *1Cardiobacterium valvarum_HMT-540, Fusobacterium Cluster-AE01 (Generalized Periodontitis-Stage-I vs. Gingivitis_p<0.001_Levels, OR: 9.1 and 4.7), *2Porphyromonas gingivalis HMT-619 (OR: 4.7), ƗPorphyromonas pasteri_HMT-279 (Gingivitis vs. Generalized Periodontitis-Stage-I and II_p<0.01/p<0.001_Levels), *3Streptococcus constellatus_HMT-576/Streptococcus intermedius_HMT-644 (Generalized Periodontitis-Stages-II, III vs. Gingivitis_p<0.05_%), and †Saccharibacteria (TM7)[G-1]_bacterium_HMT-347,350_Gingivitis_p<0.05_Levels), some of the Human-Microbial-Taxon identified, presented correlation with total triglycerides (≥150mg/dl, Ɨ0.521), total lipids (≥800mg/dl, †0.478), and obesity (*10.279, *20.280, *30.312). The microbiome of Type 2 diabetes subjects with gingivitis presented the classical microbial profile with representative pathogenic species, while the Generalized Periodontitis Stage I-II subjects presented a microbiome with representative putative and saccharolytic species, some of them strongly associated with the poor control of lipid profile or obesity, and to periodontal-severity.

The authors have declared no competing interest.

NA

Yes

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

The present study was approved by the Ethics Committees of Dentistry School at the Universidad Nacional Autónoma de México and of the of the Health Sciences Institute at Universidad Autónoma del Estado de Hidalgo (ICSA, UAEH) with record numbers UAEH-DIICSA-ODO-CF-011 and CEEI-00005-2019.

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Yes

I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes

I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

Yes

The data are all contained within the manuscript.