Table 1.

Disease specific microbiota alterations at the species level and associated relevant biological findings.

Disease	Microbiota alteration	Relevant associated biological findings	Future directions ?
Rheumatoid arthritis	Oral microbiota -Overall diversity preserved, but different taxa repartition in RA (Mikuls et al., 2018). In particular, Prevotella species and Leptotrichia species almost absent in healthy controls (Scher et al., 2012; Chen et al., 2018),and depletion of Haemophilus spp in RA patients (Zhang et al., 2015; Corrêa et al., 2019). -Infection with Porphyromonas gingivalis or Aggregatibacter actinomycetemcomitans (Aa) (Konig et al., 2016) more frequent in RA patients.	-Analysis of gingival crevicular fluid from patients with periodontitis revealed extensive protein citrullination with same patterns as observed in RA joints (Konig et al., 2016)-Incubation of neutrophils with Aa, but not with P. gingivalis, reproduced this hypercitrullination (Konig et al., 2016) - Periodontitis status correlates with anti-citrullinated-peptides antibodies (Corrêa et al., 2019).	-Unravel associations between smoking, periodontitis, oral dysbiosis and rheumatoid arthritis onset. -Homogenize sampling methodology across the various oral sites (saliva, crevicular fluid, dental plaque, etc.).
	Gut microbiota -Increase of Prevotella species, in particular Prevotella copri, in early RA and preclinical stages of RA (Scher et al., 2013). - Eggerthella genus (Zhang et al., 2015; Chen J et al., 2016), and Collinsella aerofaciens was also more abundant in some RA patients (Chen J et al., 2016).	- Serological immunity against P copri is specific for RA patients (Pianta et al., 2017b). - Prevotella species have potentially cross-reactive antigens (Pianta et al., 2017a). -Patient-derived Collinsella aerofaciens (Chen J et al., 2016), as well as Prevotella species aggravate arthritis in mice models.	-Longitudinal follow-up of at-risk population to allow proper causal inference. - Identification of targeted approaches to shape gut microbiota (probiotics, FMT, functional foods, etc.).
Ankylosing spondylitis	Gut microbiota -Higher abundance of five families of bacteria Lachnospiraceae, Ruminococcaceae, Rikenellaceae, Porphyromonadaceae and Bacteroidaceae, and lower abundance of two families of Veilonellaceae (Costello et al., 2015b) and Prevotellaceae. -A higher prevalence of sulfate-reducing bacteria was also reported in patients with AS.	-A higher prevalence of sulfate-reducing bacteria, also known as hydrogen scavengers. These bacteria can reduce inorganic sulphate to hydrogen sulfide. The higher prevalence of these bacteria may indicate gut inflammation (Stebbings, 2002).	-Modifiye risk factors including nutritional habits (fiber-enriched cereal bars or dietary interventions). - To investigate the effectiveness of fecal transplantation and its long-term results. - Further studies in AS patient’s microbiota needs to focus more on strain level identification of bacteria and plans to study on limitations of 16S-based analysis.
Psoriatic arthritis	-High-throughput 16S rRNA pyrosequencing method in a cohort of PsA and psoriasis patients indicated a decrease in taxonomic diversity due to lower abundances of several taxa compared to the microbiota of healthy controls (Scher et al., 2015), including decreased Coprococcus in both psoriasis and PsA patients, while significantly lower levels of Akkermansia and Ruminococcus only in the PsA (Scher et al., 2015; Scher et al., 2016). - Higher abundance of Firmicutes and lower abundance of phylum Actinobacteria, Staphylococci and Propionibacteria in psoriasis patients and in affected skin (Gao et al., 2008; Fahlén et al., 2012; Costello et al., 2015a).	- The decreased abundance of Ruminococcus and Akkermansia specific to PsA has been evaluated as a chronological loss of diversity that may potentially associate with the natural history of disease (Scher et al., 2015). -The decrease of Propionibacteria may be the cause or result of changes in diseased skin. It still remains unknown if it is a potential biomarker to predict who finally improve PsA (Coit and Sawalha, 2016).	-Homogenize sampling methodology across the skin both psoriasis and PsA patients. -Future preventive or treatment strategies could be including microbiota-targeted interventions, such as dietary interventions, probiotics or FMT.
Juvenile spondylarthritis	-Patients with ERA were reported to display decreased abundance of C. leptum, similar to AS (Stebbings, 2002; Stoll et al., 2014)., a decrease in F. prausnitzii and in cellular immune response to Salmonella typhimurium were also reported in patients with juvenile SpA.	-In children with enthesitis-related arthritis (juvenile idiopathic arthritis subtype), the relative abundance of F. prausnitzii was presented lower as compared to healthy controls (Stoll et al., 2014).	-Planning of further and larger studies on microbiota analysis of children with ERA. -Education of patients and parents about probiotics and nutritional habits.