Oral microbiome - Streptococcus overgrowth (test results)

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Aeon

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Hi, my test results (Oralis 1, shotgun metagenomics method) show overgrowth of Streptococcus species in my oral microbiome.


My test shows the Streptococcus genus at 35.3%, while the healthy average is around 20.8%.


They produce a lot of lactic acid and cause different taste because of this.


How to reduce them? I already reduced sugars in my diet, take xylitol 5x day, K12 with M18, and added a lot of green leafs vegetables to support Rothia and Nesseria with nitrates.


Mouthwashes are not an option, because they kill all, good and bad bacteria.


Streptococcus mitis: 8.0% (Normal range: 0 - 4.7%)


Streptococcus oralis: 4.5% (0.1 - 2.3%)


Streptococcus pneumoniae: 3.5% (0 - 1.2%)


Streptococcus sp. A12: 2.1% (0.09 - 1.2%)


Streptococcus sanguinis: 1.9% (0.04 - 1.2%)


Streptococcus australis: 1.8% (0.1 - 1.3%)


Streptococcus sp. Marseille-Q3533: 1.8% (0.1 - 1.7%)


Streptococcus sp. Marseille-Q6470: 1.2% (0.2 - 1.1%)


Streptococcus gwangjuense: 0.8% (0 - 0.3%)


Streptococcus toyakuensis: 0.7% (0 - 0.4%)


Streptococcus sp. D7B5: 0.7% (0 - 0.1%)


Streptococcus pseudopneumoniae: 0.6% (0 - 0.2%)


Streptococcus sp. 116-D4: 0.5% (0 - 0.2%)


Streptococcus sp. oral taxon 064: 0.5% (0 - 0.1%)


Streptococcus sp. NPS 308: 0.5% (0.003 - 0.1%)


Streptococcus agalactiae: 0.2% (0 - 0.09%)


Streptococcus sp. 1643: 0.2% (0.003 - 0.08%)

Thank you.
 
Thanks for sharing this test here! I didn't know such a thing existed. Aside from reducing sugars and simple carbohydrates, or trying to get bacteria from a healthy donor, I don't know of a way to reduce Streptococcus. Many probiotics contain their own species of Streptococcus, which are probably relatively more benign as far as Streptococcus go, but it's still adding more of something similar. Even Lactobacillus is very close to Streptococcus--so again it's kind of more of the same group, even if it's less-bad species within that group.

There's no probiotic on the market that contains anything even remotely like Rothia or Neisseria. You MAY want to try a Bifidobacterium-only probiotic like ProBiota if you haven't already done so, only because they are evolutionarily far removed from Streptococcus, and though they fill a similar niche of carbohydrate fermentation they do it in a different way (using something called the "bifid shunt" and producing mostly acetate, not lactate).

Out of curiosity, do you have a substantial amount of species like Rothia and Neisseria, just at a slightly lower percent than normal, or are the levels of these almost undetectable?
 
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Thank you for your kindness and willingess to help.

Yesterday I bought this:
www.amazon.co.uk/dp/B0DZX4CR63

Is it a good idea in the discussed context to also take xylitol and arginine powder a few times a day?

I do not think that a donation (except kissing, and some experimental, closed trials starting now in USA) is available.
  • Rothia mucilaginosa: 2.7% (normal range 3.9–21.0%)
  • Rothia aeria: 1.0% (normal range 0–0.7%)
  • Rothia dentocariosa: 1.2% (normal range 0–1.7%)

  • Neisseria subflava: 8.8% (normal range 1.1–14.9%)
  • Neisseria cinerea: 0.07% (normal range 0–0.7%)
  • Neisseria polysaccharea: 0.05% (normal range 0–0.06%)
  • Neisseria gonorrhoeae: 0.1% (normal range 0–0.2%)
  • Neisseria bacilliformis: 0.02% (normal range 0–0.1%)
 
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Aeon said:
I do not think that a donation (except kissing, and some experimental, closed trials starting now in USA) is available.
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I'm hoping to change that.
Aeon said:
  • Rothia mucilaginosa: 2.7% (normal range 3.9–21.0%)
  • Rothia aeria: 1.0% (normal range 0–0.7%)
  • Rothia dentocariosa: 1.2% (normal range 0–1.7%)

  • Neisseria subflava: 8.8% (normal range 1.1–14.9%)
  • Neisseria cinerea: 0.07% (normal range 0–0.7%)
  • Neisseria polysaccharea: 0.05% (normal range 0–0.06%)
  • Neisseria gonorrhoeae: 0.1% (normal range 0–0.2%)
  • Neisseria bacilliformis: 0.02% (normal range 0–0.1%)
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Aside from Rothia mucilaginosa and possibly Neisseria cinerea, nothing looks significantly low here. Is there anything else (Prevotella, Actinomyces, etc.) that really is strikingly low, (like <5% of the midpoint of the normal range)? or just a wide variety of bacteria, each of which is toward the lower end of normal but with none in particular standing out?

I'd suspect that your problem really were missing microbes, there'd be some genera/species that are totally or near-totally missing. If there really is an empty niche for something you have at, say, 25% of normal, then it should be able to expand to fill it within well under a day. It's also possible that you're missing specific strains more than specific species.
 
SFBayFMT5 said:
I'd suspect that your problem really were missing microbes, there'd be some genera/species that are totally or near-totally missing. If there really is an empty niche for something you have at, say, 25% of normal, then it should be able to expand to fill it within well under a day.
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This is not evidence-based. As previously pointed out, current knowledge does not allow one to make these kinds of inferences. Doing so is spreading misinformation.
 
SFBayFMT5 said:
I'm hoping to change that.

Aside from Rothia mucilaginosa and possibly Neisseria cinerea, nothing looks significantly low here. Is there anything else (Prevotella, Actinomyces, etc.) that really is strikingly low, (like <5% of the midpoint of the normal range)? or just a wide variety of bacteria, each of which is toward the lower end of normal but with none in particular standing out?

I'd suspect that your problem really were missing microbes, there'd be some genera/species that are totally or near-totally missing. If there really is an empty niche for something you have at, say, 25% of normal, then it should be able to expand to fill it within well under a day. It's also possible that you're missing specific strains more than specific species.
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Thank you. Please find the full results below:

Neisseria subflava: 8.8% (normal range 1.1–14.9%)
Streptococcus mitis: 8.0% (0–4.7%)
Gemella sanguinis: 5.0% (0.2–1.9%)
Streptococcus oralis: 4.5% (0.1–2.3%)
Haemophilus parainfluenzae: 4.1% (1.1–8.4%)
Streptococcus pneumoniae: 3.5% (0–1.2%)
Granulicatella adiacens: 3.3% (0.3–1.8%)
Actinomyces sp. oral taxon 169: 2.9% (0–0.7%)
Rothia mucilaginosa: 2.7% (3.9–21.0%)
Actinomyces oris: 2.6% (0–1%)
Neisseria mucosa: 2.5% (0.06–1.6%)
Veillonella rogosae: 2.5% (0.4–4.1%)
Prevotella sp. oral taxon 299: 2.5% (0–1.2%)
Neisseria sp. RH3002v2g: 2.3% (0–1.6%)
Streptococcus sp. A12: 2.1% (0.09–1.2%)
Streptococcus sanguinis: 1.9% (0.04–1.2%)
Streptococcus australis: 1.8% (0.1–1.3%)
Streptococcus sp. Marseille-Q3533: 1.8% (0.1–1.7%)
Schaalia odontolytica: 1.8% (1.8–9.6%)
Gemella haemolysans: 1.6% (0–1.1%)
Neisseria perflava: 1.3% (0–1.4%)
Neisseria sp. Marseille-Q5346: 1.3% (0.03–1.5%)
Streptococcus sp. Marseille-Q6470: 1.2% (0.2–1.1%)
Rothia dentocariosa: 1.2% (0–1.7%)
Haemophilus haemolyticus: 1.1% (0–0.6%)
Streptococcus sp. oral taxon 061: 1.1% (0.2–1.3%)
Rothia aeria: 1.0% (0–0.7%)
Neisseria sicca: 1.0% (0.06–1.3%)
Neisseria meningitidis: 0.9% (0.07–0.6%)
Streptococcus sp. oral taxon 431: 0.9% (0.1–1.4%)
Streptococcus gwangjuense: 0.8% (0–0.3%)
Fusobacterium pseudoperiodonticum: 0.8% (0–1.9%)
Actinomyces sp. HMT 175: 0.8% (0–0.2%)
Streptococcus toyakuensis: 0.7% (0–0.4%)
Streptococcus ilei: 0.7% (0–1.6%)
Capnocytophaga gingivalis: 0.7% (0.003–0.5%)
Streptococcus sp. D7B5: 0.7% (0–0.1%)
Haemophilus sp. oral taxon 036: 0.7% (0–0.4%)
Streptococcus pseudopneumoniae: 0.6% (0–0.2%)
Haemophilus influenzae: 0.6% (0–0.4%)
Candidatus Nanosynbacter sp. HMT-352: 0.6% (0–8.2%)
Neisseria macacae: 0.6% (0–0.5%)
Streptococcus sp. 116-D4: 0.5% (0–0.2%)
Streptococcus sp. oral taxon 064: 0.5% (0–0.1%)
Streptococcus infantis: 0.5% (0.1–0.7%)
Streptococcus sp. NPS 308: 0.5% (0.003–0.1%)
Gemella morbillorum: 0.4% (0–0.4%)
Streptococcus parasanguinis: 0.4% (0.03–2.9%)
Streptococcus rubneri: 0.4% (0–1%)
Neisseria flavescens: 0.4% (0.02–0.5%)
Streptococcus koreensis: 0.4% (0–0.7%)
Porphyromonas sp. oral taxon 275: 0.4% (0–0.4%)
Veillonella parvula: 0.4% (0.04–1.3%)
Eikenella corrodens: 0.3% (0–0.2%)
Abiotrophia defectiva: 0.3% (0–0.3%)
Actinomyces pacaensis: 0.3% (0–1%)
Actinomyces naeslundii: 0.3% (0–0.5%)
Streptococcus gordonii: 0.3% (0–0.6%)
Veillonella nakazawae: 0.3% (0.3–2.0%)
Capnocytophaga sputigena: 0.2% (0–0.3%)
Leptotrichia sp. oral taxon 212: 0.2% (0–0.6%)
Cardiobacterium hominis: 0.2% (0–0.2%)
Streptococcus cristatus: 0.2% (0–0.5%)
Streptococcus agalactiae: 0.2% (0–0.09%)
Parvimonas micra: 0.2% (0–0.3%)
Streptococcus sp. 1643: 0.2% (0.003–0.08%)
Actinomyces sp. oral taxon 171: 0.2% (0–0.3%)
Morococcus cerebrosus: 0.2% (0–0.2%)
Neisseria lactamica: 0.2% (0–0.1%)
Veillonella sp. S12025-13: 0.2% (0.2–1.0%)
Fusobacterium nucleatum: 0.2% (0–0.2%)
Campylobacter concisus: 0.2% (0.1–2.1%)
Streptococcus salivarius: 0.1% (0.2–9.1%)
Streptococcus sp. LPB0220: 0.1% (normal range 0–3.1%)
Streptococcus anginosus: 0.1% (0.02–0.1%)
Porphyromonas endodontalis: 0.1% (0–0.8%)
Fusobacterium periodonticum: 0.1% (0–0.2%)
Streptococcus sp. HSISM1: 0.1% (0–2.6%)
Neisseria elongata: 0.1% (0–0.6%)
Aggregatibacter segnis: 0.1% (0–0.1%)
Lancefieldella parvula: 0.1% (0.06–1.3%)
Arachnia propionica: 0.1% (0–0.2%)
Prevotella melaninogenica: 0.1% (0.2–10.9%)
Corynebacterium durum: 0.1% (0–0.2%)
Capnocytophaga sp. FDAARGOS737: 0.1% (0–0.5%)
Veillonella dispar: 0.1% (0–1.1%)
Lachnoanaerobaculum gingivalis: 0.1% (0.04–0.3%)
Kingella oralis: 0.1% (0–0.2%)
Neisseria gonorrhoeae: 0.1% (0–0.2%)
Candidatus Minimicrobia vallesae: 0.1% (0–0.6%)
Lautropia mirabilis: 0.1% (0–1.1%)
Pauljensenia hongkongensis: 0.09% (0.01–0.1%)
Fusobacterium polymorphum: 0.09% (0–0.2%)
Prevotella intermedia: 0.08% (0.05–0.5%)
Veillonella atypica: 0.09% (0.05–4.2%)
Neisseria sp. Marseille-Q6792: 0.08% (0–0.2%)
Candidatus Nanosynbacter lyticus: 0.08% (0–0.2%)
Fusobacterium hwasookii: 0.07% (0–0.05%)
Neisseria sp. oral taxon 014: 0.08% (0–0.4%)
Capnocytophaga leadbetteri: 0.07% (0–0.4%)
Aggregatibacter sp. 2125159857: 0.07% (0–0.3%)
Actinomyces viscosus: 0.06% (0.006–0.03%)
Corynebacterium matruchotii: 0.06% (0–0.4%)
Eikenella exigua: 0.07% (0–0.03%)
Campylobacter showae: 0.06% (0–0.4%)
Neisseria cinerea: 0.07% (0–0.7%)
Prevotella nigrescens: 0.05% (0–2.3%)
Prevotella sp. oral taxon 475: 0.05% (0–0.09%)
Cardiobacterium sp. Marseille-Q4385: 0.05% (0–0.1%)
Prevotella bivia: 0.06% (0–0.1%)
Neisseria polysaccharea: 0.05% (0–0.06%)
Streptococcus lactarius: 0.06% (0–0.3%)
Haemophilus parahaemolyticus: 0.06% (0–0.3%)
Aggregatibacter sp. Marseille-P9115: 0.05% (0–0.1%)
Aggregatibacter sp. oral taxon 513: 0.06% (0–0.2%)
Streptococcus thermophilus: 0.05% (0.01–0.1%)
Tannerella serpentiformis: 0.05% (0–1.1%)
Capnocytophaga endodontalis: 0.04% (0–0.05%)
Ottowia sp. oral taxon 894: 0.05% (0–0.1%)
Aggregatibacter aphrophilus: 0.05% (0–0.2%)
Lachnoanaerobaculum umeaense: 0.04% (0–0.2%)
Neisseria sp. KEM232: 0.04% (0–0.08%)
Bibersteinia trehalosi: 0.04% (not detected)
Streptococcus intermedius: 0.04% (0–0.1%)
Streptococcus sp. LPB0220: 0.1% (normal range 0–3.1%)
Streptococcus anginosus: 0.1% (0.02–0.1%)
Porphyromonas endodontalis: 0.1% (0–0.8%)
Fusobacterium periodonticum: 0.1% (0–0.2%)
Streptococcus sp. HSISM1: 0.1% (0–2.6%)
Neisseria elongata: 0.1% (0–0.6%)
Aggregatibacter segnis: 0.1% (0–0.1%)
Lancefieldella parvula: 0.1% (0.06–1.3%)
Arachnia propionica: 0.1% (0–0.2%)
Prevotella melaninogenica: 0.1% (0.2–10.9%)
Corynebacterium durum: 0.1% (0–0.2%)
Capnocytophaga sp. FDAARGOS737: 0.1% (0–0.5%)
Veillonella dispar: 0.1% (0–1.1%)
Lachnoanaerobaculum gingivalis: 0.1% (0.04–0.3%)
Kingella oralis: 0.1% (0–0.2%)
Neisseria gonorrhoeae: 0.1% (0–0.2%)
Candidatus Minimicrobia vallesae: 0.1% (0–0.6%)
Lautropia mirabilis: 0.1% (0–1.1%)
Pauljensenia hongkongensis: 0.09% (0.01–0.1%)
Fusobacterium polymorphum: 0.09% (0–0.2%)
Prevotella intermedia: 0.08% (0.05–0.5%)
Veillonella atypica: 0.09% (0.05–4.2%)
Neisseria sp. Marseille-Q6792: 0.08% (0–0.2%)
Candidatus Nanosynbacter lyticus: 0.08% (0–0.2%)
Fusobacterium hwasookii: 0.07% (0–0.05%)
Neisseria sp. oral taxon 014: 0.08% (0–0.4%)
Capnocytophaga leadbetteri: 0.07% (0–0.4%)
Aggregatibacter sp. 2125159857: 0.07% (0–0.3%)
Actinomyces viscosus: 0.06% (0.006–0.03%)
Corynebacterium matruchotii: 0.06% (0–0.4%)
Eikenella exigua: 0.07% (0–0.03%)
Campylobacter showae: 0.06% (0–0.4%)
Neisseria cinerea: 0.07% (0–0.7%)
Prevotella nigrescens: 0.05% (0–2.3%)
Prevotella sp. oral taxon 475: 0.05% (0–0.09%)
Cardiobacterium sp. Marseille-Q4385: 0.05% (0–0.1%)
Prevotella bivia: 0.06% (0–0.1%)
Neisseria polysaccharea: 0.05% (0–0.06%)
Streptococcus lactarius: 0.06% (0–0.3%)
Haemophilus parahaemolyticus: 0.06% (0–0.3%)
Aggregatibacter sp. Marseille-P9115: 0.05% (0–0.1%)
Aggregatibacter sp. oral taxon 513: 0.06% (0–0.2%)
Streptococcus thermophilus: 0.05% (0.01–0.1%)
Tannerella serpentiformis: 0.05% (0–1.1%)
Capnocytophaga endodontalis: 0.04% (0–0.05%)
Ottowia sp. oral taxon 894: 0.05% (0–0.1%)
Aggregatibacter aphrophilus: 0.05% (0–0.2%)
Lachnoanaerobaculum umeaense: 0.04% (0–0.2%)
Neisseria sp. KEM232: 0.04% (0–0.08%)
Bibersteinia trehalosi: 0.04% (not detected)
Streptococcus intermedius: 0.04% (0–0.1%)
Weissella cibaria: 0.04% (not detected)
Streptococcus suis: 0.04% (0.001–0.01%)
Schaalia meyeri: 0.04% (0.03–0.3%)
Streptococcus constellatus: 0.04% (0–0.07%)
Granulicatella elegans: 0.05% (0–0.2%)
Mogibacterium diversum: 0.04% (0.01–0.7%)
Capnocytophaga ochracea: 0.03% (0–0.1%)
Porphyromonas gingivalis: 0.04% (0–0.3%)
Fusobacterium animalis: 0.03% (0–0.2%)
Streptococcus dysgalactiae: 0.03% (0–0.03%)
Streptococcus vestibularis: 0.03% (0–0.2%)
Hoylesella loescheii: 0.03% (0–0.2%)
Prevotella denticola: 0.02% (0–1.1%)
Capnocytophaga sp. oral taxon 878: 0.02% (0–0.05%)
Arachnia rubra: 0.02% (0–0.09%)
Actinobacillus equuli: 0.02% (0–0.006%)
Fusobacterium canifelinum: 0.02% (0–0.01%)
Fusobacterium sp. oral taxon 203: 0.02% (0–0.03%)
Kingella denitrificans: 0.02% (0–0.4%)
Streptococcus parasuis: 0.02% (0–0.005%)
Hoylesella pleuritidis: 0.02% (0–0.2%)
Streptococcus sp. FDAARGOS192: 0.02% (0–0.3%)
Haemophilus pittmaniae: 0.02% (0–0.08%)
Fusobacterium vincentii: 0.02% (0–0.1%)
Streptococcus milleri: 0.02% (0–0.03%)
Mannheimia varigena: 0.02% (not detected)
Streptococcus mutans: 0.02% (0–0.2%)
Bacteroides heparinolyticus: 0.02% (0–0.02%)
Neisseria bacilliformis: 0.02% (0–0.1%)
Actinomyces israelii: 0.009% (0–0.08%)
Leyella stercorea: 0.01% (0–0.007%)
Prevotella jejuni: 0.009% (0–4.9%)
Prevotella histicola: 0.01% (0–3.0%)
Prevotella veroralis: 0.02% (0–2.1%)
Prevotella oris: 0.02% (0–0.9%)
Neisseria shayeganii: 0.006% (not detected)
Neisseria dumasiana: 0.006% (not detected)
Streptococcus respiraculi: 0.006% (not detected)
Streptococcus oriscaviae: 0.006% (not detected)
Streptococcus pyogenes: 0.01% (0–0.4%)
Streptococcus pluranimalium: 0.006% (not detected)
Streptococcus equinus: 0.01% (not detected)
Simonsiella muelleri: 0.007% (0–0.01%)
Streptococcus marmotae: 0.007% (not detected)
Streptococcus himalayensis: 0.006% (not detected)
Streptococcus equi: 0.009% (0–0.01%)
Leptotrichia hofstadii: 0.007% (0–0.05%)
Schaalia cardiffensis: 0.006% (0–0.02%)
Actinomyces capricornis: 0.007% (not detected)
Actinomyces sp. oral taxon 414: 0.009% (0–0.3%)
Bulleidia sp. zg-1006: 0.01% (0–0.02%)
Filifactor alocis: 0.01% (0–0.08%)
Selenomonas sp. oral taxon 136: 0.008% (0–0.5%)
Neisseria yangbaofengii: 0.01% (0–0.007%)
Neisseria lisongii: 0.008% (0–0.003%)
Neisseria sp. KH1003-01: 0.006% (0–0.02%)
Selenomonas sp. oral taxon 478: 0.01% (0–0.7%)
Veillonella rodentium: 0.009% (0.002–0.03%)
Streptococcus alactolyticus: 0.007% (not detected)
Neisseria animalis: 0.01% (not detected)
Neisseria brasiliensis: 0.01% (0–0.005%)
Neisseria animaloris: 0.01% (not detected)
Neisseria chenwenguii: 0.008% (not detected)
Neisseria dentiae: 0.007% (not detected)
Neisseria weixii: 0.007% (not detected)
Neisseria weaveri: 0.007% (0–0.004%)
Neisseria wadsworthii: 0.006% (not detected)
Tannerella forsythia: 0.007% (0–0.3%)
Porphyromonas somerae: 0.006% (0–0.007%)
Porphyromonas cangingivalis: 0.006% (0–0.006%)
Porphyromonas asaccharolytica: 0.007% (0–0.01%)
Pseudoprevotella muciniphila: 0.006% (0–0.006%)
Prevotella buccae: 0.01% (0–0.07%)
Prevotella scopos: 0.007% (0.008–0.2%)
Prevotella baroniae: 0.006% (0–0.04%)
Prevotella corporis: 0.009% (0.003–0.1%)
Leptotrichia wadei: 0.006% (0–1%)
Pseudoleptotrichia goodfellowii: 0.009% (0–0.02%)
Campylobacter rectus: 0.01% (0–0.1%)
Treponema pedis: 0.005% (not detected)
Treponema denticola: 0.009% (0–0.1%)
Schaalia turicensis: 0.006% (0–0.03%)
Aggregatibacter actinomycetemcomitans: 0.005% (0–0.09%)
Actinobacillus porcitonsillarum: 0.01% (not detected)
Actinobacillus genomosp. 1: 0.009% (not detected)
Actinobacillus suis: 0.008% (not detected)
Mannheimia haemolytica: 0.01% (not detected)
Mannheimia granulomatis: 0.01% (not detected)
Pasteurella multocida: 0.007% (0–0.006%)
Candidatus Ornithobacterium hominis: 0.005% (0–0.01%)
Streptococcus uberis: 0.006% (not detected)
Burkholderia multivorans: 0.004% (0–0.003%)
Burkholderia vietnamiensis: 0.002% (not detected)
Leptotrichia trevisanii: 0.005% (0–0.05%)
Actinomyces radicidentis: 0.004% (0–0.003%)
Actinomyces slackii: 0.005% (not detected)
Caproicibacterium sp. BJN0003: 0.005% (not detected)
Barnesiella viscericola: 0.005% (not detected)
Prevotella fusca: 0.005% (0–0.06%)
Prevotella dentalis: 0.004% (0–0.02%)
Prevotella micans: 0.005% (0–0.03%)
Prevotella disiens: 0.005% (0.002–0.07%)
Hoylesella enoeca: 0.005% (0–0.1%)
Hoylesella timonensis: 0.005% (0–0.02%)
Hoylesella shahii: 0.005% (0–0.6%)
Haemophilus ducreyi: 0.005% (0–0.003%)
Neisseria canis: 0.003% (not detected)
Neisseria arctica: 0.004% (not detected)
Streptococcus sobrinus: 0.004% (not detected)
Neisseria musculi: 0.003% (not detected)
Streptococcus ferus: 0.005% (not detected)
Streptococcus merionis: 0.003% (not detected)
Actinobacillus indolicus: 0.005% (not detected)
Mogibacterium pumilum: 0.004% (0–0.04%)
Streptococcus canis: 0.004% (not detected)
Actinomyces howellii: 0.003% (0–0.002%)
Neisseria zalophi: 0.005% (not detected)
Leptotrichia hongkongensis: 0.005% (0–0.04%)
Glaesserella parasuis: 0.004% (not detected)
Fretibacterium fastidiosum: 0.003% (0–0.03%)
Actinomyces trachealis: 0.003% (0–0.004%)
Actinomyces respiraculi: 0.003% (not detected)
Prevotella ruminicola: 0.003% (not detected)
Segatella copri: 0.003% (not detected)
Hoylesella oralis: 0.003% (0–0.04%)
Streptococcus porcinus: 0.005% (0–0.003%)
 
I've been meaning to respond to this sooner... but I sorted these by "percentile" a few weeks ago given the ranges you provided in parentheses (not a "real" percentile, but a fraction of the way between the lower and upper bound given). Around half of the ones below the 5th percentile (shown below) are Bacteroidetes, mostly Prevotella but also Tannerella, Hoylesella, and Leptotrichia (most of the rest are Veillonellaceae, which are a kind of weird offshoot of the Clostridia). None of the Neisseria show up below the 10th percentile.

[('Rothia mucilaginosa', -0.07017543859649121),
('Streptococcus salivarius', -0.011235955056179775),
('Prevotella melaninogenica', -0.009345794392523364),
('Prevotella melaninogenica', -0.009345794392523364),
('Prevotella scopos', -0.005208333333333333),
('Schaalia odontolytica', 0.0),
('Veillonella nakazawae', 0.0),
('Veillonella sp. S12025-13', 0.0),
('Prevotella jejuni', 0.0018367346938775507),
('Prevotella histicola', 0.0033333333333333335),
('Leptotrichia wadei', 0.006),
('Hoylesella shahii', 0.008333333333333333),
('Prevotella veroralis', 0.009523809523809523),
('Veillonella atypica', 0.009638554216867467),
('Veillonella atypica', 0.009638554216867467),
('Selenomonas sp. oral taxon 478', 0.014285714285714287),
('Selenomonas sp. oral taxon 136', 0.016),
('Prevotella denticola', 0.01818181818181818),
('Prevotella nigrescens', 0.02173913043478261),
('Prevotella nigrescens', 0.02173913043478261),
('Prevotella oris', 0.022222222222222223),
('Tannerella forsythia', 0.023333333333333334),
('Streptococcus pyogenes', 0.024999999999999998),
('Actinomyces sp. oral taxon 414', 0.03),
('Lancefieldella parvula', 0.03225806451612904),
('Lancefieldella parvula', 0.03225806451612904),
('Schaalia meyeri', 0.03703703703703704),
('Streptococcus sp. HSISM1', 0.038461538461538464),
('Streptococcus sp. HSISM1', 0.038461538461538464),
('Mogibacterium diversum', 0.043478260869565216),
('Prevotella disiens', 0.044117647058823525),
('Tannerella serpentiformis', 0.045454545454545456),
('Tannerella serpentiformis', 0.045454545454545456),
('Kingella denitrificans', 0.049999999999999996),
('Hoylesella enoeca', 0.049999999999999996)]

I wasn't able to find good info on the food preferences of these Prevotella and related species, as they're not well studied. The only one that has been grown enough in culture to establish these things is Prevotella (now Segatella) copri. But extrapolating as best we can from that, the other Prevotella probably like plant fibers, which Streptococcus can't grow on--so if you wanted a dietary way to try and feed them that's what I'd try.
 
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