Clostridium spp.

Optimal Result: 0 - 15000000 CFU/g stool.

Clostridium spp. is a genus belonging to the phylum Firmicutes. While interpreting the literature, careful attention should be paid to the phylogenetic classification of this group due to minor spelling differences between the taxonomic levels. Beyond the phylum level, it is broken down as follows: Class: Clostridia, Order: Clostridiales, Family: Clostridiaceae, and finally, Genus: Clostridium. 

The Clostridium genus contains more than 100 species, most of which are commensal, however it does include pathogens. The literature discusses Clostridial clusters, which may include other species belonging to Eubacterium, Ruminococcus, Roseburia, Butyrivibrio, Faecalibacterium and other genera. These clusters exist due to historic issues with classification, where unclassified species would be moved into the Clostridium category.

Clostridium spp. is part of the intestinal indigenous microbiota and they can produce several endogenous infections.

- Clostridia are one of the most commonly studied anaerobes that cause disease in humans.

- The Clostridium genus contains more than 100 species.

- Clostridia spp are vegetative cells that are rod shaped and arranged in pairs or short chains.

- Clostridium genus bacteria are often described as a biological threat but many of them have positive properties and are used in cosmetic and medicine manufacturing.

- Clostridia typically live in dust, soil, water and in human and animal intestines.

- When the environment is hostile, Clostridia produce spores which are resistant to many disinfectants, including some with antimicrobial properties.

- The odour produced by the Clostridia metabolism can be likened to that of mud, manure and the decay of plant materials.

Clostridium is a genus of bacteria that includes over one hundred distinct species, many of which are abundant and normal inhabitants (commensal) of the human gastrointestinal tract (GIT). Most of the Clostridium species are not virulent and can even have beneficial effects on health and integrity of the GIT in part by breakdown of polysaccharides and fermentation of carbohydrates to short chain fatty acids. However a few species are well-established opportunistic pathogens that produce specific toxins that cause diseases such as food-borne illnesses and, antibiotic-associated diarrhea and pseudomembranous colitis. Some species of Clostridium have been associated with neurological disorders and are the subject of ongoing research. Due to the biodiversity within the Clostridium genus it may be helpful to identify the prevalence of specific Clostridium species that are transiently or permanently present in the GIT of symptomatic patients.

The genus Clostridium includes two serious human pathogens:

1. C.botulinum produces the toxin that causes botulism, which occurs primarily from food poisoning but can also result from wounds or injecting street drugs with infected needles.

2. C.difficile, a normal part of the gut bacteriome, can cause severe diarrhea and abdominal pain when the balance of normal bacteria is impacted. C. difficile is disrupted by taking antibiotics. The elderly or those with Irritable Bowel Syndrome or Colorectal cancer are at a greater risk of developing a C. difficile infection.


Lopetuso, L.R., Scaldaferri, F., Petito, V. et al. Commensal Clostridia: leading players in the maintenance of gut homeostasis. Gut Pathog 5, 23 (2013). [L]

Halmos EP, Christophersen CT, Bird AR, Shepherd SJ, Gibson PR, Muir JG. Diets that differ in their FODMAP content alter the colonic luminal microenvironment. Gut. 2015 Jan;64(1):93-100. doi: 10.1136/gutjnl-2014-307264. Epub 2014 Jul 12. PMID: 25016597. [L]

Basson A, Trotter A, Rodriguez-Palacios A, Cominelli F. Mucosal Interactions between Genetics, Diet, and Microbiome in Inflammatory Bowel Disease. Front Immunol. 2016 Aug 2;7:290. doi: 10.3389/fimmu.2016.00290. PMID: 27531998; PMCID: PMC4970383. [L]

Lin P-Y, Whang L-M, Wu Y-R, et al. Biological hydrogen production of the genus Clostridium: metabolic study and mathematical model simulation. Int J Hydrog Energ. 2007;32(12):1728-1735. [L]

Triantafyllou K, Chang C, Pimentel M. Methanogens, methane and gastrointestinal motility. J Neurogastroenterol Motil. 2014 Jan;20(1):31-40. doi: 10.5056/jnm.2014.20.1.31. Epub 2013 Dec 30. PMID: 24466443; PMCID: PMC3895606. [L]

Gori A, Rizzardini G, Van't Land B, Amor KB, van Schaik J, Torti C, Quirino T, Tincati C, Bandera A, Knol J, Benlhassan-Chahour K, Trabattoni D, Bray D, Vriesema A, Welling G, Garssen J, Clerici M. Specific prebiotics modulate gut microbiota and immune activation in HAART-naive HIV-infected adults: results of the "COPA" pilot randomized trial. Mucosal Immunol. 2011 Sep;4(5):554-63. doi: 10.1038/mi.2011.15. Epub 2011 Apr 27. PMID: 21525866; PMCID: PMC3158294. [L]

Mroczynska M, Galecka M, Szachta P, Kamoda D, Libudzisz Z, Roszak D. Beta-glucuronidase and Beta-glucosidase activity in stool specimens of children with inflammatory bowel disease. Pol J Microbiol. 2013;62(3):319-25. PMID: 24459840. [L]

Leite AZ, Rodrigues NC, Gonzaga MI, Paiolo JCC, de Souza CA, Stefanutto NAV, Omori WP, Pinheiro DG, Brisotti JL, Matheucci Junior E, Mariano VS, de Oliveira GLV. Detection of Increased Plasma Interleukin-6 Levels and Prevalence of Prevotella copri and Bacteroides vulgatus in the Feces of Type 2 Diabetes Patients. Front Immunol. 2017 Sep 15;8:1107. doi: 10.3389/fimmu.2017.01107. PMID: 28966614; PMCID: PMC5605568. [L]

Toscano M, De Grandi R, Miniello VL, Mattina R, Drago L. Ability of Lactobacillus kefiri LKF01 (DSM32079) to colonize the intestinal environment and modify the gut microbiota composition of healthy individuals. Dig Liver Dis. 2017 Mar;49(3):261-267. doi: 10.1016/j.dld.2016.11.011. Epub 2016 Dec 6. PMID: 27939319. [L]

What does it mean if your Clostridium spp. result is too low?

- Both higher and lower abundance of Clostridium has been observed in Irritable Bowel Disease.

- Lactobacillus kefiri was given to 20 healthy volunteers for one month and after the probiotic was discontinued for a month, Bacteroides, Barnesiella, Clostridium, Veillonella and other species were significantly reduced compared to baseline samples. After 12 weeks, a significant increase in Bifidobacteria, and decrease in pathogenic Clostridium spp. (C. histolyticum and C. coccoides clusters) were observed in 57 HIV positive adults supplemented with a prebiotic oligosaccharide powder (15 or 30g short chain galactooligosaccharides/long chain fructooligosaccharides/pectin hydrolysate-derived acidic oligosaccharides (scGOS/lcFOS/pAOS).

What does it mean if your Clostridium spp. result is too high?

- Cigarette smoking is associated with increased levels.

- Coffee was positively associated with the relative abundance of Clostridium, Lactobacillus, and Lactococcus in 23 allergic patients.

- A high beef diet was associated with increases in Bacteroides and Clostridium spp. in 10 volunteers.

- Higher Clostridium counts and increased number of Clostridium species have been reported in people with autism.

- Both higher and lower abundance of Clostridium has been observed in Irritable Bowel Disease (IBS).

10 000+ happy customers
100% satisfaction
★ ★ ★ ★ ★ customer support

Understand blood, stool, and urine medical results from all your laboratories.

Upload Your Personal Results

Upload Personal Results

For professional account plans go here

for professional account plans go here

Monthly plan

Annual plan

Own it for life

  • Subscription
  • Data entry service included

    Data entry service

    Our exclusive data entry service is a convenient way to get your results into your private dashboard. Simply attach an image or a file of your lab test results, and one of our qualified data entry team members will add the results for you. We support all sorts of files, whether PDFs, JPGs, or Excel. This service is excellent whether you have a lot of reports to upload or are too busy to do the data entry yourself.

  • Instant interpretation
  • Use free data entry form

    Free data entry form

    We strive to make the data entry process easy for you. Whether by offering dozens of templates to choose from that pre-populate the most popular laboratory panels or by giving you instant feedback on the entered values. Our data entry forms are an easy, fast, and convenient way to enter the reports yourself. There is no limit on how many lab reports you can upload.

  • 4000+ biomarkers explained
  • Nutrition recommendations
  • Cancel anytime


$15 /month

billed every month

  • monthly
  • $15 per report
  • ✓ Instant interpretations
  • ✓ 4000+ biomarkers explained
  • ✓ Nutrition recommendations
  • ✓ Free data entry form
  • ✓ Unlimited data
  • ✓ $15 data entry service
  • ✓ Cancel anytime

Most popular

Data entry included


$79 /year

$6.60/month billed annually

  • yearly
  • 5 reports free
  • ✓ Instant interpretations
  • ✓ 4000+ biomarkers explained
  • ✓ Nutrition recommendations
  • ✓ We enter 5 reports for you
  • ✓ Yearly subscription
  • ✓ Cancel anytime

Data entry included


$250 /once

own it for life

  • pay once
  • 10 reports free
  • ✓ Instant interpretations
  • ✓ 4000+ biomarkers explained
  • ✓ Nutrition recommendations
  • ✓ We enter 10 reports for you
  • ✓ No subscription
  • ✓ Dedicated support
  • ✓ Unlimited access

Are You a Health Professional?

Get started with our professional plan

Welcome to Healthmatters Pro.

Save time on interpreting lab results with the largest database of biomarkers online. In-depth research on any test at your fingertips, all stored and tracked in one place. Learn more

Pro Monthly Plus

for health professionals

  • ✓ Track multiple clients results
  • ✓ No setup fees
  • ✓ No hidden costs
  • ✓ Instant interpretations
  • ✓ 4000+ biomarkers explained
  • ✓ Includes data entry service
  • ✓ Personal training and support
  • ✓ Cancel anytime

$75 per month

Use promo code to save 10% off any plan.

We implement proven measures to keep your data safe.

At HealthMatters, we're committed to maintaining the security and confidentiality of your personal information. We've put industry-leading security standards in place to help protect against the loss, misuse, or alteration of the information under our control. We use procedural, physical, and electronic security methods designed to prevent unauthorized people from getting access to this information. Our internal code of conduct adds additional privacy protection. All data is backed up multiple times a day and encrypted using SSL certificates. See our Privacy Policy for more details.