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We have good clostridia in the gut and some of them prevent allergies

21st March 2015

Clostridia: who are they ?

The clostridia or Clostridiales, with Clostridium and other related genera, are Gram-positive sporulating bacteria. They are obligate anaerobes, and belong to the taxonomic phylum Firmicutes. This phylum includes clostridia, the aerobic sporulating Bacillales (Bacillus, Listeria, Staphylococcus and others) and also the anaerobic aero-tolerant Lactobacillales (id est, lactic acid bacteria: Lactobacillus, Leuconostoc, Oenococcus, Pediococcus, Lactococcus, Streptococcus, etc.). All Firmicutes have regular shapes of rod or coccus, and they are the evolutionary branch of gram-positive bacteria with low G + C content in their DNA. The other branch of evolutionary bacteria are gram-positive Actinobacteria, of high G + C and irregular shapes, which include Streptomyces, Corynebacterium, Propionibacterium, and Bifidobacterium, among others.




Being anaerobes, the clostridia have a fermentative metabolism of both carbohydrates and amino acids, being primarily responsible for the anaerobic decomposition of proteins, known as putrefaction. They can live in many different habitats, but especially in soil and on decaying plant and animal material. As we will see below, they are also part of the human intestinal microbiota and of other vertebrates.

The best known clostridia are the bad ones (Figure 1): a) C. botulinum, which produces botulin, the botulism toxin, although nowadays has medical and cosmetic applications (Botox); b) C. perfringens, the agent of gangrene; c) C. tetani, which causes tetanus; and d) C. difficile, which is the cause of hospital diarrhea and some postantibiotics colitis.



Figure 1. The four more pathogen species of Clostridium. Image from


Clostridia in gut microbiota

As I mentioned in a previous post (Bacteria in the gut …..) of this blog, we have a complex ecosystem in our gastrointestinal tract, and diverse depending on each person and age, with a total of 1014 microorganisms. Most of these are bacteria, besides some archaea methanogens (0.1%) and some eukaryotic (yeasts and filamentous fungi). When classical microbiological methods were carried out from samples of colon, isolates from some 400 microbial species were obtained, belonging especially to proteobacteria (including Enterobacteriaceae, such as E. coli), Firmicutes as Lactobacillus and some Clostridium, some Actinobacteria as Bifidobacterium, and also some Bacteroides. Among all these isolates, some have been recognized with positive effect on health and are used as probiotics, such as Lactobacillus and Bifidobacterium, which are considered GRAS (Generally Recognized As Safe).

But 10 years ago culture-independent molecular tools began to be used, by sequencing of ribosomal RNA genes, and they have revealed many more gut microorganisms, around 1000 species. As shown in Figure 2, taken from the good review of Rajilic-Stojanovic et al (2007), there are clearly two groups that have many more representatives than thought before: Bacteroides and Clostridiales.


Rajilic 2007 Fig 1

Figure 2. Phylogenetic tree based on 16S rRNA gene sequences of various phylotypes found in the human gastrointestinal tract. The proportion of cultured or uncultured phylotypes for each group is represented by the colour from white (cultured) passing through grey to black (uncultured). For each phylogenetic group the number of different phylotypes is indicated (Rajilic-Stojanovic et al 2007)


In more recent studies related to diet such as Walker et al (2011) — a work done with faecal samples from volunteers –, population numbers of the various groups were estimated by quantitative PCR of 16S rRNA gene. The largest groups, with 30% each, were Bacteroides and clostridia. Among Clostridiales were included: Faecalibacterium prausnitzii (11%), Eubacterium rectale (7%) and Ruminococcus (6%). As we see the clostridial group includes many different genera besides the known Clostridium.

In fact, if we consider the population of each species present in the human gastrointestinal tract, the most abundant seems to be a clostridial: F. prausnitzii (Duncan et al 2013).


Benefits of some clostridia

These last years it has been discovered that clostridial genera of Faecalibacterium, Eubacterium, Roseburia and Anaerostipes (Duncan et al 2013) are those which contribute most to the production of short chain fatty acids (SCFA) in the colon. Clostridia ferment dietary carbohydrate that escape digestion producing SCFA, mainly acetate, propionate and butyrate, which are found in the stool (50-100 mM) and are absorbed in the intestine. Acetate is metabolized primarily by the peripheral tissues, propionate is gluconeogenic, and butyrate is the main energy source for the colonic epithelium. The SCFA become in total 10% of the energy obtained by the human host. Some of these clostridia as Eubacterium and Anaerostipes also use as a substrate the lactate produced by other bacteria such as Bifidobacterium and lactic acid bacteria, producing finally also the SCFA (Tiihonen et al 2010).


Clostridia of microbiota protect us against food allergen sensitization

This is the last found positive aspect of clostridia microbiota, that Stefka et al (2014) have shown in a recent excellent work. In administering allergens (“Ara h”) of peanut (Arachis hypogaea) to mice that had been treated with antibiotics or to mice without microbiota (Germ-free, sterile environment bred), these authors observed that there was a systemic allergic hyper reactivity with induction of specific immunoglobulins, id est., a sensitization.

In mice treated with antibiotics they observed a significant reduction in the number of bacterial microbiota (analysing the 16S rRNA gene) in the ileum and faeces, and also biodiversity was altered, so that the predominant Bacteroides and clostridia in normal conditions almost disappeared and instead lactobacilli were increased.

To view the role of these predominant groups in the microbiota, Stefka et al. colonized with Bacteroides and clostridia the gut of mice previously absent of microbiota. These animals are known as gnotobiotic, meaning animals where it is known exactly which types of microorganisms contain.

In this way, Stefka et al. have shown that selective colonization of gnotobiotic mice with clostridia confers protection against peanut allergens, which does not happen with Bacteroides. For colonization with clostridia, the authors used a spore suspension extracted from faecal samples of healthy mice and confirmed that the gene sequences of the extract corresponded to clostridial species.

So in effect, the mice colonized with clostridia had lower levels of allergen in the blood serum (Figure 3), had a lower content of immunoglobulins, there was no caecum inflammation, and body temperature was maintained. The mice treated with antibiotics which had presented the hyper allergic reaction when administered with antigens, also had a lower reaction when they were colonized with clostridia.


fig 4 skefta

Figure 3. Levels of “Ara h” peanut allergen in serum after ingestion of peanuts in mice without microbiota (Germ-free), colonized with Bacteroides (B. uniformis) and colonized with clostridia. From Stefka et al (2014).


In addition, in this work, Stefka et al. have conducted a transcriptomic analysis with microarrays of the intestinal epithelium cells of mice and they have found that the genes producing the cytokine IL-22 are induced in animals colonized with clostridia, and that this cytokine reduces the allergen uptake by the epithelium and thus prevents its entry into the systemic circulation, contributing to the protection against hypersensitivity. All these mechanisms, reviewed by Cao et al (2014), can be seen in the diagram of Figure 4.

In conclusion, this study opens new perspectives to prevent food allergies by modulating the composition of the intestinal microbiota. So, adding these anti-inflammatory qualities to the production of butyrate and other SCFA, and the lactate consumption, we must start thinking about the use of clostridia for candidates as probiotics, in addition to the known Lactobacillus and Bifidobacterium.


fig 4 Cao b

Figure 4. Induction of clostridia on cytokine production by epithelial cells of the intestine, as well as the production of short chain fatty acids (SCFA) by clostridia (Cao et al 2014).



Cao S, Feehley TJ, Nagler CR (2014) The role of commensal bacteria in the regulation of sensitization to food allergens. FEBS Lett 588, 4258-4266

Duncan SH, Flint HJ (2013) Probiotics and prebiotics and health in ageing populations. Maturitas 75, 44-50

Rajilic-Stojanovic M, Smidt H, de Vos WM (2007) Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 9, 2125-2136

Rosen M (2014) Gut bacteria may prevent food allergies. Science News 186, 7, 4 oct 2014

Russell SL, et al. (2012) Early life antibiotic-driven changes in microbiota enhance 
susceptibility to allergic asthma. EMBO Rep 13(5):440–447

Stefka AT et al (2014) Commensal bacteria protect against food allergen sensitization. Proc Nat Acad Sci 111, 13145-13150

Tiihonen K, Ouwehand AC, Rautonen N (2010) Human intestinal microbiota and healthy aging. Ageing Research Reviews 9:107–16

Walker AW et al (2011) Dominant and diet-responsive groups of bacteria within the human colonic microbiota. The ISME J 5, 220-230




Bacteria in the gut are controlling what we eat

It seems to be so: the microbes in our gastrointestinal tract (GIT) influence our choice of food. No wonder: microbes, primarily bacteria, are present in significant amounts in GIT, more than 10 bacterial cells for each of our cells, a total of 1014 (The human body has about 1013 cells). This amounts to about 1-1.5 kg. And these bacteria have lived with us always, since all mammals have them. So, they have evolved with our ancestors and therefore they are well suited to our internal environment. Being our bodies their habitat, much the better if they can control what reaches the intestine. And how can they do? Then giving orders to the brain to eat such a thing or that other, appropriate for them, the microbes.

Imagen1Figure 1.Command centre of the gastrointestinal tract” (own assembly,  Albert Bordons)

Well, gone seriously, there is some previous work in this direction. It seems there is a relationship between preferences for a particular diet and microbial composition of GIT (Norris et al 2013). In fact, it is a two-way interaction, one of the many aspects of symbiotic mutualism between us and our microbiota (Dethlefsen et al 2007).

There is much evidence that diet influences the microbiota. One of the most striking examples is that African children fed almost exclusively in sorghum have more cellulolytic microbes than other children (De Filippo et al 2010).

The brain can also indirectly influence the gut microbiota by changes in intestinal motility, secretion and permeability, or directly releasing specific molecules to the gut digestive lumen from the sub epithelial cells (neurons or from the immune system) (Rhee et al 2009).

The GIT is a complex ecosystem where different species of bacteria and other microorganisms must compete and cooperate among themselves and with the host cells. The food ingested by the host (human or other mammal) is an important factor in the continuous selection of these microbes and the nature of food is often determined by the preferences of the host. Those bacteria that are able to manipulate these preferences will have advantages over those that are not (Norris et al 2013).

Recently Alcock et al (2014) have reviewed the evidences of all this. Microbes can manipulate the feeding behaviour of the host in their own benefit through various possible strategies. We’ll see some examples in relation to the scheme of Figure 2.


Fig 2 human microbiome behaviour appetite

Figure 2. As if microbes were puppeteers and we humans were the puppets, microbes can control what we eat by a number of marked mechanisms. Adapted from Alcock et al 2014.


People who have “desires” of chocolate have different microbial metabolites in urine from people indifferent to chocolate, despite having the same diet.

Dysphoria, id est, human discomfort until we eat food which improve microbial “welfare”, may be due to the expression of bacterial virulence genes and perception of pain by the host. This is because the production of toxins is often triggered by a low concentration of nutrients limiting growth. The detection of sugars and other nutrients regulates virulence and growth of various microbes. These directly injure the intestinal epithelium when nutrients are absent. According to this hypothesis, it has been shown that bacterial virulence proteins activate pain receptors. It has been shown that fasting in mice increases the perception of pain by a mechanism of vagal nerve.

Microbes can also alter food preferences of guests changing the expression of taste receptors on the host. In this sense, for instance germ-free mice prefer more sweet food and have a greater number of sweet receptors on the tongue and intestine that mice with a normal microbiota.

The feeding behaviour of the host can also be manipulated by microbes through the nervous system, through the vagus nerve, which connects the 100 million neurons of the enteric nervous system from the gut to the brain via the medulla. Enteric nerves have receptors that react to the presence of certain bacteria and bacterial metabolites such as short chain fatty acids. The vagus nerve regulates eating behaviour and body weight. It has been seen that the activity of the vagus nerve of rats stimulated with norepinephrine causes that they keep eating despite being satiated. This suggests that GIT microbes produce neurotransmitters that can contribute to overeating.

Neurotransmitters produced by microbes are analogue compounds to mammalian hormones related to mood and behaviour. More than 50% of dopamine and most of serotonin in the body have an intestinal origin. Many persistent and transient inhabitants of the gut, including E. coli, several Bacillus, Staphylococcus and Proteus secrete dopamine. In Table 1 we can see the various neurotransmitters produced by GIT microbes. At the same time, it is known that host enzymes such as amine oxidase can degrade neurotransmitters produced by microorganisms, which demonstrates the evolutionary interactions between microbes and hosts.


Table 1. Diversity of neurotransmitters isolated from several microbial species (Roschchina 2010)

Neurotransmitter Genera
GABA (gamma-amino-butyric acid) Lactobacillus, Bifidobacterium
Norepinephrine Escherichia, Bacillus, Saccharomyces
Serotonin Candida, Streptococcus, Escherichia, Enterococcus
Dopamine Bacillus, Serratia
Acetylcholine Lactobacillus


Some bacteria induce hosts to provide their favourite nutrients. For example, Bacteroides thetaiotaomicron inhabits the intestinal mucus, where it feeds on oligosaccharides secreted by goblet cells of the intestine, and this bacterium induces its host mammal to increase the secretion of these oligosaccharides. Instead, Faecalibacterium prausnitzii, a not degrading mucus, which is associated with B. thetaiotaomicron, inhibits the mucus production. Therefore, this is an ecosystem with multiple agents that interact with each other and with the host.

As microbiota is easily manipulated by prebiotics, probiotics, antibiotics, faecal transplants, and changes in diet, controlling and altering our microbiota provides a viable method to the otherwise insoluble problems of obesity and poor diet.



Alcock J, Maley CC, Aktipis CA (2014) Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms. BioEssays 36, DOI: 10.1002/bies.201400071

De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, et al (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA 107:14691–6

Dethlefsen L, McFall-Ngai M, Relman DA (2007) An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449:811-818

Lyte M (2011) Probiotics function mechanistically as delivery for neuroactive compounds: Microbial endocrinology in teh design and use of probiotics. BioEssays 33:574-581

Norris V, Molina F, Gewirtz AT (2013) Hypothesis: bacteria control host appetites. J Bacteriol 195:411–416

Rhee SH, Pothoulakis C, Mayer EA (2009) Principles and clinical implications of the brain–gut–enteric microbiota axis. Nature Reviews Gastroenterology and Hepatology 6:306-314

Roschchina VV (2010) Evolutionary considerations of neurotransmitters in microbial, plant, and animal cells. In Lyte M, Freestone PPE, eds; Microbial Endocrinology: Interkingdom Signaling in Infectious Disease and Health. New York: Springer. pp. 17–52

Hyenas communicate by scent through symbiotic bacteria

The spotted hyena (Crocuta crocuta), also known as laughing hyena, is the best known and greatest species of hyena, living in Sub-Saharan Africa. Although not considered in immediate danger of extinction, their numbers have been increasingly shrinking, like all other large African mammals and their total number is estimated at about 40,000. Most of them live in national parks of the East Africa, especially in the Serengeti in Tanzania. In the rest of western and southern Africa, populations in many cases are lower than 1000 individuals in each country, and isolated from each other, so in real danger of extinction.

The spotted hyena (Crocuta crocuta). Photo: Tophat21 (

It is the carnivorous mammal with more complexity of social behaviour, similar to the cercopithecine primates (baboons and macaques), and because of this, his intelligence is comparable to those primates and in some respects even to the chimpanzees.

They live in communities, clans, of about 40 to 80 individuals and these societies are matriarchal: females, larger than males, are dominant, with even the lowest ranking females being dominant over the highest ranking males. Maybe they could be caught by the radical feminists as a symbol, right?

Social relationships among hyenas may have to do with maintaining the hierarchy, or to find food (hunting or scavenging), or reproduce, or control of the territory against other clans, and are based on communication systems that manifest with multiple sensory modalities, both body language and vocalizations. Of these, a wide range of sounds (about 12 different) have been registered, the best known of which are a howl and a kind of laughing where the nickname comes from. Body language is also quite complex, with different attitudes and positions of the ears, tail, etc., sometimes similar to wolves.

Like primates, spotted hyenas recognize individual conspecifics, are conscious that some clan-mates may be more reliable than others, recognize foreign family groups and rank relationships among clan-mates, and adaptively use this knowledge during social decision making.

Creamy secretion of anal scent glands, and olfactory communication

The title of this blog post refers to a particular form of communication, but very common among these hyenas: a chemical signal, olfactively detectable. It is an odorous marking, with a smelly white creamy secretion, called paste, produced by a pair of anal sebaceous glands. This secretion is composed of lipid-rich sebum and desquamated epithelial cells. The paste is deposited on grass stalks, and produces a powerful soapy odour, which even humans can detect. They do it on several occasions, as when lions are present, or the males do it near the dens, and most often in their territory limits. Often, after the pasting, they scratch the ground with their front legs, which adds even more flavours that come from the secretions of their interdigital glands. Clans mark their territories by either pasting or pawing in special latrines located on clan range boundaries.

In addition, this odorous secretion is also part of usual greetings among members of the clan. So, two of the individuals are placed in parallel and in opposite directions from one another, lifting one leg back and smelling each other anogenital areas [1].

Spotted hyenas greeting one another. Photo: Tony Camacho, Science Photo Library

The scent of paste secretion

The major volatile constituents of paste are fatty acids, esters, hydrocarbons, alcohols and aldehydes. Collectively, they give paste a pungent, sour mulch odour that persists, detectable by the human nose, for more than a month after paste is deposited on grass stalks.

It has been shown that odour of spotted hyena paste varies based on the individual identity, sex and group membership of the scent donor. Hyenas’ group-specific odours, in particular, are due to underlying variation in the structure of short-chain fatty acid (mainly acetic, propionic and butyric acids) and ester profiles of paste.

These odorants are well-documented products of bacterial fermentation. These scent glands are warm, moist, organic-rich and largely anaerobic, and thus appear highly conducive to the proliferation of fermentative symbiotic bacteria.

Symbiotic bacterial communities that produce social odour of hyenas

The bacteria use protein and lipid of glands as substrates, producing odoriferous metabolites, which are used by their mammal guests as chemical signals. The bacterial communities differ according to the hyena individuals and especially to the clans, according to symbiotic microbial communities are slightly different among clans, they are group-specific. Bacterial communities arise from the contact between the hyenas of the same clan, as they share the same space and common areas where they deposit the paste secretion. Spotted hyenas frequently scent mark the same grass stalks as their clan-mates (i.e. overmarking), and they often do so in rapid succession to one another. Therefore, overmarking appears to be a viable pathway for the transmission of bacterial communities among members of hyena clans. Although average genetic relatedness within hyena clans is low, it is higher within than among clans.

This mechanism to explain the social scent specific for group has also been proposed for some other mammals such as bats (Eptesicus fuscus, Myotis bechsteinii) and badger (Meles meles), but precisely in the spotted hyena it has been well demonstrated recently in an article published by scientists from Michigan (USA) [2].

These authors have worked with anal scent secretions of female hyenas from Masai Mara reserve in Kenya. They have shown by electron microscopy the presence of bacteria in the paste.

bacteria in pasteBacilli- and cocci-shaped bacteria surrounded by the paste secretion, with lipid droplets (asterisk) [2].

Bacterial DNA was extracted from samples of paste secretion and 16S rRNA genes were amplified and sequenced. Comparing the obtained sequences with data from GenBank ® (public database of genetic sequences,, different bacteria were identified. The genera found were some of the groups of gram-positive Actinobacteria (Corynebacterium and Propionibacterium) and Firmicutes (Anaerococcus and others), and some of the gram-negative group of bacteroides. While the types found were more or less the same in the different clans of hyenas, the proportions of bacterial types were significantly different according to the clan.

Propionibacterium, coloured electron microscopy image: Dennis Kunkel Microscopy, Inc./Visuals Unlimited, Inc. Other species of this bacterial genus producing propionic acid are involved in the production of Emmental cheese types.

So, using the latest molecular techniques, culture independent techniques and sequencing, this work [2] shows that symbiotic bacteria may be helpful to their animal guests, by increasing diversity of odoriferous signals available, with variability among hyenas’ clans.

Importance of symbiosis

This is a quite peculiar symbiosis of bacteria with mammals. But, as you know, most mammals, including us the humans, live with millions of bacteria inside, many of which are beneficial, like most that inhabit the digestive tract or other body parts, which constitute the so-called “microbiome”. The probiotics we eat with some fermented dairy products contribute to maintaining populations of these symbiotic bacteria.

More and more data on the importance of symbiosis in multiple aspects of living beings is being known, as well as symbiosis is a key factor in evolution. Just remember that the most likely hypothesis for the origin of the first eukaryotic cells (about 2000 million years), is that it was due to a combination of the two types of prokaryotes, bacteria and archaea. Some millions of years later, the two well known endosymbiosis took place in the eukaryotic cell: bacteria carrying aerobic respiration that gave rise to mitochondria, and photosynthetic oxygenogenic cyanobacteria that were the origin of chloroplasts in algae and plants.

Other important evolutionary symbiosis were the establishment of mycorrhizae between fungi and plants, which led to the colonization of land by these, or nitrogen-fixing bacteria (Rhizobium) with legume plants, or a group of organisms, lichens, which are symbiosis of fungi with some algae or cyanobacteria, and live in many very different and hostile environments. And many other cases of symbiosis between distinct species getting benefits because live together.

So, symbiosis is a good lesson from biological evolution: by cooperation, benefits for both participants are always obtained.


[1] Mills, G., H. Hofer (1998). Hyaenas: status survey and conservation action plan. IUCN/SSC Hyena Specialist Group.

[2] Theis, K.R., T.M. Schmidt, K.E. Holekamp (2012) Evidence for a bacterial mechanism for group-specific social odors among hyenas. Nature Scientific Reports 2, 615

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