Bacteria belonging to the Actinobacteria phylum can be found naturally in the human body on sites ranging from the skin to mucosal surfaces within the gastrointestinal tract. These bacteria are considered important members of a normal microbiota and scientists have found that their presence and abundance in specific sites correlates with the individual’s health status. Knowledge of these species is clinically important.

Actinobacteria have assumed highly variable lifestyles, including pathogens (e.g., Corynebacterium, Tropheryma, Mycobacterium, Propionibacterium, and Nocardia), soil dwellers (Streptomyces), plant commensals (Leifsonia), and even gastrointestinal commensals and symbionts (Bifidobacterium). Actinobacteria has long deviated from other bacteria, which makes it nearly impossible to identify any bacterial group phylogenetically close to this phylum. However, state-of-the-art sequencing technology has recently transformed bacterial biology by enhancing our understanding of genetics, physiology, and evolutionary development of bacteria. Various Actinobacteria genomes have been sequenced, revealing a wide genomic heterogeneity, which reflect their vast biodiversity.

ACTINOBACTERIA IN THE HUMAN MICROBIOME

Bacteria belonging to the Actinobacteria phylum can be found naturally in the human body on sites ranging from the skin to mucosal surfaces within the gastrointestinal tract. These bacteria are considered important members of a normal microbiota and scientists have found that their presence and abundance in specific sites correlates with the individual’s health status. Knowledge of these species is clinically important.

Some of the commensals, symbionts, and opportunistic pathogens found in the human microbiome are bacteria found within the phylum Actinobacteria, which includes 219 genera in 48 families and five orders. The majority of these bacteria live in the soil, but a few groups inhabit the healthy human microbiota. These are predominantly members in the genera Corynebacterium, Propionibacterium, Rothia, Actinomyces, and Bifidobacterium. The presence and abundance of these specific bacteria on certain sites of the human body accurately reflects the individuals’ health status. In terms of clinical significance, the genome sequences for certain strains of each genus were recently decoded and have given insight into how Actinobacteria adapt within the human body.

ACTINOBACTERIA IN MEDICINE & AGRICULTURE

Actinobacteria, especially the most commonly found Actonobacteria genus, Streptomyces spp., produce many bioactive metabolites that are critical to modern-day medicine, such as antibacterials, antifungals, antivirals, immunomodifiers, antithrombotics, anti-tumor drugs, and enzyme inhibitors. Specific Actinobacteria-derived antibiotics commonly used in medicine include aminoglycosides, anthracyclines, chloramphenicol, macrolide, and tetracyclines.

In agriculture, Actinobacteria bacteria is used for insecticides, herbicides, fungicides, and growth promoting substances for plants and animals.

References:  

Bressan, W. Biological control of maize seed pathogenic fungi by use of actinomycetes. Biocontrol. 2003. 48 (2): 233–240. doi:10.1023/a:1022673226324.

Akkermansia currently only has one known species, Akkermansia muciniphila. This bacteria naturally occurs in the human gut microbiome and might be linked to human metabolism. Studies have shown that increased abundances of A. muciniphila are correlated to lean humans, while decreased abundances are observed more often in overweight or obese patients.

Akkermansia, from the phylum Verrucomicrobia, is known for its ability to efficiently use mucus as a carbon and nitrogen source.Akkermansia is a Gram-negative, non-motile, anaerobic, oval-shaped, and non-spore-forming bacteria.

References: 
Caesar, Robert; Tremaroli, Valentina; Kovatcheva-Datchary, Petia; Cani, Patrice D.; Bäckhed, Fredrik. Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling. Cell Metabolism. 2015. 22: 658–668. doi:10.1016/j.cmet.2015.07.026.

Derrien, M. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. International Journal of Systematic and Evolutionary Microbiology. 2004. 54 (5): 1469–1476. doi:10.1099/ijs.0.02873-0. ISSN 1466-5026.

Van Passel MW, Kant R, Zoetendal EG, et al. The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes. Plos One. 2011. 6(3): e16876. doi: 10.1371/journal.pone.0016876.

Researchers consider low levels of the genus Alistipes to be commensal bacteria in the human gut microbiome. Small numbers of these bacteria may indicate good gut health. Alistipes are, however, seen in decreased numbers in plant-based diets and thrive on high-fat diets. They also grow particularly strong colonies in the guts of obese patients. Alistipes are particularly sensitive to antibiotic treatments, which might indicate an obesity therapy. They can also be observed in higher abundances in patients with inflammatory bowel diseases (IBD) as well as in autism.

Bacteroides, one of the most extensively studied bacteria in the human gut, is considered a commensal or mutualistic genus of bacteria when found in the human gut microbiome. They help us in digesting veggies and other foods in lean, low-fat diets. Some of these bacteria might help break down cholesterol and complex sugars.

The common gut microbes, Bacteroidetes, are thought to be key players in protecting us against obesity and disease because they do not digest fat well. In the modern human gut microbiome, Bacteroidetes are often seen in decreased numbers due to poor diet and lifestyle choices like smoking. Scientists believe that we are able to shift our microbiome into a more friendly environment for Bacteroidetes, which reduces risk of disease like obesity.

Bifidobacterium bifidum occurs naturally in the human gut microbiome, is commonly used as a probiotic, and may provide a variety of benefits, including aiding vitamin K and B-complex vitamins production within the intestines, which are essential to human function.

Supplementing the diet with B. bifidum has been shown to improve digestion and boost immune function. B. bifidum promotes microbiota equilibrium and optimal digestion, creating an unfavorable environment for the production of histamine, a chemical responsible for triggering allergic reactions. In addition, B. bifidum may enhance the body's natural antibody immune response. These conclusions may indicate that B. bifidum can help fight intestinal pathogens, digestive irregularities, and histamine production, ultimately improving the body's immunity and reducing risk of allergic reactions.

One study revealed short-term supplementation with B. bifidum may result in restoration of balanced gastrointestinal (GI) tract microflora. In addition, notable improvements in alcohol-induced liver injury were seen with B. bifidum when compared to standard therapy alone.

Probiotics like B. bifidum can be particularly effective in diarrheal treatment, including infectious diarrhea and antibiotic associated diarrhea. Rebalancing the GI tract microflora with probiotic supplements can result in a decrease in stool frequency, fecal weight, and abdominal cramps.

References: 
C. Picard, J. Fioramonti, A. Francois et al. Review article: bifidobacteria as probiotic agents – physiological effects and clinical benefits. Alimentary Pharmacology and Therapeutics. 2005. 22 (6): 495-512.doi: 10.1111/j.1365-2036.2005.02615.x

Chitapanarux, I., Chitapanarux, T., Traisathit, P. et al. Randomized controlled trial of live lactobacillus acidophilus plus bifidobacterium bifidum in prophylaxis of diarrhea during radiotherapy in cervical cancer patients. Radiation Oncology. 2010. 5(31). doi: 10.1186/1748-717X-5-31

Bifidobacterium lactis, an extremely versatile and efficient bacteria in the human gastrointestinal (GI) tract, can be found in fermented dairy products and vegetables as well as probiotic supplements.

In studies, B. lactis has been shown to reduce and maintain healthy levels of cholesterol, ease ulcerative colitis discomfort, and fight Celiac disease symptoms. In combination with other probiotic strains as well as prebiotics, B. lactis could prove helpful in the support of regular bowel movements, overall GI tract health, and metabolism.

B. lactis is essential to the digestion of sugars, fibers, and macronutrients and has been shown to help reduce antibiotic-associated diarrhea risks. In addition, recent studies indicate B. lactis may also be beneficial when fighting respiratory and other infections.

References: 
Bordoni, A., Amaretti, A., Leonardi, A. et al. Cholesterol-lowering probiotics: in vitro selection and in vivo testing of bifidobacteria. Applied Microbiology and Biotechnology. 2013. 97(18):8273-81. DOI: 10.1007/s00253-013-5088-2

Guyonnet, D., Woodcock, A., Stefani, B. et al. Fermented milk containing Bifidobacterium lactis DN-173 010 improves gastrointestinal well-being and digestive symptoms in women reporting minor digestive symptoms: a randomised, double-blind, parallel, controlled study. British Journal of Nutrition. 2009. 102(11):1654-1662. DOI: 10.1111/j.1751-2980.2008.00366.x

Blautia, a recently discovered bacterial genus, groups several abundant gastrointestinal (GI) bacteria previously assigned to the Ruminococcus genus – particularly those related to Ruminococcus obeum. Blautia is capable of using hydrogen and carbon dioxide to create acetate. Species within this genus are among the most abundant members of the GI tract, ranging from 2.5% to 16% of the total human microbiota.

Researchers have found levels of species within this genus are often diminished in elderly patients. In addition, diminished levels have also been found in mucosal samples of colorectal cancer patients, although more research is needed. Alternatively, increased levels of Blautia species have been observed in irritable bowel syndrome (IBS) patients, but this may reflect higher gas levels, which are produced by Dorea, a genus of bacteria that can be utilized by Blautia.

Other interesting research done by the Memorial Sloan Kettering Cancer Center may indicate that small amounts of Blautia within a patients’ microbiome may reduce the risk of graft-versus-host-disease (GVHD) after a bone marrow transplant (BMT). Researchers found that despite Blautia’s presence prior to transplantation, patients often lose this common microbe due to the treatment or not eating, which is common in BMT patients. If a patient still carried Blautia in their gut microbiome after the transplant, they were significantly less at risk for GVHD, a life-threatening condition.

References: 
Chen, W., Liu, F., Ling, Z. et al. “Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer.” PloS ONE. 7(6): e39743; doi: 10.1371/journal.pone.0039743

Grisham, J. “Bacteria May Hold the Key to Preventing Dangerous Side Effect of Transplants.” Memorial Sloan Kettering Cancer Center. (2014). Memorial Sloan Kettering Cancer Center

Coprococcus, a common genus of beneficial bacteria, has been utilized in research to gauge an individual’s gut health. High levels of stress can reduce or deplete levels of Coprococcus and allow potentially bad bacteria, such as Clostridia spp., to overgrow and cause dysbiosis. In addition, researchers have often observed a lack of Coprococcus in the gut microbiomes of autistic children.

References: 
Holdeman, L.V., Moore, W.E.C. New Genus, Coprococcus, Twelve New Species, and Emended Descriptions of Four Previously Described Species of Bacteria from Human Feces. International Journal of Systematic Bacteriology. 1974. 24(2): 260-77; doi: 10.1099/00207713-24-2-260

Berni Canani, R., Sangwan, N., Stefka, A.T. et al. Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants. The ISME Journal. 2016. 10; 742-50; doi: 10.1038/ismej.2015.151

Desulfovibrio, a genus of bacteria commonly found in human guts, is a sulfate-reducing bacteria (SRB). Desulfovibrio spp. are often found in increased abundances in inflammatory bowel disease (IBD) patients.

Increased abundances of Dorea have been found in patients with Irritable Bowel Syndrome (IBS).

Faecalibacterium, which has only one species Faecalibacterium prausnitzii, typically makes up 5 to 20% of the gut microbiome in healthy adults. It is considered one of the most common gut bacteria. Researchers have observed lower than normal levels of Faecalibacterium might be correlated to irritable bowel diseases (IBD) like Crohn's Disease, colon cancer, obesity, and asthma, although more studies are needed to definitively prove this.

The species Faecalibacterium prausnitzii typically makes up 5 to 20% of the bacteria in a healthy adult intestine, making it one of the most common gut bacteria. Studies have shown that low levels of F. prausnitzii within the intestines may potentially be linked to Crohn's Disease, colon cancer, obesity, and asthma, although more studies are needed to definitively prove this.

Recently, Faecalibacterium prausnitzii, an acetate-consuming and butyrate-synthesizing gut bacteria, has attracted attention because of its potentially important role in promoting gut health.

Studies have demonstrated that Faecalibacterium may play a probiotic role. F. prausnitzii, the only species known within the Faecalibacterium genus, may exhibit anti-inflammatory effects on colitis by blocking NF-κB expression and IL-8 secretion. Furthermore, F. prausnitzii encourages resistance against potential pathogens.

References: 
Chen W, Liu F, Ling Z, Tong X, Xiang C. Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer. PLoS ONE. 2012. 7(6);e39743. doi: 10.1371/journal.pone.00397435

Gałęcka M, Szachta, P et al. Faecalibacterium prausnitzii and Crohns Disease – is There any Connection? Polish Journal of Microbiology. 2013. 62(1); 91–5. PMID: 23829084

Often the most common phylum found in the modern human gut microbiome, Firmicutes aid in the digestion of fat, which is required for energy. Previously, these bacteria helped Europeans survive tough winters; however, Firmicutes are now linked to a higher risk of obesity and inflammation. Some Firmicutes are known pathogens for diseases like anthrax, but many Firmicutes are considered commensal bacteria. Beyond the gut microbiome, this phylum of bacteria can be used in a wide variety of processes, including fermenting wine and beer, creating yogurt from milk, and bioremediation.

The phylum Fusobacteria are often found in the gut microbiome, with many of these bacteria belonging to the Fusobacterium genus.

Fusobacteria are gram-negative, anaerobic bacilli. Fusobacteria was first reported as a pathogen connected to appendicitis in 1886. Recent studies have also revealed that acute appendicitis cases can often be linked to a local infection of Fusobacteria species.

Although Fusobacteria can be isolated from fecal samples of healthy humans in relatively high densities, research has found that these bacteria may be linked to inflammation. Increased abundance of Fusobacteria can be linked to ulcerative colitis and colon cancer.

References: 

A.D. Kostic et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host & Microbe. 2013. 14: 207-215. doi: http://dx.doi.org/10.1016/j.chom.2013.07.007

Benno, Y., Endo, K., Takeo, M. et al. Comparison of fecal microflora of elderly persons in rural and urban areas of Japan. Applied Environ Microbiology. 1989. 55: 1100–1105. PMID: 2547333

Lachnospiraceae, a family of bacteria commonly found in your oral cavity, throat, and gut microbiome, aid in the digestion of insoluble fibers. These bacteria are extremely sensitive to prescription medicine, and are often found in decreased abundances after a round of antibiotics.

Lactobacillus (pl. Lactobacilli), a genus from the phylum Firmicutes, are gram-positive facultative anaerobic or microaerophilic rod-shaped bacteria. Lactobacilli make up a significant portion of the lactic acid bacteria (LAB) group. Lactobacillus spp. are naturally found in the human gut and vaginal microbiota. In addition, these bacteria and are often found in probiotic products, like yogurt, and are used to help maintain a healthy gut. Scientists recognize and have sequenced over 50 known species.

References: 
Chen, X., Fruehauf, J., Goldsmith, J. D. et al. Saccharomyces boulardii Inhibits EGF Receptor Signaling and Intestinal Tumor Growth in Apcmin Mice. Gastroenterology. 2009. 137(3): 914–923. doi: 10.1053/j.gastro.2009.05.050

Fijan, Sabina. Microorganisms with Claimed Probiotic Properties: An Overview of Recent Literature. International Journal of Environmental Research and Public Health. 2014.11(5): 4745–4767. doi:10.3390/ijerph110504745

Lactobacillus fermentum is often found in the human gastrointestinal tract and is considered a safe probiotic. Specific strains have been linked to reduction in cholesterol.

One mechanism of this is through the absorption of cholesterol, which accelerates cholesterol metabolism. L. fermentum is also hypothesized to incorporate cholesterol in the host body into cell membranes or walls, ultimately increasing the bacterial resistance to environmental factors. In addition, it may cause the body to consume more cholesterol, interfering with bile salt recycling and aiding in its removal, increasing the demand for bile salt through cholesterol production.

Studies have also linked L. fermentum with improvements in antioxidant enzyme function, immune response, and increased resistance to bacterial infections like E. coli. 

References: 

Tomaro-Duchesneau, C., et al. “Lactobacillus fermentum NCIMB 5221 and NCIMB 2797 as cholesterol-lowering probiotic biotherapeutics: in vitro analysis. Beneficial Microbes. Wageningen Academic Publishers. 2015. 861-869. doi: http://dx.doi.org/10.3920/BM2015.0021

Lactobacillus salivarius is a probiotic that is found in the GI tract and employs a variety of helpful properties, including suppression of pathogenic bacteria.

L. salivarius produces natural antibiotics, which are specifically targeted against invading pathogenic bacteria, especially E. coli and Salmonella spp. It also produces lactic acids, which aid in fighting pathogenic or otherwise bad bacteria, and create an ideal atmosphere for beneficial bacteria.

L. salivarius, a hardy probiotic that replicates extremely quickly, crowding out bad bacteria quickly, too. Other beneficial effects of L. salivarius include aiding in the digestion of proteins, inhibiting candida (yeast) growth, reducing cavities and gingivitis, preventing strep throat, decreasing risk of mastitis (also called mammitis), and easing symptoms of ulcerative colitis and IBS.

The trillions of microbes, including bacteria, fungi, and viruses, in one environment (for example your gut), are collectively known as a microbiome. These microbes may be commensal, symbiotic, or pathogenic.

Researchers estimate the microbiome to account for one to three percent of the human body mass, which can total as high as three pounds. Bacterial DNA was once considered to outnumber human DNA by nearly 10 times; however, today that number is estimated to be around 3 times. So if you think about it, you are more bacteria than you are human!

Your first reaction to this information might be disgust; however, there is a common misconception surrounding bacteria and their potential for disease. Many of the bacteria and other microbes in and on the human body are actually considered commensals, which means that there is no harm to the human host. In addition, a majority of the microbes may also play symbiotic roles, which is a mutually beneficial relationship for the microbe and human host. The balance of gut microbes playing a role in our health is a revolutionary idea that is literally changing the medical field and how we think about and treat disease.

The human gut microbiome is considered one of the most important microbial environments in regards to the role it plays in human health; however, we still have a lot to learn. Research on the gut microbiome only began in the late 1990s. Some scientists have hailed the gut microbiome as a new organ, and believe it plays a major role in immune health. Some disease states, including obesity, diabetes, asthma, autism, and many more, have been linked to specific balances of microbes, or dysbiosis.