Phocaeicola vulgatus

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Phocaeicola vulgatus
Bacteroides biacutis 01.jpg
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Bacteria
Phylum: Bacteroidota
Class: Bacteroidia
Order: Bacteroidales
Family: Bacteroidaceae
Genus: Phocaeicola
Species:
P. vulgatus
Binomial name
Phocaeicola vulgatus
García-López et al. 2020

Phocaeicola vulgatus, (formerly Bacteroides vulgatus ), [1] is a mutualistic anaerobic Gram negative rod bacteria commonly found in the human gut microbiome and isolated from feces. [2] P. vulgatus has medical relevance and has been notable in scientific research due to its production of fatty acids, potential use as a probiotic, and associations with protecting against and worsening some inflammatory diseases. [3] [4] [5] Due to the difficulties in culturing anaerobic bacteria, P. vulgatus is still highly uncharacterised so efforts are being made to make use of multi-omic approaches to investigate the human gut microbiome more thoroughly in hopes to fully understand the role of this species in the development of and protection against diseases, as well as its potential uses in medicine and research. [6] Generally, P. vulgatus is considered as a beneficial bacteria that contributes to digestion and a balanced microbiome, but it has been known to cause opportunistic infections and induce or worsen inflammatory responses. Due to its abundance in the microbiome, some researchers are investigating these species in hopes that it will be a suitable model organism for gut microbiome research, like Bacteroides thetaiotaomicron .

Contents

Biology and biochemistry

P. vulgatus does not form spores and is able to grow in mesophilic conditions (37 °C), it is an anaerobe with a DNA GC content of around 41–42%. [7] P. vulgatus is one of the more predominant species in the Bacteroidaceae family, which are one of the five main genera in the human gut microbiome, Bacteroidaceae make up around 30% of fecal isolates. [8] P. vulgatus is found globally and most samples have been isolated from humans. [7] P. vulgatus has more rarely been isolated from companion animals like dogs and cats, and also from sewage, sediment, farms, and plants. [9]

Global distribution of 16S sequence AB510712 Phocaeicola vulgatus subclade from BacDrive, made with Microbeatlas 1.0 Global distribution of 16S sequence AB510712 Phocaeicola vulgatus subclade.png
Global distribution of 16S sequence AB510712 Phocaeicola vulgatus subclade from BacDrive, made with Microbeatlas 1.0

Structure and metabolism

P. vulgatus is a Gram negative rod bacterium. The structure and metabolism of P. vulgatus is still not fully understood, but it is known that P. vulgatus is indole and urea negative and is capable of growing on a range of sugars, the most notable carbon source being glucose. [10] [7] A nitrogen source is also required, with its preferred source being ammonia. [10] In regards to its cell membrane, the species has a lipopolysaccharide structure consisting of a mix of penta- and tetra-acylated mono-phosphorylated molecules, [11] and P. vulgatus produces RagB/SusD protein which is an outer membrane family of proteins involved in bacterial nutrient uptake. [12]

Culturing

P. vulgatus is a biosafety level 1 organism that can be grown in anaerobic laboratory conditions at 37 °C with a growth time[ vague ] of 1–2 days. [7] P. vulgatus can be exposed to 0.03% dissolved oxygen with no effect on growth, and it is believed that anaerobes like P. vulgatus possess specific mechanisms to survive or cope with small levels of oxygen in the environment. [13] A variety of liquid and solid media can be used to grow P. vulgatus; some of these include chopped meat medium supplemented with haemine 5 μg/ml and vitamin K1, Columbia blood medium, fastidious anaerobe broth, brain heart infusion medium, and tryptone yeast extract with glucose. [14] [15] [10] Anaerobic bacteria like P. vulgatus are normally grown in an anaerobic chamber, glove box or anaerobic jar, or with the use of Hungate tubes, syringes, and resazurin oxygen indicator. [10] The addition of vitamin B12 and NaHCO3 helps ensure cell survival. [10]

Diversity

Phylogeny and taxonomy

P. vulgatus belongs to the Bacteroidaceae family and was formerly considered to be part of the Bacteroides genus, but was reclassified in 2020 to the Phocaeicola genus. This was due to phylogenetic analysis suggesting it to be more closely related to the Phocaeicola genus than to B. fragilis . [1] B. barnesiae, B. caecicola, B. caecigallinarum, B. chincillae, B. coprocola,B. coprophilus, B. dorei, B. gallinaceum, B. massiliensis, B. paurosaccharolyticus, B. plebeius, B. salanitronis, B. sartorii were all reclassified to Phocaeicola at the same time. [1] P. vulgatus is often hard to distinguish from its close relative P. dorei through matrix-assisted laser desorption/ionization identification, so 16S sequencing is used. [16]

The name Phocaeicola was first proposed in 2009 when a bacteria known as Phocaeicola abscessus was isolated from the brain of a man from the town Foça, which was known as Phocaea in the 11th century BC. The name vulgatus comes from the Latin vulgatus, meaning common or popular. [17] [18]

Type strain

The type strain for this species is Phocaeicola vulgatus ATCC 8482. [19]

Genomics

Genome

The genome of P. vulgatus is around 5 Mbp in length. [20]

Plasmids

Some strains of P. vulgatus and its close relative P. dorei have been known to carry a plasmid (called pBUN24) of around 9 kbp which is the vector for its toxin, BcpT. [21] A version of this plasmid is also found in B. uniformis at around 90% similarity. Some cases have seen this plasmid present in isolates of P. vulgatus, B. intestinalis, and P. distasonis from the same individual, suggesting that the plasmid is mobilisable between multiple species of bacteria. [21]

The plasmid pBI143 is mobilisable to P. vulgatus. This plasmid was first identified in 1985 in Bacteroides fragilis . [22] [23]

Role in the gut microbiome

P. vulgatus seems to be present from early in an individual's development, and abundance is affected by type of diet the neonate has – formular or milk. [24] Studies suggest that P. vulgatus is important in breaking down the complex carbohydrates in breast milk and therefore may be more abundant in babies who are breastfed. Infants as young at 2 months have been found to have species of Bacteroidaceae in their fecal microbiome. [25]

P. vulgatus becomes more abundant as a human ages [24] and will be involved in breakdown and digestion of other foods in the human diet, as well as the production of important molecules needed by the human body. [26] [27] It is capable of degrading complex heteropolysaccharides, like xylan into small chain fatty acids to be used in the human body. P. vulgatus also possess the ldh gene, which codes for the production of D-lactate dehydrogenase, an enzyme that is responsible for the conversion of lactate into pyruvate. [28] These are important metabolic fuels for the function of mitochrondria in cells in the body. [29] [30] P. vulgatus is also known to produce acetate, and succinate from hexose sugars as well as being involved in synthesising vitamins and bioactive compounds. [31] [28]

Antibacterial toxin

This bacteria likely has a very complex role in the microbiome and interacts with many of the species present. Exposure to treatment that lowers the abundance of E. coli and C. sporogenes increases abundance of P. vulgatus P. vulgatus produces an antibacterial protein called BcpT which is encoded on a small conjugative plasmid. [21] This protein's receptor is Lipid A-core glycan which is found in other Bacteroidales families. The protein has a unique structure, unlike other characterised toxin proteins and it requires a two site cleavage to activate its antibacterial activity. Due to this, it is suggested to be a newly identified family of antibacterial toxins found in the gut microbiome. [21] Bacteria will often produce toxins like these in order to pose a threat to other bacteria competing for the same niche, in doing this they will kill or inhibit growth of these competitors, and therefore gain the nutrients and habitats [32]

Role in disease

Ulcerative Colitis

Higher levels of dipeptides and oligopeptides have been observed in fecal samples from ulcerative colitis patients, and are believed to be due to an overproduction of proteases from P. vulgatus and related species. [6] In a study looking at investigating this observation by investigating the transepithelial electrical resistance, which is a reliable method for testing the integrity of a cell monolayer, [33] in the presence of these peptides from P. vulgatus. They saw that mouse epithelial layer integrity was lower in the presence of the proteases from P. vulgatus, hinting to damage of the intestinal wall, and saw that this was significantly reduced when a protease inhibitor was given to the mouse. [6] Other work has seen similar results to this in rats. [34] Ulcerative colitis has also been seen to be induced more severely in guinea pigs exposed to both P. vulgatus and carrageenan, a polysaccharide found in red seaweed that is known to induce inflammation and worsen symptoms of ulcerative colitis, [35] [36] animals exposed to just P. vulgatus showed no signs of ulcerative colitis unless exposure was daily, in which smaller signs of inflammation were observed in the epithelium.

While some research has shown P. vulgatus plays a role in worsening symptoms of ulcerative colitis, a study expanding on previous findings that E. coli Nissle could act as a probiotic, protecting against ulcerative colitis, [37] [38] found that P. vulgatus had the same impact as E. coli Nissle and reduced diseases expression in IL-2-/- mice [39]

Obesity

P. vulgatus is reported to be a member of the healthy microbiota, preventing obesity phenotypes from worsening in some studies [40]

Role in biotechnology

While P. vulgatus does prefer anaerobic conditions, it is capable of surviving exposure to oxygen for short periods of time., [8] [13] and is known to produce very little gas during growth, the gas it produces is hydrogen. [41] Due to its low hydrogen production, P. vulgatus has been used in developing gas production measuring systems in biotechnology, allowing for testing the lower detection limits of gas sensors [3]

History

P. vulgatus was first described in 1932 by Arnold H. Eggerth and Bernard H. Gagnon. [2] In this study, it was recognised that P. vulgatus was very common compared to other species isolated from human feces, and made up the majority of the isolates in this study.

Related Research Articles

An anaerobic organism or anaerobe is any organism that does not require molecular oxygen for growth. It may react negatively or even die if free oxygen is present. In contrast, an aerobic organism (aerobe) is an organism that requires an oxygenated environment. Anaerobes may be unicellular or multicellular. Most fungi are obligate aerobes, requiring oxygen to survive. However, some species, such as the Chytridiomycota that reside in the rumen of cattle, are obligate anaerobes; for these species, anaerobic respiration is used because oxygen will disrupt their metabolism or kill them. The sea floor is possibly one of the largest accumulation of anaerobic organisms on our planet, where microbes are primarily concentrated around hydrothermal vents. These microbes produce energy in absence of sunlight or oxygen through a process called chemosynthesis, where by inorganic compounds such as hydrogen gas, hydrogen sulfide or ferrous ions are converted into organic matter.

<span class="mw-page-title-main">Human microbiome</span> Microorganisms in or on human skin and biofluids

The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside, including the gastrointestinal tract, skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, and the biliary tract. Types of human microbiota include bacteria, archaea, fungi, protists, and viruses. Though micro-animals can also live on the human body, they are typically excluded from this definition. In the context of genomics, the term human microbiome is sometimes used to refer to the collective genomes of resident microorganisms; however, the term human metagenome has the same meaning.

<i>Fusobacterium</i> Genus of bacteria

Fusobacterium is a genus of obligate anaerobic, Gram-negative, non-sporeforming bacteria belonging to Gracilicutes. Individual cells are slender, rod-shaped bacilli with pointed ends. Fusobacterium was discovered in 1900 by Courmont and Cade and is common in the flora of humans.

<span class="mw-page-title-main">Bacteroidota</span> Phylum of Gram-negative bacteria

The phylum Bacteroidota is composed of three large classes of Gram-negative, nonsporeforming, anaerobic or aerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments, and sea water, as well as in the guts and on the skin of animals.

<span class="mw-page-title-main">Gut microbiota</span> Community of microorganisms in the gut

Gut microbiota, gut microbiome, or gut flora are the microorganisms, including bacteria, archaea, fungi, and viruses, that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the gut microbiota. The gut is the main location of the human microbiome. The gut microbiota has broad impacts, including effects on colonization, resistance to pathogens, maintaining the intestinal epithelium, metabolizing dietary and pharmaceutical compounds, controlling immune function, and even behavior through the gut–brain axis.

<i>Bacteroides</i> Genus of bacteria

Bacteroides is a genus of Gram-negative, obligate anaerobic bacteria. Bacteroides species are non endospore-forming bacilli, and may be either motile or nonmotile, depending on the species. The DNA base composition is 40–48% GC. Unusual in bacterial organisms, Bacteroides membranes contain sphingolipids. They also contain meso-diaminopimelic acid in their peptidoglycan layer.

<i>Bacteroides fragilis</i> Species of bacterium

Bacteroides fragilis is an anaerobic, Gram-negative, pleomorphic to rod-shaped bacterium. It is part of the normal microbiota of the human colon and is generally commensal, but can cause infection if displaced into the bloodstream or surrounding tissue following surgery, disease, or trauma.

<span class="mw-page-title-main">Vaginal flora</span> Microorganisms present in the vagina

Vaginal flora, vaginal microbiota or vaginal microbiome are the microorganisms that colonize the vagina. They were discovered by the German gynecologist Albert Döderlein in 1892 and are part of the overall human flora. The amount and type of bacteria present have significant implications for an individual's overall health. The primary colonizing bacteria of a healthy individual are of the genus Lactobacillus, such as L. crispatus, and the lactic acid they produce is thought to protect against infection by pathogenic species.

<span class="mw-page-title-main">Microbial symbiosis and immunity</span>

Long-term close-knit interactions between symbiotic microbes and their host can alter host immune system responses to other microorganisms, including pathogens, and are required to maintain proper homeostasis. The immune system is a host defense system consisting of anatomical physical barriers as well as physiological and cellular responses, which protect the host against harmful microorganisms while limiting host responses to harmless symbionts. Humans are home to 1013 to 1014 bacteria, roughly equivalent to the number of human cells, and while these bacteria can be pathogenic to their host most of them are mutually beneficial to both the host and bacteria.

Faecalibacterium is a genus of bacteria. The genus contains several species including Faecalibacterium prausnitzii, Faecalibacterium butyricigenerans, Faecalibacterium longum, Faecalibacterium duncaniae, Faecalibacterium hattorii, and Faecalibacterium gallinarum. Its first known species, Faecalibacterium prausnitzii is gram-positive, mesophilic, rod-shaped, and anaerobic, and is one of the most abundant and important commensal bacteria of the human gut microbiota. It is non-spore forming and non-motile. These bacteria produce butyrate and other short-chain fatty acids through the fermentation of dietary fiber. The production of butyrate makes them an important member of the gut microbiota, fighting against inflammation.

Prevotella is a genus of Gram-negative bacteria.

Anaerobic infections are caused by anaerobic bacteria. Obligately anaerobic bacteria do not grow on solid media in room air ; facultatively anaerobic bacteria can grow in the presence or absence of air. Microaerophilic bacteria do not grow at all aerobically or grow poorly, but grow better under 10% carbon dioxide or anaerobically. Anaerobic bacteria can be divided into strict anaerobes that can not grow in the presence of more than 0.5% oxygen and moderate anaerobic bacteria that are able of growing between 2 and 8% oxygen. Anaerobic bacteria usually do not possess catalase, but some can generate superoxide dismutase which protects them from oxygen.

Microbiota-accessible carbohydrates (MACs) are carbohydrates that are resistant to digestion by a host's metabolism, and are made available for gut microbes, as prebiotics, to ferment or metabolize into beneficial compounds, such as short chain fatty acids. The term, ‘‘microbiota-accessible carbohydrate’’ contributes to a conceptual framework for investigating and discussing the amount of metabolic activity that a specific food or carbohydrate can contribute to a host's microbiota.

Bifidobacterium breve is a bacterial species of the genus Bifidobacterium which has probiotic properties. Bifidobacteria are a type of bacteria that live symbiotically in the intestines of humans. They have been used to treat a number of conditions including constipation, diarrhea, irritable bowel syndrome and even the cold and flu. Some of these uses have been backed up by scientific research, but others have not. B. breve is a gram positive, anaerobic, rod shaped organism that is non motile and forms branches with its neighbors.

Christensenella is a genus of non-spore-forming, anaerobic, and nonmotile bacteria from the family Christensenellaceae. They are also part of the order Clostridiales, the class Clostridia and the phylum Firmicutes. Phylogenetic analyzes of 16S rRNA gene sequences are used to describe this family. Due to the recent discovery of the Christensenellaceae family, it was not given importance until a few years ago. This is why very little is known about its ecology and how it may be associated with host factors and other microbiota. However, recent studies establish that members of this family, with exceptions, may be associated with a healthy phenotype for humans. The species C. minuta has been published and validated, and C. timonensis and C. massiliensis have been proposed as novel species of the genus Christensenella, all isolated from human feces.

Bacteroides dorei is a species of bacteria within the genus Bacteroides, first isolated in 2006. It is found in the intestinal systems of humans and animals. Research is being conducted to better understand the relationship Bacteroides dorei has on the human intestinal system and the autoimmune disease, Type 1 Diabetes (T1D).

<span class="mw-page-title-main">Microbial drug delivery</span> Form of drug administration

Microbial drug delivery is an emerging form of drug administration characterized by the use of commensal microbes that have been genetically modified to produce medications for chronic diseases in humans. Only proteinaceous drugs can be produced by microbes, as DNA encodes for protein. Research into microbial drug delivery refers to this route of administration as topical, since the microbes release the drug directly to the surface of affected tissues, namely the gastrointestinal (GI) epithelium. Microbial drug delivery is not currently used as a standard route of drug administration due to its experimental nature. During clinical trials, it has been used to treat forms of inflammatory bowel disease (IBD). The most prominently studied vehicles of microbial drug administration are the bacterial species, Lactococcus lactis and Bacteroides ovatus.

Anaerococcus is a genus of bacteria. Its type species is Anaerococcus prevotii. These bacteria are Gram-positive and strictly anaerobic. The genus Anaerococcus was proposed in 2001. Its genome was sequenced in August 2009. The genus Anaerococcus is one of six genera classified within the group GPAC. These six genera are found in the human body as part of the commensal human microbiota.

<i>Bacteroides thetaiotaomicron</i> Species of bacterium

Bacteroides thetaiotaomicron is a gram-negative, rod shaped obligate anaerobic bacterium that is a prominent member of the normal gut microbiome in the distal intestines. Its proteome, consisting of 4,779 members, includes a system for obtaining and breaking down dietary polysaccharides that would otherwise be difficult to digest. B. thetaiotaomicron is also an opportunistic pathogen, meaning it may become virulent in immunocompromised individuals. It is often used in research as a model organism for functional studies of the human microbiota.

Bacteroides caccae is a saccharolytic gram-negative bacterium from the genus Bacteroides. They are obligate anaerobes first isolated from human feces in the 1980s. Prior to their discovery, they were known as the 3452A DNA homology group. The type strain is now identified as ATCC 43185.

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