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Higher order taxa

Domain: Bacteria; Phylum: Verrucomicrobia; Class: Verrucomicrobiales; Order: Verrucomicrobiales; Family: Planctobacteria/Gracilicutes



2. Description and significance

Verrucomicrobia is a phylum of Gram-negative bacteria that are found in freshwater, marine, and soil environments and human feces [Bergmann et al., 2011]. This phylum plays an important role in biogeochemical cycles globally [Freitas et al., 2012] and is a component of the human gut microbiota [Wertz et al., 2012] as it contributes to the nitrogen content of animal guts. It has two “sister phyla”, Chlamydiae and Lentisphaerae within the Planctobacteria group, also known as the PVC group. Verrucomicrobia can be distinguished to have an exclusive relation specifically to chlamydiae in comparison to other bacteria. Furthermore, Verrucomicrobia is suggested to have a common ancestry and an independent lineage with other bacteria and is more closely related than planctomycetes. Verrucomicrobia bacteria are also closely related to eukaryotes and can be essential to a healthy gut, due to its anti-inflammatory properties [Fujio-Vejar et al., 2017].

3. Genome structure

The genome of TAV2, a strain of Verrucomicrobia in the gut of termites, has been sequenced. The TAV2 genome is 5.2 mB in size with one 16S rRNA copy per cell [Wertz et al., 2012]. The TAV2 genome has all the necessary genes for glycolysis and the tricarboxylic acid cycle, as well as a terminal oxidase encoding gene, meaning that the microbe potentially can oxidize glucose to CO2 and is a potential microaerophile [Wertz et al., 2012]. The Verrucomicrobia genome also revealed that it uses plant biomass as an energy source and exhibits optimal growth at 2-8% oxygen confirming that it is microaerophilic [Wertz et al., 2012]. Initial analysis of the TAV2 genome also revealed regions containing genes encoding nitrogenase [Wertz et al., 2012], which is involved in nitrogen fixation may contribute to the nitrogen content of animal guts.

Currently, six monophyletic classes are recognized in the phylum Verrucomicrobia based on 16S rRNA gene library studies. There are more than 500 different Verrucomicrobia 16S rRNA gene sequences in a publicly accessible database [Lee, K.-C. et al., 2009].

4. Cell structure

Verrucomicrobium spinosum are heterotrophic, Gram-negative. Its morphology is coccoid or rod-shaped. The spore formation was not observed and no spore forming genes were annotated in the genome sequence. The cells of Verrucomicrobium spinosum have a cell extension known as the prostate. At present, six monophyletic classes are recognized within the phylum Verrucomicrobia on the basis of 16S rRNA gene library studies [Lee, K.-C. et al., 2009].

5. Metabolic processes

Verrucomicrobia is involved in the metabolism of two glycosphingolipids (neutral glycosphingolipids and negatively charged glycosphingolipids), galactosylceramide, and sulfate [Cabello-Yeves,et al 2018]. Verrucomicrobia bacteria conduct aerobic and heterotrophic metabolism, though some synthesize anaerobic reductase complexes [Cabello-Yeves et al., 2017]. Verrucomicrobia bacterial populations had significant differences between the two lakes in terms of glycoside hydrolase gene abundance and functional profiles, reflecting the natural and terrestrial carbon sources of the two ecosystems, respectively. Verrucomicrobia are potential saccharide degraders . These molecules allow Verrucomicrobia to live a phototrophic lifestyle through rhodopsin pumps. The TAV2 genome has all the genes which are necessary for glycolysis and the TCA, as well as a terminal oxidase encoding gene, meaning that the microbe potentially can oxidize glucose to CO2 and is a potential microaerophile [Wertz et al., 2012]. Verrucomicrobia are oligotrophs that aid in methanol oxidation in soil, which regulates methane emissions to the atmosphere [Dunfield et al., 2007]. Researchers found that Verrucomicrobia bacteria have an abundance of glycoside hydrolase genes, which allows the bacteria to degrade carbohydrates [Cardman et al., 2014].

6. Ecology

Verrucomicrobia are oligotrophs that aid in methanol oxidation in soil, which regulates methane emissions to the atmosphere [Dunfield et al., 2007]. They are also known to possess a symbiotic relationship with nematodes in soil and grasslands [Cardman et al., 2014]. Bacteria in the phylum Verrucomicrobia are responsible for polysaccharide hydrolysis in aquatic systems, which plays a significant role in heterotrophic activity in the ocean [Chiang et al., 2018]. Species in the phylum Verrucomicrobia, such as Methylacidiphilum fumariolicum, are present in many ecosystems and conduct ammonia oxidation and nitrite reduction, important processes in ecosystem nitrogen cycling [Mohammadi et al., 2017].

7. Pathology

Verrucomicrobia resides in the mucous lining of the intestinal tract, where they can be found in high abundance in healthy individuals [Fujio-Vejar et al., 2017]. This discovery suggests that Verrucomicrobia aid in glucose homeostasis of the human gut [Fujio-Vejar et al., 2017]. Verrucomicrobia is not known to cause gastrointestinal related problems in the human gut [Dubourg et al., 2013].

Verrucomicrobia has anti-inflammatory properties that further aid in intestinal health. Studies have shown a positive correlation between the foxp3 gene, a gene that expresses anti-inflammatory and immunity in humans [Lindenberg et al., 2019]. Researchers have also suggested the use of microbes in this phylum may enhance patient care through dietary and therapeutic intervention [Fujio-Vejar et al., 2017]. A. muciniphila, a species in the Verrucomicrobia phylum, contains genomes with codes for beta-lactamase and genes, and an antibiotic resistance protein called 5-nitroimidazole [Van Passel et al., 2011].

8. Current Research

Current research on Verrucomicrobia focuses on its role in the environment and the human body. A recent experiment showed that there were a large proportion of Verrucomicrobia sequences in the gut of patients with Coxiella burnetii vascular infection (44.%) and another patient who was admitted to the intensive care unit (84.6%) after receiving a broad-spectrum antibiotics regimen [Dubourg et al., 2013].

Although Verrucomicrobia only constitutes a small amount of the total microbial community, results suggested that a few Verrucomicrobia phylotypes make an unexpected and considerable contribution to polysaccharide degradation [Martinez-Garcia et al., 2012] of laminarin and xylan. The genomic sequencing of five cells that represent the most dominant active polysaccharide of the Verrucomicrobia phylotype encoded a wide variety of glycoside hydrolases, sulfatases, peptidases, carbohydrate lyases, and esterases. This meant that these organisms had the machinery to hydrolyze a variety of polysaccharides. Although Bacteroidetes are usually considered more efficient biopolymer degraders, the enrichment of these organisms was higher on average comparatively [Martinez-Garcia et al., 2012]. This research is important as it highlights the role of Verrucomicrobia in ecology and helps readers understand how specific taxa can be used in the biotech world.

In 2018, Chiang et al. conducted a study in order to determine what drives Verrucomicrobia abundance in lake ecosystems. The distribution of Verrucomicrobia across 12 lakes in Michigan, ranging in depth, size, and tropic states were analyzed and 228 sequencing data sets of the V4 region of the 16S rRNA gene were generated [Chiang et al., 2018]. It was determined that Verrucomicrobia was the fourth most abundant phylum. This study highlights the importance of the continual information to be learned about Verrucomicrobia, as well as the range of drivers in the abundance of the microbiota.

9. References

Bergmann, G. T., Bates, S. T., Eilers, K. G., Lauber, C. L., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2011). The under-recognized dominance OF Verrucomicrobia in Soil bacterial communities. Soil Biology and Biochemistry, 43(7), 1450–1455.

Cabello-Yeves, P. J., Ghai, R., Mehrshad, M., Picazo, A., Camacho, A., & Rodriguez-Valera, F. (2017). Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs. Frontiers in Microbiology, 8, 2131–2131.

Cabello-Yeves, P. J., Zemskaya, T. I., Rosselli, R., Coutinho, F. H., Zakharenko, A. S., Blinov, V. V., & Rodriguez-Valera, F. (2018). Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal. Applied and Environmental Microbiology, 84(1).

Cardman, Z., Arnosti, C., Durbin, A., Ziervogel, K., Cox, C., Steen, A. D., & Teske, A. (2014). Verrucomicrobia are candidates for polysaccharide-degrading bacterioplankton in an arctic fjord of Svalbard. Applied and environmental microbiology, 80(12), 3749–3756.

Chiang E. et al. (2018) Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats. PLoS ONE 13(3): e0195112.

Dubourg, G., Lagier, J.-C., Armougom, F., Robert, C., Audoly, G., Papazian, L., & Raoult, D. (2013). High-level colonization of the human gut by Verrucomicrobia FOLLOWING broad-spectrum antibiotic treatment. International Journal of Antimicrobial Agents, 41(2), 149–155.

Dunfield, P., Yuryev, A., Senin, P. et al. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450, 879–882 (2007).

Freitas, S., Hatosy, S., Fuhrman, J. A., Huse, S. M., Mark Welch, D. B., Sogin, M. L., & Martiny, A. C. (2012). Global distribution and diversity of marine Verrucomicrobia. The ISME Journal, 6(8), 1499–1505.

Fujio-Vejar, S., Vasquez, Y., Morales, P., Magne, F., Vera-Wolf, P., Ugalde, J. A., Navarrete, P., & Gotteland, M. (2017). The Gut Microbiota of Healthy Chilean Subjects Reveals a High Abundance of the Phylum Verrucomicrobia. Frontiers in Microbiology, 8, 1221–1221.

Lee, K.-C., Webb, R. I., Janssen, P. H., Sangwan, P., Romeo, T., Staley, J. T., & Fuerst, J. A. (2009). Phylum Verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum Planctomycetes. BMC Microbiology, 9(1), 5–5.

Lindenberg, F., Krych, L., Fielden, J. et al. Expression of immune regulatory genes correlate with the abundance of specific Clostridiales and Verrucomicrobia species in the equine ileum and cecum. Sci Rep 9, 12674 (2019).

Martinez-Garcia M, Brazel DM, Swan BK, Arnosti C, Chain PSG, Reitenga KG, et al. (2012) Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia. PLoS ONE 7(4): e35314.

Mohammadi, S. S., Pol, A., van Alen, T., Jetten, M., & Op den Camp, H. (2017). Ammonia Oxidation and Nitrite Reduction in the Verrucomicrobial Methanotroph Methylacidiphilum fumariolicum SolV. Frontiers in microbiology, 8, 1901.

Van Passel, M. W., Kant, R., & Zoetendal, E. G. (2011). Plug-ge CM, Derrien M, Malfatti SA, Chain PS, Woyke T, Palva A, de Vos WM, Smidt H. The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes. PLoS One, 6(3), e16876

Wertz, J. T., Kim, E., Breznak, J. A., Schmidt, T. M., & Rodrigues, J. L. (2012). Genomic and physiological characterization of the Verrucomicrobia isolate Geminisphaera colitermitum gen. nov., sp. nov., reveals microaerophile and nitrogen fixation genes. Applied and environmental microbiology, 78(5), 1544–1555.

Edited by [Aanchal Swarup, Tori Calbo, Ellie King, Preeti Iyengar, and Tu Vu], student of Jennifer Bhatnagar for BI 311 General Microbiology, 2015, Boston University.