Staff Advice Report
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Staff Advice Report 11 January 2021 Advice to the Decision-making Committee to determine the new organism status of 18 gut bacteria species Application code: APP204098 Application type and sub-type: Statutory determination Applicant: PSI-CRO Date application received: 4 December 2020 Purpose of the Application: Information to support the consideration of the determination of 18 gut bacteria species Executive Summary On 4 December 2020, the Environmental Protection Authority (EPA) formally received an application from PSI-CRO requesting a statutory determination of 18 gut bacteria species, Anaerotruncus colihominis, Blautia obeum (aka Ruminococcus obeum), Blautia wexlerae, Enterocloster aldenensis (aka Clostridium aldenense), Enterocloster bolteae (aka Clostridium bolteae), Clostridium innocuum, Clostridium leptum, Clostridium scindens, Clostridium symbiosum, Eisenbergiella tayi, Emergencia timonensis, Flavonifractor plautii, Holdemania filiformis, Intestinimonas butyriciproducens, Roseburia hominis, ATCC PTA-126855, ATCC PTA-126856, and ATCC PTA-126857. In absence of publicly available data on the gut microbiome from New Zealand, the applicant provided evidence of the presence of these bacteria in human guts from the United States, Europe and Australia. The broad distribution of the species in human guts supports the global distribution of these gut bacteria worldwide. After reviewing the information provided by the applicant and found in scientific literature, EPA staff recommend the Hazardous Substances and New Organisms (HSNO) Decision-making Committee (the Committee) to determine that the 18 bacteria are not new organisms for the purpose of the HSNO Act. Recommendation 1. Based on the information available, the bacteria appear to be globally ubiquitous and commonly identified in environments that are also found in New Zealand (human guts). 2. There is sufficient weight of evidence for the Committee to agree that the 18 bacteria species were present in New Zealand prior to 29 July 1998 and continuously after that, and therefore are not new for the purpose of the Act. Purpose of this document 3. This document has been prepared by the EPA staff to advise the Committee of our assessment of application APP204098 submitted under the HSNO Act (the Act). This document discusses information provided in the application and other sources. 4. The decision path for this application can be found in Appendix 1. The application 5. On 4 December 2020, PSI-CRO applied to the EPA under section 26 of the HSNO Act seeking a determination on the new organism status of 18 gut bacteria species. 6. The applicant provides evidence that these bacteria naturally occur in human guts from various countries and have a ubiquitous global distribution. Therefore, the applicant considers these bacteria to be not new for the purpose of the HSNO Act. 7. EPA staff have also investigated information on these species in scientific literature and other local sources for evidence of the existence of these organisms both before and after 29 July 1998 in New Zealand. Moreover, we have considered the histories of these organisms from the perspective of the taxonomic literature and the state of scientific knowledge regarding these species and their classification prior to 29 July 1998. 8. The EPA considered the ubiquity argument as evidence for the presence of a microorganism in New Zealand based on a commissioned report ‘The Biogeography of Environmental Microorganisms’, by Clark Ehlers and Gavin Lear of the University of Auckland . This report considers and discusses global phenomena that cause the distribution of Archaea and Bacteria to widely dispersed on the globe (Ehlers C & Lear G 2014). Among these are natural phenomena, such as the intercontinental transport of dust particles by wind and rain clouds, as well as unintentional transport by human beings, for example in ship ballast water or via air travel. 2 Organism description Family Lachnospiraceae Table 1: Taxonomic description of Blautia wexlerae, B. obeum, Eisenbergiella tayi, Roseburia hominis, Enterocloster aldensis and E. bolteae. Taxonomic Unit Classification Order Eubacteriales Family Lachnospiraceae Genus Blautia Eisenbergiella Roseburia Enterocloster Species Blautia wexlerae Liu Eisenbergiella tayi Roseburia Enterocloster aldenensis et al. 2008 Amir et al. 2014 hominis corrig. (Warren et al. 2007) Blautia obeum Duncan et al. Haas and Blanchard 2020, (Moore et al. 1976) 2006 aka Clostridium aldenense Lawson and Enterocloster bolteae Finegold 2015, aka (Song et al. 2003) Haas Ruminococcus and Blanchard 2020, aka obeum Clostridium bolteae Blautia wexlerae and B. obeum (aka Ruminococcus obeum) 9. Blautia wexlerae and B. obeum are gram-positive, non-motile, anaerobic bacteria isolated from animal and human faeces (MOORE et al. 1976; Liu et al. 2008). 10. Blautia obeum is also known as Ruminococcus obeum (Moore et al. 1976). However, taxonomic authorities are waiting for a second deposit of R. obeum in a different collection and country to be recognised as a new species (LPSN ND). Eisenbergiella tayi 11. Eisenbergiella tayi is the only species in the genus Eisenbergiella. The bacteria is strictly an anaerobic, non-motile bacterium with thin elongated rods. The main fermentation end product produced by the bacterium is butyric acid suggesting a beneficial effect in the human gastrointestinal tract (Amir et al. 2014). Roseburia hominis 12. Species in the genus Roseburia are butyrate-producing bacteria. Roseburia hominis cells are gram- variable to gram-negative, slightly curved rods. They are motile thanks to the presence of multiple flagella. The species has been isolated from human faeces (Duncan et al. 2006). Enterocloster aldenensis (aka Clostridium aldenense) and E. bolteae (aka Clostridium bolteae) 13. Following their complete genome sequencing, the species, C. aldenense and C. bolteae, were recently reclassified under the genus Enterocloster. Their basonym names, C. aldenense and C. bolteae, are validly published, however, their preferred names are E. aldenensis and E. bolteae (Haas & Blanchard 2020). 14. Species in this genus are anaerobic fusiform rods that rarely produce spores. 3 Family Ruminococcaceae Table 2: Taxonomic description of Flavonifractor plautii and Anaerotruncus colihominis Taxonomic Unit Classification Order Eubacteriales Family Oscillospiraceae Genus Flavonifractor Anaerotruncus Species Flavonifractor plautii (Seguin Anaerotruncus colihominis 1928) Carlier et al. 2010 Lawson et al. 2004 Flavonifractor plautii 15. The bacteria Flavonifractor plautii is a gram-positive anaerobic bacterium of the family Clostridiales commonly found in the human gut microbiome. This bacterium seems to play a role in the immune system and could be used as an anti-allergy probiotic (Ogita et al. 2020). Anaerotruncus colihominis 16. Anaerotruncus is a newly described bacterial genus in the family Clostridiaceae. The species, A. colihominis, is a gram-positive, anaerobic, thin rod bacterium. It does not produce spores and forms colonies of 2-3 mm diameter. It has been isolated from human faeces (Lawson et al. 2004). Family Clostridiaceae Table 3: Taxonomic description of Clostridium innocuum, C. scindens, C. symbiosum and C. leptum. Taxonomic Unit Classification Order Eubacteriales Family Clostridiaceae Genus Clostridium Species Clostridium innocuum Smith and King 1962 Clostridium scindens Morris et al. 1985 Clostridium symbiosum (Stevens 1956) Kaneuchi et al. 1976 Clostridium leptum Moore et al., 1976 Clostridium species 17. Species in the genus Clostridium are gram-variable rod-shaped bacteria widely distributed in the environment. They are found in soils, water, intestinal tracts of humans and animals (Elsayed & Zhang 2004). Most species are anaerobic. They produce bottle-shaped endospores1 (Maczulak 2011). 1 Endospore: a dormant, tough, and non-reproductive structure produced by certain bacteria. The primary function of most endospores is to ensure the survival of a bacterium through periods of environmental stress. 4 18. The bacterium C. leptum was recognised by the EPA as present in New Zealand (PNZ1000141) due to its natural occurrence in the human colon (Lay et al. 2007) and identification in New Zealand patients (Stebbings et al. 2002). Family Oscillospiraceae Table 4: Taxonomic description of Intestinimonas butyriciproducens. Taxonomic Unit Classification Order Eubacteriales Family Oscillospiraceae Genus Intestinimonas Species Intestinimonas butyriciproducens Kläring et al. 2013 Intestinimonas butyriciproducens 19. Species in this newly described genus within the family Oscillospiraceae are gram-positive and anaerobic (Kläring et al. 2013). They have unique metabolic features such as the production of butyrate from sugars and amino acids. There is a lack of data on their diversity, however, the species I. butyriciproducens appears to be the most commonly found (Bui et al. 2016). It has been isolated from mouse intestines (Kläring et al. 2013) as well as human stool samples (Bui et al. 2015). Family Erysipelotrichaceae Table 5: Taxonomic description of Holdemania filiformis and the new strain in the family Erysipelotrichaceae. Taxonomic Unit Classification Order Erysipelotrichales Family Erysipelotrichaceae Genus Holdemania Unknown Species Holdemania filiformis ATCC PTA-126855 Willems et al. 1997 Holdemania filiformis 20. The genus Holdemania was recently described with currently only two species. The species H. filiformis, previously known as Eubacterium-like strains, is a gram-positive