Archaebiotics: Archaea as Pharmabiotics for Treating Chronic Disease in Humans?

Recent findings highlight the role of the human gut microbiota in various disorders. For example, atherosclerosis frequently seems to be the consequence of gut microbiota–derived metabolism of some dietary components. Pharmabiotics (i.e., live/dead microbes and microbe-derived substances) and probiotics (live microorganisms with a health benefit when administered in adequate amounts) are a means to counteract these deleterious effects. Among the latter, microbes now being used or, being currently developed, are bacteria and eukaryotes (yeasts), so omitting the third domain of life—the archaea, despite their unique properties that could be of great interest to human health. Here, we promote the idea that some specific archaea are potential next-generation probiotics. This is based on an innovative example of the bioremediation of a gut microbial metabolite. Indeed, besides the fact that they are archaea (i.e. originating from a domain of life from which no pathogens of humans/animals/plants are currently known), they are rationally selected based on (i) being naturally human-hosted, (ii) having a unique metabolism not performed by other human gut microbes, (iii) depleting a deleterious atherogenic compound generated by the human gut microbiota and (iv) generating a health inert gas

Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat

During a study of the anaerobic microbial community of a lithifying hypersaline microbial mat of Lake 21 on the Kiritimati atoll (Kiribati Republic, Central Pacific) strain L21-RPul-D2(T) was isolated. The closest phylogenetic neighbor was Spirochaeta africana Z-7692(T) that shared a 16S rRNA gene sequence identity value of 90% with the novel strain and thus was only distantly related. A comprehensive polyphasic study including determination of the complete genome sequence was initiated to characterize the novel isolate. Cells of strain L21-RPul-D2(T) had a size of 0.2 - 0.25 x 8-9 mu m, were helical, motile, stained Gram-negative and produced an orange carotenoid-like pigment. Optimal conditions for growth were 35 degrees C, a salinity of 50 g/l NaCl and a pH around 7.0. Preferred substrates for growth were carbohydrates and a few carboxylic acids. The novel strain had an obligate fermentative metabolism and produced ethanol, acetate, lactate, hydrogen and carbon dioxide during growth on glucose. Strain L21-RPul-D2(T) was aerotolerant, but oxygen did not stimulate growth. Major cellular fatty acids were C-14:0, iso-C-15:0, C-16:0 and C-18:0. The major polar lipids were an unidentified aminolipid, phosphatidylglycerol, an unidentified phospholipid and two unidentified glycolipids. Whole cell hydrolysates contained L-ornithine as diagnostic diamino acid of the cell wall peptidoglycan. The complete genome sequence was determined and annotated. The genome comprised one circular chromosome with a size of 3.78 Mbp that contained 3450 protein-coding genes and 50 RNA genes, including 2 operons of ribosomal RNA genes. The DNA G + C content was determined from the genome sequence as 51.9 mol%. There were no predicted genes encoding cytochromes or enzymes responsible for the biosynthesis of respiratory lipoquinones. Based on significant differences to the uncultured type species of the genus Spirochaeta, S. plicatilis, as well as to any other phylogenetically related cultured species it is suggested to place strain L21-RPul-D2(T) (=DSM 27196(T) = JCM 18663(T)) in a novel species and genus, for which the name Salinispira pacifica gen. nov., sp. nov. is proposed

Etudes moléculaires et culturales de boues issues de bioréacteurs anaérobies mésothermiques traitant le phosphogypse : Isolement et caractérisation de nouveaux genres chez les thermotogales

Les représentants de l'ordre des Thermotogales se trouvent généralement dans les puits pétroliers et les sources hydrothermales aquatiques et terrestres. Récemment, des études moléculaires basées sur l'analyse des gènes codant l'ARNr 16S ont prouvé l'existence de représentants thermophiles, mais également mésophiles de cet ordre dans les boues de bioréacteurs et dans les sédiments contaminés par des composés toxiques. Les expériences que nous avons conduites pour traiter notamment le lactosérum en présence de phosphogypse ou de sulfate dans des bioréacteurs anaérobies mésothermiques nous ont permis de mettre en évidence de nouvelles populations de bactéries et plus précisément de Thermotogales par des approches moléculaires et culturales, avec la description de deux nouveaux genres, « Mesotoga sulfurireducens » et Defluviitoga tunisiensis. En ce qui concerne « M. sulfurireducens», il correspond à la première bactérie mésophile isolée chez les Thermotogales avec un métabolisme original centré sur la sulfo-réduction. Toujours dans le but de traiter le phosphogypse, mais cette fois-ci en utilisant les margines comme composantes organiques dans le procédé anaérobie, une nouvelle espèce du genre Fusibacter a pu être isolée, F. tunisiensis. Globalement, nos résultats démontrent le rôle important joué par les Firmicutes fermentaires et sulfato-réductrices (ordre des Clostridiales) et celui des Proteobacteria sulfato-réductrices (deltaproteobacteria) chez les Bacteria, mais également par les Methanoarchaea acétoclastes aux côtés des Thermotogales dans la digestion anaérobie de la matière organique lorsque les effluents sont riches en sulfate.The representatives of the order Thermotogales are usually found in oil reservoirs and hot aquatic and terrestrial springs. Recently, the existence of thermophilic and mesophilic representatives of the Thermotogales was proved by analysis of SSU rRNA genes of clones from bioreactors sludges and sediments contaminated by toxic compounds.Experiments which were led to treat lactoserum in the presence of phosphogypsum or sulphate in the mesothermic anaerobic digesters permitted to detect new populations of bacteria, in particular, Thermotogales by molecular and cultural approaches, with the description of two new genera, “Mesotoga sulfurireducens” and “Defluviitoga tunisiensis”. “Mesotoga sulfurireducens” is the first mesophilic bacterium isolated in the order of Thermotogales with an original metabolism axed on sulfo-reduction. During the treatment of phosphogypsum in the presence of margines as organic compounds in the anaerobic processus, a new species of Fusibacter was isolated: F.tunisiensis, sp. nov.Our results show the important role played by fermentative and sulphate-reducing Firmicutes (order Clostridiales) and sulphate-reducing Proteobacteria (deltaproteobacteria) within the Bacteria, but also by the acetoclastic Methanoarchaea beside Thermotogales in the anaerobic digestion of organic matter when the effluents are rich in sulphate

Insights into Dynamics of Mobile Genetic Elements in Hyperthermophilic Environments from Five New Thermococcus Plasmids

Mobilome of hyperthermophilic archaea dwelling in deep-sea hydrothermal vents is poorly characterized. To gain insight into genetic diversity and dynamics of mobile genetic elements in these environments we have sequenced five new plasmids from different Thermococcus strains that have been isolated from geographically remote hydrothermal vents. The plasmids were ascribed to two subfamilies, pTN2-like and pEXT9a-like. Gene content and phylogenetic analyses illuminated a robust connection between pTN2-like plasmids and Pyrococcus abyssi virus 1 (PAV1), with roughly half of the viral genome being composed of genes that have homologues in plasmids. Unexpectedly, pEXT9a-like plasmids were found to be closely related to the previously sequenced plasmid pMETVU01 from Methanocaldococcus vulcanius M7. Our data suggests that the latter observation is most compatible with an unprecedented horizontal transfer of a pEXT9a-like plasmid from Thermococcales to Methanococcales. Gene content analysis revealed that thermococcal plasmids encode Hfq-like proteins and toxin-antitoxin (TA) systems of two different families, VapBC and RelBE. Notably, although abundant in archaeal genomes, to our knowledge, TA and hfq-like genes have not been previously found in archaeal plasmids or viruses. Finally, the plasmids described here might prove to be useful in developing new genetic tools for hyperthermophiles

PROCESS FOR THE CO-CULTURE OF A BACTERIUM OF THE MESOTOGA LINEAGE AND AT LEAST ONE HYDROGENOTROPHIC SULFATE REDUCING BACTERIUM

The present invention concerns a process for the co-culture of an anaerobic mesophilic bacterium of the Mesotoga lineage with at least one hydrogenotrophic sulfate-reducing bacterium

PROCESS FOR THE CO-CULTURE OF A BACTERIUM OF THE MESOTOGA LINEAGE AND AT LEAST ONE HYDROGENOTROPHIC SULFATE REDUCING BACTERIUM

The present invention concerns a process for the co-culture of an anaerobic mesophilic bacterium of the Mesotoga lineage with at least one hydrogenotrophic sulfate-reducing bacterium

Balneicella halophila gen. nov., sp nov., an anaerobic bacterium, isolated from a thermal spring and description of Balneicellaceae fam. nov.

International audienceA mesophilic anaerobic bacterium, designated KHALHBd91(T) was isolated from the moderately hot spring of Hammam Biadha, Tunisia. The strain was Gram-staining-negative, non-sporulating, non-motile and rod-shaped, appearing singly (0.5-2.0 x 0.5-1 mu m). It grew anaerobically at temperatures between 20 and 50 degrees C (optimum 37 degrees C) and at pH values between 5.5 and 7.8 (optimum 7.0). It required NaCl for growth, with growth observed at up 8.5% and an optimum at 2.5 %. KHALHBd91(T) used glucose, galactose, maltose, pyruvate, lactate, fumarate and yeast extract as electron donors. The end-products from glucose fermentation were acetate, propionate, succinate and CO2. Nitrate, nitrite, thiosulfate, elemental sulfur, sulfate and sulfite were not used as terminal electron acceptors. The predominant cellular fatty acids were anteiso-C-15 : 0 and iso-C-15 : 0. The respiratory quinone was MK-6. The main polar lipids consisted of lipids, phospholipids, glycolipids, aminolipids, phosphoaminoglycolipids and phosphatidylethanolamine. The DNA G+C content was 35.0 mol%. Phylogenetic analysis of the small-subunit ribosomal 16S rRNA gene sequence indicated that KHALHBd91(T) had Marinifilum fragile and Marinifilum flexuosum (phylum Bacteroidetes, class Bacteroidia, order Bacteroidales) as its closest relatives (similarity of 86.7 and 87.8% respectively). The phylogenetic and physiological data fro the present study strongly indicate that the isolate represents a novel genus and species of a novel family, Balneicella halophila gen. nov., sp. nov., in the family Balneicellaceaefam. nov. The type strain is KHALHBd91(T) (=DSM28579(T) =JCM19909(T))

Isolation and characterization of Fonticella tunisiensis gen nov., sp. nov., a novel bacterium isolated from a Tunisian hot spring.

International audienceA strictly anaerobic, moderately thermophilic, halotolerant, rod-shaped bacterium, was isolated from a water sample of a Tunisian hot spring. The strain designated BELH25T was non motile with cells appearing singly or in pairs (0.4-0.6 µm x 2-6 µm). It grew at temperatures between 45°C and 70°C (optimum 55°C), pH between 6.2 and 8.0 (optimum 7.0) and NaCl concentration between 0 and 4 % (optimum 0-2.0 %). Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Strain BELH25T used cellobiose, fructose, galactose, glucose, maltose, mannose, saccharose, starch and yeast extract as electron donors. The main fermentation products from glucose metabolism were formate, acetate, ethanol and CO(2). The predominant cellular fatty acids were iso- C15:0, iso- C17:0 and anteiso-C15:0. The DNA G+C content was 37.2 mol %. Phylogenetic analysis of the small-subunit (SSU) ribosomal RNA (rRNA) gene sequence indicated that strain BELH25T had Caloramator viterbiensis and Fervidicella metallireducens as its closest relatives (identity of 92.2 and 92.1 % respectively) and that the strain was positioned approximatively equidistantly between the two genera. Based on phenotypic, phylogenetic and taxonomic characteristics, strain BELH25T is proposed as a novel species of a new genus within the order Clostridiales, family Clostridiaceae for which the name Fonticella tunisiensis is proposed. The type strain is BELH25T (= DSM 24455 T = JCM 17559T)

Reclassification of Anaerobaculum mobile, Anaerobaculum thermoterrenum, Anaerobaculum hydrogeniformans as Acetomicrobium mobile comb. nov., Acetomicrobium thermoterrenum comb. nov and Acetomicrobium hydrogeniformans comb. nov., respectively, and emendation of the genus Acetomicrobium

Taking into account their 16S rRNA gene sequences, it appears that Acetomicrobium flavidum and the three species of the genus Anaerobaculum described so far belong to the same phylogenetic clade with high levels (>95 %) of similarity. In this respect, these three Anaerobaculum species should be reclassified within the genus Acetomicrobium, which has priority over the genus Anaerobaculum, which was validated since the genus Acetomicrobium. The DNA G+ C content of Acetomicrobium flavidum is 47.1 mol%, which is of the same order as that of the three Anaerobaculum species. All these bacteria have in common iso-C-15 : 0 as their main fatty acid. Based on further phylogenetic, genetic and chemotaxonomic studies, we propose that Anaerobaculum mobile (=DSM 13181(T) =JCM 12221(T)), Anaerobaculum thermoterrenum (5DSM 13490(T) =5ACM 5076(T)) and Anaerobaculum hydrogeniformans (5DSM 22491(T) 5ATCC BAA-1850(T)) be reclassified as Acetomicrobium mobile comb. nov., Acetomicrobium thermoterrenum comb. nov. and Acetomicrobium hydrogeniformans comb. nov., respectively. The four bacterial species belong to the phylum Synergistetes