Observation of time quasicrystal and its transition to superfluid time crystal

We report experimental realization of a quantum time quasicrystal, and its transformation to a quantum time crystal. We study Bose-Einstein condensation of magnons, associated with coherent spin precession, created in a flexible trap in superfluid $^3$He-B. Under a periodic drive with an oscillating magnetic field, the coherent spin precession is stabilized at a frequency smaller than that of the drive, demonstrating spontaneous breaking of discrete time translation symmetry. The induced precession frequency is incommensurate with the drive, and hence the obtained state is a time quasicrystal. When the drive is turned off, the self-sustained coherent precession lives a macroscopically-long time, now representing a time crystal with broken symmetry with respect to continuous time translations. Additionally, the magnon condensate manifests spin superfluidity, justifying calling the obtained state a time supersolid or a time super-crystal

Akkermansia muciniphila - friend or foe in colorectal cancer?

Akkermansia muciniphila is a gram-negative anaerobic bacterium, which represents a part of the commensal human microbiota. Decline in the abundance of A. muciniphila among other microbial species in the gut correlates with severe systemic diseases such as diabetes, obesity, intestinal inflammation and colorectal cancer. Due to its mucin-reducing and immunomodulatory properties, the use of probiotics containing Akkermansia sp. appears as a promising approach to the treatment of metabolic and inflammatory diseases. In particular, a number of studies have focused on the role of A. muciniphila in colorectal cancer. Of note, the results of these studies in mice are contradictory: some reported a protective role of A. muciniphila in colorectal cancer, while others demonstrated that administration of A. muciniphila could aggravate the course of the disease resulting in increased tumor burden. More recent studies suggested the immunomodulatory effect of certain unique surface antigens of A. muciniphila on the intestinal immune system. In this Perspective, we attempt to explain how A. muciniphila contributes to protection against colorectal cancer in some models, while being pathogenic in others. We argue that differences in the experimental protocols of administration of A. muciniphila, as well as viability of bacteria, may significantly affect the results. In addition, we hypothesize that antigens presented by pasteurized bacteria or live A. muciniphila may exert distinct effects on the barrier functions of the gut. Finally, A. muciniphila may reduce the mucin barrier and exerts combined effects with other bacterial species in either promoting or inhibiting cancer development

Dissimilatory sulfate reduction in the archaeon ‘Candidatus Vulcanisaeta moutnovskia’ sheds light on the evolution of sulfur metabolism

Dissimilatory sulfate reduction (DSR)—an important reaction in the biogeochemical sulfur cycle—has been dated to the Palaeoarchaean using geological evidence, but its evolutionary history is poorly understood. Several lineages of bacteria carry out DSR, but in archaea only Archaeoglobus, which acquired DSR genes from bacteria, has been proven to catalyse this reaction. We investigated substantial rates of sulfate reduction in acidic hyperthermal terrestrial springs of the Kamchatka Peninsula and attributed DSR in this environment to Crenarchaeota in the Vulcanisaeta genus. Community profiling, coupled with radioisotope and growth experiments and proteomics, confirmed DSR by ‘Candidatus Vulcanisaeta moutnovskia’, which has all of the required genes. Other cultivated Thermoproteaceae were briefly reported to use sulfate for respiration but we were unable to detect DSR in these isolates. Phylogenetic studies suggest that DSR is rare in archaea and that it originated in Vulcanisaeta, independent of Archaeoglobus, by separate acquisition of qmoABC genes phylogenetically related to bacterial hdrA genes.This work was supported by the Russian Science Foundation (grant number 17-74-30025) and in part by the grant from the Russian Ministry of Science and Higher Education (to N.A.C., A.V.L., E.N.F., M.L.M., A.Y.M., N.V.P. and E.A.B.-O.). Sequencing of PCR amplicons was performed using the scientific equipment of the core research facility ‘Bioengineering’ by T. Kolganova. The proteomics analysis was performed at the Proteomics Facility of the Spanish National Center for Biotechnology (CNB-CSIC), which belongs to ProteoRed, PRB2-ISCIII, supported by grant PT13/0001 (to S.C., M.C.M. and M.F.). P.N.G. acknowledges funding from the UK Biotechnology and Biological Sciences Research Council (BBSRC) within the ERA NET-IB2 programme, grant number ERA-IB-14-030 and the European Union Horizon 2020 Research and Innovation programme (Blue Growth: Unlocking the Potential of Seas and Oceans) under grant agreement number 634486, as well as support from the Centre for Environmental Biotechnology project, part funded by the European Regional Development Fund (ERDF) through the Welsh Government, and support from the Centre of Environmental Biotechnology. D.Y.S. was supported by the SIAM/Gravitation Program (Dutch Ministry of Education, Culture and Science; grant 24002002) and RFBR grant 19-04-00401. F.L.S. and S.N. acknowledge support from the Wiener Wissenschafts, Forschungs- und Technologiefonds (Austria) through the grant VRG15-007. F.L.S. gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation programme (grant agreement 803768). I.A.C.P. acknowledges support from the Fundação para a Ciência e Tecnologia (Portugal) through grant PTDC/BIA-BQM/29118/2017 and R&D unit MOSTMICRO-ITQB (UIDB/04612/2020 and UIDP/04612/2020)

Genomic analysis of Caldithrix abyssi, the thermophilic anaerobic bacterium of the novel bacterial phylum Calditrichaeota

The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of C. abyssi to synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylum Calditrichaeota.The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231. OS and MSG were supported by the Russian Science Foundation (RSF, grant 14-24-00155). EB-O and SG were supported by the RSF grant 14-24-00165. IK, NC, AL, and MM were supported by the Russian Foundation for Basic Research grant 14-04-00503.http://www.frontiersin.orgam2017Biochemistr

Caldithrix palaeochoryensis sp. nov., a thermophilic, anaerobic, chemo-organotrophic bacterium from a geothermally heated sediment, and emended description of the genus Caldithrix

A novel thermophilic, strictly anaerobic, chemo-organotrophic bacterium, designated MCT, was isolated from a geothermally heated sediment of a marine hydrothermal system at Palaeochory Bay, Milos, Greece. Cells of strain MCTwere rods of variable length (4–12 μm) and width (0.2–0.3 μm), occurring as single cells or forming large aggregates that were visible as flocs. Strain MCTgrew optimally at pH 7.0 and 60 °C and with 3 % (w/v) NaCl. Strain MCTgrew chemo-organoheterotrophically and fermented peptides and di- and polysaccharides in the presence of 0.1 g yeast extract l−1. The DNA G+C content of strain MCTwas 43.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed strain MCTwithin the genusCaldithrix. However, strain MCTpossessed certain phenotypic features that differentiated it from the type strain of the only species of the genusCaldithrixdescribed to date. On the basis of phylogenetic and phenotypic characteristics, it is proposed that strain MCTrepresents a novel species,Caldithrix palaeochoryensissp. nov. The type strain is MCT(=DSM 21940T=VKM B-2536T). In addition, an emended description of the genusCaldithrixis presented.</jats:p