TY  - JOUR
AB  - The human gut virome is comprised of diverse commensal and pathogenic viruses. The colonization by these viruses begins right after birth through vaginal delivery, then continues through breastfeeding, and broader environmental exposure. Their constant interaction with their bacterial hosts in the body shapes not only our microbiomes but us. In addition, these viruses interact with the immune cells, trigger a broad range of immune responses, and influence different metabolic pathways. Besides its key role in regulating the human gut homeostasis, the intestinal virome contributes to disease development in distant organs, both directly and indirectly. In this review, we will describe the changes in the gut virome through life, health, and disease, followed by discussing the interactions between the virome, the microbiome, and the human host as well as providing an overview of their contribution to gut disease and disease of distant organs.
AU  - Tiamani, K.
AU  - Luo, S.
AU  - Schulz, S.
AU  - Xue, J.
AU  - Costa, R.
AU  - Mirzaei, M.K.
AU  - Deng, L.
C1  - 65430
C2  - 52278
TI  - The role of virome in the gastrointestinal tract and beyond.
JO  - FEMS Microbiol. Rev.
VL  - 46
IS  - 6
PY  - 2022
SN  - 0168-6445
ER  - 

TY  - JOUR
AB  - This review summarizes aspects of the current knowledge about the ecology of ammonia-oxidizing and denitrifying bacteria. The development of molecular techniques has contributed enormously to the rapid recent progress in the field. Different techniques for doing so are discussed. The characterization of ammonia-oxidizing and -denitrifying bacteria by sequencing the genes encoding 16S rRNA and functional proteins opened the possibility of constructing specific probes. It is now possible to monitor the occurrence of a particular species of these bacteria in any habitat and to get an estimate of the relative abundance of different types, even if they are not culturable as yet. These data indicate that the composition of nitrifying and denitrifying communities is complex and apparently subject to large fluctuations, both in time and in space. More attempts are needed to enrich and isolate those bacteria which dominate the processes, and to characterize them by a combination of physiological, biochemical and molecular techniques. While PCR and probing with nucleotides or antibodies are primarily used to study the structure of nitrifying and denitrifying communities, studies of their function in natural habitats, which require quantification at the transcriptional level, are currently not possible.
AU  - Bothe, H.*
AU  - Jost, G.*
AU  - Schloter, M.
AU  - Ward, B.B.*
AU  - Witzel, K.-P.
C1  - 24406
C2  - 32737
SP  - 673-690
TI  - Molecular analysis of ammonia oxidation and denitrification in natural environments.
JO  - FEMS Microbiol. Rev.
VL  - 24
IS  - 5
PB  - Elsevier
PY  - 2000
SN  - 0168-6445
ER  - 

TY  - JOUR
AB  - Using high resolution molecular fingerprinting techniques like random amplification of polymorphic DNA, repetitive extragenic palindromic PCR and multilocus enzyme electrophoresis, a high bacterial diversity below the species and subspecies level (microdiversity) is revealed. It became apparent that bacteria of a certain species living in close association with different plants either as associated rhizosphere bacteria or as plant pathogens or symbiotic organisms, typically reflect this relationship in their genetic relatedness. The strain composition within a population of soil bacterial species at a given field site, which can be identified by these high resolution fingerprinting techniques, was markedly influenced by soil management and soil features. The observed bacterial microdiversity reflected the conditions of the habitat, which select for better adapted forms. In addition, influences of spatial separation on specific groupings of bacteria were found, which argue for the occurrence of isolated microevolution. In this review, examples are presented of bacterial microdiversity as influenced by different ecological factors, with the main emphasis on bacteria from the natural environment. In addition, information available from some of the first complete genome sequences of bacteria (Helicobacter pylori and Escherichia coli) was used to highlight possible mechanisms of molecular evolution through which mutations are created; these include mutator enzymes. Definitions of bacterial species and subspecies ranks are discussed in the light of detailed information from whole genome typing approaches.
AU  - Schloter, M.
AU  - Lebuhn, M.
AU  - Heulin, T.*
AU  - Hartmann, A.
C1  - 23021
C2  - 31142
SP  - 647-660
TI  - Ecology and evolution of bacterial microdiversity.
JO  - FEMS Microbiol. Rev.
VL  - 24
IS  - 5
PB  - Elsevier
PY  - 2000
SN  - 0168-6445
ER  -