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Multicellular organisms contain numerous symbiotic microorganisms, collectively called microbiomes. Recently, microbiomic research has shown that these microorganisms are responsible for the proper functioning of many of the systems (digestive, immune, nervous, etc.) of multicellular organisms. This has inclined some scholars to argue that it is about time to reconceptualise the organism and to develop a concept that would place the greatest emphasis on the vital role of microorganisms in the life of plants and animals. We believe that, unfortunately, there is a problem with this suggestion, since there is no such thing as a universal concept of the organism which could constitute a basis for all biological sciences. Rather, the opposite is true: numerous alternative definitions exist. Therefore, comprehending how microbiomics is changing our understanding of organisms may be a very complex matter. In this paper we will demonstrate that this pluralism proves that claims about a change in our understanding of organisms can be treated as both true and untrue. Mainly, we assert that the existing concepts differ substantially, and that only some of them have to be reconsidered in order to incorporate the discoveries of microbiomics, while others are already flexible enough to do so. Taking into account the plurality of conceptualisations within different branches of modern biology, we will conduct our discussion using the developmental and the cooperation-conflict concepts of the organism. Then we will explain our results by referring to the recent philosophical debate on the nature of the concept of the organism within biology., Author(s): Adrian Stencel [sup.1] , Agnieszka M. Proszewska [sup.1] [sup.2] Author Affiliations: (Aff1) 0000 0001 2162 9631, grid.5522.0, Faculty of Philosophy, Jagiellonian University, , ul. Golebia 24, 31-007, Kraków, Poland [...]

In September 2017, a healthy boy was born at 35 weeks' gestation in Brazil. The newborn was fed breast milk and reconstituted powdered infant formula (PIF) while in the hospital. [...]

Research has been conducted on the single-stranded-DNA-binding protein-like proteins from thermophilic bacteria. The identification and biochemical characterization of these proteins have been carried out and the results demonstrate that the single-stranded-DNA-binding protein-like proteins are homodimers.

Research has been conducted on Streptomyces rishiriensis methyltransferase genes from the coumermycin A (sub)1 cluster. The identification of these genes carried out via gene inactivation and secondary metabolite inactivation is described.

Research has been conducted on Rhodococcus erythropolis SQ1. The results of molecular characterization of R. erythropolis kstD2 gene indicate functional involvement of 3-ketosteroid Delta isoenzymes in microbial steroid catabolism.

Research has been conducted on HPr kinase/phosphatase, a regulatory protein encoded by Mycoplasma pneumoniae. Results demonstrate that this protein has both phosphatase and kinase activities.

Research has been conducted on Slr1295, a cyanobacterium Synechocystis sp. PCC 6803 homologue of IdiA. Results suggest that Slr1295 is a protein protecting photosystem II under iron limitation, its localization has been investigated and the study of the Slr1295-free mutant grown under iron-deficient and iron-sufficient conditions is presented.

Research has been conducted on the receptor methylation in Escherichia coli chemotaxis. The role of this receptor in adaptation has been investigated and the details are reported.

Research has been conducted on oxidative stress tolerance in Streptococcus gordonii. The role of Mn (super)2+ permease in this oxidative stress tolerance has been investigated and the results indicate that Mn (super)2 regulates superoxide dismutase expression and thiol peroxidase activities.

Research has been conducted on group B streptococcus. The identification and characterization of the genes bsp and femH which play a role in group B streptococcus peptidoglycan metabolism and cell morphogenesis have been carried out, and the results indicate that genes' overexpression and disruption altere cell morphology and changes peptidoglycan's amino acid composition.

Research has been conducted on Staphylococcus aureus gene svrA. Results indicate that this gene is required for accessory gene regulator and RNAIII transcripts expression and is an accessory gene regulator's regulatory network component which controlls virulence gene expression in S. aureus.

Research has been conducted on Bacillus methanolicus MGA3 steady-state methanol-limited cultures. The role of the growth-inhibitory effects of methanol pulses which perturb steady-state methanol concentrations has been investigated and the results are reported.

Research has been conducted on nucleoid segregation in Escherichia coli. The disturbances in this segregation have been investigated and the comparison of nucleoid segregation in min mutant and its wild-type parent have been carried out and discussed.

Research has been conducted on gamma-Proteobacteria. The occurrence of the NifL-like protein outside these bacteria has been detected and the details are reported.

Research has been conducted on Pseudomonas aeruginosa PAO1 physiological responses to oxidative stress. The role of the oxygen transfer blockage in P. aeruginosa defense against reactive oxygen intermediates has been investigated and the results are reported.

Research has been conducted on the exotoxin A regulation in Pseudomonas aeruginosa. The role of pvdS in this regulation during chronic lung infections associated with the genetic disease cystic fibrosis has been investigated and the results are reported.

Research has been conducted on Mycobacterium avium. The effect of natural exposure to low M. avium doses in immunocompetent BALB/c or athymic BALB/c mice has been investigated in studying the acquired resistance rate and immune response and the details are reported.

Research has been conducted on Mycobacterium avium growth. The study of the bacteria growth restriction has been carried out in wild-type and NADPH oxidase-deficient macrophages and the results indicate that the reactive oxygen species are not involved in the M. avium activities of the macrophage.

Research has been conducted on Mycobacterium thermoresistibile. The role of growth temperature in M. thermoresistibile complex lipid composition, mycolic and fatty acids has been investigated and the details are reported.

Research has been conducted on Mycobacterium tuberculosis ahpC gene. The role of this gene in M. tuberculosis biology and in resistance to the reactive nitrogen species and survival in macrophages has been investigated and the details are reported.

Research has been conducted on transcriptional regulation of Mycobacterium tuberculosis heat-shock proteins. The study of this regulation has been carried out via the use of microarrays prepared by spotting DNA sequences, and the contribution of the regulatory circuits to the heat-shock response is discussed.

Research has been conducted on Mycobacterium gordonae lipidic compounds which produce HPLC-double-cluster pattern. The purification and identification of these compounds via the use of mycolic acid has been carried our and the details are reported.

Research has been conducted on the mycobacterial genomes. The two-dimensional bacterial genome display method used in producing mycobacterial genome displays and in separating genomic segments cut with different restriction endonucleases is described.

Research has been conducted on the antibiotic thiolactomycin analogues. The synthesis of these analogues has been carried out and the results indicate that they enhance activity against Mycobacterium tuberculosis H37Rv cells and against mycolic acid biosynthesis in M. smegmatis cell extracts.

Research has been conducted on Mycobacterium smegmatis glycopeptidolipids. The effect of the C-type glycopeptidolipids' absence on the surface properties and architecture of M. smegmatis cell envelope and on bacteria interaction with host cells has been investigated and the results are reported.

Research has been conducted on Mycobacterium smegmatis glycopeptidolipids. The biosynthetic gene cluster of these glycopeptidolipids and the methyltransferase catalyzing the fatty acid conversion to the 3-methoxy form have been investigate and are discussed.

Research has been conducted on Mycobacterium tuberculosis strains with defects in amino acid biosynthesis pathway. Results indicate that the gene which encodes shikimate kinase catalyzing chorismate biosynthesis steps is essential in M. tuberculosis.

Research has been conducted on Mycobacterium smegmatis cell wall assembly. The study of the assembly events has been carried out in vivo via radiolabelling of exponentially growing liquid cultures and the ability of M. smegmatis to take up radioactive N-acetylglucosamine from the culture medium and incorporate it into peptidoglycan has been investigated.

Research has been conducted on Mycobacterium smegmatis polar glycopeptolipids. The synthesis of these carbon-starved M. smegmatis glycopeptolipids has been carried out and the results demonstrate that the molecule contains a monosaccharide and is a new form of polar glycopeptolipids.

Research has been conducted on Mycobacterium tuberculosis mannosylated lipoarabinomannans extracted from the M. tuberculosis wild-type strain and phoP mutant. The functional domains of these lipoarabinomannans have been investigated and it was found that both strains shared the same acyl forms and that there was a proportion difference between mannosylated lipoarabinomannans acyl forms and the reduce virulence of the phoP mutant.

Research has been conducted on Mycobacterium bovis illegitimate mutants. The screening of these mutants has been carried out via the use of the fragment made from another M. bovis gene and the results are reported.

Research has been conducted on mycobacteria. The genetic method developed for generation of the targeted deletion mutant by allelic exchange is described.

Research has been conducted on Mycobacterium tuberculosis mce3 operon. The regulation of operon expression has been carried out in investigating the role of this operon in M. tuberculosis and the results indicate that the repressor controls mce3 transcription.

Research has been conducted on Mycobacterium abscessus strain 390R. The characterization of this strain and its mutant derivative has been carried out and the discovery of the insertion sequence with nucleotide identity to insertion sequence elements from the environmental mycobacteria is reported.

Research has been conducted on Mycobacterium tuberculosis virulence. The identification of the genes important for this virulence has been carried out via the use of transposon mutagenesis and the results indicate that this approach allowes to recognize each mutant and provides the candidates to screen in vivo.

Research has been conducted on Mycobacterium tuberculosis strain H37Rv genome sequence. The re-annotation of this sequence has been performed and results indicate that eighty-two protein-coding sequences have been added and some of them have a predicted function.

Research has been conducted on the response to virulent Mycobacterium tuberculosis infection. The hypothesis that a prior tuberculosis infection or a prior vaccination with BCG could overcome the inability of the inbred mouse strains, which have poor expression of adhesion and integrin molecules, to focus on lung tissues and mediate protection has been tested and the details are reported.

Research has been conducted on the intracellular lipophilic inclusions in Mycobacterium smegmatis. The factors affecting these inclusions and the hypothesis that these factors could be formed via fatty acid uptake either directly or biosynthetically have been investigated and the results are reported.

Research has been conducted on the lipoarabinomannans of Mycobacterium species. Results indicate that the antibodies generated against these species react with lipoarabinomannans with naked arabinofuranosyl termini and that these anibodies do not bind to arabinogalactan of the mycabacterial cell walls.

The author reviews the publications on rapid-growing non-pathogenic mycobacteria. The topics of interest include the approaches based on mycobacteria dissection at the DNA level and the mycobacterial genus in the post-genomic era.

Escherichia coli RNA polymerase translocates along the DNA discontinuously during the elongation phase of transcription, spending proportionally more time at some template positions, known as pause and arrest sites, than at others. Current models of elongation suggest that the enzyme backtracks at these locations, but the dynamics are unresolved. Here, we study the role of lateral displacement in pausing and arrest by applying force to individually transcribing molecules. We find that an assisting mechanical force does not alter the translocation rate of the enzyme, but does reduce the efficiency of both pausing and arrest. Moreover, arrested molecules cannot be rescued by force, suggesting that arrest occurs by a bipartite mechanism: the enzyme backtracks along the DNA followed by a conformational change of the ternary complex (RNA polymerase, DNA and transcript), which cannot be reversed mechanically.

Research has been conducted on Delftia acidovorans MC1. The ability of this bacterium to utilize chlorophenyl acids and to detoxify dichlorophenol, dichlorocatechol and dichlorophenoxypropionic acids has been investigated via the use of the short-term response by 2D-electrophoresis and the results are reported.

Research has been conducted on Deinococcus radiodurans, an extremely radioresistant bacterium encoding genes which are homologous to those involved in bacterial lysine biosynthesis. Results indicate that this bacterium carries lysine biosynthesis in a unique way.

Research has been conducted on cyanobacterium Synechococcus elongatus PCC 7942 KaiA circadian clock protein. The study of the kaiA gene via PCR-based mutagenesis and the screening of this gene for abnormal rhythmic phenotypes are described.

Research has been conducted on the microbial population evolution. The authors discuss the Monod model explaining the clock-like behaviour of the selection-driven evolution.