The regulation of the central metabolism and fermentation pathways and its effect on antimicrobial susceptibility in the anaerobic pathogen Bacteroides fragilis is not completely understood. In this study, we show that B. fragilis encodes for two iron-dependent redox-sensitive regulatory pirin protein genes, pir1 and pir2, whose mRNA expression is upregulated following oxygen exposure and growth in iron-limiting conditions. Pir1 and Pir2 modulate short-chain fatty acids production and alter susceptibility to metronidazole (MTZ), and to amixicile (AMIX), a novel inhibitor of pyruvate:ferredoxin oxidoreductase (PFOR) in anaerobes. Consistent with this, we showed that Pir1 forms direct protein-protein interactions with PFOR as determined by two-hybrid system assays. In addition, AlphaFold2-based structural analysis predicts that Pir1 and Pir2 form stable interactions with several enzymes of the central metabolism including the 2-ketoglutarate:ferredoxin oxidoreductases Kor1AB and Kor2CDAEBG. A series of metabolic mutants and electron transport chain inhibitors were used to show a wide-ranging effect of bacterial metabolism on MTZ and AMIX susceptibility. Furthermore, we show that AMIX is an effective antimicrobial against B. fragilis in an experimental model of intra-abdominal infection. This investigation led to the discovery that the kor2AEBG genes are essential for growth, and we present evidence that kor2AEBG genes have dual functions including the reductive synthesis of 2-ketoglutarate via reverse TCA cycle. However, the metabolic activity that bypasses KorAEBG function remains to be defined. Collectively our investigation reveals new information on B. fragilis central metabolism and its modulatory control by pirin proteins which may be leveraged for the future development of new narrow-spectrum antimicrobials

The genome of Halobacterium strain 63-R2 was recently reported and provides the opportunity to resolve long-standing issues regarding the source of two widely used model strains of Hbt. salinarum, NRC-1 and R1. Strain 63-R2 was isolated in 1934 from a salted buffalo hide (epithet ‘cutirubra’), along with another strain from a salted cowhide (91-R6T, epithet ‘salinaria’, the type strain of Halobacterium salinarum). Both strains belong to the same species according to genome-based taxonomy analysis (TYGS), with chromosome sequences showing 99.64% identity over 1.85 Mb. The chromosome of strain 63-R2 is 99.99% identical to the two laboratory strains NRC-1 and R1, with only 5 indels, excluding the mobilome. The two reported plasmids of strain 63-R2 share their architecture with plasmids of strain R1 (pHcu43/pHS4, 99.89% identity; pHcu235/pHS3, 100.0% identity). We detected and assembled additional plasmids, using PacBio reads deposited at the SRA database, further corroborating that strain differences are minimal. One plasmid, pHcu190 (190,816 bp) corresponds to pHS1 (strain R1) but is even more similar in architecture to pNRC100 (strain NRC-1). Another plasmid, pHcu229, assembled partially and completed in silico (229,124 bp), shares most of its architecture with pHS2 (strain R1). In deviating regions, it corresponds to pNRC200 (strain NRC-1). Further architectural differences between the laboratory strain plasmids are not unique but are present in strain 63-R2, which contains characteristics from both of them. Based on these observations, it is proposed that the early 20th-century isolate 63-R2 is the immediate ancestor of the twin laboratory strains NRC-1 and R1.

Patterns and drivers of succession provide insight into the mechanisms that govern community assembly and are indicators of community resilience and stability but are still poorly understood in microbial communities. We assessed whether the successional trends of woody vegetation are mirrored by foliar fungal endophyte communities of three tree species that are abundant across the woody successional gradient using a total amplicon sequencing approach. Additionally, we test the relative contribution of host identity, abiotic predictors, biotic factors, and spatial distance between sites in predicting community composition and species richness of endophyte communities. Unlike the woody community, endophyte communities showed no consistent evidence of deterministic successional trends. Host identity was the most important factor structuring fungal endophyte community composition. Spatial distance played some role in explaining differences in community composition, but the effects of this and other environmental variables were small and not consistent between different host species. Much of the variation in endophyte composition remained unexplained. Host identity was most important in predicting endophyte richness. Although endophyte communities showed no deterministic succession, community assembly was most strongly influenced by host identity and spatial distance.

Biofilm communities cause many infectious diseases. Biofilms are diverse microbial species found either attached to a surface or aggregated into an extracellular matrix. Bacteria form biofilms as a default mode of growth or as a response mechanism to environmental conditions like stress. As such, biofilm strains are increasingly virulent causing a wide variety of chronic persistent diseases, are typically antibiotic-resistant and known to improve host mortality rate. Most biofilms contain polysaccharides, proteins, extracellular DNA (eDNA), RNA, and water. Determining and quantifying the major components of a biofilm may indicate an appropriate treatment for biofilm eradication. Burkholderia pseudomallei is a Gram-negative, motile bacillus typically found in surface water and/or soil in endemic regions. It is the etiologic agent of melioidosis and is capable of forming both surface adherent and air-liquid interface biofilms (pellicle) in broth cultures. This study evaluates the components of established biofilms using B. pseudomallei and Burkholderia thailandensis, a closely related nonpathogenic species. Using assays, fluorescent dyes and microscopy, we quantified the major components of biofilms produced by five genetically related B. pseudomallei strains and compared them to B. thailandensis E264. Our data show that biofilm produced by the B. pseudomallei 1026b derivatives and B. thailandensis E264 significantly differ. The molecular composition of the surface adherent biofilm is similar to the molecular composition of the air-liquid pellicle. Finally, the eDNA quantity biofilm produced by JW270 which bears a CPS I deletion, is significantly increased in comparison to 1026 and Bp82 biofilm.

The Taklimakan Desert is the largest desert in China and the second-largest mobile desert in the world. It is characterized by an increasing altitude gradient from north to south. In this study, a total of 48 sand samples were collected in the Taklimakan Desert, and variations in physicochemical parameters and bacterial communities in the samples and the correlation between them were explored. The bacterial community was characterized using 16S rRNA gene sequencing. The obtained taxonomic data revealed significant differences in the relative abundance of bacterial communities and populations among the samples. The predominant phyla were Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. The abundance of Actinobacteria increased gradually while that of Firmicutes decreased gradually with the increase in altitude. At the genus level, the abundance of Bacillus showed a gradual decrease while that of unclassified Micrococcaceae showed a gradual increase. Altitude and pH were the primary factors that shaped the bacterial communities in the desert. Besides, Ca2+ and P were also significantly correlated with the abundance of bacterial communities. The indicator taxa were significant differences in the surface and the subsurface samples.

Whether ooids are formed through biotic or abiotic progress seems to become increasingly controversial in recent decades. New studies indicate that the microbial effect could make important contributions to the construction, destruction and modification of ooids. Previous studies mainly focused on the organomineralization of carbonate minerals in ooids. This paper investigates the formation process of iron minerals in red oolitic grainstones of the Lower Jurassic Nieniexiongla Formation in the Tethyan Himalaya of southern Tibet. Petrographic studies and electron probe microanalysis revealed that the colorful minerals present in red ooids are hematites. Sulfur was detected in the hematites, which indicates that they were transformed from precursor pyrites. These hematites retain euhedral or framboid shapes of the pyrites. Hematite pseudomorphs distribute randomly in ooids and could not form a whole concentric layer of the ooids. Euhedral crystals usually have larger diameters than amorphous spheres and are scattered mostly in nuclei. Based on the distribution and morphology of hematites, we speculate that precursor pyrites were formed through metabolism of sulfate-reducing bacteria. Moreover, the timing of the pyrite formation was after the deposition but before the lithification. The decomposition of the microorganisms within the ooids by bacterial sulfate-reducing provides the HS-, the degradation of organic matters would produce spaces for the intrusion of pore water with sufficient Fe2+ to facilitate the pyrite deposition. In nuclei, the framboid aggregates of pyrites were transferred to euhedral crystals through continuous growth of the constituent microcrystals. Our study demonstrated organomineralization of sulfate-reducing bacteria mediated pyrites in carbonate ooids.

The Agnano thermal spring water (ATSW) is mainly a salso-bromo-iodic-bicarbonate-alkaline-sulphurous water. Since ancient time, the benefits of thermal spring water in the treatment of various diseases have been known. Today it is known that thermal spring water acts effectively on various physiological and pathological processes such as skin regeneration, respiratory and cardiovascular diseases and bone illnesses and most of these beneficial effects depend on the chemical and physical properties of water. However, all the benefits of thermal spring water may not be fully explained only by its mineral composition. In this regard, it is known that non-pathogenic bacterial populations play an active role in various processes in the ecological and biological fields. The aim of the present study is the microbiological characterization of ATSW through the use of two distinct methods in order to determine the total viable bacterial community.

A document by Ahmed Elkhatat. Click on the document to view its contents.

The increasingly wide knowledge of the microbiota, as well as its continuous relation with several pathologies, favours the interest, discovery and classification of all the bacteria that are part of it. The isolation of strain P3519T is possible thanks to the application of new strategies such as culturomics and taxono-genomics. Strain Marseille-P3519T isolated from the fecal flora of a 25-year-old healthy French woman was a Gram-positive anaerobic bacterium, non-motile and non-spore-forming. The 16S rRNA gene sequence of Marseille-P3519 showed 98.57% of sequence similarity with Lactobacillus caviae MOZM2, the closest species, phylogenetically. Its genome had 2,237,367 bp with 45.42 mol% of G+C content. These findings support that strain Marseille-P3519 is a new member of the genus Lactobacillus for which the name Lactobacillus caccae sp. nov., is proposed.

Hemodialysis requires repeated, reliable access to the systemic circulation; therefore, a well-functioning vascular access (VA) procedure is crucial for stable hemodialysis. VA infections (VAIs) constitute the most challenging complication and cause considerable morbidity, loss of access, and even death. In this study, we investigated the molecular profiles of different bacterial isolates retrieved from various types of VA grafts. We collected clinical isolates from hemodialysis patients with VAIs in our institution for the period between 2013 and 2018. We identified the bacterial isolates using standard biochemical procedures; we used a polymerase chain reaction for coagulase-negative staphylococcus (CoNS) and Burkholderia cepacia complex (BCC) species identification. The antibiotic resistance and molecular profile were analyzed using the disk diffusion method and multilocus sequence typing, respectively. We studied 150 isolates retrieved from patients with VAI and observed that Staphylococcus aureus was the predominant bacterial species, followed by S. argenteus, BCC, and CoNS. According to multilocus sequence typing data, we identified a wide variety of sequence types (STs) in S. aureus isolates, with ST59, ST45, and ST239 being the predominant types. Burkholderia cepacia with two new ST types, namely ST1723 and ST1724, accounted for most of the BCC infections, along with ST102 B. contaminans, which were mainly isolated from infected tunneled-cuffed catheters. In summary, the increased incidence of S. argenteus and BCC infections provides insights into their potential clinical effects in VAIs. The various STs identified in different bacterial species indicate the high genetic diversity of bacterial species isolated from VAIs in our institution.

Twenty-nine Candida isolates were assessed with green-coloured colonies using CHROMagar Candida medium with a positive germ-tube test. Based on morphological and biochemical tests, 29 strains were isolated from the oral cavity of children with leukaemia who were undergoing chemotherapy in Basrah, Iraq. Three (10.3%) of them were identified as Candida africana. Identification of the isolated yeasts was further confirmed at the molecular level by amplifying the internal transcribed spacer sequencing (ITS) region of rDNA comprising the ITS1-5.85-ITS2 regions of fungal rRNA genes. This study represented the first recovery of C. africana from the oral cavity for immunocompromised patients with leukaemia and considered the first record of species in Iraq.