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Opinion 129 addresses the status of Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980). The name has the category 'division' and was included in the Approved Lists of Bacterial Names, although that category had previously been removed from the International Code of Nomenclature of Bacteria (1975 revision onwards). When the category 'phylum' was introduced into the International Code of Nomenclature of Prokaryotes (ICNP) in 2021, equivalence between 'phylum' and 'division' was not stipulated. Since the definition of the taxonomic categories and their relative order is one of the principal tasks of every code of nomenclature, the inclusion of Firmicutes corrig. Gibbons and Murray 1978 in the Approved Lists was an error. The name is either not validly published or illegitimate because its category is not covered by the ICNP. If Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980) was a validly published phylum name, it would be illegitimate because it would contravene Rule 8, which does not permit any deviation from the requirement to derive a phylum name from the name of the type genus. Since Firmicutes corrig. Gibbons and Murray 1978 is also part of a 'misfitting megaclassification' recognized in Opinion 128, the name is rejected, without any pre-emption regarding a hypothetically validly published name Firmicutes at the rank of phylum. Gracilicutes Gibbons and Murray 1978 (Approved Lists 1980) and Anoxyphotobacteriae Gibbons and Murray 1978 (Approved Lists 1980) are also rejected. The validly published phylum names have a variety of advantages over their not validly published counterparts and cannot be replaced with ad hoc names suggested in the literature. To ease the transition, it is recommended to mention the not validly published phylum names which strongly deviate in spelling from their validly published counterparts along with the latter in publications during the next years.

Until mid-1970s, cyanobacteria have been interpreted as algae despite they differed from other members of this taxonomic group by the absence of cell nucleus (that is currently considered among the characters of prokaryotic organization). However, when bacteria were interpreted as prokaryotes, blue-green algae became reattributed as cyanobacteria, and bacteriologists began to study their cultured strains with microbiology methods. But since these objects did not obey the provisions of bacteriological code (ICNB), development of their taxonomy had certain problems, especially regarding nomenclature, that could not be solved until early-2010s. Current changes in taxonomy of cyanobacteria result from the general progress in taxonomy of prokaryotes due to explosive accumulation of 16S rRNA gene sequencing data, particularly for uncultured objects. Advances in description of new cyanobacteral taxa are as follows: (I) based on polyphasic approach, new taxa ranging from species to order were published; (II) "dark" cyanobacteria demonstrating several types of non-photosynthetic metabolism were described; I(II) strains producing red-shifted chlorophylls d and f were published. Advances in nomenclature of cyanobacteria are: (IV) taxa validly published according to botanical code (ICN) are also considered valid under prokaryotic code (ICNP); (V) the category of phylum was introduced into ICNP, and due to valid publication of the type genus Cyanobacterium, phylum name Cyanobacteriota became legitimate; (VI) names of uncultured Candidatus objects could get a standing in nomenclature based on SeqCode in which type material is represented by genomic DNA sequences. Advances in classification of cyanobacteria are: (VII) evolutionary tree of oxygenic phototrophs and related phylotypes was construed; (VIII) phylogenomic system of orders and families was elaborated; (IX) ecogenomic system combining genomie analysis with genome distribution data was offered. A subject for future research is restriction of taxonomic redundancy in cyanobacteria, and further attempts to establish their species concept. [ABSTRACT FROM AUTHOR]

Ubiquitination is an evolutionary, ancient system of post-translational modification of proteins that occurs through a cascade involving ubiquitin activation, transfer, and conjugation. The maturation of this system has followed two main pathways. The first is the conservation of a universal structural fold of ubiquitin and ubiquitin-like proteins, which are present in both Archaea and Bacteria, as well as in multicellular Eukaryotes. The second is the rise of the complexity of the superfamily of ligases, which conjugate ubiquitin-like proteins to substrates, in terms of an increase in the number of enzyme variants, greater variation in structural organization, and the diversification of their catalytic domains. Here, we examine the diversity of the ubiquitination system among different organisms, assessing the variety and conservation of the key domains of the ubiquitination enzymes and ubiquitin itself. Our data show that E2 ubiquitin-conjugating enzymes of metazoan phyla are highly conservative, whereas the homology of E3 ubiquitin ligases with human orthologues gradually decreases depending on "molecular clock" timing and evolutionary distance. Surprisingly, Chordata and Echinodermata, which diverged over 0.5 billion years ago during the Cambrian explosion, share almost the same homology with humans in the amino acid sequences of E3 ligases but not in their adaptor proteins. These observations may suggest that, firstly, the E2 superfamily already existed in its current form in the last common metazoan ancestor and was generally not affected by purifying selection in metazoans. Secondly, it may indicate convergent evolution of the ubiquitination system and highlight E3 adaptor proteins as the "upper deck" of the ubiquitination system, which plays a crucial role in chordate evolution. [ABSTRACT FROM AUTHOR]

Fungi harbor a vast diversity of mobile genetic elements (MGEs). Recently, novel fungal MGEs, tentatively referred to as ‘ambiviruses,’ were described. ‘Ambiviruses’ have single-stranded RNA genomes of about 4–5 kb in length that contain at least two open reading frames (ORFs) in non-overlapping ambisense orientation. Both ORFs are conserved among all currently known ‘ambiviruses,’ and one of them encodes a distinct viral RNA-directed RNA polymerase (RdRP), the hallmark gene of ribovirian kingdom Orthornavirae. However, ‘ambivirus’ genomes are circular and predicted to replicate via a rolling-circle mechanism. Their genomes are also predicted to form rod-like structures and contain ribozymes in various combinations in both sense and antisense orientations—features reminiscent of viroids, virusoids, ribozyvirian kolmiovirids, and yet-unclassified MGEs (such as ‘epsilonviruses,’ ‘zetaviruses,’ and some ‘obelisks’). As a first step toward the formal classification of ‘ambiviruses,’ the International Committee on Taxonomy of Viruses (ICTV) recently approved the establishment of a novel ribovirian phylum, Ambiviricota, to accommodate an initial set of 20 members with well-annotated genome sequences. [ABSTRACT FROM AUTHOR]

biological treatment is most used for domestic wastewater. The fixed-bed reactor is a biofilm of microorganisms capable of degrading organic matter, and is an efficient alternative compared to conventional systems, as it increases the contact surface between the microorganism and organic matter. The present work focuses on the adaptation, acclimatization, and use of activated sludge for the formation of a biofilm in a bioreactor for the treatment of domestic effluents with a PET support; It was proven that such material is feasible to be implemented as a means of support. The fixed bed system was kept in operation for 150 days, using domestic wastewater as a substrate, and evaluating the efficiency of the reactor by means of water quality parameters. Microbial diversity was assessed by 16S rRNA analysis. The removal efficiencies of Chemical Oxygen Demand (COD) and Biochemical Oxygen Demand (BOD) were greater than 90% and neutralization of the effluent with alkaline characteristics was achieved. The treatment time was 4 h. We identified 11 corresponding bacterial phylums for biofilm and 8 in suspension, where the main bacterial groups were Proteobacteria, Bacteroidetes and Firmicutes. Treatment time was reduced by 50% compared to conventional systems. The identification of the Phylum allows us to better understand the complexity of bacterial structures in wastewater and how it intervenes in the efficiency of wastewater treatment processes. [ABSTRACT FROM AUTHOR]

Ulcerative colitis (UC) poses a contemporary medical challenge, with its exact cause still eluding researchers. This is due to various factors, such as the rising incidence, diagnostic complexities, and difficulties associated with its management. We compared the intestinal microbiome of patients with UC to that of healthy controls to determine the qualitative and quantitative changes associated with UC that occur in the intestinal microbiota. The intestinal bacterial abundance in 40 Korean patients with UC and 25 healthy controls was assayed using via next-generation sequencing. There were five major phyla in both groups: Firmicutes (UC patients: 51.12%; healthy controls: 46.90%), Bacteroidota (UC patients: 37.04%; healthy controls: 40.34%), Proteobacteria (UC patients: 6.01%; healthy controls: 11.05%), Actinobacteriota (UC patients: 5.71%; healthy controls: 1.56%), and Desulfobacteriota (UC patients: 0.13%; healthy controls: 0.14%). Firmicutes was more prevalent in patients with UC (51.12%) compared to that of healthy controls (46.90%). Otherwise, Bacteroidota was more prevalent in healthy controls (40.34%) compared to patients with UC (37.04%). Although there was no significant difference, our results showed a substantially lower gut microbiome diversity in patients with UC (mean: 16.5; 95% confidence interval (CI) = 14.956–18.044) than in healthy controls (mean: 17.84; 95% CI = 15.989–19.691), the beta diversity and the flora structure of the microbiome in patients with UC differed from those in healthy controls. This will be helpful for the development of new treatment options and lay the groundwork for future research on UC. To understand the disease mechanism, it is essential to define the different types of microbes in the guts of patients with UC. [ABSTRACT FROM AUTHOR]

Keypoints Taxonomically distant species have a wide diversity of roseocin family lantibiotics. The phylogeny-guided approach opens new possibilities for RiPPs bioengineering. Bioactive variants of roseocin were generated using semi-in vitro reconstitution.

The purpose of studying the biodiversity and interannual variation of the meiofauna is to compare the abundance and dominance among all taxonomic groups identifying the most representative ones; being these of important relevance because, due to their sensitivity to environmental changes, they intervene as bio-indicators of the state of health of the ecosystems. The monitoring was carried out on the beaches of San Pedro de Manglaralto at the southern limit of the National Center for Aquaculture and Marine Research (CENAIM), latitude 01° 56' 30" S - longitude 80° 43' 30" W and in Salinas, located 02°12' 06" S - longitude 80° 57' 24" W on the coast of Ecuador, in February and August 2004, 2007 and 2013, collecting 3 replicates per station obtaining a total of 36 samples, considering February as the wet season and August as the dry season. Samples were collected by burying a plastic core in the sediment, obtaining subsamples in a surface of 10cm² at a depth of 15 cm, in the intertidal zone at low tide of sicily; then sealed and labeled, taking care to disturb as little as possible the sampling area. In the laboratory, the species were decanted, washed, centrifuged and counted, identifying them by groups, where nematodes were the most dominant. Biodiversity for the communities of San Pedro and Salinas is related to zones of medium diversity, reporting maximum values of 2.30 bits/org in August 2007 and 2.09 bits/org in August 2004, respectively. The San Pedro station reported the highest diversity in August 2007 with 2.30 bits/org for H' (Margalef) and 0.es39 bits/org for H'(Shannon and Weaver). Significant difference was found in the multivariate structure of the meiofauna between seasons, but not between groups. Nematoda was the most abundant and dominant phylum at the group level. Nine meiofaunal groups were recorded, the Salinas station reported the highest abundance with 625 ± 238 ind/10cm² and the highest density values ranging from 173 to 1004 ind/10cm² (using a 95% confidence interval). The dominant phylum was Nematoda with 18344 ind/10cm² representing 85% of the total density. [ABSTRACT FROM AUTHOR]

Objective: The real causal relationship between human gut microbiota and T1D remains unclear and difficult to establish. Herein, we adopted a two-sample bidirectional mendelian randomization (MR) study to evaluate the causality between gut microbiota and T1D. Methods: We leveraged publicly available genome-wide association study (GWAS) summary data to perform MR analysis. The gut microbiota-related GWAS data from 18,340 individuals from the international consortium MiBioGen were used. The summary statistic data for T1D (n = 264,137) were obtained from the latest release from the FinnGen consortium as the outcome of interest. The selection of instrumental variables conformed strictly to a series of preset inclusion and exclusion criteria. MR-Egger, weighted median, inverse variance weighted (IVW), and weighted mode methods were used to assess the causal association. The Cochran's Q test, MR-Egger intercept test, and leaveone-out analysis were conducted to identify heterogeneity and pleiotropy. Results: At the phylumlevel, only Bacteroidetes was indicated to have causality on T1D (OR = 1.24, 95% CI = 1.01-1.53, P = 0.044) in the IVW analysis. When it comes to their subcategories, Bacteroidia class (OR = 1.28, 95% CI = 1.06-1.53, P = 0.009, PFDR = 0.085), Bacteroidales order (OR = 1.28, 95% CI = 1.06-1.53, P = 0.009, PFDR = 0.085), and Eubacterium eligens group genus (OR = 0.64, 95% CI = 0.50-0.81, P= 2.84×10-4, PFDR = 0.031) were observed to have a causal relationship with T1D in the IVW analysis. No heterogeneity and pleiotropy were detected. Conclusions: The present study reports that Bacteroidetes phylum, Bacteroidia class, and Bacteroidales order causally increase T1D risk, whereas Eubacterium eligens group genus, which belongs to the Firmicutes phylum, causally decreases T1D risk. Nevertheless, future studies are warranted to dissect the underlying mechanisms of specific bacterial taxa's role in the pathophysiology of T1D. [ABSTRACT FROM AUTHOR]

Bantang hot spring is natural, geologically formed by the aggregation of both cold and hot spring water. For the first time, this study combined 16S rRNA genes high-throughput sequencing and bioinformatics analyses to determine the prokaryotic microbe diversity and community structure in the water. A total of 5266 OTUs were obtained, and the community of water was found to comprise 32 bacterial phyla with the most abundant phylum of members belonging to Proteobacteria, and six archaeal phyla with the most abundant phylum of members belonging to Woesearchaeota. Alphaproteobacteria, Burkholderiales, and Comamonadaceae were the highest represented classified species at the level of class, order, and family, respectively. The most abundant bacterial and archaeal genus were Subdivision3 genera incertae sedis and Pacearchaeota Incertae Sedis AR13, and more than a quarter of microorganisms were unclassified genus. Among the top 50 most abundant OTUs, 18 OTUs including the earliest and latest species in evolution have not yet been classified. In the COG analysis, ‘General function prediction only’ was found to be the highest represented category, whereas among predicted KEGG pathways, ‘Membrane Transport’ was the most abundant. Thus, findings from this study greatly improve our understanding to explore novel microorganisms in future.

Describing diet-related effects on the gut microbiome is essential for understanding its interactions with fat and/or sugar-rich diets to promote obesity-related metabolic diseases. Here, we sequenced the V3-V4 hypervariable region of the bacterial 16S rRNA gene to study the composition and dynamics of the gut microbiome of adult mice fed diets rich in fat and/or sugar, at 9 and 18 weeks of diet. Under high-fat, high-sugar diet, the abundances of Tuzzerella and Anaerovorax were transiently increased at 9 weeks, while Lactobacillus remained elevated at 9 and 18 weeks. The same diet decreased the abundances of Akkermansia, Paludicola, Eisenbergiella, and Butyricicoccus at 9 and 18 weeks, while Intestinimonas and UCG-009 of the Butyricicoccaceae family responded only at 18 weeks. The high-fat diet decreased the abundances of UBA1819 at 9 weeks, and Gastranaerophilales, Clostridia UCG-014, and ASF356 at 9 and 18 weeks. Those of Marvinbryantia, Harryflintia, Alistipes, Blautia, Lachnospiraceae A2, Eubacterium coprostanoligenes group, and Eubacterium brachy group were lowered only at 18 weeks. Interestingly, these genera were not sensitive to the high-sugar diet. The mouse gut microbiome was differentially affected by diets rich in fat or fat and sugar. The differences observed at 9 and 18 weeks indicate a progressive microbiome response. [ABSTRACT FROM AUTHOR]

Roseocin, the two-peptide lantibiotic from Streptomyces roseosporus, carries extensive intramolecular (methyl)lanthionine bridging in the peptides and exhibits synergistic antibacterial activity against clinically relevant Gram-positive pathogens. Both peptides have a conserved leader but a diverse core region. The biosynthesis of roseocin involves post-translational modification of the two precursor peptides by a single promiscuous lanthipeptide synthetase, RosM, to install an indispensable disulfide bond in the Rosα core along with four and six thioether rings in Rosα and Rosβ cores, respectively. RosM homologs in the phylum actinobacteria were identified here to reveal twelve other members of the roseocin family which diverged into three types of biosynthetic gene clusters (BGCs). Further, the evolutionary rate among the BGC variants and analysis of variability within the core peptide versus leader peptide revealed a phylum-dependent lanthipeptide evolution. Analysis of horizontal gene transfer revealed its role in the generation of core peptide diversity. The naturally occurring diverse congeners of roseocin peptides identified from the mined novel BGCs were carefully aligned to identify the conserved sites and the substitutions in the core peptide region. These selected sites in the Rosα peptide were mutated for permitted substitutions, expressed heterologously in E. coli, and post-translationally modified by RosM in vivo. Despite a limited number of generated variants, two variants, RosαL8F and RosαL8W exhibited significantly improved inhibitory activity in a species-dependent manner compared to the wild-type roseocin. Our study proves that a natural repository of evolved variants of roseocin is present in nature and the key variations can be used to generate improved variants. Keypoints: Taxonomically distant species have a wide diversity of roseocin family lantibiotics. The phylogeny-guided approach opens new possibilities for RiPPs bioengineering. Bioactive variants of roseocin were generated using semi-in vitro reconstitution. [ABSTRACT FROM AUTHOR]

Intestinal microbiome and gut-brain axis have been receiving increasing attention for their role in the regulation of brain/behavior and possible biological basis of psychiatric disorders. Several recent clinical studies have linked the microbiome with neuropsychiatric conditions, although the literature on schizophrenia is quite limited. This study investigated gut microbiome composition in 50 individuals, including 25 persons with chronic schizophrenia and 25 demographically-matched non-psychiatric comparison subjects (NCs). Stool samples were collected and assayed using 16S rRNA sequencing of the V4 region. Examination of unweighted UniFrac and Bray-Curtis dissimilarity revealed significant community-level separation in microbiome composition between the two subject groups. At the phylum level, Proteobacteria were found to be relatively decreased in schizophrenia subjects compared to NCs. At the genus level, Anaerococcus was relatively increased in schizophrenia while Haemophilus, Sutterella, and Clostridium were decreased. Within individuals with schizophrenia, abundance of Ruminococcaceae was correlated with lower severity of negative symptoms; Bacteroides was associated with worse depressive symptoms; and Coprococcus was related to greater risk for developing coronary heart disease. Our findings provide evidence of altered gut microbial composition in persons with chronic schizophrenia and suggest a need for larger and longitudinal studies of microbiome in schizophrenia.

Intestinal microbiome and gut-brain axis have been receiving increasing attention for their role in the regulation of brain/behavior and possible biological basis of psychiatric disorders. Several recent clinical studies have linked the microbiome with neuropsychiatric conditions, although the literature on schizophrenia is quite limited. This study investigated gut microbiome composition in 50 individuals, including 25 persons with chronic schizophrenia and 25 demographically-matched non-psychiatric comparison subjects (NCs). Stool samples were collected and assayed using 16S rRNA sequencing of the V4 region. Examination of unweighted UniFrac and Bray-Curtis dissimilarity revealed significant community-level separation in microbiome composition between the two subject groups. At the phylum level, Proteobacteria were found to be relatively decreased in schizophrenia subjects compared to NCs. At the genus level, Anaerococcus was relatively increased in schizophrenia while Haemophilus, Sutterella, and Clostridium were decreased. Within individuals with schizophrenia, abundance of Ruminococcaceae was correlated with lower severity of negative symptoms; Bacteroides was associated with worse depressive symptoms; and Coprococcus was related to greater risk for developing coronary heart disease. Our findings provide evidence of altered gut microbial composition in persons with chronic schizophrenia and suggest a need for larger and longitudinal studies of microbiome in schizophrenia.

Ulcerative colitis (UC) poses a contemporary medical challenge, with its exact cause still eluding researchers. This is due to various factors, such as the rising incidence, diagnostic complexities, and difficulties associated with its management. We compared the intestinal microbiome of patients with UC to that of healthy controls to determine the qualitative and quantitative changes associated with UC that occur in the intestinal microbiota. The intestinal bacterial abundance in 40 Korean patients with UC and 25 healthy controls was assayed using via next-generation sequencing. There were five major phyla in both groups: Firmicutes (UC patients: 51.12%; healthy controls: 46.90%), Bacteroidota (UC patients: 37.04%; healthy controls: 40.34%), Proteobacteria (UC patients: 6.01%; healthy controls: 11.05%), Actinobacteriota (UC patients: 5.71%; healthy controls: 1.56%), and Desulfobacteriota (UC patients: 0.13%; healthy controls: 0.14%). Firmicutes was more prevalent in patients with UC (51.12%) compared to that of healthy controls (46.90%). Otherwise, Bacteroidota was more prevalent in healthy controls (40.34%) compared to patients with UC (37.04%). Although there was no significant difference, our results showed a substantially lower gut microbiome diversity in patients with UC (mean: 16.5; 95% confidence interval (CI) = 14.956–18.044) than in healthy controls (mean: 17.84; 95% CI = 15.989–19.691), the beta diversity and the flora structure of the microbiome in patients with UC differed from those in healthy controls. This will be helpful for the development of new treatment options and lay the groundwork for future research on UC. To understand the disease mechanism, it is essential to define the different types of microbes in the guts of patients with UC.

Background: Post-stroke depression (PSD) is a common neuropsychological complication after a stroke with a range of poor outcomes. Evidence of gut microbiota disorder for PSD has recently accumulated. This study aimed to systematically evaluate the association between PSD and gut microbiota. Methods: We searched PubMed, Web of Science, Embase, and VIP, CNKI, Wangfang without language restrictions for eligible studies and performed a meta-analysis and systematic review to assess the pooled differences in gut microbiota compositions between PSD and healthy individuals. Results: We included nine eligible studies reporting the differences in the intestinal microbiome between PSD and healthy control. The pooled results demonstrated that the sequencing depth index (Good's coverage), richness indexes (Chao1 and ACE), evenness, and alpha diversity (Shannon and Simpson) were not significantly changed in PSD patients as compared to healthy controls. The observed species (operational taxonomic unit, OUT) in PSD was significantly higher than that in healthy individuals (SMD, 1.86, 95%CI: 1.47 to 2.25). Furthermore, we observed significant differences between PSD and healthy individuals at the phylum level. The pooled estimation of relative abundance of Proteobacteria (SMD, 0.37, 95%CI: 0.19 to 0.55), Bacteroidetes (SMD, 1.87, 95%CI: 1.25 to 2.48), and Fusobacteria (SMD, 1.06, 95%CI: 0.76 to 1.37) in patients with PSD significantly was increased as compared to controls, while the pooled relative abundance of Firmicutes (SMD, -0.84, 95%CI: -1.21 to -0.47) was significantly decreased in PSD as compared to healthy controls. Moreover, significant differences in intestinal microbiota were observed between PSD patients and healthy controls at the family and genus levels. Conclusions: This meta-analysis indicates a significant alteration of observed species and microbiota composition at the phylum, family and genus levels in PSD as compared to healthy individuals.

The Cape fynbos biome in South Africa is home to highly diverse and endemic shrub legumes, which include species of Aspalathus, Polhillia, Wiborgia and Wiborgiella. These species play a significant role in improving soil fertility due to their ability to fix N2. However, information regarding their microbiome is still unknown. Using the 16S rRNA Miseq illumina sequencing, this study assessed the bacterial community structure associated with the rhizospheres of Polhillia pallens, Polhillia brevicalyx, Wiborgia obcordata, Wiborgia sericea and Wiborgiella sessilifolia growing at different locations during the wet and dry seasons in the Cape fynbos. The results showed that the most dominant bacterial phylum was Actinobacteria during both the dry (56.2–37.2%) and wet (46.3–33.3%) seasons. Unclassified bacterial genera (19.9–27.7%) were the largest inhabitants in the rhizospheres of all five species during the two seasons. The other dominant phyla included Bacteroidetes, Acidobacteria, Proteobacteria and Firmicutes. Mycobacterium and Conexibacter genera were the biggest populations found in the rhizosphere soil of all five test species during both seasons, except for W. obcordata soil sampled during the dry season, which had Dehalogenimonas as the major inhabitant (6.08%). In this study plant species and growth season were the major drivers of microbial community structure, with W. obcordata having the greatest influence on its microbiome than the other test species. The wet season promoted greater microbial diversity than the dry season. [ABSTRACT FROM AUTHOR]

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.

This research focused on in vitro and in vivo biocontrol of two major rice diseases, Bacterial Leaf Blight caused by Xanthomonus oryzae pv oryzae (Xoo) and Sheath Blight caused by Rhizoctonia solani. Furthermore, the soil of paddy fields in Kansai region, Japan was analysed for the presence of these pathogens, and their microbial communities were evaluated according to the location and management systems. For biocontrol, the rhizospheric bacteria were isolated and molecularly identified. The results indicated that DAR17225040 and DAR17225017 were 99% similar to Bacillus aryabhattai and Bacillus megaterium. The isolated bacteria were able to suppress Bacterial Leaf Blight and Sheath Blight disease 78% and 86% respectively, under greenhouse conditions. The 16S amplicon sequencing (Illumina MiSeq 250bp) was used to analyse the bacterial community in paddy fields of soil taken from five locations under conventional and organic systems. Xoo and R. solani were detected in sampled soil, however, no clear difference was noted, regarding systems. From amplicon sequencing data, Chloroflexi, Acidobacteria, Proteobacteria, Actinobacteria, Planctomycetes were the dominant phyla of rice soil in Kansai region. The phylum Kazan-3B-28 was found more in organic system than conventional. The bacterial community was more affected by location and soil type than by management systems.

The Cape fynbos biome in South Africa is home to highly diverse and endemic shrub legumes, which include species of Aspalathus, Polhillia, Wiborgia and Wiborgiella. These species play a significant role in improving soil fertility due to their ability to fix N2. However, information regarding their microbiome is still unknown. Using the 16S rRNA Miseq illumina sequencing, this study assessed the bacterial community structure associated with the rhizospheres of Polhillia pallens, Polhillia brevicalyx, Wiborgia obcordata, Wiborgia sericea and Wiborgiella sessilifolia growing at different locations during the wet and dry seasons in the Cape fynbos. The results showed that the most dominant bacterial phylum was Actinobacteria during both the dry (56.2–37.2%) and wet (46.3–33.3%) seasons. Unclassified bacterial genera (19.9–27.7%) were the largest inhabitants in the rhizospheres of all five species during the two seasons. The other dominant phyla included Bacteroidetes, Acidobacteria, Proteobacteria and Firmicutes. Mycobacterium and Conexibacter genera were the biggest populations found in the rhizosphere soil of all five test species during both seasons, except for W. obcordata soil sampled during the dry season, which had Dehalogenimonas as the major inhabitant (6.08%). In this study plant species and growth season were the major drivers of microbial community structure, with W. obcordata having the greatest influence on its microbiome than the other test species. The wet season promoted greater microbial diversity than the dry season.

Although fungal communities are known to vary along latitudinal gradients, mechanisms underlying this pattern are not well-understood. We used high-throughput sequencing to examine the large-scale distributions of soil fungi and their relation to evolutionary history. We tested the Tropical Conservatism Hypothesis, which predicts that ancestral fungal groups should be more restricted to tropical latitudes and conditions than would more recently derived groups. We found support for this hypothesis in that older phyla preferred significantly lower latitudes and warmer, wetter conditions than did younger phyla. Moreover, preferences for higher latitudes and lower precipitation levels were significantly phylogenetically conserved among the six younger phyla, possibly because the older phyla possess a zoospore stage that is vulnerable to drought, whereas the younger phyla retain protective cell walls throughout their life cycle. Our study provides novel evidence that the Tropical Conservatism Hypothesis applies to microbes as well as plants and animals.

Soil microorganisms play important roles in crop production and sustainable agricultural management. However, soil conditions and crop selection are key determining factors for soil microbial communities. This study investigated the effect of plant types and soil salinity on the microbial community of interspecific interaction zone (II) based on the sorghum/peanut intercropping system. Microbial community diversity and composition were determined through PacBio single molecule, real-time sequencing of 16S rDNA and internal transcribed spacer (ITS) genes. Results showed Proteobacteria, Bacteroidota, and Acidobacteriota to be the dominant bacterial phyla in IP, II, and IS, whereas Ascomycota, Basidiomycota, and Mucoromycota were the dominant fungal phyla. Under salt-treated soil conditions, the plants-specific response altered the composition of the microbial community (diversity and abundance). Additionally, the interspecific interactions were also helpful for maintaining the stability and ecological functions of microbial communities by restructuring the otherwise stable core microbiome. The phylogenetic structure of the bacterial community was greatly similar between IP and II while that of the fungal community was greatly similar between IP and IS; however, the phylogenetic distance between IP and IS increased remarkably upon salinity stress. Overall, salinity was a dominant factor shaping the microbial community structure, although plants could also shape the rhizosphere microenvironment by host specificity when subjected to environmental stresses. In particular, peanut still exerted a greater influence on the microbial community of the interaction zone than sorghum.

Soil microorganisms play important roles in crop production and sustainable agricultural management. However, soil conditions and crop selection are key determining factors for soil microbial communities. This study investigated the effect of plant types and soil salinity on the microbial community of interspecific interaction zone (II) based on the sorghum/peanut intercropping system. Microbial community diversity and composition were determined through PacBio single molecule, real-time sequencing of 16S rDNA and internal transcribed spacer (ITS) genes. Results showed Proteobacteria, Bacteroidota, and Acidobacteriota to be the dominant bacterial phyla in IP, II, and IS, whereas Ascomycota, Basidiomycota, and Mucoromycota were the dominant fungal phyla. Under salt-treated soil conditions, the plants-specific response altered the composition of the microbial community (diversity and abundance). Additionally, the interspecific interactions were also helpful for maintaining the stability and ecological functions of microbial communities by restructuring the otherwise stable core microbiome. The phylogenetic structure of the bacterial community was greatly similar between IP and II while that of the fungal community was greatly similar between IP and IS; however, the phylogenetic distance between IP and IS increased remarkably upon salinity stress. Overall, salinity was a dominant factor shaping the microbial community structure, although plants could also shape the rhizosphere microenvironment by host specificity when subjected to environmental stresses. In particular, peanut still exerted a greater influence on the microbial community of the interaction zone than sorghum. [ABSTRACT FROM AUTHOR]

Introduction: Distinct microbial communities reside in the oral cavity and the composition of the oral microbiota has important implications for human health and disease. Identification of bacterial flora of the microbiome is done by metagenomic analysis of 16S ribosomal RNA sequences. Aim: The aim of this study was to characterise the human microbiome in patients with Coronary Artery Disease (CAD) in comparison with the normal human microbiome. Materials and Methods: A pilot study was carried out in tertiary hospital, Chennai. Oral mouthwash samples collected from nine patients with CAD were selected, with one control group. They were studied by metagenomic analysis of V3-V4 region of 16SrRNA gene sequences.. Sequencing of the variable V3 and V4 regions was done using Illumina platform. Results: The six major phyla, Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes, and Fusobacteria contained 99% of the taxa in all the samples analysed. Conclusion: Diversity of the microbiome in patients with CAD was similar to the normal human microbiome.

Xylan is one of the most abundant polysaccharides present in softwoods and hardwoods. Microbial xylanases mainly mediate its degradation. Xylanase has biotechnological potential with enormous demand in industries. The present study was initiated to investigate the diversity of culturable bacteria in mangrove sediments of Goa (India) and study the xylanase-coding gene in the isolated bacteria. Phylogenetic diversity was determined, in which proteobacteria was the dominant phylum (57%) with the abundance of Vibrio (36%) and Photobacterium (9%), while the second most abundant phylum Firmicutes (40%) was dominated by Bacillus (32%). Among all the culturable isolates screened for xylan degradation, the Bacillus genus was dominant (86%) xylan degrader. Bacillus isolates were further screened for the xylanase gene. The xylanase gene fragments of representative Bacillus were sequenced. All sequences matched to glycoside hydrolase (GH) family 10, thus, showing the dominance of GH10 xylanases in the mangroves regions of Goa (India). GH10 xylanases isolated from Bacillus sp. showed a broad pH optima ranged from pH 5.0 to 9.0 and temperature optima ranged from 50 to 60°C. These properties can be of potential interest for a variety of industrial processes where degradation of lignocelluloses is a crucial process. [ABSTRACT FROM AUTHOR]

This research focused on in vitro and in vivo biocontrol of two major rice diseases, Bacterial Leaf Blight caused by Xanthomonus oryzae pv oryzae (Xoo) and Sheath Blight caused by Rhizoctonia solani. Furthermore, the soil of paddy fields in Kansai region, Japan was analysed for the presence of these pathogens, and their microbial communities were evaluated according to the location and management systems. For biocontrol, the rhizospheric bacteria were isolated and molecularly identified. The results indicated that DAR17225040 and DAR17225017 were 99% similar to Bacillus aryabhattai and Bacillus megaterium. The isolated bacteria were able to suppress Bacterial Leaf Blight and Sheath Blight disease 78% and 86% respectively, under greenhouse conditions. The 16S amplicon sequencing (Illumina MiSeq 250bp) was used to analyse the bacterial community in paddy fields of soil taken from five locations under conventional and organic systems. Xoo and R. solani were detected in sampled soil, however, no clear difference was noted, regarding systems. From amplicon sequencing data, Chloroflexi, Acidobacteria, Proteobacteria, Actinobacteria, Planctomycetes were the dominant phyla of rice soil in Kansai region. The phylum Kazan-3B-28 was found more in organic system than conventional. The bacterial community was more affected by location and soil type than by management systems. [ABSTRACT FROM AUTHOR]

The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum. [ABSTRACT FROM AUTHOR]

Data pre-processing is an important strategy in chemometrics and related fields because in many cases the transformation of data has a great effect on the performance of the method (model). However, a careful examination of the literature clearly points out that only very few systematic studies are dedicated to the effect of the derivative spectra on the performance of the pattern recognition methods. This comprehensive study compares the impact of the order of derivative spectra and other data pre-processing procedures (normalization and standardization) on the performance of cluster analysis, principal component analysis and discriminant analysis applied for characterization and classification of medicinal plants according to their phylum using UV spectra. The efficiency of the pre-processing methods was estimated by comparing the accuracy of classification and prediction measured by internal cross-validation. Derivatization method (1st order) resulted in the best classification (100%) of medicinal plants according to their phylum (Pteridophyte , Magnoliophyte and Spermatophyte) as compared to other pre-processing methods (normalized spectra-71.4%, standardized spectra-76.2% and original spectra-78.6%). Unlabelled Image • Derivatization, normalization and standardization of UV-spectra have been compared. • The first order derivative spectra improve significantly the performance of PCA-LDA. • The advantages provided by derivatization were clearly highlighted in the manuscript. • Medicinal plants were successfully classified according to their phylum. • Correct classification rates, including leave-one-out approach, were computed for all data. [ABSTRACT FROM AUTHOR]

Intestinal microbiome and gut-brain axis have been receiving increasing attention for their role in the regulation of brain/behavior and possible biological basis of psychiatric disorders. Several recent clinical studies have linked the microbiome with neuropsychiatric conditions, although the literature on schizophrenia is quite limited. This study investigated gut microbiome composition in 50 individuals, including 25 persons with chronic schizophrenia and 25 demographically-matched non-psychiatric comparison subjects (NCs). Stool samples were collected and assayed using 16S rRNA sequencing of the V4 region. Examination of unweighted UniFrac and Bray-Curtis dissimilarity revealed significant community-level separation in microbiome composition between the two subject groups. At the phylum level, Proteobacteria were found to be relatively decreased in schizophrenia subjects compared to NCs. At the genus level, Anaerococcus was relatively increased in schizophrenia while Haemophilus, Sutterella, and Clostridium were decreased. Within individuals with schizophrenia, abundance of Ruminococcaceae was correlated with lower severity of negative symptoms; Bacteroides was associated with worse depressive symptoms; and Coprococcus was related to greater risk for developing coronary heart disease. Our findings provide evidence of altered gut microbial composition in persons with chronic schizophrenia and suggest a need for larger and longitudinal studies of microbiome in schizophrenia. [ABSTRACT FROM AUTHOR]