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The gut microbiota (GM) can regulate bone mass, but its association with incident fractures is unknown. We used Cox regression models to determine whether the GM composition is associated with incident fractures in the large FINRISK 2002 cohort (n = 7043, 1092 incident fracture cases, median follow-up time 18 years) with information on GM composition and functionality from shotgun metagenome sequencing. Higher alpha diversity was associated with decreased fracture risk (hazard ratio [HR] 0.92 per standard deviation increase in Shannon index, 95% confidence interval 0.87-0.96). For beta diversity, the first principal component was associated with fracture risk (Aitchison distance, HR 0.90, 0.85-0.96). In predefined phyla analyses, we observed that the relative abundance of Proteobacteria was associated with increased fracture risk (HR 1.14, 1.07-1.20), while the relative abundance of Tenericutes was associated with decreased fracture risk (HR 0.90, 0.85-0.96). Explorative sub-analyses within the Proteobacteria phylum showed that higher relative abundance of Gammaproteobacteria was associated with increased fracture risk. Functionality analyses showed that pathways related to amino acid metabolism and lipopolysaccharide biosynthesis associated with fracture risk. The relative abundance of Proteobacteria correlated with pathways for amino acid metabolism, while the relative abundance of Tenericutes correlated with pathways for butyrate synthesis. In conclusion, the overall GM composition was associated with incident fractures. The relative abundance of Proteobacteria, especially Gammaproteobacteria, was associated with increased fracture risk, while the relative abundance of Tenericutes was associated with decreased fracture risk. Functionality analyses demonstrated that pathways known to regulate bone health may underlie these associations.

Leaf litter microbes collectively degrade plant polysaccharides, influencing land-atmosphere carbon exchange. An open question is how substrate complexity-defined as the structure of the saccharide and the amount of external processing by extracellular enzymes-influences species interactions. We tested the hypothesis that monosaccharides (i.e. xylose) promote negative interactions through resource competition, and polysaccharides (i.e. xylan) promote neutral or positive interactions through resource partitioning or synergism among extracellular enzymes. We assembled a three-species community of leaf litter-degrading bacteria isolated from a grassland site in Southern California. In the polysaccharide xylan, pairs of species stably coexisted and grew equally in coculture and in monoculture. Conversely, in the monosaccharide xylose, competitive exclusion and negative interactions prevailed. These pairwise dynamics remained consistent in a three-species community: all three species coexisted in xylan, while only two species coexisted in xylose, with one species capable of using peptone. A mathematical model showed that in xylose these dynamics could be explained by resource competition. Instead, the model could not predict the coexistence patterns in xylan, suggesting other interactions exist during biopolymer degradation. Overall, our study shows that substrate complexity influences species interactions and patterns of coexistence in a synthetic microbial community of leaf litter degraders.

To investigate the influence of immigration on the selection in structuring local water bacterial communities, we conducted a new community assembly experiment using microcosms filled with sterile original water medium under outdoor conditions. We collected air particulate matter from dust pooled from samples collected at 10 locations across ~20 km in a warm temperate region in Linfen City (northern China). The immigration rates were increased by introducing air particulate matter into the microcosms. The diversity, structure, and composition of the bacterial community in the water were assessed using 16S rRNA gene amplicon sequencing on the 13th and 60th days after the start of the experiment. Our results showed that increasing immigration did not lead to significant changes in the overall diversity of the total bacterial community on the 13th day. However, on the 60th day, diversity significantly increased. The variation explained by the environment substantially decreased from the 13th to the 60th day. The amount decreased from the control to the high immigration treatments, with a range of 65.0 to 29.8% on the 13th day and 34.0 to 15.4% on the 60th day. The dominant phyla differed significantly. In the early stage, Proteobacteria (69.6%) accounted for a higher relative average abundance, while Firmicutes (4.6%), Cyanobacteria (6.0%), Planctomycetota (8.1%), Verrucomicrobiota (2.0%), and Halobacterota (0.9%) were more abundant in the late stage. Additionally, the late stage had an average of 33 phyla, compared to 15 phyla in the early stage. All the results suggested a minimal role of dispersal limitation in structuring water bacterial communities in the early stage, whereas, in the late stage, the bacterial communities might experience dispersal swamping in our study area. Variance partitioning indicated that throughout the experiment, increasing immigration weakened the signal of environmental selection in the water microbial community assembly. These results expand our understanding of the impact of immigration on environmental selection and provide insights into the varying importance of dispersal and selection on microbial community assembly at different stages of succession. [ABSTRACT FROM AUTHOR]

Damqiong Co Lake (DCL) is a high-altitude (4,450 m) soda lake with high salinity (122.45 ± 6.20 g/L) and carbonate concentrations ((10 ± 0.21 g/L of CO32- and 8.77 ± 0.07 g/L of HCO3-) in the Qinghai-Tibet Plateau (QTP). High-throughput sequencing of 16S rRNA genes was used to examine bacterial and archaeal community compositions in the DCL. The result showed that bacterial diversity (Shannon index values of 4.18 ± 0.42) in DCL were significantly higher (P = 0.012) than Archaeal (2.27 ± 1.01). Bacterial communities comprised by 25 phyla, 40 classes, and 205 genera. The dominant bacterial phyla were the Firmicutes (11.23%–70.05%), Proteobacteria (15.47%–45.27%), Bacteroidetes (9.87%–27.88%) and Actinobacteria (0.98%–11.55%). The dominant bacterial genera were Gracilimonas (1.25%–18.95%), Halomonas (3.99%–15.02%), Nitriliruptor (0.76%–11.30%), Bradymonas (0.08%–6.66%), and Brumimicrobium (0.04%–6.47%). Archaeal communities comprised by 5 phyla, 4 classes, and 26 genera. The dominant archaeal phyla were Euryarchaeota (3.69%–97.12%) and Woesearchaeota (2.85%–92.26%), while the dominant genera were Methanomassiliicoccus (0.36%–76.88%), Woesearchaeota AR16 (2.18%–48.61%), Methanolobus (0.32%–19.87%), and Woesearchaeota AR15 (0.27%–18.20%). Correlation heatmap indicated that the diversity in DCL was highly correlated with pH, CO32-, Cl-, Na+, Mg2+, and temperature (P < 0.001). The unique dominant genera of Bacteria (Bradymonas) and Archaea (Methanomassiliicoccus) in DCL suggests that valuable microbial resources may exist in high-altitude soda lakes like the DCL. [ABSTRACT FROM AUTHOR]

Cyanobacterial harmful algal blooms (CyanoHABs) represent a significant threat to freshwater ecosystems globally. To investigate the bacterial communities associated with these blooms, we conducted a metabarcoding analysis of water samples collected during the blooming events in various freshwater reservoirs, including Veeranam, Wellington, Perumal lake at Cuddalore and Trichy Kottapattu Pond, Tamil Nadu, India. Utilizing Metabarcoding of 16S rRNA amplicon sequencing, we characterized the taxonomic composition of bacterial communities in freshwater reservoirs. Our study revealed the dominance of key phyla such as Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria across all four freshwater reservoirs. Predominantly, the abundance of cyanobacterial genera, notably toxin-producing Microcystis sp. and Nostoc sp., were identified, which played a crucial role in driving cyanobacterial bloom formation. Multifaceted interactions between bacteria and cyanobacteria, including core microbiomes and beta diversity patterns, shed light on the microbial dynamics underlying CyanoHABs. This provides a comprehensive understanding of freshwater reservoir Cyanobacterial dynamics, highlighting the bacterial communities involved in bloom events. These findings are crucial for protecting freshwater ecosystems and public health from the harmful effects of cyanobacterial blooms. [ABSTRACT FROM AUTHOR]

The impact of combined heat and drought stress was investigated in Arabidopsis thaliana and compared to individual stresses to reveal additive effects and interactions. A combination of plant metabolomics and root and rhizosphere bacterial metabarcoding were used to unravel effects at the plant holobiont level. Hierarchical cluster analysis of metabolomics signatures pointed out two main clusters, one including heat and combined heat and drought, and the second cluster that included the control and drought treatments. Overall, phenylpropanoids and nitrogen-containing compounds, hormones and amino acids showed the highest discriminant potential. A decrease in alpha-diversity of Bacteria was observed upon stress, with stress-dependent differences in bacterial microbiota composition. The shift in beta-diversity highlighted the pivotal enrichment of Proteobacteria , including Rhizobiales , Enterobacteriales and Azospirillales. The results corroborate the concept of stress interaction, where the combined heat and drought stress is not the mere combination of the single stresses. Intriguingly, multi-omics interpretations evidenced a good correlation between root metabolomics and root bacterial microbiota, indicating an orchestrated modulation of the whole holobiont. [ABSTRACT FROM AUTHOR]

The canonical function of glutamyl‐tRNA synthetase (GluRS) is to glutamylate tRNAGlu. Yet not all bacterial GluRSs glutamylate tRNAGlu; many glutamylate both tRNAGlu and tRNAGln, while some glutamylate only tRNAGln and not the cognate substrate tRNAGlu. Understanding the basis of the unique specificity of tRNAGlx is important. Mutational studies have hinted at hotspot residues, both on tRNAGlx and GluRS, which play crucial roles in tRNAGlx‐specificity. However, its underlying structural basis remains unexplored. The majority of biochemical studies related to tRNAGlx‐specificity have been performed on GluRS from Escherichia coli and other proteobacterial species. However, since the early crystal structures of GluRS and tRNAGlu‐bound GluRS were from non‐proteobacterial species (Thermus thermophilus), proteobacterial biochemical data have often been interpreted in the context of non‐proteobacterial GluRS structures. Marked differences between proteobacterial and non‐proteobacterial GluRSs have been demonstrated; therefore, it is important to understand tRNAGlx‐specificity vis‐a‐vis proteobacterial GluRS structures. To this end, we solved the crystal structure of a double mutant GluRS from E. coli. Using the solved structure and several other currently available proteo‐ and non‐proteobacterial GluRS crystal structures, we probed the structural basis of the tRNAGlx‐specificity of bacterial GluRSs. Specifically, our analyses suggest a unique role played by the tRNAGlx D‐helix contacting loop of GluRS in the modulation of tRNAGln‐specificity. While earlier studies have identified functional hotspots on tRNAGlx that control the tRNAGlx‐specificity of GluRS, this is the first report of complementary signatures of tRNAGlx‐specificity in GluRS. [ABSTRACT FROM AUTHOR]

Polychaete annelids are one of the main components of the oceanic benthos, but little is known about their microbial symbionts. The purpose of this work is to study the microbiome associated with representatives of Terebellides cf. stroemii and to describe their lifestyle in the White Sea. To do this, the worms and their tubes were examined using light and electron microscopy, and the composition of the microbiome was studied by sequencing the hypervariable V4 regions of the 16S rRNA gene. The tubes of Terebellides cf. stroemii are shown to be loose and, most likely, temporary, whereas the worms dig actively into the ground, yet spend part of their time collecting food from the ground surface with the help of tentacles. Bacteria were found neither in integument cells nor in the intestinal epithelium. Phylogenetic and cluster analyses revealed significant differences in the taxonomic composition of the microbiomes of T. cf. stroemii worms from the soil microbiome and allowed us to determine to specific components of the microbiomes of intestines and tentacles, whereas the microbiomes of bottom sediments and worm tubes appeared to be similar. The microbiomes of the tubes are dominated by Pseudomonadota, Desulfobacterota, and Bacteroidota. While the intestines are home to Pseudomonadota, Actinomycetota, Bacillota, CyanobacteriotaChloroflexota, and Planctomycetota, this bacterial community is very different from the microbiomes of both the surrounding sediment and the tentacles. The microbiome of the tentacles of T. cf. stroemii differs significantly from that of the surrounding soil, tube, and intestine, as it contains Pseudomonadota, Bacillota, and Bacteroidota, in addition to a significant number of representatives of the archaeal superfilium DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaeota) observed in two samples. Modern technologies for studying microbiomes demonstrate the presence of specific communities of microorganisms associated with the study species, with a combination of morphological and molecular methods being promising for studying the microbiomes associated with marine annelids and their functional relationships with the animals. [ABSTRACT FROM AUTHOR]

Probiotic sour beer (PRO) fermented with Lacticaseibacillus paracasei Lpc‐37 is a novel beverage option, which may potentially offer health benefits. In this study, the effects of PRO are evaluated on the inflammatory, immunity, lipid profile, and gut microbiome of consumers in a 5‐week, participant‐blinded, randomized‐controlled within‐subject crossover study. Twenty‐one healthy male participants consumed 330 mL of PRO and normal sour beer (CON) daily for 2 weeks each with a 1 week of washout. Stool and blood samples were collected before and after each intervention. Significant increases for Proteobacteria and Bacteroides and a significant decrease in Dialister (p < 0.05) were observed in the CON group, while gut microbiome populations remained relatively stable in the PRO group. A significant increase was also found in HDL‐cholesterol after PRO (p < 0.05), while no significant differences were observed in inflammatory and immunity profiles. Further research is warranted to explore its HDL‐cholesterol increasing potential. [ABSTRACT FROM AUTHOR]

Background: The gut microbiota, comprising billions of microorganisms, plays a pivotal role in health and disease. This study aims to investigate the effect of sepsis on gut microbiome of neonates admitted to the Neonatal Intensive Care Unit. Methods: A prospective cohort study was carried out in the NICU of tertiary care hospital in Karnataka, India, from January 2021 to September 2023. Preterm neonates with birth weight < 1500 g and gestational age < 37 weeks were recruited, excluding those with congenital gastrointestinal anomalies, necrotizing enterocolitis, or blood culture-negative infections. The study population was divided into three groups: healthy neonates (Group A), neonates with drug-sensitive GNB sepsis (Group B), and neonates with pan drug-resistant GNB sepsis (Group C). Stool samples were collected aseptically, snapped in liquid nitrogen, and stored at -80⁰C for extraction of DNA and microbiome analysis. Results: The gut microbiota of healthy neonates (Group A) was dominated by Proteobacteria (24.04%), Actinobacteria (27.13%), Firmicutes (12.74%), and Bacteroidetes (3%). Predominant genera included Bifidobacterium (55.17%), Enterobacter (12.55%), Enterococcus (50.69%), Streptococcus (7.92%), and Bacteroides (3.58%).Groups B and C, the microbiota exhibited higher Proteobacteria abundance (57.16% and 66.58%, respectively) and reduced diversity of beneficial bacteria. Notably, the presence of sepsis was associated with an increase in pathogenic bacteria and a decrease in beneficial commensal bacteria. Conclusion: Neonates with sepsis exhibited significant gut microbiome dysbiosis, characterized by increased Proteobacteria and reduced beneficial bacteria diversity. These findings highlight the potential of microbiome profiling as a diagnostic tool and underscore the importance of gut microbiota modulation in managing neonatal sepsis. [ABSTRACT FROM AUTHOR]

This study aimed to investigate the growth characteristics of Sageretia thea and analyze the correlations between soil physicochemical properties and microbial communities in its native habitats. Soil physicochemical properties were characterized by organic matter (0.37–36.43%), available phosphate (57.96–315.90 mg/kg), potassium (0.11–1.17 cmol+kg−1), calcium (1.23–25.97 cmol+kg−1), magnesium (0.43–15.01 cmol+kg−1), sodium (0.04–6.16 cmol+kg−1), and pH (4.68–7.05), indicating slightly acidic to neutral conditions. S. thea exhibited variable growth characteristics across habitats; leaf length and width were largest in Jangnam-ri and Hacka-ri, respectively, whereas Docheong-ri promoted higher fruit growth. The soil microbial community composition was dominated by Proteobacteria, Actinobacteria, and Acidobacteria at the phylum level (76.09%) and by Alphaproteobacteria, Actinobacteria_c, and Vicinamibacter_c at the class level (40%). Soil physicochemical properties were significantly correlated with Actinobacteria, Acidobacteria, and Chloroflexi at the phylum level, and all microbial groups except Spartobacteria at the class level. Furthermore, growth characteristics were significantly correlated with all microbial communities except Acidobacteria and Firmicutes at the phylum level, and Acidobacteria, Thermoleophilia, and Rubrobacteria at the class level. These findings provide a foundation for developing efficient cultivation techniques for S. thea based on its soil microbiome and habitat conditions. [ABSTRACT FROM AUTHOR]

Endometriosis (EMT) has a significant impact on women's physical and mental health. In this study, high-throughput sequencing technology was employed to detect differences in gut microbiota between EMT patients and healthy individuals (CTL). Additionally, Spearman correlation analysis was utilized to analyze the correlation between different bacterial genera and EMT biomarkers (CA125 and CA199). The results demonstrated that at the phylum level, the relative abundances of Proteobacteria and Desulfobacterota_G_459546 in the EMT group were significantly higher than those in the CTL group, while the relative abundances of Bacteroidota and Firmicutes_A in the EMT group were significantly lower than those in the CTL group. At the genus level, the relative abundances of Burkholderiales and Sphingomonadales in the EMT group were significantly higher than those in the CTL group, while the relative abundances of Bacteroidales and Roseburia in the EMT group were significantly lower than those in the CTL group. The correlation analysis results show that CA125 and CA199 are significantly positively correlated with Burkholderiales and Sphingomonadales , and significantly negatively correlated with Bacteroidales , Oscillospirales , and Roseburia. The PICRUSt2 results show that the relative abundance in the cell motility and xenobiotics biodegradation and metabolism pathways in the EMT group was higher than that in the CTL group, while the relative abundance in the translation, replication and repair, folding, sorting and degradation, metabolism of terpenoids and polyketides and metabolism of cofactors and vitamins pathways in the EMT group was lower than that in the CTL group. In brief, there is a close correlation between the imbalance of gut microbiota and the onset of EMT. The intestinal microbiota has great significance broad prospects for the prevention, diagnosis and treatment of EMT. [ABSTRACT FROM AUTHOR]

Objective To investigate the microbiome composition of deep invasive endometriosis lesions, offering novel insights into its pathogenesis, diagnosis, and treatment strategies. Methods From May 2021 to May 2022, we collected samples of normal endometrium (normal group, n = 10), endometrium from patients with deep infiltrating endometriosis (DIE endometrium group, n = 14), and lesions from these patients (DIE lesion group, n = 10) for 16s rRNA sequencing analysis. We employed the bacterial community diversity algorithm (alpha diversity and beta diversity), principal coordinate analysis (PCoA) distance matrix algorithms (Bray-Curtis and Unifrac matrices), as well as the biological identification algorithm (LeFSe) to investigate microbiome differences between groups and identify differentially abundant bacteria and enriched KEGG functions. Results The diversity of the three groups did not show any significant difference, while the P diversity exhibited a statistically significant distinction (P = 0.005 5). The focus group had a relatively low abundance of Firmicutes at the phylum level and a relatively increased abundance of Fusobacteria. At the genus level, there was an increased relative abundance of Enterococcus and Prevotella. LEFse analysis suggested that Proteobacteria and Gammaproteobacteria were the main dominant in the lesion group. Notably, Gamma proteobacteria emerged as a key differential species among the three groups' microbial flora with statistical significance (P = 0.021 2). Conclusion Compared to the normal group and DIE group, there was a significant increase in the abundance of Fusobacteria, Proteobacteria, Gammaproteobacteria, Enterococcus, and Prevotella. These findings offer novel therapeutic targets for the prevention and intervention of deep infiltrating endometriosis. [ABSTRACT FROM AUTHOR]

AIM: To explore the effects of moderate-altitude exposure on intestinal flora in healthy individuals. METHODS: The aid-Tibet cadres, who were sent to work from Guangdong（ average altitude < 50 m） to Nyingchi（ average altitude of 2 900 m）, were recruited. A total of 76 samples were collected, including 42 samples from healthy adults with plateau living for 0 day and 34 samples from healthy adults with plateau living for 6 months. Fecal samples DNA were extracted, sequenced by the 16S rDNA high-throughput sequencing technology and analyzed bioinformatically. RESULTS: Compared with the base group, α diversity was increased （P=4. 00×10-4） and β diversity was decreased （P=1. 00×10-3）. After moderate altitude exposure, the relative abundance of phylum Proteobacteria （|LDA|>4, P<0. 05）, genus Escherichia-Shigella, species Enterococcus_faecalis, Haemophilus_influenzae and Helicobacter_sp. _UNSW1. 7sp decreased（ adjusted P<0. 05）, wheras the relative abundance of phylum Bacteroidetes （|LDA|>4, P<0. 05）, genusButyricimona, species Lactobacillus_sp. _RA2113 （s） and Butyricimonas_sp. _Marseille-P2440 （s） increased （adjusted P<0. 05）. The functional prediction by PICRUSt showed a decrease in the relative abundance of pathway related to xenobiotics biodegradation and metabolism, membrane transport and amino acid metabolism （adjusted P<0. 05）. Conversely, the relative abundance of pathway related to biosynthesis of other secondary metabolites and nucleotide metabolism was increased （adjusted P< 0. 05）. Finally, the results of microbiome phenotype prediction by BugBase showed that moderate altitude exposure improves the gut microbiota functions involving anaerobic oxygen tolerance and gram positive （adjusted P<0. 05）. And bacteria containing facultatively anaerobic oxygen tolerance, oxidative stress tolerance, gram negative and biofilm formation in the six-group decreased significantly compared with those in base group （adjusted P<0. 05）. CONCLUSION: Moderate altitude exposure impacts the diversity, abundance and function of intestinal flora in healthy population, suggesting that altitude factors may have some influence on gut microbiota. [ABSTRACT FROM AUTHOR]

The purpose of this study is to characterize the ocular surface microbiota of patients with an anophthalmic cavity. An eNAT with 1 mL of Liquid Amies Medium was used to collect samples. Microbial DNA from anophthalmic socket and healthy fellow control eye samples was isolated and sequenced. Raw reads were analyzed with GAIA (v 2.02). The richness and Shannon alpha diversity metrics, as well as Bray–Curtis beta diversity and Wilcoxon signed-rank test values, were computed with R packages such as phyloseq, mia, or DESeq2 to allow for microbiome analysis. Principal coordinate analysis (PCoA) was performed using the function plotReducedDim from the R package scater. The different taxonomic profiles were described under the concept of eye community state type (ECST). The microbiomes of both eyes from 25 patients with an anophthalmic cavity were analyzed in this study. While the microbial communities of paired eyes from the same patients showed notable dissimilarity, no consistent patterns emerged when comparing healthy eyes to anophthalmic sockets. Alpha diversity values did not significantly differ between healthy eyes and anophthalmic socket samples, though there was considerable variability within each group. Notably, anophthalmic socket samples generally exhibited lower abundances of genera such as Staphylococcus, Enterococcus, Paenibacillus, and Sediminibacterium compared to their healthy counterparts. Microbial variability between healthy eyes and anophthalmic sockets may be due to anatomical differences. Further research is needed to determine whether patients without anophthalmic sockets exhibit similar microbiome patterns in both eyes. [ABSTRACT FROM AUTHOR]

To provide the necessary nitrite for the Anaerobic Ammonium Oxidation (ANAMMOX) process, the effect of nitrite accumulation in the partial sulfide autotrophic denitrification (PSAD) process was investigated using an SBR reactor. The results revealed that the effectiveness of nitrate removal was unsatisfactory when the S/N ratio (mol/mol) fell below 0.6. The optimal conditions for nitrate removal and nitrite accumulation were achieved within the S/N ratio range of 0.7-0.8, resulting in an average Nitrate Removal Efficiency (NRE) of 95.84%±4.89% and a Nitrite Accumulation Rate (NAR) of 75.31%±6.61%, respectively. It was observed that the nitrate reduction rate was three times faster than that of nitrite reduction during a typical cycle test. Furthermore, batch tests were conducted to assess the influence of pH and temperature conditions. In the pH tests, it became evident that the PSAD process performed more effectively in alkaline environment. The highest levels of nitrate removal and nitrite accumulation were achieved at an initial pH of 8.5, resulting in a NRE of 98.30%±1.93% and a NAR of 85.83%±0.47%, respectively. In the temperature tests, the most favourable outcomes for nitrate removal and nitrite accumulation were observed at 22±1 ℃, with a NRE of 100.00% and a NAR of 81.03%±1.64%, respectively. Moreover, a comparative analysis of 16S rRNA sequencing results between the raw sludge and the sulfide-enriched culture sludge sample showed that Proteobacteria (49.51%) remained the dominant phylum, with Thiobacillus (24.72%), Prosthecobacter (2.55%), Brevundimonas (2.31%) and Ignavibacterium (2.04%) emerging as the dominant genera, assuming the good nitrogen performance of the system. [ABSTRACT FROM AUTHOR]

The generation of surplus sludge during biological wastewater treatment has become a prevalent issue, necessitating the development of a dewatering approach that is efficient, economically feasible, and ecologically sound. Bdellovibrio-and-like-organisms (BALOs) are obligatory parasitic bacteria that prey on an array of bacteria. In this study, different BALO strains were isolated and purified from waste activited sludge (WAS). Anti-predation host strains were applied to screen the BALO strains with different host-range to minimize the overlap of the biolysis prey spectrum. In addition, the BALO strains with different host preferences were mixed for sludge biolysis treatment efficiency comparison. The results indicated that the capillary suction time and the bound water content in the WAS treated with the mixed BALOs were significantly decreased by 25.9% ± 1.7% and 5.2% ± 1.2%, respectively, compared to those treated with the single BALO strain. The soluble chemical oxygen demand concentration in the mixed BALOs treated group was increased by 31.2% ± 0.7% than that treated with the single strain. The findings indicate that the mixed strains used in the treatment process resulted in a notable enhancement of both sludge dewatering performance and lysis degree. In addition, the abundance of Proteobacteria treated with the BALO mixtures decreased by 69.1% than the single strain treated one which demonstrated that the BALO mixture expanded the sludge host lysis spectrum. This study revealed the different effects of single and mixed strains on sludge community structure, suggesting that the BALO host-range expansion is crucial to further improve sludge dewatering performances. [ABSTRACT FROM AUTHOR]

BACKGROUND: Giardia duodenalis (Gd) causes intestinal parasitosis. The involvement of the intestinal microbiome in determining the infections clinical phenotype is unknown. OBJECTIVE: Investigate the fecal microbiome features in dogs with giardiasis. ANIMALS AND METHODS: Cross-sectional study, including fecal samples of kenneled dogs with Gd diagnosed by fecal Giardia antigen dot ELISA. The fecal microbial compositional characteristics and dysbiosis index (DI) were compared between diarrheic and nondiarrheic dogs. RESULTS: Fecal samples of 38 Gd-infected dogs (diarrheic, 21; nondiarrheic, 17) were included. No differences were found in Faiths phylogenic diversity and beta diversity (weighted UniFrac distances) and in specific taxa abundances at the phylum, genus, and species levels, as well as in alpha and beta diversities between diarrheic and nondiarrheic dogs, and also when divided by sex or age. Among diarrheic dogs, alpha diversity was higher in males than in females (pairwise Kruskal-Wallis, q = 0.01). Among males, fecal abundances of the genus Clostridium (W = 19) and Clostridium spiroforme species (W = 33) were higher in diarrheic compared to nondiarrheic dogs. In diarrheic dog fecal samples, Proteobacteria were more prevalent (W = 1), whereas Verrucomicrobia were less prevalent in dogs

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Abstract The extreme conditions of the deep-sea environment, including limited light, low oxygen levels, high pressure, and nutrient scarcity, create a natural habitat for deep-sea bacteria. These remarkable microorganisms have developed unique strategies to survive and adapt to their surroundings. However, research on the diversity of deep-sea bacteria, both culture-dependent and culture-independent, in Indonesian waters remains insufficient. This study focused on exploring the biodiversity of deep-sea bacteria, specifically in the Makassar and Lombok Strait, the main Indonesian throughflow pathway characterized by relatively fertile water, which serves as an important deep-sea region. High-throughput DNA sequencing of full-length 16S rRNA was employed to construct a genomic database. The results of the bioinformatic analysis revealed that two stations, 48 and 50 (Makassar Strait), exhibited a more similar community structure of deep-sea bacteria than did station 33 (Lombok Strait). Among the predominant phyla found at a depth of 1000 m, the top ten were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Nitrospinae, Verrucomicrobia, Candidatus Melainabacteria, and Cyanobacteria. Furthermore, the genera Colwellia, Moritella, Candidatus Pelagibacter, Alteromonas, and Psychrobacter consistently appeared at all three stations, albeit with varying relative abundance values. These bacterial genera share common characteristics, such as psychrophilic, halophilic, and piezophilic tendencies, and are commonly found in deep-sea ecosystem. The environmental conditions at a depth of 1000 m were relatively stable, with an average pressure 10 MPa, temperature 4.68 °C, salinity 34.58 PSU, pH 8.06, chlorophyll-a 0.29 µg/L, nitrate 3.19 µmol/L, phosphate 6.32 µmol/L and dissolved oxygen (DO) 2.90 mg/L. The bacterial community structures at the three sampling stations located at the same depth (1000 m) exhibited similarities, as indicated by the closely aligned similarity index values.

Abstract Background The gut microbiota, comprising billions of microorganisms, plays a pivotal role in health and disease. This study aims to investigate the effect of sepsis on gut microbiome of neonates admitted to the Neonatal Intensive Care Unit. Methods A prospective cohort study was carried out in the NICU of tertiary care hospital in Karnataka, India, from January 2021 to September 2023. Preterm neonates with birth weight

Abstract Glaciers, which form due to the accumulation of snow, play a crucial role in providing freshwater resources, supporting river systems, and maintaining ecosystem stability. Pakistan is habitat to over 5000 glaciers, primarily located in the Hindukash, Himalaya, and Karakoram mountain ranges. Understanding the microbial communities thriving in these extreme environments becomes of utmost importance. These glaciers offer a unique perspective on extremophile adaptation, as they harbor microorganisms that are capable of surviving and thriving under harsh conditions. Glacial melting poses a significant threat to ancient microbiomes, potentially leading to the resurgence of epidemics and exposure of life to paleomicrobiota. Mostly glacial microbiome is evenly distributed and shows similar diversity. With the threat of resurrection of ages old microbiome and its incorporation into the waters have raised a major concern for revival of epidemics and exposure of life with paleanmicrobiota again. This has led the scientist to deeply observe the bacterial flora embedded in the cryonite holes of glaciers. This study aims to investigate the bacterial diversity within various glaciers of Pakistan using metagenomic techniques. Kamri, Burzil, Siachin, Baltoro, Shigar Basin, Biafo and Panama Glaciers designated from G1 to G7 respectively were chosen from Pakistan. Through rigorous physicochemical analyses, distinct characteristics among glaciers are revealed, including variations in temperature, depth, electrical conductivity, pH levels, and nutrient concentrations. The exploration of alpha diversity, employing metrics such as Chao1, Shannon, Simpson, and Inverse Simpson indices, offers valuable insights into the richness, evenness, and dominance of species within different samples. Beta diversity was calculated by using R software. The vegan package was used for NMSD, cluster and PCoA analysis based on Bray–Curtis distance. PCA analysis was done by using prcomp package from R software. Based on OTU abundance and environmental factor data, DCA analysis was done to determine the linear model from the gradient value (RDA) and the unimodal model (CCA). results were compiled by drawing cluster dendrogram which predicts the patterns of similarity and dissimilarity between different samples. Notably, phyla Proteobacteria emerge as the dominant phylum, accompanied by Actinobacteria, Firmicutes, and Bacteroidetes. The dendrogram shows five clusters, with close similarity between G1 and G4, glacier samples G3 and G8, and G2 and G7. Seasonal variations in glacier physicochemical properties were also observed, with summer samples having shallower depths, lower temperatures, and slightly acidic pH. In contrast, winter samples have higher electrical conductivity and sulfur content. Ultimately, this research provides a foundational framework for comprehending glacier ecosystems, their resident microbial communities, and their broader ecological significance. The study highlights the potential public health risks linked to the release of ancient microorganisms due to climate change, emphasizing the need for comprehensive monitoring and research to mitigate potential public health threats.

Introduction: Traditional fermented foods have long been recognized for their numerous health benefits along with their potential to aid in the treatment of gastrointestinal disorders. These fermented foods have been shown to promote gut health and contribute to a longer, healthier life. Methods: The high-throughput sequencing using the Illumina MiSeq platform was employed to investigate the microbiome communities of rice-based fermented beverages consumed by ethnic tribes in Southern Assam, namely Zeme Naga, Dimasa Kachari, Hmar, Karbi and Tea tribes. Results: The fermented rice-based beverages were highly predominated by Firmicutes, Bacteroides, Proteobacteria, and Actinobacteria exhibiting the highest relative abundance across all tribes. At genus level, significant abundance of pediococcus, lactobacillus, bacillus, leuconostoc, acetobacter, staphylococcus, delftia, erwinia, klebsiella and chrysebacterium were found amongst these ethnic tribes. Discussion: Understanding the fermented food microbiome will help to know the relationships between microbial communities and their effect on health of humans amongst the tribes. Furthermore, the use of these fermented products could provide enhanced health benefits to southern Assam region of India. [ABSTRACT FROM AUTHOR]

Background: The gut microbiota plays an important role in primates, which may be associated with their habitat. In Malaysia, pig‐tailed macaques (Macaca nemestrina) live in different habitat environments and have traditionally been used for coconut plucking for more than a century. There is currently no information regarding the gut microbiota of this macaque in Malaysia. To address this oversight, this study employed a fecal metabarcoding approach to determine the gut microbiota composition of pig‐tailed macaques and establish how these microbial communities correspond with the macaque external environments of residential area, forest edge, and fragmented forest. Methods: To determine this connection, 300 paired‐end sequences of 16S rRNA were amplified and sequenced using the MiSeq platform. Results: In the pig‐tailed macaque fecal samples, we identified 17 phyla, 40 orders, 52 families, 101 genera, and 139 species of bacteria. The most prevalent bacterial families in the gut of pig‐tailed macaques were Firmicutes (6.31%) and Proteobacteria (0.69%). Our analysis did not identify a significant difference between the type of environmental habitat and the gut microbiota composition of these macaques. Conclusions: There was great variation in the population richness and bacterial community structure. The abundance of Firmicutes and Proteobacteria helps this macaque digest food more easily while maintaining a healthy gut microbiota diversity. Exploring the gut microbiota provides an initial effort to support pig‐tailed macaque conservation in the future. [ABSTRACT FROM AUTHOR]

A novel bacterium, designated as strain LOR1-02T and isolated from a lichen sample collected from Kham Riang Subdistrict, Kantharawichai District, Maha Sarakham Province, Thailand, underwent thorough investigation utilizing a polyphasic taxonomic approach. Strain LOR1-02T demonstrated growth within a temperature range of 20–42 °C (optimal at 30 °C), pH range of 5.0–7.5 (optimal at pH 7.0), and tolerance to 4.0% (w/v) NaCl. Phylogenetic analysis revealed its close relation to Paracraurococcus ruber JCM 9931T, with a 16S rRNA gene sequence similarity of 97.16%, placing it within the genus Paracraurococcus. The approximate genome size of strain LOR1-02T was determined to be 8.6 Mb, with a G + C content of 70.9 mol%. Additionally, ANIb, ANIm, and AAI values between the whole genomes of strain LOR1-02T and type strains were calculated as 82.6–83.4%, 86.1–86.8%, and 81.4–82.2%, respectively, while the dDDH value was determined to be 26.3–28.5% (C.I. 24.0–31.0%). The predominant fatty acids detected were C18:1ω7c and/or C18:1ω6c, C16:0, and C18:12OH. The major ubiquinone identified was Q-10, and the polar lipids included phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, along with unidentified phosphoaminolipid, lipids, and an amino lipid. Based on comprehensive phenotypic, chemotaxonomic, and genotypic characterization, it is concluded that strain LOR1-02T represents a novel species within the genus Paracraurococcus, for which the name Paracraurococcus lichenis sp. nov. is proposed. The type strain designation is LOR1-02T (= JCM 33121T = NBRC 112776T = TISTR 2503T). [ABSTRACT FROM AUTHOR]

Actinobacteria cells Rhodococcus erythropolis 4-1 and Rhodococcus erythropolis 11-2 and Proteobacteria Alcaligenes faecalis 2, which have amidase activity, were immobilized by entrapping barium alginate and agarose into the gel structure, as well as by obtaining biofilms on thermally expanded graphite (TEG). The operational stability of such immobilized biocatalysts after storage in frozen and dehydrated form was determined, and a prototype of a conductometric acrylamide biosensor based on such a bioselective agent was developed. The most preferred method for storing immobilized cells was freezing at temperatures from –20 to –80°C; long-term storage is also possible wet at 4–25°C. It was shown that these cells were most preferable for the biodetection of acrylamide A. faecalis 2, immobilized in an agarose gel structure. An agarose gel with bacterial cells immobilized in its structure had greater mechanical strength and stability during successive cycles of conversion of acrylamide into acrylic acid compared to barium alginate gel. The mechanical strength of barium alginate gel can be enhanced by the addition of carbon nanomaterials during cell immobilization. Growing biofilms on carbon materials used for manufacturing electrodes is also promising. Biofilms of R. erythropolis 11-2 on TEG are capable of converting acrylamide into acrylic acid in more than 20 reaction cycles while maintaining at least 50% amidase activity. [ABSTRACT FROM AUTHOR]

The impact of pollution on the Ologe Lagoon was assessed by comparing physicochemical properties, hydrocarbon concentrations and microbial community structures of the sediments obtained from distinct sites of the lagoon. The locations were the human activity site (OLHAS), industrial-contaminated sites (OLICS) and relatively undisturbed site (OLPS). The physicochemical properties, heavy metal concentrations and hydrocarbon profiles were determined using standard methods. The microbial community structures of the sediments were determined using shotgun next-generation sequencing (NGS), taxonomic profiling was performed using centrifuge and statistical analysis was done using statistical analysis for metagenomics profile (STAMP) and Microsoft Excel. The result showed acidic pH across all sampling points, while the nitrogen content at OLPS was low (7.44 ± 0.085 mg/L) as compared with OLHAS (44.380 ± 0.962 mg/L) and OLICS (59.485 ± 0.827 mg/L). The levels of the cadmium, lead and nickel in the three sites were above the regulatory limits. The gas chromatography flame ionization detector (GC-FID) profile revealed hydrocarbon contaminations with nC14 tetradecane > alpha xylene > nC9 nonane > acenaphthylene more enriched at OLPS. Structurally, the sediments metagenomes consisted of 43 phyla,75 classes each, 165, 161, 166 orders, 986, 927 and 866 bacterial genera and 1476, 1129, 1327 species from OLHAS, OLICS and OLPS, respectively. The dominant phyla in the sediments were Proteobacteria, Firmicutes, Actinobacteria, and Chloroflexi. The principal component ordination (PCO) showed that OLPS microbial community had a total variance of 87.7% PCO1, setting it apart from OLHAS and OLICS. OLICS and OLHAS were separated by PCO2 accounting for 12.3% variation, and the most polluted site is the OLPS. [ABSTRACT FROM AUTHOR]

Deep-sea trenches representing an intriguing ecosystem for exploring the survival and evolutionary strategies of microbial communities in the highly specialized deep-sea environments. Here, 29 metagenomes were obtained from sediment samples collected from Kermadec and Diamantina trenches. Notably, those samples covered a varying sampling depths (from 5321 m to 9415 m) and distinct layers within the sediment itself (from 0~40 cm in Kermadec trench and 0~24 cm in Diamantina trench). Through metagenomic binning process, we reconstructed 982 metagenome assembled genomes (MAGs) with completeness >60% and contamination <5%. Within them, completeness of 351 MAGs were >90%, while an additional 331 were >80%. Phylogenomic analysis for the MAGs revealed nearly all of them were distantly related to known cultivated isolates. The abundant bacterial MAGs affiliated to phyla of Proteobacteria, Planctomycetota, Nitrospirota, Acidobacteriota, Actinobacteriota, and Chlorofexota, while the abundant archaeal phyla affiliated with Nanoarchaeota and Thermoproteota. These results provide a dataset available for further interrogation of diversity, distribution and ecological function of deep-sea microbes existed in the trenches. [ABSTRACT FROM AUTHOR]

Glaciers, which form due to the accumulation of snow, play a crucial role in providing freshwater resources, supporting river systems, and maintaining ecosystem stability. Pakistan is habitat to over 5000 glaciers, primarily located in the Hindukash, Himalaya, and Karakoram mountain ranges. Understanding the microbial communities thriving in these extreme environments becomes of utmost importance. These glaciers offer a unique perspective on extremophile adaptation, as they harbor microorganisms that are capable of surviving and thriving under harsh conditions. Glacial melting poses a significant threat to ancient microbiomes, potentially leading to the resurgence of epidemics and exposure of life to paleomicrobiota. Mostly glacial microbiome is evenly distributed and shows similar diversity. With the threat of resurrection of ages old microbiome and its incorporation into the waters have raised a major concern for revival of epidemics and exposure of life with paleanmicrobiota again. This has led the scientist to deeply observe the bacterial flora embedded in the cryonite holes of glaciers. This study aims to investigate the bacterial diversity within various glaciers of Pakistan using metagenomic techniques. Kamri, Burzil, Siachin, Baltoro, Shigar Basin, Biafo and Panama Glaciers designated from G1 to G7 respectively were chosen from Pakistan. Through rigorous physicochemical analyses, distinct characteristics among glaciers are revealed, including variations in temperature, depth, electrical conductivity, pH levels, and nutrient concentrations. The exploration of alpha diversity, employing metrics such as Chao1, Shannon, Simpson, and Inverse Simpson indices, offers valuable insights into the richness, evenness, and dominance of species within different samples. Beta diversity was calculated by using R software. The vegan package was used for NMSD, cluster and PCoA analysis based on Bray–Curtis distance. PCA analysis was done by using prcomp package from R software. Based on OTU abundance and environmental factor data, DCA analysis was done to determine the linear model from the gradient value (RDA) and the unimodal model (CCA). results were compiled by drawing cluster dendrogram which predicts the patterns of similarity and dissimilarity between different samples. Notably, phyla Proteobacteria emerge as the dominant phylum, accompanied by Actinobacteria, Firmicutes, and Bacteroidetes. The dendrogram shows five clusters, with close similarity between G1 and G4, glacier samples G3 and G8, and G2 and G7. Seasonal variations in glacier physicochemical properties were also observed, with summer samples having shallower depths, lower temperatures, and slightly acidic pH. In contrast, winter samples have higher electrical conductivity and sulfur content. Ultimately, this research provides a foundational framework for comprehending glacier ecosystems, their resident microbial communities, and their broader ecological significance. The study highlights the potential public health risks linked to the release of ancient microorganisms due to climate change, emphasizing the need for comprehensive monitoring and research to mitigate potential public health threats. [ABSTRACT FROM AUTHOR]

The aim of this experiment was to study the difference of intestinal microflora of Kazakh horses in grass group and hay group after transfer. Twenty Kazakh mares aged five to six years old under uniform feeding and management conditions in the Tacheng area of Xinjiang were selected and divided into two groups: Fresh Grass Group (QC group) and Dry Grass Group (GC group). They were fed 2 kg of concentrate feed per horse per day. QC group consumed fresh grass daily, while the GC group consumed dry grass daily. At 30 days of the experiment, fecal samples of all horses were collected, and the characteristic sequences of microbial species such as 16S amplified by PCR were detected by high-throughput sequencing technology. There were 28 865 OTU in fecal flora of Kazakh horses in the two groups, and the OTU amount in fecal flora of Kazakh horses in QC group was higher than that in GC group. The results showed that Firmicute, Bacteroidota, Proteobacteria, Verrucomicrobiota, and Spirochaetota were the dominant bacteria in the manure of Kazakh horses in the two groups. The dominant bacteria genera were Solibacillus, Acinetobacter, Rikenellaceae_RC9_gut_group, Treponema, and Ruminococcaceae NK4A214_group. Compared with the GC group, the relative abundances of Actinobacteriota and Rummeliibacillus in feces of Kazakh horses in QC group were significantly increased (P<0.05). LEfSe analysis showed that 65 kinds of bacteria were significantly different in fecal flora of Kazakh horses in the two groups, among which 36 kinds of bacteria were significantly up-regulated in QC group and 29 kinds of bacteria were significantly up-regulated in GC group. The study indicates that the composition structure and community of fecal flora of Kazakh horses were affected by different forage, but the diversity and richness of intestinal flora did not change significantly. More important microbial groups played an important role in fecal flora of Kazakh horses in QC group than in GC group. [ABSTRACT FROM AUTHOR]

Glycoside hydrolases belonging to family 48 (GH48) are one of the most important cellulases responsible for the synergistic degradation of crystalline cellulose (CC) to glucose. Microbial DNA was extracted from soils and compost followed by PCR amplification to detect bacterial GH48 genes. Amplified fragments were cloned to develop DNA libraries to determine the diversity and community structure of bacterial genes responsible for cellulose degradation using GH48 genes. Soil bacterial communities were predominantly based upon unidentified GH48 genes (66%). When identification was possible, community composition analysis of soil samples showed 4 known bacterial phyla with Proteobacteria (23%), Actinobacteria (9%), Firmicutes (1%), and Bacteroidetes (1%). Phylogenetic analysis of unidentified clones showed 2% of clones clustered with a reference sequence from the Chloroflexota genus Herpetosiphon sp. Compost GH48 sequences were predominantly comprised of 3 different bacterial phyla belonging to Firmicutes (72%), Actinobacteria (16%), Myxococcota (5%) with 7% of sequences not matching any known bacteria. The most abundant microbial species in soil with GH48 genes was the Proteobacteria species Massilia violaceinigra (13%) while in compost the Firmicutes species Bacillus licheniformis showed the highest percentage (70%). Soil communities showed a higher genetic diversity than compost predominantly composed of unknown genetic sequences showing the potential to isolate and characterize new cellulases from soil. The contribution of different bacterial phyla, genera, and species to the synergistic CC degradation by GH48 genes demonstrated the importance of diverse bacterial communities to optimize carbon recycling in the environment. [ABSTRACT FROM AUTHOR]

This study investigated the effects of adding earthworm mucus on the changes in sludge compost bacterial community structure and its response to environmental factors. The results showed that adding earthworm mucus improved the composting effect of sludge, reducing nitrogen loss and increasing nutrients; nitrogen loss decreased by 5.55%, and potassium and phosphorus increased by 10.23 and 16.28%, respectively. Firmicutes, Chloroflexi, Actinobacteria, and Proteobacteria were the main bacterial phyla in the sludge, with a combined relative abundance of over 60%. The addition of earthworm mucus significantly impacted bacterial community structure and composting activity, increasing the relative abundance of dominant bacteria during the process. Redundancy analysis showed that environmental factors significantly impacted the changes in bacterial community structure during composting. The results indicate that the addition of earthworm mucus increases the relative abundance of advantageous bacteria playing essential roles in sludge composting, enhancing the fertility and maturity of sludge composting products by significantly reducing nitrogen loss and increasing potassium and phosphorus. Based on the response relationship between environmental factors and bacterial communities, the bacterial community structure in sludge composting can be improved by regulating environmental factors (such as pH and moisture content), enhancing the effectiveness of sludge composting. [ABSTRACT FROM AUTHOR]

Ologe Lagoon, in Lagos State Nigeria, is one of the freshwaters exposed to chemical and hydrocarbon pollution. The impacts of anthropogenic pollution on lagoon microbial communities were assessed. Three sampling points were identified, namely Ologe industrial contaminated water (OLICW), Ologe human activity water (OLHAW), and relatively undisturbed water (OLPW). The microbial community structure of samples was determined via Illumina shotgun next-generation sequencing, while taxonomic classification was done by centrifuge. Acidic pH of (3.8 ± 0.02; 4.6 ± 0.01; and 6.5 ± 0.04) were observed for OLHAW, OLICW and OLPW. The heavy metals nickel and lead showed increase at OLICW > OLPW > OLHAW with their values higher than the WHO permissible limit. The gas chromatography flame ionization detector (GC-FID) fingerprints of the samples showed presence of aliphatic (nC1-nC17) and aromatic hydrocarbons like pyrene, anthracene, phenanthraquinone, and phenanthridine which is evidence of pollution. Structurally, the water metagenomes comprised of 40, 43, and 42 phyla, 67, 74, and 72 classes, 666, 982, and 920 genera from OLHAW, OLICW, and OLPW metagenomes. Dominant phyla across the three sites were Proteobacteria (37.1–64.1%), Actinobacteria (6.1–21.6%), Cyanobacteria (5.3–14.0%), Planctomycetes (6.6%), Firmicutes (6.6–5.7%). Archaea phyla like Euryarchaeota and Creanarchaeota were encountered. Principal component ordination (PCO) showed that OLHAW prokaryotic community had total variance of 88.2% PCO1 separating it from OLICW and OLPW, also OLICW and OLPW were separated by PCO2 accounting for 11.8% variation but clustered showing 60% similarity. The study showed abundance of Cyanobacteria, Nitrospira and Clostridia which are biological indicator of pollution and their presence signify eutrophication. [ABSTRACT FROM AUTHOR]

Despite the highly conserved nature of the genetic code, the frequency of usage of each codon can vary significantly. The evolution of codon usage is shaped by two main evolutionary forces: mutational bias and selection pressures. These pressures can be driven by environmental factors, but also by the need for efficient translation, which depends heavily on the concentration of transfer RNAs (tRNAs) within the cell. The data presented here supports the proposal that tRNA modifications play a key role in shaping the overall preference of codon usage in proteobacteria. Interestingly, some codons, such as CGA and AGG (encoding arginine), exhibit a surprisingly low level of variation in their frequency of usage, even across genomes with differing GC content. These findings suggest that the evolution of GC content in proteobacterial genomes might be primarily driven by changes in the usage of a specific subset of codons, whose usage is itself influenced by tRNA modifications. [ABSTRACT FROM AUTHOR]

The sub-lakes of Poyang Lake have significant ecological value. To date, the diazotrophs in sub-lakes are unknown. Moreover, no study has simultaneously focused on diazotrophic communities in the water and sediment in natural freshwater ecosystems. In this study, we investigated the diazotrophic alpha diversity, structure, abundance, molecular ecological network, and community assembly mechanism in the water and sediment of sub-lakes using Illumina MiSeq sequencing and a quantitative polymerase chain reaction assay. The results showed that the sediment had a greater diversity of diazotrophs than the water. Proteobacteria and Spirochaetes were the dominant diazotrophic phyla in the water, whereas Proteobacteria was the dominant diazotrophic phylum in the sediment. There were significant differences in the composition of diazotrophic communities between the water and sediment. The sediment had a more complex co-occurrence network of diazotrophs than the water. Deterministic processes dominate the community assembly of diazotrophs in both the water and sediment of the sub-lakes, and the relative role of deterministic processes was stronger for sediment than water. Our study is the first to reveal the differences in the diazotrophic communities between the water and sediment in natural freshwater ecosystems and provides the fundamental scientific datasets for understanding the nitrogen fixation process in sub-lakes. [ABSTRACT FROM AUTHOR]

Kaliningrad region has a rich historical heritage, including several water sources with high iron content, known since the end of 19th century. They are rich in divalent iron, which is oxidized by bacterial communities. They include many different taxonomic groups of bacteria. In this paper, for the first time, the microbial communities of iron-bearing springs in the Kaliningrad region were profiled, and 6 samples were taken from four geographical locations during the study. The results of profiling revealed taxonomic groups belonging to phylum: Acidobacteriota, Desulfobacteriota, Cyanobacteriia, Proteobacteria, Nitrospirota, and among the predominant groups stands out a gamma-proteobacterium of the genus Gallionella. [ABSTRACT FROM AUTHOR]

Introduction: Cholesteatoma usually harbors a poly-microbial infection. As the diversity of bacterial pathogens in the Indian COM is unknown, we set out to identify the bacteria associated with cholesteatoma disease in different patients of North India using targeted metagenomic analysis of the 16 S rRNA gene. Methods: We recruited 15 patients of cholesteatomatous chronic otitis media (COM), who underwent surgical disease clearance. We divided these patients into four groups based on the four clinic-radiological stages categorized as per the EAONO/JOS joint consensus statement classification. Representative samples were extracted during the surgery and sent for bacterial culture and sensitivity and 16 S rRNA gene metagenomic analysis. Results: While 12 (80%) of the patients belonged to clinical Stage I/II; one patient had an extracranial complication (stage III) and two patients had an intracranial complication (stage IV). Our detailed bacterial metagenomics analyses showed that while phylum Proteobacteria was most abundant (reads up to ∼ 95%) in specimens from nine patients, phylum Firmicutes was most abundant (up to ∼ 80%) in specimens from four patients. Gamma (γ) Proteobacteria and Epsilon (ε) Proteobacteria were the most abundant class amongst Proteobacteria. Class Tissierellia stood out as the most abundant Firmicutes (40–60%), followed by Clostridia (20%) and Bacilli (10%). There was negligible difference in the bacterial profiles across all four clinical stages. Conclusion: Cholesteatoma is primarily associated with Proteobacteria and Firmicutes phyla, even in complicated disease. Further studies with a larger sample size are required to validate our findings. [ABSTRACT FROM AUTHOR]

The distinct microbiological and physicochemical characteristics of sheep milk enable the production of cheeses with unique organoleptic properties. The scenario of sheep cheeses in Brazil is still uncertain, lacking data and regulations. This study aims to characterize the diversity of bacterial groups with potential pathogenic and/or harmful properties to milk technology and correlate the presence of these bacteria with the physicochemical properties of sheep cheese. Additionally, it investigates the presence of virulence genes, resistance genes, and toxins in reference genomes. The main steps were (a) sample preparation and fractionation; (b) physicochemical analysis; (c) analysis of the free fatty acids profile by GC-FID; (d) analysis of the volatile compounds profile by GC-MS; (e) molecular analysis—Next Generation Sequencing of the 16S rRNA gene (V3-V4 region); and (f) in silico analysis—Genomics. A total of 1,061,392 sequences were identified, corresponding to 45 genera and 57 species. Of the total abundance, 95.7% were considered beneficial, while 3.9% were classified as bacteria with pathogenic potential (BPP) and/or bacteria harmful to milk technology (BHMT). Five phyla were identified: Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, and Fusobacteriota. The genera Acinetobacter, Pseudomonas, and Staphylococcus stood out in the BPP and BHMT groups, showing higher abundance. Alpha diversity of the cheese samples showed that the cheese origin significantly influences the richness, evenness, and abundance of bacterial species. Some physicochemical parameters, fatty acids, and volatile organic compounds showed a negative correlation with Staphylococcus. Reference genomes of two species exhibited a higher number of resistance and virulence genes. This reinforces the need to monitor bacteria considered of lesser relevance to prevent the transmission, through food, of potentially resistant and virulent pathogens. [ABSTRACT FROM AUTHOR]

A novel coupling process to replace the traditional multi-stage anammox process—sulfur autotrophic denitrification (SAD) coupled anaerobic ammonium oxidation (anammox) system was designed, which solved problems of nitrate produced in anammox process and low nitrate conversion rate caused by nitrite accumulation in SAD process. Different filter structures (SAD filter and anammox granular sludge) were investigated to further explore the excellent performance of the novel integrated reactor. The results of sequential batch experiments indicated that nitrite accumulation occurred during SAD, which inhibited the conversion of nitrate to dinitrogen gas. When SAD filter and anammox granular sludge were added to packed bed reactor simultaneously, the nitrate removal rate increased by 37.21% and effluent nitrite concentration decreased by 100% compared to that achieved using SAD. The stratified filter structure solved groove flow. Different proportion influence of SAD filter and anammox granular sludge on the stratified filter structure was evaluated. More suitable ratio of SAD filter to anammox granular sludge was 2:1. Proteobacteria (57.26%), Bacteroidetes (20.12%) and Chloroflexi (9.95%) were the main phyla. The dominant genera of denitrification functional bacteria were Thiobacillus (39.80%), Chlorobaculum (3.99%), norank_f_PHOs-HE36 (2.90%) and Ignavibacterium (2.64%). The dominant genus of anammox bacterium was Candidatus_Kuenenia (3.05%). [ABSTRACT FROM AUTHOR]

The impact of combined heat and drought stress was investigated in Arabidopsis thaliana and compared to individual stresses to reveal additive effects and interactions. A combination of plant metabolomics and root and rhizosphere bacterial metabarcoding were used to unravel effects at the plant holobiont level. Hierarchical cluster analysis of metabolomics signatures pointed out two main clusters, one including heat and combined heat and drought, and the second cluster that included the control and drought treatments. Overall, phenylpropanoids and nitrogen-containing compounds, hormones and amino acids showed the highest discriminant potential. A decrease in alpha-diversity of Bacteria was observed upon stress, with stress-dependent differences in bacterial microbiota composition. The shift in beta-diversity highlighted the pivotal enrichment of Proteobacteria, including Rhizobiales, Enterobacteriales and Azospirillales. The results corroborate the concept of stress interaction, where the combined heat and drought stress is not the mere combination of the single stresses. Intriguingly, multi-omics interpretations evidenced a good correlation between root metabolomics and root bacterial microbiota, indicating an orchestrated modulation of the whole holobiont.

To date, the association of potato tuber microbiota is poorly understood. In this study, the endophytic bacterial flora of seed potato tubers was identified and the diversity of healthy and unhealthy tubers was compared. Metagenomic DNA extracted from healthy and unhealthy samples of seed potato tubers was used for the analysis of microbial communities. Next generation sequencing of the ∼460 bp v3–v4 region of the 16S rRNA gene was carried out using the Illumina Miseq platform. The data were analysed using the Divisive Amplicon Denoising Algorithm 2 pipeline. Sequence analysis of the potato metagenome identified amplicon sequence variants (ASVs) assigned to 745 different taxa belonging to eight Phyla: Firmicutes (46.2%), Proteobacteria (36.9%), Bacteroidetes (1.8%), Actinobacteria (0.1%), Tenericutes (0.005%), Saccharibacteria (0.003%), Verrucomicrobiota (0.003%), and Acidobacteria (0.001%). In healthy seed potato tubers, 55–99% of ASVs belonged to Firmicutes, including Bacillus, Salinibacillus, Staphylococcus, Lysinibacillus, Paenibacillus, and Brevibacillus genera within the taxonomic order Bacillales. However, in the visually unhealthy tubers, only 0.5–3.9% of ASVs belonged to Firmicutes while 84.1–97% of ASVs belonged to Proteobacteria. This study highlights that diverse bacterial communities colonize potato tubers, which contributes to the understanding of plant–microbe interactions and underscores the significance of metagenomic approaches in agricultural research.

Violacein is a water-insoluble violet pigment produced by various Gram-negative bacteria. The compound and the bacteria that produce it have been gaining attention due to the antimicrobial and proposed antitumour properties of violacein and the possibility that strains producing it may have broad industrial uses. Bacteria that produce violacein have been isolated from diverse environments including fresh and ocean waters, glaciers, tropical soils, trees, fish and the skin of amphibians. We report here the isolation and characterization of six violacein-producing bacterial strains and three non-violacein-producing close relatives, each isolated from either an aquatic environment or moist food materials in northern California, USA. For each isolate, we characterized traditional phenotypes, generated and analysed draft genome sequences, and carried out multiple types of taxonomic, phylogenetic and phylogenomic analyses. Based on these analyses we assign putative identifications to the nine isolates, which include representatives of the genera Chromobacterium, Aquitalea, Iodobacter, Duganella, Massilia and Janthinobacterium. In addition, we discuss the utility of various metrics for taxonomic assignment in these groups including average nucleotide identity, whole genome phylogenetic analysis and extent of recent homologous recombination using the software program PopCOGenT.

Judicial Opinion 128 addresses nomenclatural issues related to the names of classes validly published under the International Code of Nomenclature of Prokaryotes. It is confirmed that the common ending -proteobacteria of some class names is not indicative of a joint taxonomic or phylogenetic placement; that the nomenclatural type of Mollicutes Edward and Freundt 1967 (Approved Lists 1980) is Mycoplasmatales Freundt 1955 (Approved Lists 1980); and that the placement of a name on the list of rejected names does not imply that another name with the same spelling but a distinct rank is also placed on that list. The names at the rank of class Anoxyphotobacteria (Gibbons and Murray 1978) Murray 1988, Archaeobacteria Murray 1988, Bacteria Haeckel 1894 (Approved Lists 1980), Firmibacteria Murray 1988, Microtatobiotes Philip 1956 (Approved Lists 1980), Oxyphotobacteria (ex Gibbons and Murray 1978) Murray 1988, Photobacteria Gibbons and Murray 1978 (Approved Lists 1980), Proteobacteria Stackebrandt et al. 1988, Schizomycetes Nägeli 1857 (Approved Lists 1980), Scotobacteria Gibbons and Murray 1978 (Approved Lists 1980) are placed on the list of rejected names. For three common nominative singular suffixes of genus names their genitive singular and nominative plural forms are confirmed: -bacter (-bacteris, -bacteres); -fex (-ficis, -fices); and -genes (-genis, -genes). The class names Aquificae Reysenbach 2002, Chrysiogenetes Garrity and Holt 2002, Chthonomonadetes Lee et al. 2011, Gemmatimonadetes Zhang et al. 2003, Opitutae Choo et al. 2007 and Verrucomicrobiae Hedlund et al. 1998 are orthographically corrected to Aquificia, Chrysiogenia, Chthonomonadia, Gemmatimonadia, Opitutia and Verrucomicrobiia, respectively.

Methane-oxidizing bacteria (MOB) is a group of planktonic microorganisms that use methane as their primary source of cellular energy. For tropical lakes in monsoon Asia, there is currently a knowledge gap on MOB community diversity and the factors influencing their abundance. Herewith, we present a preliminary assessment of the MOB communities in three maar lakes in tropical monsoon Asia using Catalyzed Reporter Deposition, Fluorescence In-Situ Hybridization (CARD-FISH), 16S rRNA amplicon sequencing, and pmoA gene sequencing. Correlation analysis between MOB abundances and lakes' physicochemical parameters following seasonal monsoon events were performed to explain observed spatial and temporal patterns in MOB diversity. The CARD-FISH analyses detected the three MOB types (I, II, and NC10) which aligned with the results from 16S rRNA amplicons and pmoA gene sequencing. Among community members based on 16S rRNA genes, Proteobacterial Type I MOB (e.g., Methylococcaceae and Methylomonadaceae), Proteobacterial Type II (Methylocystaceae), Verrucomicrobial (Methylacidiphilaceae), Methylomirabilota/NC10 (Methylomirabilaceae), and archaeal ANME-1a were found to be the dominant methane-oxidizers in three maar lakes. Analysis of microbial diversity and distribution revealed that the community compositions in Lake Yambo vary with the seasons and are more distinct during the stratified period. Temperature, DO, and pH were significantly and inversely linked with type I MOB and Methylomirabilota during stratification. Only MOB type I was influenced by monsoon changes. This research sought to establish a baseline for the diversity and ecology of planktonic MOB in tropical monsoon Asia to better comprehend their contribution to the CH4 cycle in tropical freshwater ecosystems. [ABSTRACT FROM AUTHOR]