Class Betaproteobacteria Research Articles

Microbiome analysis of saliva from oral squamous cell carcinoma (OSCC) patients and tobacco abusers with potential biomarkers for oral cancer screening

Oral squamous cell carcinoma (OSCC) is the most common type of oral cancer and accounts for about 95% of all head and neck cancers with high mortality, usually at a late stage. Dysbiosis in the oral microbiome can lead to chronic inflammatory responses and may predispose to the development and progression of OSCC. Tobacco abuse plays an essential role in oral microbiome dysregulation and OSCC pathogenesis. We used 16S rRNA gene amplicon next-generation sequencing to examine microbial signatures unique to saliva from OSCC patients, tobacco abusers (TA) and controls (n = 10 for each group) to elucidate oral microbiome changes associated with tobacco abuse and OSCC. Overall, the oral microbiome compositions of class Betaproteobacteria and Epsilonproteobacteria, order Neisseriales, Burkholderiales and Campylobacterales, family Burkholderiaceae and Campylobacteraceae and genera Campylobacter and Leptotrichia revealed significant differences among OSCC patients, TA and control. Our preliminary pilot study not only serves as a basis for future studies with large sample size but also gives an indication of microbiome-based potential non-invasive biomarkers for early screening and monitoring of oral carcinogenesis transition due to tobacco abuse.

Correlation between cognitive impairment and metabolic imbalance of gut microbiota in patients with schizophrenia.

The gut microbiome interacts with the central nervous system through the gut-brain axis, and this interaction involves neuronal, endocrine, and immune mechanisms, among others, which allow the microbiota to influence and respond to a variety of behavioral and mental conditions. To explore the correlation between cognitive impairment and gut microbiota imbalance in patients with schizophrenia. A total of 498 untreated patients with schizophrenia admitted to our hospital from July 2020 to July 2022 were selected as the case group, while 498 healthy volunteers who underwent physical examinations at our hospital during the same period were selected as a control group. Fluorescence in situ hybridization was employed to determine the total number of bacteria in the feces of the two groups. The cognitive function test package was used to assess the score of cognitive function in each dimension. Then, the relationship between gut microbiota and cognitive function was analyzed. There were statistically significant differences in the relative abundance of gut microbiota at both phylum and class levels between the case group and the control group. In addition, the scores of cognitive function, such as atten-tion/alertness and learning ability, were significantly lower in the case group than in the control group (all P < 0.05). The cognitive function was positively correlated with Actinomycetota, Bacteroidota, Euryarchaeota, Fusobacteria, Pseudomonadota, and Saccharibacteria, while negatively correlated with Bacillota, Tenericutes, and Verrucomicrobia at the phylum level. While at the class level, the cognitive function was positively correlated with Class Actinobacteria, Bacteroidia, Betaproteobacteria, Proteobacteria, Blastomycetes, and Gammaproteobacteria, while negatively correlated with Bacilli, Clostridia, Coriobacteriia, and Verrucomicrobiae. There is a relationship between the metabolic results of gut microbiota and cognitive function in patients with schizophrenia. When imbalances occur in the gut microbiota of patients, it leads to more severe cognitive impairment.

Sequence similarity network and protein structure prediction offer insights into the evolution of microbial pathways for ferrous iron oxidation.

Dissimilatory ferrous iron [Fe(II)] oxidation is a well-established microbial energy generation strategy. This study aims to comprehensively investigate the distribution and evolution of recognized Fe(II) oxidation pathways through comparative analysis. Interestingly, we have discovered a wide range of taxonomic groups that harbor homologs to known Fe(II) oxidation proteins. The presence of these homologs among phylogenetically distant lineages and their frequent association with mobile genetic elements strongly suggest horizontal gene transfer events involving Fe(II) oxidation proteins, such as the rus operon of Acidithiobacillus and Cyc572 from Leptospirillum lineages belonging to classes Gammaproteobacteria and Betaproteobacteria often present at the hub positions of the protein sequence similarity networks from which homologs of other taxa are derived. In addition, RoseTTAFold predictions have provided valuable insights into the structural characteristics of previously unknown Fe(II) oxidation components. Despite having limited sequence identity, a significant number of acknowledged proteins involved in different Fe(II) oxidation pathways exhibit close structural similarities, including Cyc2 and Cyc572. Collectively, this study significantly enhances our understanding of the distribution and evolution of microbial ferrous iron oxidation pathways. IMPORTANCE Microbial Fe(II) oxidation is a crucial process that harnesses and converts the energy available in Fe, contributing significantly to global element cycling. However, there are still many aspects of this process that remain unexplored. In this study, we utilized a combination of comparative genomics, sequence similarity network analysis, and artificial intelligence-driven structure modeling methods to address the lack of structural information on Fe(II) oxidation proteins and offer a comprehensive perspective on the evolution of Fe(II) oxidation pathways. Our findings suggest that several microbial Fe(II) oxidation pathways currently known may have originated within classes Gammaproteobacteria and Betaproteobacteria.

Silvimonas soli sp. nov., a new member of Chromobacteriaceae isolated from soil in Norrbyskär island, Sweden.

A novel bacterial species is described that was isolated from the soil of Norrbyskär island (Sweden). This Gram-negative, facultatively anaerobic and motile rod, designated 17-6T, was classified in the family Chromobacteriaceae, class Betaproteobacteria, and further characterized by a polyphasic approach. Comparative 16S rRNA gene analysis revealed the potential species novelty of the strain, with Silvimonas terrae (98.20 % similarity) and Silvimonas amylolytica (98.13 %) being its closest type strains. The phylogenetic novelty of the isolate at the level of species was confirmed using phylogenetic analyses based on the whole genome: average nucleotide identity values ranged from 79 to 81 %, average amino acid identity values from 75 to 81 % and percentage of conserved proteins values from 69-81 % with the members of genera Silvimonas and Amantichitinum. On the basis of phenotypic, phylogenetic, functional and genotypic analyses, we propose the isolate as the type strain of a novel species within the genus Silvimonas with the designation Silvimonas soli 17-6T (=DSM 115342T=CCM 9308T).

Betaproteobacteria are a key component of surface water biofilters that maintain sustained manganese removal in response to fluctuations in influent water temperature

The health risks associated with manganese (Mn) in drinking water, and an improved understanding of Mn accumulation within, and subsequent release from, distribution systems, have increased the need for robust, sustainable treatment options to minimize Mn concentrations in finished water. Biofiltration is an established and effective method to remove Mn in groundwater however, Mn removal in surface water biofilters is an emerging treatment process that has not been extensively studied. Seasonal variations in water temperature can present an operational challenge for surface water biofilters which may see reduced Mn removal under colder conditions. This study examined the microbiomes of surface water biofilters at three utilities (ACWD WTP, WTP B, and WTP D) which all experienced similar seasonal fluctuations in influent water temperature. High Mn removal was observed at the ACWD WTP for much of the year, but Mn removal decreased with a concurrent decrease in the influent water temperature (58% ± 22%). In contrast, both WTP B and WTP D achieved year-round Mn removal (84% ± 5% and 93% ± 8% respectively). Marker gene (16S rRNA) sequencing analysis of the biofilter microbiomes identified a high abundance of Betaproteobacteria in WTP B and WTP D (37% ± 12% and 21% ± 3% respectively), but a low abundance of Betaproteobacteria in the ACWD WTP (2% ± 2%). The microbiomes of new bench-scale biofilters, in operation at the ACWD WTP, were also investigated. The abundance of Betaproteobacteria was significantly greater (p < 0.05) after the biofilters had acclimated than before acclimation, and differential abundance analysis identified 6 genera within the Betaproteobacteria class were enriched in the acclimated microbiome. Additionally, the acclimated biofilters were able to maintain high Mn removal performance (87% ± 10%) when the influent water temperature decreased to 10 °C or less. Further analysis of previously published studies found the abundance of Betaproteobacteria was also significantly greater (p < 0.001) in biofilters with sustained Mn removal than in biofilters which did not treat for Mn as a contaminant, despite differences in design scale, source water, and media type. Microbiome network analysis identified multiple co-occurrence relationships between Betaproteobacteria and Mn oxidizing bacteria in the WTP B and WTP D biofilters, suggesting indirect contributions by Betaproteobacteria to biological Mn oxidation. These co-occurrence relationships were not present in the full-scale ACWD WTP microbiome. Whether the role of Betaproteobacteria in biological Mn oxidation is direct, indirect, or a combination of both, they are consistently present at a high abundance in both groundwater and surface water biofilters with sustained Mn removal, and their absence may contribute to the seasonal fluctuations in Mn removal observed at the ACWD WTP. This new insight to Betaproteobacteria and their role in Mn biofiltration could contribute to water innovation and design that would improve the reliability of Mn removal.

Bioprospection of the bacterial β-myrcene-biotransforming trait in the rhizosphere

The biocatalysis of β-myrcene into value-added compounds, with enhanced organoleptic/therapeutic properties, may be performed by resorting to specialized enzymatic machinery of β-myrcene-biotransforming bacteria. Few β-myrcene-biotransforming bacteria have been studied, limiting the diversity of genetic modules/catabolic pathways available for biotechnological research. In our model Pseudomonas sp. strain M1, the β-myrcene catabolic core-code was identified in a 28-kb genomic island (GI). The lack of close homologs of this β-myrcene-associated genetic code prompted a bioprospection of cork oak and eucalyptus rhizospheres, from 4 geographic locations in Portugal, to evaluate the environmental diversity and dissemination of the β-myrcene-biotransforming genetic trait (Myr+).Soil microbiomes were enriched in β-myrcene-supplemented cultures, from which β-myrcene-biotransforming bacteria were isolated, belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia classes. From a panel of representative Myr+ isolates that included 7 bacterial genera, the production of β-myrcene derivatives previously reported in strain M1 was detected in Pseudomonas spp., Cupriavidus sp., Sphingobacterium sp., and Variovorax sp. A comparative genomics analysis against the genome of strain M1 found the M1-GI code in 11 new Pseudomonas genomes. Full nucleotide conservation of the β-myrcene core-code was observed throughout a 76-kb locus in strain M1 and all 11 Pseudomonas spp., resembling the structure of an integrative and conjugative element (ICE), despite being isolated from different niches.Furthermore, the characterization of isolates not harboring the Myr+-related 76-kb locus suggested that they may biotransform β-myrcene via alternative catabolic loci, being thereby a novel source of enzymes and biomolecule catalogue for biotechnological exploitation.Key points• The isolation of 150 Myr+bacteria hints the ubiquity of such trait in the rhizosphere.• The Myr+trait is spread across different bacterial taxonomic classes.• The core-code for the Myr+trait was detected in a novel ICE, only found in Pseudomonas spp.

Hexameric structure of the flagellar master regulator FlhDC from Cupriavidus necator and its interaction with flagellar promoter DNA

Bacterial flagella are assembled with ∼30 different proteins in a defined order via diverse regulatory systems. In gram-negative bacteria from the Gammaproteobacteria and Betaproteobacteria classes, the transcription of flagellar genes is strictly controlled by the master regulator FlhDC. In Gammaproteobacteria species, the FlhDC complex has been shown to activate flagellar expression by directly interacting with the promoter region in flagellar genes. To obtain the DNA-binding mechanism of FlhDC and determine the conserved and distinct structural features of Betaproteobacteria and Gammaproteobacteria FlhDCs that are necessary for their functions, we determined the crystal structure of Betaproteobacteria Cupriavidus necator FlhDC (cnFlhDC) and biochemically analyzed its DNA-binding capacity. cnFlhDC specifically recognized the promoter DNA of the class II flagellar genes flgB and flhB. cnFlhDC adopts a ring-like heterohexameric structure (cnFlhD4C2) and harbors two Zn-Cys clusters, as observed for Gammaproteobacteria Escherichia coli FlhDC (ecFlhDC). The cnFlhDC structure exhibits positively charged surfaces across two FlhDC subunits as a putative DNA-binding site. Noticeably, the positive patch of cnFlhDC is continuous, in contrast to the separated patches of ecFlhDC. Moreover, the ternary intersection of cnFlhD4C2 behind the Zn-Cys cluster forms a unique protruding neutral structure, which is replaced with a charged cavity in the ecFlhDC structure.

Phylogenetic analyses of Candidatus Branchiomonas cysticola refine the taxonomic classification of Betaproteobacteria associated with epitheliocystis in fish

Candidatus Branchiomonas cysticola is recognized as the most prevalent bacterial agent causing epitheliocystis in Atlantic salmon (Salmo salar). Based on its partial 16S rRNA sequence, the bacterium has previously been found to be a member of Burkholderiales in the class Betaproteobacteria. Multilocus Sequence Analysis (MLSA) of the bacterium and 60 type strains of Betaproteobacteria using newly identified housekeeping genes (dnaK, rpoC, and fusA) and ribosomal subunit sequences (16S and 23S), instead supported the bacterium’s affiliation to Nitrosomodales. Taxonomic rank normalization by Relative Evolutionary Divergence (RED) showed the phylogenetic distinction between Cand. B. cysticola and its closest related type strain to be at the family level. A novel bacterial family named Branchiomonaceae has thus been proposed to include a monophyletic clade of Betaproteobacteria exclusively associated with epitheliocystis in fish.

Glycoside Hydrolases of the Obligate Methanotroph &lt;i&gt;Methyloferula stellata&lt;/i&gt;: an Unusual Evolutionary Strategy not Involving Distant Lateral Transfers

Abstract—The genome of the obligately methanotrophic bacterium Methyloferula stellata AR4 encodes thirty glycoside hydrolases. The closest homologues for most of these proteins belong to other members of the class Alphaproteobacteria. Two exceptions are represented by the genes encoding glycoside hydrolases of the families GH39 and GH65, which presumably appeared in M. stellata AR4 due to the lateral transfer from distantly related bacteria. This work was devoted to the study of the evolutionary history of these two genes. In the case of a member of the GH65 family of glycoside hydrolases, this scenario was not confirmed. Kojibiose phosphorylase encoded by this gene is common among Alphaproteobacteria. The suggested lateral transfer of the corresponding gene had an opposite direction, into one of the evolutionary lineages of the class Betaproteobacteria. The potential glycoside hydrolase of the GH39 family was shown to be the only one which gene is not of proteobacterial origin. The role of lateral transfers in the evolution of glycoside hydrolases and their homologues in methanotrophs and other bacteria is discussed.

A Nitrate-Transforming Bacterial Community Dominates in the Miscanthus Rhizosphere on Nitrogen-Deficient Volcanic Deposits of Miyake-jima.

The perennial gramineous grass Miscanthus condensatus functions as a major pioneer plant in colonizing acidic volcanic deposits on Miyake-jima, Japan, despite a lack of nitrogen nutrients. The nitrogen cycle in the rhizosphere is important for the vigorous growth of M. condensatus in this unfavorable environment. In the present study, we identified the nitrogen-cycling bacterial community in the M. condensatus rhizosphere on these volcanic deposits using a combination of metagenomics and culture-based analyses. Our results showed a large number of functional genes related to denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in the rhizosphere, indicating that nitrate-transforming bacteria dominated the rhizosphere biome. Furthermore, nitrite reductase genes (i.e., nirK and nirS) related to the denitrification and those genes related to DNRA (i.e., nirB and nrfA) were mainly annotated to the classes Alpha-proteobacteria, Beta-proteobacteria, and Gamma-proteobacteria. A total of 304 nitrate-succinate-stimulated isolates were obtained from the M. condensatus rhizosphere and were classified into 34 operational taxonomic units according to amplified 16S rRNA gene restriction fragment pattern analysis. Additionally, two strains belonging to the genus Cupriavidus in the class Beta-proteobacteria showed a high in vitro denitrifying activity; however, metagenomic results indicated that the DNRA-related rhizobacteria appeared to take a major role in the nitrogen cycle of the M. condensatus rhizosphere in recent Miyake-jima volcanic deposits. This study elucidates the association between the Miscanthus rhizosphere and the nitrate-reducing bacterial community on newly placed volcanic deposits, which furthers our understanding of the transformation of nitrogen nutrition involved in the early development of vegetation.

Soybean extracts can improve plant development

Microbial biodiversity of an environment can contribute to plant growth and increase crop yield. Plant extracts from soybean (Glycine max (L.) Merrill) were investigated on soybean plants grown after inoculation with these extracts. Soil samples were collected from two important Brazilian soybean-growing regions to produce the extracts used in the experiments. The extracts were produced with material collected from aboveground biomass and rhizosphere of soybean plants cultivated in a controlled greenhouse (phase 1). The extracts produced in phase 1 were applied in a sequential experiment (phase 2). Phase 2 was conducted to examine the plant microbiome after the microbial alteration process in the greenhouse through seed inoculation with the extracts produced previously. Samples of aboveground biomass were collected to determine root dry matter and crop yield. Bacterial 16S rRNA sequences were processed to determine the final microbial content of soybean. The inoculated treatments had lower species diversity; however, the phyla Firmicutes and Bacteroidetes were more abundant in the treatments than in the non-inoculated treatment. The soybean plant stem in the inoculated treatment also had a positive response to enrichment of the bacterial classes Betaproteobacteria, Bacilli and Flavobacteria. Inoculation affected the microbial composition of soybean plants. The alteration of microbiome changes revealed differences for crop yield between the inoculated and non-inoculated treatments, with up to 93.5 % higher crop yields per plant according to the extract applied.

Multi-omics analysis on seasonal variations of the biofilm microbial community in a full-scale pre-denitrification biofilter.

The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.

Genetically proxied gut microbiota, gut metabolites with risk of epilepsy and the subtypes: A bi-directional Mendelian randomization study.

An increasing number of observational studies have revealed an association among the gut microbiota, gut metabolites, and epilepsy. However, this association is easily influenced by confounders such as diet, and the causality of this association remains obscure. Aiming to explore the causal relationship and ascertain specific gut microbe taxa for epilepsy, we conducted a bi-directional Mendelian randomization (MR) study based on the genome-wide association study (GWAS) data of epilepsy from the International League Against Epilepsy, with the gut microbiota GWAS results from MiBioGen, and summary-level GWAS data of gut microbiota-dependent metabolites trimethylamine N-oxide and its predecessors. Nine phyla, 15 classes, 19 orders, 30 families, and 96 genera were analyzed. A suggestive association of host-genetic-driven increase in family Veillonellaceae with a higher risk of childhood absence epilepsy (odds ratio [OR]: 1.033, confidential interval [CI]: 1.015-1.051, P IVW = 0.0003), class Melainabacteria with a lower risk of generalized epilepsy with tonic-clonic seizures (OR = 0.986, CI = 0.979-0.994, P IVW = 0.0002), class Betaproteobacteria (OR = 0.958, CI = 0.937-0.979, P IVW = 0.0001), and order Burkholderiales (OR = 0.960, CI = 0.937-0.984, P IVW = 0.0010) with a lower risk of juvenile myoclonic epilepsy were identified after multiple-testing correction. Our sensitivity analysis revealed no evidence of pleiotropy, reverse causality, weak instrument bias, or heterogeneity. This is the first MR analysis to explore the potential causal relationship among the gut microbiota, metabolites, and epilepsy. Four gut microbiota features (two class levels, one order level, and one family level) were identified as potential interventional targets for patients with childhood absence epilepsy, generalized epilepsy with tonic-clonic seizures, and juvenile myoclonic epilepsy. Previous associations in numerous observational studies may had been interfered by confounders. More rigorous studies were needed to ascertain the relationship among the gut microbiota, metabolites, and epilepsy.

The lung microbiome, peripheral gene expression, and recurrence-free survival after resection of stage II non-small cell lung cancer

BackgroundCancer recurrence after tumor resection in early-stage non-small cell lung cancer (NSCLC) is common, yet difficult to predict. The lung microbiota and systemic immunity may be important modulators of risk for lung cancer recurrence, yet biomarkers from the lung microbiome and peripheral immune environment are understudied. Such markers may hold promise for prediction as well as improved etiologic understanding of lung cancer recurrence.MethodsIn tumor and distant normal lung samples from 46 stage II NSCLC patients with curative resection (39 tumor samples, 41 normal lung samples), we conducted 16S rRNA gene sequencing. We also measured peripheral blood immune gene expression with nanoString®. We examined associations of lung microbiota and peripheral gene expression with recurrence-free survival (RFS) and disease-free survival (DFS) using 500 × 10-fold cross-validated elastic-net penalized Cox regression, and examined predictive accuracy using time-dependent receiver operating characteristic (ROC) curves.ResultsOver a median of 4.8 years of follow-up (range 0.2–12.2 years), 43% of patients experienced a recurrence, and 50% died. In normal lung tissue, a higher abundance of classes Bacteroidia and Clostridia, and orders Bacteroidales and Clostridiales, were associated with worse RFS, while a higher abundance of classes Alphaproteobacteria and Betaproteobacteria, and orders Burkholderiales and Neisseriales, were associated with better RFS. In tumor tissue, a higher abundance of orders Actinomycetales and Pseudomonadales were associated with worse DFS. Among these taxa, normal lung Clostridiales and Bacteroidales were also related to worse survival in a previous small pilot study and an additional independent validation cohort. In peripheral blood, higher expression of genes TAP1, TAPBP, CSF2RB, and IFITM2 were associated with better DFS. Analysis of ROC curves revealed that lung microbiome and peripheral gene expression biomarkers provided significant additional recurrence risk discrimination over standard demographic and clinical covariates, with microbiome biomarkers contributing more to short-term (1-year) prediction and gene biomarkers contributing to longer-term (2–5-year) prediction.ConclusionsWe identified compelling biomarkers in under-explored data types, the lung microbiome, and peripheral blood gene expression, which may improve risk prediction of recurrence in early-stage NSCLC patients. These findings will require validation in a larger cohort.

Effects of combined aerobic and resistance training on gut microbiota and cardiovascular risk factors in physically active elderly women: A randomized controlled trial.

Background: Exercise can modulate gut microbiota and lower the risk of cardiovascular disease (CVD). However, the association between exercise-induced changes in gut microbiota and CVD risk have not been investigated. Objective: This study determined the effects of exercise training on CVD risk and gut microbiota in physically active elderly women and whether exercise-induced gut microbiota changes were associated with CVD risk. Methods: An 8-week randomized controlled trial was conducted with 14 elderly women assigned to exercise group (n = 8) or control group (n = 6). Physical function, sarcopenic obesity, and metabolic syndrome were evaluated as components of CVD risk. Gut microbiota composition was determined using 16S rRNA gene sequencing. Repeated-measures analysis of variance was used to examine intra-group and inter-group differences. Results: A significant group × time interaction was observed for chair sit-and-reach (F = 8.262, p = 0.014), single-leg standing with eyes closed (F = 7.340, p = 0.019), waist circumference (F = 6.254, p = 0.028), and body fat mass (F = 12.263, p = 0.004), for which the exercise group showed improved trends. The exercise group exhibited significant improvements in skeletal muscle mass (p = 0.041) and fasting blood glucose (p = 0.017). Regarding gut microbiota, a significant interaction was observed for the class Betaproteobacteria (F = 6.822, p = 0.023) and genus Holdemania (F = 4.852, p = 0.048). Conclusion: The 8-week exercise training improved physical function, lowered CVD risk, and modulated relative abundance of gut microbiota associated with CVD in physically active elderly women.

Temperature modulation alters the gut and skin microbial profiles of chum salmon (Oncorhynchus keta)

Fish-associated microbiota are an integral part to the health of the host fish. The ongoing climate changes including global warming of water may disrupt the composition and diversity of host-microbiota, and subsequently, destabilize the fish homeostasis. Since the knowledge on temperature-sensitive marine fish and environmental bacteria is scarce, we investigated the effects of rearing temperatures on community structure, diversity and assembly process of bacteria on chum salmon (Oncorhynchus keta), which is a temperate salmon species found in the Pacific. Over the course of two weeks, laboratory-raised chum salmon were exposed to three temperatures: high (18°C), low (8°C) and, control (13°C). Their feces, cutaneous mucus, and surrounding water were sampled for community structure analysis based on 16S rRNA gene amplicon sequencing. Temperature changes from the control level triggered significant dysbiosis in the fecal and skin mucus microbiota. In particular, Vibrio and Tenacibaculum sequence variants were highly abundant at high and low temperatures, respectively, and the opportunistic growth of these pathogenic species may impede host immunity. Two temperature-specific taxonomic microbial biomarkers, the class Betaproteobacteria and the genus Flavobacterium were identified at both high and low temperatures. An analysis of bacterial community assembly processes revealed that environmental selection significantly affected the gut microbial community assembly, while the assembly process of the skin microbiota was stochastic. Our study elucidated the potential crisis of fish health when the equilibrium of the cutaneous and intestinal microbiota was disrupted by temperature changes. Our data will be a valuable tool to better understand the effects of climate change, a very pressing and important challenge now and in the future, on the fish microbiota and its homeostasis.

Phosphorus Removal from Aerobic Granular Sludge: Proliferation of Polyphosphate-Accumulating Organisms (PAOs) under Different Feeding Strategies

Aerobic granular sludge (AGS) is known for high phosphorus removal from wastewaters, and phosphorus can be recovered from high phosphorus-containing waste sludge granules. This study aimed at determining the feeding strategy that provides the best performance in terms of the proliferation of polyphosphate-accumulating organisms (PAOs) and phosphorus removal. Using three AGS bioreactors, this study compared phosphorus removal and the proliferation dynamics of PAOs under three different feeding strategies: anaerobic slow feeding (R1), pulse feeding + anaerobic mixing (R2), and pulse feeding (R3). Results indicate that R1 and R2 achieved significantly higher phosphorus removal (97.6 ± 3% for R1 and 98.3 ± 1% for R2) than R3 (55 ± 11%). The anaerobic slow feeding procedure (R1) achieved the highest specific phosphorus release rate (SPRR) and specific phosphorus uptake rate (SPUR) as compared to the other two feeding conditions. 16S ribosomal ribonucleic acid (rRNA) gene sequencing assay of the microbial community for the three feeding strategies indicated that although the feeding strategy impacted reactor performance, it did not significantly alter the microbial community. The bacteria community composition maintained a similar degree of diversity. Proteobacteria, Bacteroidetes, and Verrucomicrobia were the dominant bacterial phyla in the system. Dominant PAOs were from the class Betaproteobacteria and the genera Paracoccus and Thauera. Glycogen-accumulating organisms were significantly inhibited while other less-known bacteria such as Wandonia and Hyphomonas were observed in all three reactors.

Global genomic and proteomic analysis indicates co-evolution of Neisseria species and with their human host

Neisseria, a genus from the beta-proteobacteria class, is of potential clinical importance. This genus contains both pathogenic and commensal strains. Gonorrhea and meningitis are two major diseasescaused by pathogens belonging to this genus. With the increased use of antimicrobial agents against these pathogens they have evolved the antimicrobial resistance capacity making these diseases nearly untreatable. The set of anti-bacterial resistance genes (resistome) and genes associated with signal processing (secretomes) are crucial for the host-microbial interaction. With the virtue of whole-genome sequences and computational biology, it is now possible to study the genomic and proteomic riddles ofNeisseriaalong with their comprehensive evolutionary and metabolic profiling. We have studied relative synonymous codon usage, amino acid usage, reverse ecology, comparative genomics, evolutionary analysis andpathogen-host (Neisseria-human) interaction through bioinformatics analysis. Our analysis revealed the co-evolution ofNeisseriagenomes with the human host. Moreover, the co-occurrence ofNeisseriaand humans has been supported through reverse ecology analysis. A differential pattern of the evolutionary rate of resistomes and secretomes was evident among the pathogenic and commensal strains. Comparative genomics supported the presence of virulent genes in both pathogenic and commensal strains of the select genus. Our analysis also indicated a transition from commensal to pathogenicNeisseriastrains through the long run of evolution.

Bacterioplankton community indicators for seasonal variation in a fragmented subtropical river.

In this study, spatiotemporal investigations were conducted along five cascade dams in the main channel of the North River of China during 2019 to explore bacterioplankton community indicators of water environments in a fragmented, highly regulated river. Bacterioplankton communities were good bioindicators of temporal variation in river environments, especially when considering the bacterial class level. Specifically, the most dominant bacterial classes (Gammaproteobacteria, Oxyphotobacteria, and Actinobacteria) and sub-dominant bacterial classes (Bacteroidia, Betaproteobacteria, and Acidimicrobiia) exhibited obvious temporal variation. Rainfall, water temperature (WT), water transparency (SD), and pH were all highly associated with temporal variation. In contrast, bacterioplankton indicators of spatial variation were limited to individual dominant bacterial classes for individual study periods, while rainfall, total phosphorus (TP), and pH were also associated with spatial variation. Clustering of bacterioplankton community compositions revealed that temporal differences were much stronger than spatial differences, which is consistent with most environmental parameters exhibiting obvious temporal differences, but minimal spatial differences. A possible reason for these observations could be that river fragmentation caused by cascade dams weakened spatial differences in communities, with WT, rainfall, and river runoff playing key roles in these patterns. In conclusion, bacterioplankton communities were good bioindicators of water environments in the fragmented river ecosystem of this study and their temporal variation was more apparent than their spatial variation.

Dimethoate residues in Pakistan and mitigation strategies through microbial degradation: a review.

Organophosphate pesticides (OPs) are used extensively for crop protection worldwide due to their high water solubility and relatively low persistence in the environment compared to other pesticides, such as organochlorines. Dimethoate is a broad-spectrum insecticide that belongs to the thio-organophosphate group of OPs. It is applied to cash crops, animal farms, and houses. It has been used in Pakistan since the 1960s, either alone or in a mixture with other OPs or pyrethroids. However, the uncontrolled use of this pesticide has resulted in residual accumulation in water, soil, and tissues of plants via the food chain, causing toxic effects. This review article has compiled and analyzed data reported in the literature between 1998 and 2021 regarding dimethoate residues and their microbial bioremediation. Different microorganisms such as bacteria, fungi, and algae have shown potential for bioremediation. However, an extensive role of bacteria has been observed compared to other microorganisms. Twenty bacterial, three fungal, and one algal genus with potential for the remediation of dimethoate have been assessed. Active bacterial biodegraders belong to four classes (i) alpha-proteobacteria, (ii) gamma-proteobacteria, (iii) beta-proteobacteria, and (iv) actinobacteria and flavobacteria. Microorganisms, especially bacterial species, are a sustainable technology for dimethoate bioremediation from environmental samples. Yet, new microbial species or consortia should be explored.