Pairs Of Sequences Research Articles

Equipment layout modeling method for forging lines based on equipment profile layering method

Forging equipment is equipped with an access platform with a size that significantly differs from that of the equipment body, so modeling methods such as envelopes and sequence pairs cannot be used to accurately describe the equipment or layout. In this paper, we propose a profile layering method for forging equipment, and establish a model of production line layout by setting a layering level using the Cartesian coordinate system, so as to lay a foundation for the subsequent research on interference detection, layout optimization and trajectory planning for production lines.

Based on point merge for paired approach sequencing on closely spaced parallel runways

Based on point merge for paired approach sequencing on closely spaced parallel runways

Differentiating patients with obstructive sleep apnea from healthy controls based on heart rate-blood pressure coupling quantified by entropy-based indices.

We introduce an entropy-based classification method for pairs of sequences (ECPS) for quantifying mutual dependencies in heart rate and beat-to-beat blood pressure recordings. The purpose of the method is to build a classifier for data in which each item consists of two intertwined data series taken for each subject. The method is based on ordinal patterns and uses entropy-like indices. Machine learning is used to select a subset of indices most suitable for our classification problem in order to build an optimal yet simple model for distinguishing between patients suffering from obstructive sleep apnea and a control group.

Stereo vision-based measurement of wave evolution around square column in laboratory

The spatial-temporal measurement of complex wave evolution is significant in studying wave-structure interactions. Current methods, such as that using wave probes, have shown limitations in measuring the wave evolution around structures in laboratories. In this study, an improved stereo imaging method is proposed for measuring the wave evolution around a fixed structure. Regular wave tests were conducted on a fixed surface-piercing square column in a wave flume to validate the reliability and accuracy of the proposed method. A flexible marker-net made of foam particles was arranged around the column to provide Lambertian features for the water surface. Two synchronized stereo imaging systems covered all the surrounding areas of the column and provided stereo pair sequences for wave evolution. Subsequently, image segmentation techniques were used to mask the low-confidence disparities in stereo matching, and finally, three-dimensional (3D) wave surfaces were reconstructed in the time sequence. The time histories of the wave elevations at particular locations were extracted and agreed well with the measurements of wave probes with an average bias of 2.4 %. Subsequently, the reconstructed 3D wave field was sliced, exhibiting the instantaneous profiles that agreed with the measurements of wave probes. Moreover, the wave run-up height ratios were consistent with those of a previous study, thereby verifying the method's accuracy from the perspective of spatial evolution. The results demonstrated that the proposed method was capable of precisely measuring the spatial-temporal evolution of the wave field around the square column and displayed potential for application in more studies on wave-structure interactions.

Prospective, Cell-Free Circulating Tumor DNA (ctDNA) Profiling in Locally Advanced Lung Cancer Treated with Chemoradiation

Liquid biopsy for cell-free circulating tumor DNA (ctDNA) allows for non-invasive, comprehensive genomic profiling. We explored the utility prospective liquid biopsy for (ctDNA) in among non-small cell lung cancer (NSCLC) patients treated with definitive chemoradiation. This prospective clinical cohort consists of unresectable, locally advanced NSCLC patients who had liquid biopsy testing prior to initiation of cancer therapy. Liquid biopsy testing was performed using a next-generation sequencing assay (MSK-ACCESS) which includes 129 genes and paired white blood cell sequencing. An FDA-recognized database (OncoKB) was utilized to classify alterations associated with radiation resistance (including KEAP1, NFE2L2, STK11, and PIK3CA) and radiation sensitivity (including ATM, ATR, BRCA1/2, ARID1A, MLH1 and other DNA Damage Repair Pathway alterations). We evaluated progression-free survival (PFS) from the completion of chemoradiation using the Log-rank test. Among 25 patients with prospective ctDNA testing prior to therapy initiation, 17 patients had stage III disease (68%), 8 patients had stage II disease (32%), 18 patients had adenocarcinoma (72%), 7 patients had squamous cell carcinoma (28%), and 23 (92%) were former or current smokers. The median radiation dose was 60 Gy in 30 fractions (range: 55 to 66 Gy in 20 to 33 fractions). 76% of patients (n = 18) had one or more alterations detected (median: 3 alterations, range: 1 - 8) including genomic markers of radiation response in 2 patients in BRCA1/2 (n = 2) and radiation resistance in 1 patient in KEAP1. The most common driver alteration detected was KRAS in 24% of the cohort (n = 6). Among patients with baseline detectable ctDNA, the median PFS was 21.3 months and was not reached among patients without baseline ctDNA detection (HR 4.54, p = 0.04). Using an institutional assay, the presence of baseline cell-free ctDNA appeared prognostic in patients with unresectable, locally advanced NSCLC treated with definitive chemoradiation. We also detected driver alterations and potential markers of radiation resistance and response using ctDNA testing. Prospective cell-free ctDNA profiling may offer pathways to therapy personalization among patients with locally advanced unresectable lung cancer.

MSI-XGNN: an explainable GNN computational framework integrating transcription- and methylation-level biomarkers for microsatellite instability detection.

Microsatellite instability (MSI) is a hypermutator phenotype caused by DNA mismatch repair deficiency. MSI has been reported in various human cancers, particularly colorectal, gastric and endometrial cancers. MSI is a promising biomarker for cancer prognosis and immune checkpoint blockade immunotherapy. Several computational methods have been developed for MSI detection using DNA- or RNA-based approaches based on next-generation sequencing. Epigenetic mechanisms, such as DNA methylation, regulate gene expression and play critical roles in the development and progression of cancer. We here developed MSI-XGNN, a new computational framework for predicting MSI status using bulk RNA-sequencing and DNA methylation data. MSI-XGNN is an explainable deep learning model that combines a graph neural network (GNN) model to extract features from the gene-methylation probe network with a CatBoost model to classify MSI status. MSI-XGNN, which requires tumor-only samples, exhibited comparable performance with two well-known methods that require tumor-normal paired sequencing data, MSIsensor and MANTIS and better performance than several other tools. MSI-XGNN also showed good generalizability on independent validation datasets. MSI-XGNN identified six MSI markers consisting of four methylation probes (EPM2AIP1|MLH1:cg14598950, EPM2AIP1|MLH1:cg27331401, LNP1:cg05428436 and TSC22D2:cg15048832) and two genes (RPL22L1 and MSH4) constituting the optimal feature subset. All six markers were significantly associated with beneficial tumor microenvironment characteristics for immunotherapy, such as tumor mutation burden, neoantigens and immune checkpoint molecules such as programmed cell death-1 and cytotoxic T-lymphocyte antigen-4. Overall, our study provides a powerful and explainable deep learning model for predicting MSI status and identifying MSI markers that can potentially be used for clinical MSI evaluation.

Natural restoration exhibits better soil bacterial network complexity and stability than artificial restoration on the Loess Plateau, China

Natural restoration (NR, e.g., secondary succession) and artificial restoration (AR, e.g., afforestation) are key approaches for rehabilitating degraded land; however, a comparative assessment of microbial network between these approaches is lacking. We compared bacterial networks under NR and AR in two different watersheds on the Loess Plateau. Our findings revealed significantly heightened network complexity under NR compared to AR, including metrics such as node, edge, modularity, degree, centrality, and keystone nodes. NR's network robustness exceeded AR by 19.45–35.9% and 7.79–17.74% in the two watersheds, aligning with the ecological principle that complexity begets stability. The significantly higher negative/positive cohesion and natural connectivity under NR also support its better network stability than AR. Integrated analysis of paired sequencing data from five Loess Plateau studies conducted on the Loess Plateau further confirmed the higher complexity and stability of bacterial networks under NR. Further analysis unveiled “biological interactions” as primary drivers of bacterial co-occurrence (on average 84.21% of links), surpassing the influence of environmental filtering (5.17%) or dispersal limitation (4.2%). Importantly, networked communities under NR exhibited generally stronger linkages with various ecosystem function than AR. Overall, our study provides insights into vegetation restoration strategies from the perspective of microbial network, underscoring natural regeneration's potential as a superior remedy for degraded-land restoration.

Germline pathogenic variants in neuroblastoma patients are enriched in BARD1 and predict worse survival.

Neuroblastoma is an embryonal cancer of the developing sympathetic nervous system. The genetic contribution of rare pathogenic or likely pathogenic germline variants in patients without a family history remains unclear. Germline DNA sequencing was performed on 786 neuroblastoma patients. The frequency of rare cancer predisposition gene pathogenic or likely pathogenic variants in patients was compared with 2 cancer-free control cohorts. Matched tumor DNA sequencing was evaluated for second hits, and germline DNA array data from 5585 neuroblastoma patients and 23 505 cancer-free control children were analyzed to identify rare germline copy number variants. Patients with germline pathogenic or likely pathogenic variants were compared with those without to test for association with clinical characteristics, tumor features, and survival. We observed 116 pathogenic or likely pathogenic variants involving 13.9% (109 of 786) of neuroblastoma patients, representing a statistically significant excess burden compared with cancer-free participants (odds ratio [OR] = 1.60, 95% confidence interval [CI] = 1.27 to 2.00). BARD1 harbored the most statistically significant enrichment of pathogenic or likely pathogenic variants (OR = 32.30, 95% CI = 6.44 to 310.35). Rare germline copy number variants disrupting BARD1 were identified in patients but absent in cancer-free participants (OR = 29.47, 95% CI = 1.52 to 570.70). Patients harboring a germline pathogenic or likely pathogenic variant had a worse overall survival compared with those without (P = 8.6 x 10-3). BARD1 is an important neuroblastoma predisposition gene harboring both common and rare germline pathogenic or likely pathogenic variations. The presence of any germline pathogenic or likely pathogenic variant in a cancer predisposition gene was independently predictive of worse overall survival. As centers move toward paired tumor-normal sequencing at diagnosis, efforts should be made to centralize data and provide an infrastructure to support cooperative longitudinal prospective studies of germline pathogenic variation.

Protein remote homology detection and structural alignment using deep learning

Exploiting sequence–structure–function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec and DeepBLAST. TM-Vec allows searching for structure–structure similarities in large sequence databases. It is trained to accurately predict TM-scores as a metric of structural similarity directly from sequence pairs without the need for intermediate computation or solution of structures. Once structurally similar proteins have been identified, DeepBLAST can structurally align proteins using only sequence information by identifying structurally homologous regions between proteins. It outperforms traditional sequence alignment methods and performs similarly to structure-based alignment methods. We show the merits of TM-Vec and DeepBLAST on a variety of datasets, including better identification of remotely homologous proteins compared with state-of-the-art sequence alignment and structure prediction methods.

Superharmonic and triadic resonances in a horizontally oscillated stably stratified square cavity

The response to harmonic horizontal oscillations of a stably stratified fluid-filled two-dimensional square container is examined as the forcing amplitude is increased. For the studied forcing frequency, the response flow at very small forcing amplitudes is a synchronous periodic flow with piecewise-constant vorticity in regions delineated by the characteristics emanating from the corners of the container, regularized by viscosity. The second temporal harmonic of the forced response flow resonantly excites an intrinsic mode of the stratified container, whose magnitude grows as the square of the forcing amplitude. Above a critical forcing amplitude, a sequence of pairs of other container modes are excited via triadic resonances with the second-harmonic-driven mode. The flows are computed from the Navier–Stokes–Boussinesq equations and the ensuing dynamics is analysed using Fourier techniques, providing a comprehensive picture of the transition to internal wave turbulence.

Psychometric indicators and adaptation ch. Osgud's method "semantic differential" (ukrainian version of the method

The article presents the results of adaptation and standardization of the Semantic Differential method (Ch. Osgood). The purpose of the article was to adapt the Ukrainian version of the Semantic Differential method and determine the possibilities of its use in further psychological research. In order to meaningfully validate the adapted version of the Semantic Differential method, five experts were involved - philological specialists in the field of English-Ukrainian translation. In the course of joint work with experts, the following was carried out: direct translation of the original text of the method of semantic differential by Ch. Osgood; retroversion; correction of the translated material in order to increase the degree of compliance with the linguistic features of Ukrainian speakers (taking into account compliance with the theoretical construct of the methodology); final substantive and linguistic evaluation of the Ukrainian-language version; selection of the optimal sequence of pairs of adjectives. The work was carried out in several stages: translation; expert substantive evaluation of the preliminary translation; standardization of the questionnaire; collection of relevant norms on the domestic sample (563 persons (24.01-11.95 years old), among whom 198 are carriers of the male gender; 365 – female). All subjects were fluent in the Ukrainian language; the level of knowledge of English is not lower than B1 (Intermediate). Language knowledge was tested using express methods on the eve of testing. The testing took place in the following order: the original (English) version of the Semantic Differential (the attitude towards oneself was assessed); Rosenberg self-esteem scale; subjective scaling of one's self; adapted author's Ukrainian modification of the Semantic Differential (attitude towards oneself was also assessed). During the analysis of the psychometric indicators of the adapted version of the methodology, its content and construct validity were checked; reliability and coherence of its points; in addition, test norms for the Ukrainian-speaking sample were obtained. Test norms were determined separately for groups of men and women. It was established that the adapted version of the Semantic Differential is characterized by high psychometric indicators, so it allows the use of the method for further study of the attitude to phenomena determined by the purpose of a separate study.

Effect of Carcinomas on Autosomal Trait Screening: A Review Article.

This review highlights the effect of carcinomas on the results of the examination of autosomal genetic traits for identification and paternity tests when carcinoid tissue is the only source and no other samples are available. In DNA typing or genetic fingerprinting, variable elements are isolated and identified within the base pair sequences that form the DNA. The person's probable identity can be determined by analysing nucleotide sequences in particular regions of DNA unique to everyone. Genetics plays an increasingly important role in the risk stratification and management of carcinoma patients. The available information from previous studies has indicated that in some incidents, including mass disasters and crimes such as terrorist incidents, biological evidence may not be available at the scene of the accident, except for some unknown human remains found in the form of undefined human tissues. If these tissues have cancerous tumours, it may affect the examination of the genetic traits derived from these samples, thereby resulting in a failure to identify the person. Pathology units, more often, verify the identity of the patients who were diagnosed with cancer in reference to their deceased tumorous relatives. Genetic fingerprinting (GF) is also used in paternity testing when the alleged parent disappeared or died and earlier was diagnosed and treated for cancer.

New Record: Molecular Depiction of Rhamnolipids (rhlA) Gene in Locally Isolated Strains of Pseudomonas aeruginosa

Soil samples were collected from oil-contaminated sites which were located in west Qurna, Basrah, Iraq. Pseudomonas species were initially isolated on mineral salts and Pseudomonas agar media and identified using morphological and biochemical characterizations. Then, specific primers for the rhlA gene belonging to Pseudomonas aeruginosa were designed based on the primer design conditions, and PCR was performed to amplify the 888 bp size fragment of the rhlA gene; additionally, the primary PCR products were purified and sent for sequencing. The band of about 888bp was determined on the gel, the amplified rhlA gene sequencing findings were revised, only 366 bp were ready to analyze using the (BLAST) software, and the final result was identified as a partial sequence of chromosomal rhlA gene related to Pseudomonas aeruginosa with percent identity of 99.45%. The query gene’s incomplete matching with another partial rhlA record on NCBI was caused by variations in two base pair sequences (T in sequence 348 and C in sequence 353, respectively), and despite the small difference, this results in variation in the amino acids produced; so that a new record number, ON637169, was assigned when the sequence was deposited in GenBank. The relation among the new record of partial rhlA gene with the same number of the other rhlA gene sequences (60 records) was demonstrated by creating a phylogenetic tree.

Base pair compositional variability influences DNA structural stability and tunes hydration thermodynamics and dynamics.

DNA deformability and differential hydration are crucial determinants of biological processes ranging from genetic material packaging to gene expression; their associative details, however, remain inadequately understood. Herein, we report investigations of the dynamic and thermodynamic responses of the local hydration of a variety of base pair sequences. Leveraging in silico sampling and our in-house analyses, we first report the local conformational propensity of sequences that are either predisposed toward the canonical A- or B-conformations or are restrained to potential transitory pathways. It is observed that the transition from the unrestrained A-form to the B-form leads to lengthwise structural deformation. The insertion of intermittent -(CG)- base pairs in otherwise homogeneous -(AT)- sequences bears dynamical consequences for the vicinal hydration layer. Calculation of the excess (pair) entropy suggests substantially higher values of hydration water surrounding A conformations over the B- conformations. Applying the Rosenfeld approximation, we project that the diffusivity of water molecules proximal to canonical B conformation is least for the minor groove of the canonical B-conformation. We determine that structure, composition, and conformation specific groove dimension together influence the local hydration characteristics and, therefore, are expected to be important determinants of biological processes.

LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules.

Many RNAs function through RNA-RNA interactions. Fast and reliable RNA structure prediction with consideration of RNA-RNA interaction is useful, however, existing tools are either too simplistic or too slow. To address this issue, we present LinearCoFold, which approximates the complete minimum free energy structure of two strands in linear time, and LinearCoPartition, which approximates the cofolding partition function and base pairing probabilities in linear time. LinearCoFold and LinearCoPartition are orders of magnitude faster than RNAcofold. For example, on a sequence pair with combined length of 26,190nt, LinearCoFold is 86.8× faster than RNAcofold MFE mode, and LinearCoPartition is 642.3× faster than RNAcofold partition function mode. Surprisingly, LinearCoFold and LinearCoPartition's predictions have higher PPV and sensitivity of intermolecular base pairs. Furthermore, we apply LinearCoFold to predict the RNA-RNA interaction between SARS-CoV-2 genomic RNA (gRNA) and human U4 small nuclear RNA (snRNA), which has been experimentally studied, and observe that LinearCoFold's prediction correlates better with the wet lab results than RNAcofold's.

Uncovering Molecular Quencher Effects on FRET Phenomena in Microsphere-Immobilized Probe Systems.

Double-stranded (ds) oligonucleotide probes composed of quencher-dye sequence pairs outperform analogous single-stranded (ss) probes due to their superior target sequence specificity without any prerequisite target labeling. Optimizing sequence combinations for dsprobe design requires promoting a fast, accurate response to a specific target sequence while minimizing spontaneous dsprobe dissociation events. Here, flow cytometry is used to rapidly interrogate the stability and selective responsiveness of 20 candidate LNA and DNA dsprobes to a 24 base-long segment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and ∼243 degenerate RNA sequences serving as model variants. Importantly, in contrast to quantifying binding events of dye-labeled targets via flow cytometry, the current work employs the Förster resonance energy transfer (FRET)-based detection of unlabeled RNA targets. One DNA dsprobe with a 15-base-long hybridization partner containing a central abasic site emerged as very stable yet responsive only to the SARS-CoV-2 RNA segment. Separate displacement experiments, however, indicated that ∼12% of these quencher-capped hybridization partners remain bound, even in the presence of an excess SARS-CoV-2 RNA target. To examine their quenching range, additional titration studies varied the ratios and spatial placement of nonquencher and quencher-capped hybridization partners in the dsprobes. These titration studies indicate that these residual, bound quencher-capped partners, even at low percentages, act as nodes, enabling both static quenching effects within each residual dsprobe as well as longer-range quenching effects on neighboring FAM moieties. Overall, these studies provide insight into practical implications for rapid dsprobe screening and target detection by combining flow cytometry with FRET-based detection.

Evaluation of Compressed SENSE on Image Quality and Reduction of MRI Acquisition Time: A Clinical Validation Study

To evaluate the effect of compressed SENSE (CS)in clinical settings on scan time reduction and image quality. Ninety-five magnetic resonance imaging (MRI) scans from different anatomical regions were acquired, consisting of a standard protocol sequence (SS) and sequence accelerated with CS. Anonymized paired sequences were randomly displayed and rated by six blinded subspecialty radiologists. Side-by-side evaluation on perceived sharpness, perceived signal-to-noise-ratio (SNR), lesion conspicuity, and artifacts were compared and scored on a five-point Likert scale, and individual image quality was evaluated on a four-point Likert scale. CS reduced overall scan time by 32% while maintaining acceptable MRI quality for all regions. The largest time savings were seen in the spine (mean = 68 seconds, 44% reduction) followed by the brain (mean = 86seconds, 37% reduction). The sequence with maximum time savings was intracranial 3D-time-of-flight magnetic resonance angiography (202seconds, 56% reduction). CS was mildly inferior to SS on perceived sharpness, perceived SNR, and lesion conspicuity (mean scores = 2.32-2.96, P<.001 [1:SS superior; 3: equivalent; 5: CS superior]). CS was equivalent to SS for joint and body scans on overall image quality (CS = 3.02-3.37, SS = 3.04-3.68, P>.05, [1: lowest quality and 4: highest quality]). The overall image quality of CS was slightly less for brain and spine scans (mean CS = 2.79-3.05, mean SS = 3.13-3.43, P=.021) but still diagnostic. Good overall clinical acceptance for CS (88%) was noted with full clinical acceptance for body scans (100%)and high acceptance for other regions (68%-95%). CS significantly reduced MR acquisition time while maintaining acceptable image quality. The implementation of CS may improve departmental workflows and enhance patient care.

The complete sequence of a human Y chromosome.

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1-3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.

The mitochondrial genomes of Panax notoginseng reveal recombination mediated by repeats associated with DNA replication

Panax notoginseng is one of the most valuable medicinal species. However, its mitochondrial genome has not been reported yet. We aimed to determine the mitogenome sequence of P. notoginseng. We de novo assembled the mitogenome with Illumina short reads and Nanopore long reads. The mitochondrial genome of P. notoginseng has a multipartite structure consisting of interconversion between a “master circle” and numerous “subgenomic circles” through recombinations mediated by 64 pairs of repetitive sequences. Among the multipartite structure, seven subgenomic circles were best supported. Six of the seven subgenomic circles shared an 852 bp conserved fragment. The complete mitogenome of P. notoginseng was 662,479 bp long including 34 mitochondrial protein-coding genes (PCGs), three rRNA, and 19 tRNA genes. We identified 166 microsatellite repeats and 26 long-tandem repeats. Phylogenetic analysis resolved a tree that was mostly congruent with the phylogeny of Apiales species described in the APG IV system and the tree built with the chloroplast genome sequences. A total of 12 mitochondrial plastid DNA fragments were identified. Lastly, we predicted 591C-to-U RNA editing sites in the coding regions of mitochondrial PCGs. The mitochondrial genome will lay the foundation for understanding the evolution of Panax species.

Immediate impacts of soybean cover crop on bacterial community composition and diversity in soil under long-term Saccharum monoculture.

Saccharum yield decline results from long-term monoculture practices. Changes in cropping management can improve soil health and productivity. Below-ground bacterial community diversity and composition across soybean (Glycine max (L.) Merr) cover crop, Saccharum monoculture (30+ year) and fallowed soil were determined. Near full length (~1,400 base pairs) of 16S rRNA gene sequences were extracted from the rhizospheres of sugarcane and soybean and fallowed soil were compared. Higher soil bacterial diversity was observed in the soybean cover crop than sugarcane monoculture across all measured indices (observed operationational taxonomic units, Chao1, Shannon, reciprocal Simpson and Jackknife). Acidocateria, Proteobacteria, Bacteroidetes and Planctomycetes were the most abundant bacterial phyla across the treatments. Indicator species analysis identified nine indicator phyla. Planctomycetes, Armatimonadetes and candidate phylum FBP were associated with soybean; Proteobacteria and Firmicutes were linked with sugarcane and Gemmatimonadetes, Nitrospirae, Rokubacteria and unclassified bacteria were associated with fallowed soil. Non-metric multidimensional scaling analysis showed distinct groupings of bacterial operational taxonomic units (97% identity) according to management system (soybean, sugarcane or fallow) indicating compositional differences among treatments. This is confirmed by the results of the multi-response permutation procedures (A = 0.541, p = 0.00045716). No correlation between soil parameters and bacterial community structure was observed according to Mantel test (r = 211865, p = 0.14). Use of soybean cover-crop fostered bacterial diversity and altered community structure. This indicates cover crops could have a restorative effect and potentially promote sustainability in long-term Saccharum production systems.