Exploring the antimicrobial and antioxidant properties of Lentzea flaviverrucosa strain E25-2 isolated from Moroccan forest soil.

The alarming rise in antimicrobial resistance (AMR) has created a significant public health challenge, necessitating the discovery of new therapeutic agents to combat infectious diseases and oxidative stress-related disorders. The Lentzea flaviverrucosa strain E25-2, isolated from Moroccan forest soil, represents a potential avenue for such research. This study aimed to identify the isolate E25-2, obtained from soil in a cold Moroccan ecosystem, and further investigate its antimicrobial and antioxidant activities. Phylogenetic analysis based on 16S rRNA gene sequences revealed the strain's classification within the Lentzea genus, with a sequence closely resembling that of Lentzea flaviverrucosa AS4.0578 (96.10% similarity). Antimicrobial activity in solid media showed moderate to strong activity against Staphylococcus aureus ATCC 25923, Bacillus cereus strain ATCC 14579, Escherichia coli strain ATCC 25922, Candida albicans strain ATCC 60193 and 4 phytopathogenic fungi. In addition, ethyl acetate extract of this isolate demonstrated potent antimicrobial activity against 7 clinically multi-drug resistant bacteria. Furthermore, it demonstrated antioxidant activity against 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) free radicals, as well as a significant increase in ferric reducing antioxidant power. A significant positive correlation was observed between antioxidant activities and total content of phenolic compounds (p < 0.0001), along with flavonoids (p < 0.0001). Furthermore, gas chromatography-mass spectrometry (GC-MS) analysis revealed the presence of amines, hydroxyl groups, pyridopyrazinone rings, esters and pyrrolopyrazines. The Lentzea genus could offer promising prospects in the fight against antibiotic resistance and in the prevention against oxidative stress related diseases.

Seasonal variation and human impacts of the river biofilm bacterial communities in the Shiting River in southeastern China.

Bacterial communities in epilithic biofilm plays an important role in biogeochemistry processes in freshwater ecosystems. Nevertheless, our understanding of the geographical and seasonal variations of the composition of bacterial communities in the biofilm of gravels on river bed is still limited. Various anthropogenic activities also influence the biofilm bacteria in gravel rivers. By taking the Shiting River in the upper Yangtze River basin in Sichuan Province as an example, we studied the geographical and seasonal variations of epilithic bacteria and the impacts of weirs and other human activities (e.g., sewage pollution). The river has experienced severe degradation since the Ms 8.0 Wenchuan Earthquake, and weirs were constructed to prevent bed erosion. We collected epilithic biofilms samples at 17 sites along ~ 30 km river reach of the Shiting River in the autumn of 2021 and the summer of 2022, respectively. We applied 16S rRNA gene high-throughput sequencing technology and Functional Annotation of Prokaryotic Taxa (FAPROTAX) to analyze the seasonal and biogeographic patterns and potential functions of the biofilm bacterial communities. The results showed that epilithic bacteria from the two surveys exhibited variation in community composition, bacterial diversity and potential functions. The bacteria samples collected in the autumn have much higher alpha diversity and richness than those collected in the summer. Bacterial richness and diversity were lower downstream of the weirs than upstream. Low diversity was observed at a sampling site influenced by sewage inflow, which contains high level of nitrogen-related chemicals.

Database of all currently known mobile colistin resistance genes.

We created a database of all currently known mobile colistin resistance genes and variants (n = 115). It contains accession numbers of the gene and protein sequences, mutations between the protein variants and the main proteins, and additional metadata. It is accompanied by all genetic and protein sequences as two aggregated FASTA files.

Essential genes identification model based on sequence feature map and graph convolutional neural network.

BACKGROUND: Essential genes encode functions that play a vital role in the life activities of organisms, encompassing growth, development, immune system functioning, and cell structure maintenance. Conventional experimental techniques for identifying essential genes are resource-intensive and time-consuming, and the accuracy of current machine learning models needs further enhancement. Therefore, it is crucial to develop a robust computational model to accurately predict essential genes. RESULTS: In this study, we introduce GCNN-SFM, a computational model for identifying essential genes in organisms, based on graph convolutional neural networks (GCNN). GCNN-SFM integrates a graph convolutional layer, a convolutional layer, and a fully connected layer to model and extract features from gene sequences of essential genes. Initially, the gene sequence is transformed into a feature map using coding techniques. Subsequently, a multi-layer GCN is employed to perform graph convolution operations, effectively capturing both local and global features of the gene sequence. Further feature extraction is performed, followed by integrating convolution and fully-connected layers to generate prediction results for essential genes. The gradient descent algorithm is utilized to iteratively update the cross-entropy loss function, thereby enhancing the accuracy of the prediction results. Meanwhile, model parameters are tuned to determine the optimal parameter combination that yields the best prediction performance during training. CONCLUSIONS: Experimental evaluation demonstrates that GCNN-SFM surpasses various advanced essential gene prediction models and achieves an average accuracy of 94.53%. This study presents a novel and effective approach for identifying essential genes, which has significant implications for biology and genomics research.

Angelica polysaccharides relieve blood glucose levels in diabetic KKAy mice possibly by modulating gut microbiota: an integrated gut microbiota and metabolism analysis.

BACKGROUND: Angelica polysaccharides (AP) have numerous benefits in relieving type 2 diabetes (T2D). However, the underlying mechanisms have yet to be fully understood. Recent many reports have suggested that altering gut microbiota can have adverse effects on the host metabolism and contribute to the development of T2D. Here, we successfully established the T2D model using the male KKAy mice with high-fat and high-sugar feed. Meanwhile, the male C57BL/6 mice were fed with a normal feed. T2D KKAy mice were fed either with or without AP supplementation. In each group, we measured the mice's fasting blood glucose, weight, and fasting serum insulin levels. We collected the cecum content of mice, the gut microbiota was analyzed by targeted full-length 16S rRNA metagenomic sequencing and metabolites were analyzed by untargeted-metabolomics. RESULTS: We found AP effectively alleviated glycemic disorders of T2D KKAy mice, with the changes in gut microbiota composition and function. Many bacteria species and metabolites were markedly changed in T2D KKAy mice and reversed by AP. Additionally, 16 altered metabolic pathways affected by AP were figured out by combining metagenomic pathway enrichment analysis and metabolic pathway enrichment analysis. The key metabolites in 16 metabolic pathways were significantly associated with the gut microbial alteration. Together, our findings showed that AP supplementation could attenuate the diabetic phenotype. Significant gut microbiota and gut metabolite changes were observed in the T2D KKAy mice and AP intervention. CONCLUSIONS: Administration of AP has been shown to improve the composition of intestinal microbiota in T2D KKAy mice, thus providing further evidence for the potential therapeutic application of AP in the treatment of T2D.

Genetic Variation versus Morphological Variability in European Peatland Violets (Viola epipsila-V. palustris Group).

In Europe, the V. epipsila-V. palustris group comprises V. epipsila Ledeb., V. palustris L., V. pubifolia (Kuta) G. H. Loos (=V. palustris subsp. pubifolia Kuta), interspecific hybrids, and putative introgressants. The genetic affinity of V. pubifolia to V. palustris, and their shared origin via hybridization followed by polyploidization, were confirmed using inter simple sequence repeat (ISSR) markers, restriction site-associated DNA sequencing (RAD-Seq), and a low-copy nuclear gene, GPI, which encodes glucose-6-phosphate isomerase. The other taxa of subsect. Stolonosae were not identified as putative parents of V. pubifolia by GPI. Our analyses indicated that V. pubifolia can be included in the morphological and genetic variation of V. palustris. The ISSR, RAD-Seq, and genome size value separated well V. palustris from V. epipsila and hybrids. The results also reopen the discussion on intraspecific variation in the context of taxa ranks and species concepts. The reduced tolerance of V. epipsila in Europe to changing environmental conditions might result from low genetic differentiation and heterozygosity, as well as the increased number of interspecific hybrids (V. epipsila × V. palustris), and eventually can possibly lead to its extinction. The disappearance of populations/individuals of this species may indicate anthropogenic changes occurring in peatlands.

Novel insights in seasonal dynamics and co-existence patterns of phytoplankton and micro-eukaryotes in drinking water reservoir, Northwest China: DNA data and ecological model.

Although associations between phytoplankton and micro-eukaryotes have been studied in aquatic ecosystems, there are still knowledge gaps in comprehending their dynamics and interactions in drinking water reservoirs. Here, the seasonal dynamics of phytoplankton and micro-eukaryotic diversities and their co-existence patterns were studied in a drinking water reservoir, Northwest China. The highest phytoplankton diversity was observed in summer, and Chlorella sp. that belongs to Chlorophyta was the most abundant genus. The highest eukaryotic diversity was also detected in summer, and Rimostrombidium sp. that belongs to Ciliophora was the most dominant genus. Mantel test showed that the phytoplankton diversity was significantly correlated with ammonia nitrogen (r = 0.561, p = 0.001) and dissolved organic carbon (r = 0.267, p = 0.017), while the eukaryotic diversity was significantly associated with ammonia nitrogen (r = 0.265, p = 0.034) and temperature (r = 0.208, p = 0.046). PLS-PM (Partial Least Squares Path Modeling) further revealed that nutrients (P < 0.01) significantly affected the phytoplankton diversity, while nutrients (P < 0.01) and temperature (P < 0.01) significantly influenced the eukaryotic diversity. Co-occurrence network displayed the primarily positive interactions (77.66% positive and 22.34% negative) between phytoplankton and micro-eukaryotes. These findings could deepen our understanding of interactions between phytoplankton and micro-eukaryotes and their driving factors under changing aquatic environments of drinking water reservoirs.

Is There a Universal Endurance Microbiota?

Billions of microbes sculpt the gut ecosystem, affecting physiology. Since endurance athletes' performance is often physiology-limited, understanding the composition and interactions within athletes' gut microbiota could improve performance. Individual studies describe differences in the relative abundance of bacterial taxa in endurance athletes, suggesting the existence of an "endurance microbiota", yet the taxa identified are mostly non-overlapping. To narrow down the source of this variation, we created a bioinformatics workflow and reanalyzed fecal microbiota from four 16S rRNA gene sequence datasets associated with endurance athletes and controls, examining diversity, relative abundance, correlations, and association networks. There were no significant differences in alpha diversity among all datasets and only one out of four datasets showed a significant overall difference in bacterial community abundance. When bacteria were examined individually, there were no genera with significantly different relative abundance in all four datasets. Two genera were significantly different in two datasets (Veillonella and Romboutsia). No changes in correlated abundances were consistent across datasets. A power analysis using the variance in relative abundance detected in each dataset indicated that much larger sample sizes will be necessary to detect a modest difference in relative abundance especially given the multitude of covariates. Our analysis confirms several challenges when comparing microbiota in general, and indicates that microbes consistently or universally associated with human endurance remain elusive.

Chromosomes in the African frog genus Tomopterna (Pyxicephalidae) and probing the origin of tetraploid Tomopterna tandyi.

Speciation by polyploidization has been documented to have independently occurred in 12 families of anuran amphibians. Tomopterna tandyi was described as a South African allotetraploid species of sand frogs in the family Pyxicephalidae. Recent taxonomic revisions and new species descriptions in the genus present problems with respect to the evolution of this tetraploid species. Chromosomes, mitochondrial and nuclear gene sequences, isozymes, and male mating calls were examined for T. tandyi and for diploid species of Tomopterna. Mitochondrial sequences confirmed the diploid species, T. adiastola, to be the maternal ancestor that gave rise to the tetraploid about 5 mya. Nuclear sequences and isozymes reveal a complex reticulation of paternal ancestry that may be explained by occasional hybridization of T. tandyi with diploid species of Tompoterna at various times in sympatric populations. Interspecific diploid to tetraploid gene introgression is suspected to have also occurred in Australian and North American tetraploid species of frogs. Diploid to tetraploid introgression is facilitated through triploid hybrids that are more viable than diploid hybrids and produce unreduced triploid eggs.

Human umbilical cord-derived mesenchymal stem cells ameliorate experimental colitis by normalizing the gut microbiota.

BACKGROUND: Crohn's disease (CD) is a chronic non-specific inflammatory bowel disease. Current CD therapeutics cannot fundamentally change the natural course of CD. Therefore, it is of great significance to find new treatment strategies for CD. Preclinical and clinical studies have shown that mesenchymal stromal cells (MSCs) are a promising therapeutic approach. However, the mechanism by which MSCs alleviate CD and how MSCs affect gut microbes are still unclear and need further elucidation. METHODS: We used 2,4,6-trinitrobenzenesulfonic acid (TNBS) to induce experimental colitis in mice and analysed the microbiota in faecal samples from the control group, the TNBS group and the TNBS + MSC group with faecal 16S rDNA sequencing. Subsequent analyses of alpha and beta diversity were all performed based on the rarified data. PICRUStII analysis was performed on the 16S rRNA gene sequences to infer the gut microbiome functions. RESULTS: MSC Treatment improved TNBS-induced colitis by increasing survival rates and relieving symptoms. A distinct bacterial signature was found in the TNBS group that differed from the TNBS + MSC group and controls. MSCs prevented gut microbiota dysbiosis, including increasing α-diversity and the amount of Bacteroidetes Firmicutes and Tenericutes at the phylum level and decreasing the amount of Proteobacteria at the phylum level. MSCs alleviated the increased activities of sulphur and riboflavin metabolism. Meanwhile some metabolic pathways such as biosynthesis of amino acids lysine biosynthesis sphingolipid metabolism and secondary bile acid biosynthesis were decreased in the TNBS group compared with the control group and the TNBS + MSC group CONCLUSIONS: Overall, our findings preliminarily confirmed that colitis in mice is closely related to microbial and metabolic dysbiosis. MSC treatment could modulate the dysregulated metabolism pathways in mice with colitis, restoring the abnormal microbiota function to that of the normal control group. This study provides insight into specific intestinal microbiota and metabolism pathways linked with MSC treatment, suggesting a new approach to the treatment of CD.

Gonadal bacterial community composition is associated with sex-specific differences in swamp eels (Monopterus albus).

Organisms are colonized by microorganism communities and play a pivotal role in host function by influencing physiology and development. In mammals, bacterial community may alter gonadal maturation and drive sex-specific differences in gene expression and metabolism. However, bacterial microbiota diversity in the gonads of early vertebrates has not been fully elucidated. Here, we focused on the swamp eel (Monopterus albus), which naturally undergoes sex reversal, and systematically analyzed the bacterial microbiota profiles between females and males using 16S rRNA gene sequences. Specifically, the microbial abundance and community diversity of gonads in males were higher than in females. Although Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were characterized as the dominating phyla in ovary and testis, the relative abundance of Firmicutes was significantly higher in males than females. Detailed analysis of the microbial community revealed that Bacilli were the dominant bacteria in ovaries and Clostridium in testes of M. albus. More importantly, we proposed that differences in the microbial composition and distribution between ovaries and testes may be linked to functional categories in M. albus, especially metabolism. These findings represent a unique resource of bacterial community in gonads to facilitate future research about the mechanism of how microbiota influence sex-specific differences and sex reversal in vertebrates.

Revision of the 'Candidatus Phytoplasma' species description guidelines.

The genus 'Candidatus Phytoplasma' was proposed to accommodate cell wall-less bacteria that are molecularly and biochemically incompletely characterized, and colonize plant phloem and insect vector tissues. This provisional classification is highly relevant due to its application in epidemiological and ecological studies, mainly aimed at keeping the severe phytoplasma plant diseases under control worldwide. Given the increasing discovery of molecular diversity within the genus 'Ca. Phytoplasma', the proposed guidelines were revised and clarified to accommodate those 'Ca. Phytoplasma' species strains sharing >98.65 % sequence identity of their full or nearly full 16S rRNA gene sequences, obtained with at least twofold coverage of the sequence, compared with those of the reference strain of such species. Strains sharing <98.65 % sequence identity with the reference strain but >98.65 % with other strain(s) within the same 'Ca. Phytoplasma' species should be considered related strains to that 'Ca. Phytoplasma' species. The guidelines herein, keep the original published reference strains. However, to improve 'Ca. Phytoplasma' species assignment, complementary strains are suggested as an alternative to the reference strains. This will be implemented when only a partial 16S rRNA gene and/or a few other genes have been sequenced, or the strain is no longer available for further molecular characterization. Lists of 'Ca. Phytoplasma' species and alternative reference strains described are reported. For new 'Ca. Phytoplasma' species that will be assigned with identity ≥98.65 % of their 16S rRNA gene sequences, a threshold of 95 % genome-wide average nucleotide identity is suggested. When the whole genome sequences are unavailable, two among conserved housekeeping genes could be used. There are 49 officially published 'Candidatus Phytoplasma' species, including 'Ca. P. cocostanzaniae' and 'Ca. P. palmae' described in this manuscript.

Morphology and phylogeny of the parasitic nematode Mooleptus rabuka (Machida, Ogawa & Okiyama, 1982) (Rhabditida, Spirurina: Mooleptinae nom. nov.), with notes on taxonomy of the family Gnathostomatidae.

The nematode Mooleptus rabuka is recorded in the digestive tract of catshark Apristurus fedorovi caught at the Imperial Ridge (Pacific Ocean). Important morphological features such as the number of cephalic and caudal papillae, the position of amphids and the shape of the gubernaculum are detailed in this parasite species. According to the phylogenetic analyses based on the 18S ribosomal RNA gene sequences, M. rabuka forms a lineage, Mooleptinae nom. nov., which is close to the gnathostomatid genus Echinocephalus (maximum likelihood analysis), or else forms a polytomy with this genus and the lineages of Anguillicola + Spiroxys and Tanqua + 'Linstowinema' sp. (Bayesian inference analysis). Overall, our findings do not support the monophyly of the Gnathostomatidae. We elevate spiroxyines to the family status, Spiroxyidae stat. nov., and temporarily consider the Gnathostomatidae to include the following subfamilies: Ancyracanthinae Yorke & Maplestone, 1926, Gnathostomatinae Railliet, 1895 sensu lato and Mooleptinae nom. nov. The name Mooleptinae nom. nov. is suggested instead of the Metaleptinae Moravec & Nagasawa, 2000, which is based on a preoccupied generic name Metaleptus Machida, Ogawa & Okiyama, 1982.

Molecular Identification, Transcriptome Sequencing and Functional Annotation of Pulex irritans.

PURPOSE: Pulex irritans are vectors of various zoonotic pathogens. However, molecular studies on P. irritans and flea-borne diseases are limited due to the lack of molecular data. This study aimed to conduct transcriptome sequencing, functional annotation, and pathogen analysis of P. irritans. METHODS: Fleas collected from a dog were identified morphologically and molecularly. RNA was extracted for transcriptome sequencing and functional annotation. Open reading frames (ORFs) of unigenes were confirmed by employing bioinformatics strategies, and maximum likelihood (ML) trees were reconstructed based on the highly expressed genes of ejaculation globulin-specific 3-like protein, salivary protein, and actin for phylogenetic relationship analysis. RESULTS: The obtained mitochondrial 16S rRNA gene sequences showed 99.71% of similarity with P. irritans obtained from GenBank database. Transcriptome sequencing generated 74,412 unigenes, of which 53,211 were functionally annotated. A total of 195 unigenes were assigned to fleas, of which 69 contained complete ORFs. Phylogenetic trees of both ejaculatory globulin and salivary protein genes demonstrated that P. irritans first clustered with Pulicidae sp., indicating the reliability of transcriptome data. It is noteworthy that 1070 unigenes were assigned to Hymenolepis microstoma and Dipylidium caninum, of which 62 contained complete ORFs. The phylogenetic tree of the actin gene showed that the unigenes had closer relationships with Echinococcus sp., suggesting the role of P. irritans as intermediate hosts of tapeworms. CONCLUSION: The results of this study provide the possibility for functional exploration of important genes and lay foundations for the prevention and control of P. irritans and flea-borne diseases.

A case of human rabies with a long incubation period in Wuhan.

Rabies remains endemic in China and continues to pose a major threat to public health with a nearly 100 % case fatality rate in humans. We confirmed a case of human rabies in Wuhan, in May 2018. The patient had got a dog bite wound 3 years before symptoms of confusion, hydrophobia, and photophobia onset. On May 14, our laboratory confirmed that the patient was infected with a rabies virus that circulates in dogs in China and died on May 24, two weeks later after admission. Complete glycoprotein gene sequences determined for this isolate indicated the source of a RABV infection was dog-related RABV variants.

Association of forkhead box P3 gene polymorphisms with premature ovarian insufficiency in Chinese women.

OBJECTIVE: Forkhead box P3 (FOXP3), a transcription factor, is regarding critical regulator of the function of regulatory T (Treg) cells and plays a crucial role in the development of autoimmune diseases. Premature ovarian insufficiency (POI) is an autoimmune disease; however, little is known about the association between FOXP3 variants and the susceptibility to POI. METHODS: Long-range polymerase chain reaction was used to analyze complete FOXP3 gene sequences from 153 patients with POI. The frequencies of genotypes and alleles of the FOXP3 gene were compared between patients with POI and 269 East Asian women from the Genome Aggregation (gnomAD) database. RESULTS: Forty-three single-nucleotide polymorphisms (SNPs) were detected, including 25 known SNPs and 18 novel SNPs. The genotype distributions and allele frequencies of two known SNPs (rs17847094 and rs76798919) and three novel SNPs (NC_000023.11:g.49112832G > A, NC_000023.11:g.49112833G > A, and NC_000023.11:g.49120479CT > C) were significantly different between the two groups. Linkage disequilibrium and haplotype analyses of the rs57734889, rs2232365, rs3761548, and rs34629506 SNPs in FOXP3 were performed and compared, and the high D' (standardized disequilibrium coefficients) value indicated that these polymorphisms may contribute to the risk of POI. CONCLUSIONS: This study is the first to show that genetic variants in the regulatory regions of FOXP3 play a vital role in idiopathic POI in the Chinese population.

CpGDB : A Comprehensive Database of Chloroplast Genomes.

Chloroplast Genome Database (CpGDB) is user friendly, web-based, freely available and dynamic relational database which provides a platform for researchers to search and download complete chloroplast genome sequences, individual gene sequences and feature records of plant species belonging to same or different families of spermatophytes. Presently, the database consists of genome sequences, individual gene sequences and feature records of chloroplast genomes of 3823 plant species belonging to 1527 genera from 256 families, which will be updated regularly with the availability of new sequences at NCBI. Extensive data mining of feature records from GenBank files, uniform nomenclature for majority of genes, enriched intron/exon feature records makes CpGDB a valuable resource for studies in chloroplast genomics while complementing existing chloroplast databases.

Allele substitution and dominance effects of CD166/ALCAM gene polymorphisms for endoparasite resistance and test-day traits in a small cattle population using logistic regression analyses.

The study investigated the effects of four single-nucleotide polymorphisms (SNPs) in the activated leukocyte cell adhesion molecule (ALCAM) gene on liver fluke (Fasciola hepatica) infections (FH-INF), gastrointestinal nematode infections (GIN-INF) and disease indicator traits [e.g. somatic cell score (SCS), fat-to-protein ratio (FPR)] in German dual-purpose cattle (DSN). A genome-wide association study inferred the chip SNP ALCAMc.73+32791A>G as a candidate for F. hepatica resistance in DSN. Because of the crucial function of ALCAM in immune responses, SNPs in the gene might influence further resistance and performance traits. Causal mutations were identified in exon 9 (ALCAMc.1017T>C) and intron 9 (ALCAMc.1104+10T>A, ALCAMc.1104+85T>C) in a selective subset of 94 DSN cows. We applied logistic regression analyses for the association between SNP genotypes with residuals for endoparasite traits (rINF-FH, rGIN-INF) and estimated breeding values (EBVs) for test-day traits. The probability of the heterozygous genotype was estimated in dependency of the target trait. Allele substitution effects for rFH-INF were significant for all four loci. The T allele of the SNPs ALCAMc.1017T>C and ALCAMc.1104+85T>C was the favourable allele when improving resistance against FH-INF. Significant allele substitution for rGIN-INF was only found for the chip SNP ALCAMc.73+32791A>G. We identified significant associations between the SNPs with EBVs for milk fat%, protein% and FPR. Dominance effects for the EBVs of test-day traits ranged from 0.00 to 0.47 SD and were in the direction of improved resistance for rFH-INF. We estimated favourable dominance effects from same genotypes for rFH-INF and FPR, but dominance effects were antagonistic between rFH-INF and SCS.

A Short-Term Assessment of Nascent HIV-1 Transmission Clusters Among Newly Diagnosed Individuals Using Envelope Sequence-Based Phylogenetic Analyses.

The identification of transmission clusters (TCs) of HIV-1 using phylogenetic analyses can provide insights into viral transmission network and help improve prevention strategies. We compared the use of partial HIV-1 envelope fragment of 1,070 bp with its loop 3 (108 bp) to determine its utility in inferring HIV-1 transmission clustering. Serum samples of recently (n = 106) and chronically (n = 156) HIV-1-infected patients with status confirmed were sequenced. HIV-1 envelope nucleotide-based phylogenetic analyses were used to infer HIV-1 TCs. Those were constructed using ClusterPickerGUI_1.2.3 considering a pairwise genetic distance of ≤10% threshold. Logistic regression analyses were used to examine the relationship between the demographic factors that were likely associated with HIV-1 clustering. Ninety-eight distinct consensus envelope sequences were subjected to phylogenetic analyses. Using a partial envelope fragment sequence, 42 sequences were grouped into 15 distinct small TCs while the V3 loop reproduces 10 clusters. The agreement between the partial envelope and the V3 loop fragments was significantly moderate with a Cohen's kappa (κ) coefficient of 0.59, p < .00001. The mean age (<38.8 years) and HIV-1 B subtype are two factors identified that were significantly associated with HIV-1 transmission clustering in the cohort, odds ratio (OR) = 0.25, 95% confidence interval (CI, 0.04-0.66), p = .002 and OR: 0.17, 95% CI (0.10-0.61), p = .011, respectively. The present study confirms that a partial fragment of the HIV-1 envelope sequence is a better predictor of transmission clustering. However, the loop 3 segment may be useful in screening purposes and may be more amenable to integration in surveillance programs.