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PubMed1979

Homology of the 3' terminal sequences of the 18S rRNA of Bombyx mori and the 16S rRNA of Escherchia coli.

The terminal 220 base pairs (bp) of the gene for 18S rRNA and 18 bp of the adjoining spacer rDNA of the silkworm Bombyx mori have been sequenced. Comparison with the sequence of the 16S rRNA gene of Escherichia coli has shown that a region including 45 bp of the B. mori sequence at the 3' end is remarkably homologous with the 3' terminal E. coli sequence. Other homologies occur in the terminal regions of the 18S and 16S rRNAs, including a perfectly conserved stretch of 13 bp within a longer homology located 150--200 bp from the 3' termini. These homologies are the most extensive so far reported between prokaryotic and eukaryotic genomic DNA.

Animals↗
PubMed1979

Intermolecular base-paired interaction between complementary sequences present near the 3' ends of 5S rRNA and 18S (16S) rRNA might be involved in the reversible association of ribosomal subunits.

Highly conserved sequences present at an identical position near the 3' ends of eukaryotic and prokaryotic 5S rRNAs are complementary to the 5' strand of the m2(6)A hairpin structure near the 3' ends of 18S rRNA and 16S rRNA, respectively. The extent of base-pairing and the calculated stabilities of the hybrids that can be constructed between 5S rRNAs and the small ribosomal subunit RNAs are greater than most, if not all, RNA-RNA interactions that have been implicated in protein synthesis. The existence of complementary sequences in 5S rRNA and small ribosomal subunit RNA, along with the previous observation that there is very efficient and selective hybridization in vitro between 5S and 18S rRNA, suggests that base-pairing between 5S rRNA in the large ribosomal subunit and 18S (16S) rRNA in the small ribosomal subunit might be involved in the reversible association of ribosomal subunits. Structural and functional evidence supporting this hypothesis is discussed.

Base Sequence↗
PubMed1979

Cyanobacterial evolution: results of 16S ribosomal ribonucleic acid sequence analyses.

We report here the sequences of oligonucleotides released by T1-ribonuclease digestion of the 16S ribosomal RNA's (rRNA's) of unicellular cyanobacteria Agmenellum quadruplicatum (strain BG-1) and Synechococcus 7502. We compare them with sequences previously obtained for the 16S RNA's of six other cyanobacteria and two chloroplasts, and conclude that: (i) Synechocystis-like unicells form a discrete cluster which also (and surprisingly) includes Agmenelium quadruplicatum, usually considered to be a Synechococcus; (ii) filamentous cyanobacteria of the genera Nostoc and Fischerella arose from within the Synechocystis group; (iii) phylogenetic diversity (and hence presumably evolutionary antiquity) within the Synechococcus group is very great; and (iv) red algal chloroplasts are of definite cyanobacterial origin, while Euglena chloroplasts are of separate and quite possibly noncyanobacterial origin. We also present the results of a computer-aided search among the 10 oligonucleotide 'catalogues' for families of related but nonidentical sequences. Examination of these families reinforces the above conclusions.

Base Sequence↗
PubMed2025

Analysis of Blood Microbiome From People Living With HIV and Donors by 16S rRNA Metagenomic Sequencing.

Utilize 16S rRNA sequencing technology to characterize bacterial species susceptible to people living with HIV (PLWH) across different stages. This mapping aims to establish a foundational framework for preventing secondary HIV infections, prolonging patient survival, enhancing quality of life, and advancing the diagnosis, treatment, and research of bacterial co-infections. In this study, we classified the participants into three groups: The blood of donors living with HIV (DI group), AIDS patients who have received ART treatment (PI group), and healthy blood donors as the control group (DH group). Each group was divided into three parallel subgroups, with 30 samples pooled from each parallel group for plasma extraction. As initial processing steps, the nine parallel subgroups were subjected to nucleic acid extraction and PCR amplification targeting the 16SV34 region. The resulting amplified products were subsequently forwarded to a sequencing company. It can be seen from the Venn diagram that the DI groups showed significantly higher bacterial diversity than the PI group and the DH group. The PI group had lower bacterial relative abundance and diversity compared to the DI group, with a community structure more similar to the control group. The DI group is particularly susceptible to several significant pathogens, including Ralstonia, Pseudomonas, Acinetobacter, Methyloversatilis, and Vibrio. The study revealed a greater quantity and diversity of bacteria in the DI blood compared to the PI and DH groups. This observation may be attributed to PI group patients in this study being hospitalized and receiving treatment.

Humans↗
PubMed2025

Evaluation of the gastric microbiota based on body mass index using 16S rRNA gene sequencing.

INTRODUCTION: Obesity is a multifactorial condition influenced by various factors, including the gut microbiota. However, the relationship between the gastric microbiota and obesity remains poorly understood. This study aimed to investigate the composition of gastric microbiota, excluding Helicobacter pylori, in relation to body mass index (BMI) and metabolic indicators. METHODS: Thirty participants undergoing health checkups were classified into three groups-normal weight (BMI 18.5-22.9), overweight (BMI 23.0-24.9), and obese (BMI ≥25.0)-with ten individuals per group. Those with H. pylori infection, atrophic gastritis, or intestinal metaplasia were excluded. Gastric microbiota from four antral biopsies per subject were analyzed using 16S rRNA sequencing and functional profiling by metagenomic prediction. RESULTS AND DISCUSSION: Alpha diversity (Gini-Simpson index) was significantly lower in the combined overweight/obese group than that in the normal group (P=0.049). Beta diversity analysis revealed clear group separation (Bray-Curtis, P=0.005; unweighted UniFrac, P=0.004). Significant species differences between the groups were observed; specifically, the abundances of Muribaculum gordoncarteri, Turicibacter bilis, and Duncaniella dubosii, were significantly reduced in the overweight/obese group. Functional predictions showed differential enrichment of pathways related to fatty acid, amino acid, vitamin, and carbohydrate metabolism across BMI categories. These findings suggest that alterations in the gastric microbiota may be linked to obesity and metabolic dysregulation.

Humans↗
PubMed2026

Oral bacteriome in pediatric patients with malignancies prior to chemotherapy: a pilot study using full-length 16S rRNA sequencing.

OBJECTIVE: To characterize the composition, diversity, and ecological features of the oral bacteriome in pediatric patients with malignancies prior to chemotherapy initiation. METHODS: In this prospective pilot study,supragingival plaque samples were collected from 10 pediatric cancer patients prior to the initiation of chemotherapy. Bacterial genomic DNA was extracted from each sample, and the full-length 16S rRNA gene was amplified and sequenced on the PacBio Sequel II platform using circular consensus sequencing (CCS). Raw CCS reads were quality-filtered and denoised into amplicon sequence variants (ASVs) using DADA2, and taxonomic assignment was performed against the SILVA 138 reference database. Alpha diversity was assessed using the Chao1, Shannon, Simpson, and Faith's phylogenetic diversity (PD whole tree) indices, while beta diversity was evaluated through principal coordinate analysis (PCoA), and non-metric multidimensional scaling (NMDS). Microbial co-occurrence networks were constructed to characterize bacterial interactions, and functional potential was predicted using PICRUSt2, and BugBase. RESULTS: A total of 614,473 high-quality CCS reads were generated, yielding 1,697 ASVs. Alpha diversity analysis revealed substantial inter-individual variation in microbial richness and diversity among the pediatric cancer patients. The bacterial community was dominated by the phyla Firmicutes, Proteobacteria, Bacteroidota, Actinobacteriota. At the genus level, Streptococcus, Prevotella, Neisseria, and Haemophilus were the most abundant taxa. Beta diversity analysis revealed distinct clustering patterns, indicating highly individualized microbial profiles. Co-occurrence network analysis identified several keystone taxa and potential pathogenic associations within the supragingival plaque community. Functional prediction indicated that the dominant metabolic pathways were related to amino acid metabolism, carbohydrate metabolism, and membrane transport. CONCLUSION: These preliminary findings reveal a taxonomically diverse, highly individualized pre-chemotherapy oral bacteriome, providing foundational baseline profiles to guide future longitudinal investigations of chemotherapy-induced dysbiosis and personalized interventions.

Humans↗
PubMed2025

16S rRNA and Metagenomic Datasets of Gastrointestinal Microbiota in Fetal and 7-Day-Old Goat Kids.

The perinatal period (from late gestation to the neonatal stage) in ruminants is a critical phase for fetal organ maturation, where ecological succession of gastrointestinal microbial communities significantly impacts livestock production efficiency. However, research remains insufficient regarding the distribution patterns and functional annotation of microbial communities across different gastrointestinal compartments during this period. This study characterized early microbiota dynamics in Hutianshi Goats using 16S rRNA sequencing (4 fetal goats at 90 ± 10 gestational days) and metagenomics (3 7-day-old goat kids). The fetal goat group generated 852,694 valid reads, yielding 688,277 high-quality reads after chimera removal for downstream analysis. The 7-day-old goat kids group produced 1,081,588,182 final valid reads, after data processing and assembly, 8,561,345 contigs were generated. Gene prediction identified 6,095,352 genes. Multi-database annotations (NR, KEGG, CAZy, etc.) revealed functional potential and antimicrobial resistance traits. The public release of this dataset facilitates academic understanding of microbial community dynamics and host-microbe interactions during this developmental stage, providing both theoretical foundations and data resources for ruminant developmental biology and precision breeding regulation.

Animals↗
PubMed1976

A comparison of the 16S ribosomal RNAs from mesophilic and thermophilic bacilli: some modifications in the Sanger method for RNA sequencing.

Two modifications in the Sanger two dimensional electrophoretic procedure for RNA analysis are reported. One increases resolution on the primary fingerprint to the point that digests of large RNAs, of the size 1500-3000 nucleotides yield well resolved fingerprint patterns. The other is a novel endonucleolytic procedure that proves useful in determining sequences of the large oligonucleotides produced by T1 ribonuclease. These modifications have been used in determining the catalogs of oligomers produced by T1 ribonuclease digestion of 16S rRNAs from three related organisms, Bacillus subtilis, B.pumilus and B.stearothermophilus. The possible effects of adaptation to a thermophilic niche on ribosomal RNA primary structure and the phylogenetic relatedness of the two mesophilic Bacilli are discussed.

Animals↗
PubMed1975

Sequence studies on 16S ribosomal RNA from a blue-green alga.

The 16S ribosomal RNA of the blue green alga Anacystis nidulans has been characterized in terms of the oligomers generated by digestion with T1 ribonuclease. A. nidulans by this criterion is definitely a procaryote; being no more distant from Bacilli or Enterics than the latter two are from one another. A. nidulans appears to be somewhat more closely related to the Bacilli than to the Enterics.

Bacillus↗
PubMed1976

Transfer RNA genes between 16S and 23S rRNA genes in rRNA transcription units of E. coli.

We have identified genes for tRNAGLU/2 on the transducing phages o80d3ilvsu7+ (see Ohtsubo et al., 1974) and lambdarifd18 (Kirschbaum and Konrad, 1973), and a gene for tRNAlle/1 on the transducing phage o80rifr (Konrad, Kirschbaum, and Austin, 1973). All these phages have previously been shown to carry genes for rRNA (Ohtsubo et al., 1974; Lindahl et al., 1975; Jaskunas et al., 1975a). We have analyzed the position of these tRNA genes by hybridizing purified RNAs to restriction fragments of the phage DNA. The tRNA genes are located inside the rRNA transcription unit in the spacer region between the 16S and 23S rRNA genes.

Chromosome Mapping↗
PubMed1978

Processing of rRNA by RNAase P: spacer tRNAs are linked to 16S rRNA in an RNAase P RNAase III mutant strain of E. coli.

To determine which enzymes are responsible for the processing cleavages of ribosomal RNA transcripts in Escherichia coli, we constructed a mutant strain lacking RNAase III and containing a thermolabile RNAase P. At the nonpermissive temperature, this strain accumulates a novel "19S" RNA species which contains 17S precursor rRNA sequences covalently linked to tRNA sequences transcribed from the ribosomal RNA spacer region between the 16S and the 23S rRNA cistrons. In vitro treatment of 19S RNA with cell extracts releases tRNA2Glu and other tRNA species. These "spacer" tRNA sequences are apparently not contained with the 18S RNA species found in an RNAase III- RNAase P+ cell. RNAase P-deficient extracts are incapable of cleaving space tRNA from 19S RNA, indicating that RNAase P is required for the release of spacer tRNAs from rRNA transcripts of E. coli cells.

Escherichia coli↗
PubMed2026

Indoor Air Quality (IAQ) analysis and 16S rRNA gene sequencing of indoor air pollutants in a 3000-capacity religious auditorium.

A thorough molecular and environmental evaluation of microbial isolates and indoor air quality (IAQ) at a place of worship is presented in this work. The study used a dual-methodological approach, including systematic environmental monitoring to assess occupant health concerns and 16S rRNA gene sequencing for taxonomic identification. Four different bacterial isolates were successfully identified by molecular analysis using BLAST and phylogenetic reconstruction: Bacillus tropicus (A11), Leclercia adecarboxylata (A12), Acinetobacter sp. (A13), and Escherichia coli (A14). The evolutionary position of isolate A13 indicated possible horizontal gene transfer, underscoring the existence of flexible, opportunistic pathogens within the indoor environment, whereas isolates A11 and A14 demonstrated significant genetic stability. Concurrently, six sessions of air quality monitoring showed a thermally demanding environment, with humidity (56.00-70.51%) and temperatures (29.21-33.79 °C) continuously surpassing ASHRAE guidelines. The average pollutant concentrations are within WHO and USEPA safety criteria, however, there were outliers that may suggest sporadic pollutant penetration (outdoor) or resuspension of dust. The results demonstrate a clear relationship between increased chemical pollutants (TVOCs) and reduced thermal comfort. To reduce the congregation's acute respiratory and cardiovascular risks, optimal ventilation systems and source-control measures are urgently needed, as evidenced by the presence of clinically relevant microorganisms combined with dangerous pollution levels.

Analysis↗
PubMed1978

Photochemical cross-linking of unmodified acetylvalyl-tRNA to 16S RNA at the ribosomal P site.

Acetylvalyl-, acetylphenylalanyl-, and formylmethionyl-tRNA which were derivatized at their 4-thiouridine residues with the photoaffinity label, p-azidophenacyl bromide, were nonenzymatically bound to salt-washed ribosomes. More than 90% of the binding was to the P site as judged by reactivity with puromycin. Subsequent irradiation (greater than 310 nm) of the tRNA-ribosome complexes resulted in the covalent linking of only the acetylvalyl-tRNA to the 30S subunit. Attachment was solely to the 16S RNA with an efficiency of cross-linking of 13--15%. Covalent linking was 90% inhibited by prior treatment with puromycin, showing that the covalent linking reaction had taken place at the P site. Cross-linking required irradiation and mRNA but was not dependent on the presence of the photoaffinity probe in the tRNA. tRNAs whose 4-thiouridine had been modified with unreactive analogues of p-azidophenacyl bromide or unmodified acetylvalyl-tRNA exhibited the same cross-linking behavior as photoaffinity probe-modified acetylvalyl-tRNA. Furthermore, even acetylvalyl-tRNA whose 4-thiouridine had been removed by treatment with H2O2 was quantitatively as active as unmodified tRNA. These results provide the first demonstration of direct photochemical cross-linking of tRNA to ribosomes.

Affinity Labels↗
PubMed1977

Sequence arrangement of the 5' ends of simian virus 40 16S and 19S mRNAs.

Electron microscopic examination of molecular hybrids between simian virus 40 DNA, that had been cleaved with EcoRI and then digested with exonuclease III, and either 16S or 19S mRNA produced late during the viral infection cycle indicated that each of these mRNAs contained a 5'-terminal "leader" sequence that was encoded in the viral genome at about map position 0.71-0.75. Hybridization of each of these mRNAs to viral DNA immobilized on nitrocellulose filters supported the electron microscopic observations.

Base Sequence↗
PubMed1977

High-resolution proton magnetic resonance study of the secondary structure of the 3'-terminal 49-nucleotide fragment of 16S rRNA from Escherichia coli.

The 3' terminus of 16S rRNA has been implicated in the recognition of mRNA's by the ribosome. A fragment containing the 3'-terminal 49 nucleotides cleaved from the rRNA by cloacin DF13 was isolated in a pure form. The secondary structure of this fragment has been studied by measuring the high-resolution proton magnetic resonance spectra. The resonances observed at low field can be assigned to hydrogen-bonded iminoprotons of base-pairs present in the fragment. From the data we conclude that the rRNA fragment, under the conditions used, exists as a hairpin consisting of eight intramolecular base-pairs, the 3'-terminal dodecanucleotide being unpaired. The implications of these findings with respect to the function of the ribosomal protein S1 are discussed.

Escherichia coli↗
PubMed1979

Rapid sequence determination of late simian virus 40 16S mRNA leader by using inhibitors of reverse transcriptase.

A method for the determination of the primary structure of spliced mRNA junction and leader sequences is described. By analogy to the DNA sequencing procedure of Sanger et al. [Sanger, F., Nicklen, S. & Coulson, A. R. (1977) Proc. Natl. Acad. Sci USA 74, 5463--5467], we use 2",3'-dideoxynucleoside triphosphates as chain-terminating inhibitors of the reverse transcriptase (RNA-dependent DNA polymerase) reaction. By using specific DNA restriction fragments as primers in combination with this technique, we have determined the sequence of the spliced junction between the body and the leader sequence of the 16S late mRNA of simian virus 40. The method described should be of general utility in mapping spliced mRNA regions for which the corresponding protein sequence (if any) is unknown.

Base Sequence↗
PubMed1979

Reverse transcriptase pauses at N2-methylguanine during in vitro transcription of Escherichia coli 16S ribosomal RNA.

A restriction fragment strand complementary to a sequence near the 3' end of Escherichia coli 16S rRNA has been used to prime reverse transcriptase (avian myeloblastosis virus RNA-directed DNA nucleotidyltransferase; deoxynucleosidetriphosphate:DNA deoxynucleotidyltransferase, EC 2.7.7.7). In addition to transcripts that were extended to the 5' end of the RNA, two major transcription intermediates were observed. These discrete-sized cDNA intermediates are the result of a kinetic barrier imposed by monomethylation of the amino group on guanine that participates in base-pairing. Both major transcription intermediates correspond to attenuation at the known positions of N2-methylguanine (m2G) in the rRNA sequence. The relaxation time for elongation of the cDNA through m2G is approximately 3 min. No other major kinetic pauses were observed in the 1340 bases transcribed.

Base Sequence↗
PubMed1979

Splicing as a requirement for biogenesis of functional 16S mRNA of simian virus 40.

Simian virus 40 deletion mutants were constructed lacking specifically the intervening sequences for a late viral mRNA. The construction method involved the replacement of portions of the late simian virus 40 genes with the DNA segment from reverse transcription of the viral mRNAs. Restriction endonuclease cleavage and sequence analysis confirmed the precise structure of the mutant DNAs and demonstrated that they contained the genetic information for VP1, including all potential 5' ends for the late viral RNAs. Thus, the primary late transcription product(s) of this mutant should have the structure of functional 16S mRNAs. Complementation analysis as well as immunoprecipitation showed, however, that deletion of the intervening sequences from this mutant prevented the expression of VP1. The nature of this failure appears to be a defect in the posttranscriptional processing of the viral RNA. These results indicate that splicing is an essential function in the biogenesis of certain mRNAs.

Animals↗