bacterial sequence
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2022 ◽  
Vol 12 ◽  
Author(s):  
Aaron J. Robinson ◽  
Hajnalka E. Daligault ◽  
Julia M. Kelliher ◽  
Erick S. LeBrun ◽  
Patrick S. G. Chain

Public sequencing databases are invaluable resources to biological researchers, but assessing data veracity as well as the curation and maintenance of such large collections of data can be challenging. Genomes of eukaryotic organelles, such as chloroplasts and other plastids, are particularly susceptible to assembly errors and misrepresentations in these databases due to their close evolutionary relationships with bacteria, which may co-occur within the same environment, as can be the case when sequencing plants. Here, based on sequence similarities with bacterial genomes, we identified several suspicious chloroplast assemblies present in the National Institutes of Health (NIH) Reference Sequence (RefSeq) collection. Investigations into these chloroplast assemblies reveal examples of erroneous integration of bacterial sequences into chloroplast ribosomal RNA (rRNA) loci, often within the rRNA genes, presumably due to the high similarity between plastid and bacterial rRNAs. The bacterial lineages identified within the examined chloroplasts as the most likely source of contamination are either known associates of plants, or co-occur in the same environmental niches as the examined plants. Modifications to the methods used to process untargeted ‘raw’ shotgun sequencing data from whole genome sequencing efforts, such as the identification and removal of bacterial reads prior to plastome assembly, could eliminate similar errors in the future.


Author(s):  
Francesco Coppolino ◽  
Letizia Romeo ◽  
Giampiero Pietrocola ◽  
Germana Lentini ◽  
Giuseppe Valerio De Gaetano ◽  
...  

Binding to plasminogen (Plg) enables bacteria to associate with and invade host tissues. The cell wall protein PbsP significantly contributes to the ability of group B streptococci, a frequent cause of invasive infection, to bind Plg. Here we sought to identify the molecular regions involved in the interactions between Plg and PbsP. The K4 Kringle domain of the Plg molecule was required for binding of Plg to whole PbsP and to a PbsP fragment encompassing a region rich in methionine and lysine (MK-rich domain). These interactions were inhibited by free L-lysine, indicating the involvement of lysine binding sites in the Plg molecule. However, mutation to alanine of all lysine residues in the MK-rich domain did not decrease its ability to bind Plg. Collectively, our data identify a novel bacterial sequence that can interact with lysine binding sites in the Plg molecule. Notably, such binding did not require the presence of lysine or other positively charged amino acids in the bacterial receptor. These data may be useful for developing alternative therapeutic strategies aimed at blocking interactions between group B streptococci and Plg.


2020 ◽  
Vol 87 (2) ◽  
Author(s):  
Laura Díaz-García ◽  
Sixing Huang ◽  
Cathrin Spröer ◽  
Rocío Sierra-Ramírez ◽  
Boyke Bunk ◽  
...  

ABSTRACT The engineering of complex communities can be a successful path to understand the ecology of microbial systems and improve biotechnological processes. Here, we developed a strategy to assemble a minimal and effective lignocellulolytic microbial consortium (MELMC) using a sequential combination of dilution-to-stimulation and dilution-to-extinction approaches. The consortium was retrieved from Andean forest soil and selected through incubation in liquid medium with a mixture of three types of agricultural plant residues. After the dilution-to-stimulation phase, approximately 50 bacterial sequence types, mostly belonging to the Sphingobacteriaceae, Enterobacteriaceae, Pseudomonadaceae, and Paenibacillaceae, were significantly enriched. The dilution-to-extinction method demonstrated that only eight of the bacterial sequence types were necessary to maintain microbial growth and plant biomass consumption. After subsequent stabilization, only two bacterial species (Pseudomonas sp. and Paenibacillus sp.) became highly abundant (>99%) within the MELMC, indicating that these are the key players in degradation. Differences in the composition of bacterial communities between biological replicates indicated that selection, sampling, and/or priority effects could shape the consortium structure. The MELMC can degrade up to ∼13% of corn stover, consuming mostly its (hemi)cellulosic fraction. Tests with chromogenic substrates showed that the MELMC secretes an array of endoenzymes able to degrade xylan, arabinoxylan, carboxymethyl cellulose, and wheat straw. Additionally, the metagenomic profile inferred from the phylogenetic composition along with an analysis of carbohydrate-active enzymes of 20 bacterial genomes support the potential of the MELMC to deconstruct plant polysaccharides. This capacity was mainly attributed to the presence of Paenibacillus sp. IMPORTANCE The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems.


2020 ◽  
Author(s):  
Bastiaan W. Haak ◽  
Ricard Argelaguet ◽  
Cormac M. Kinsella ◽  
Robert F.J. Kullberg ◽  
Jacqueline M. Lankelma ◽  
...  

AbstractBacterial microbiota play a critical role in mediating local and systemic immunity, and shifts in these microbial communities have been linked to impaired outcomes in critical illness. Emerging data indicate that other intestinal organisms, including bacteriophages, viruses of eukaryotes, fungi, and protozoa, are closely interlinked with the bacterial microbiota and their host, yet their collective role during antibiotic perturbation and critical illness remains to be elucidated. Here, multi-omics factor analysis (MOFA), a novel computational strategy to systematically integrate viral, fungal and bacterial sequence data, we describe the functional impact of exposure to broad-spectrum antibiotics in healthy volunteers and critically ill patients. We observe that a loss of the anaerobic intestinal environment is directly correlated with an overgrowth of aerobic pathobionts and their corresponding bacteriophages, as well as an absolute enrichment of opportunistic yeasts capable of causing invasive disease. These findings further illustrate the complexity of transkingdom interactions within the intestinal environment, and show that modulation of the bacterial component of the microbiome has implications extending beyond this kingdom alone.


eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Matthew D Hall ◽  
Matthew TG Holden ◽  
Pramot Srisomang ◽  
Weera Mahavanakul ◽  
Vanaporn Wuthiekanun ◽  
...  

Methicillin-resistant Staphylococcus aureus (MRSA) transmission in the hospital setting has been a frequent subject of investigation using bacterial genomes, but previous approaches have not yet fully utilised the extra deductive power provided when multiple pathogen samples are acquired from each host. Here, we used a large dataset of MRSA sequences from multiply-sampled patients to reconstruct colonisation of individuals in a high-transmission setting in a hospital in Thailand. We reconstructed transmission trees for MRSA. We also investigated transmission between anatomical sites on the same individual, finding that this either occurs repeatedly or involves a wide transmission bottleneck. We examined the between-subject bottleneck, finding considerable variation in the amount of diversity transmitted. Finally, we compared our approach to the simpler method of identifying transmission pairs using single nucleotide polymorphism (SNP) counts. This suggested that the optimum threshold for identifying a pair is 39 SNPs, if sensitivities and specificities are equally weighted.


2019 ◽  
Author(s):  
Matthew D Hall ◽  
Matthew TG Holden ◽  
Pramot Srisomang ◽  
Weera Mahavanakul ◽  
Vanaporn Wuthiekanun ◽  
...  

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S315-S315
Author(s):  
Carolyn Chang ◽  
Felicia Ruffin ◽  
Vance G Fowler ◽  
Joshua T Thaden

Abstract Background The clinical impact of Escherichia coli biofilm formation is unknown. Methods Adults with E. coli bloodstream infections (BSI) were prospectively enrolled from 2002 to 2015. All E. coli isolates were genotyped using Multilocus sequence typing (MLST) and underwent crystal violet biofilm formation assay quantified by absorbance at 540 nm (OD540) in triplicate. Associations between biofilm formation and patient/bacterial characteristics were characterized by t-tests and ANOVA tests. Results Ninety-eight percent (186) of the 189 isolates formed detectable biofilms. Bacterial sequence type (ST) was associated with biofilm formation (P < 0.001), as ST73 (average OD540 = 0.017) and ST393 (average OD540 = 0.016) had higher average biofilm formation while ST69 (average OD540 = 0.007) and ST405 (average OD540 = 0.002) had lower biofilm formation. E. coli isolates with non-multidrug-resistant (non-MDR) phenotype were associated with increased biofilm formation (MDR: average OD540 = 0.006; average non-MDR: OD540 = 0.01; P = 0.003). BSI isolates arising from pneumonia or urine/pyelonephritis were associated with the highest biofilm production (P = 0.04). No associations were identified between biofilm formation and route of infection, APACHE-II score, mortality, or complications of BSI. Conclusion In this prospective study of E. coli BSI isolates, biofilm formation was associated with ST, non-MDR phenotype, and BSI source. Disclosures All authors: No reported disclosures.


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