bacterial taxonomy
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BMC Biology ◽  
2022 ◽  
Vol 20 (1) ◽  
Author(s):  
Lin Chou ◽  
Yu-Chen Lin ◽  
Mindia Haryono ◽  
Mary Nia M. Santos ◽  
Shu-Ting Cho ◽  
...  

Abstract Background Many named species as defined in current bacterial taxonomy correspond to species complexes. Uncertainties regarding the organization of their genetic diversity challenge research efforts. We utilized the Agrobacterium tumefaciens species complex (a.k.a. Agrobacterium biovar 1), a taxon known for its phytopathogenicity and applications in transformation, as a study system and devised strategies for investigating genome diversity and evolution of species complexes. Results We utilized 35 genome assemblies, including 14 newly generated ones, to achieve a phylogenetically balanced sampling of A. tumefaciens. Our genomic analysis suggested that the 10 genomospecies described previously are distinct biological species and supported a quantitative guideline for species delineation. Furthermore, our inference of gene content and core-genome phylogeny allowed for investigations of genes critical in fitness and ecology. For the type VI secretion system (T6SS) involved in interbacterial competition and thought to be conserved, we detected multiple losses and one horizontal gene transfer. For the tumor-inducing plasmids (pTi) and pTi-encoded type IV secretion system (T4SS) that are essential for agrobacterial phytopathogenicity, we uncovered novel diversity and hypothesized their involvement in shaping this species complex. Intriguingly, for both T6SS and T4SS, genes encoding structural components are highly conserved, whereas extensive diversity exists for genes encoding effectors and other proteins. Conclusions We demonstrate that the combination of a phylogeny-guided sampling scheme and an emphasis on high-quality assemblies provides a cost-effective approach for robust analysis in evolutionary genomics. We show that the T6SS VgrG proteins involved in specific effector binding and delivery can be classified into distinct types based on domain organization. The co-occurrence patterns of VgrG-associated domains and the neighboring genes that encode different chaperones/effectors can be used to infer possible interacting partners. Similarly, the associations between plant host preference and the pTi type among these strains can be used to infer phenotype-genotype correspondence. Our strategies for multi-level investigations at scales that range from whole genomes to intragenic domains and phylogenetic depths from between- to within-species are applicable to other bacteria. Furthermore, modularity observed in the molecular evolution of genes and domains is useful for inferring functional constraints and informing experimental works.


Author(s):  
Peter Vandamme ◽  
Iain Sutcliffe

Chemotaxonomic methods played an important role in the development of the polyphasic approach to classification of Archaea and Bacteria. However, we here argue that routine application of these methods is unnecessary in an era when genomic data are available and sufficient for species delineation. Thus, authors who choose not to utilize such methods should not be forced to do so during the peer review and editorial handling of manuscripts describing novel species. Instead, we argue that chemotaxonomy will thrive if improved analytical methods are introduced and deployed, primarily by specialist laboratories, in studies at taxonomic levels above the characterisation of novel species.


Author(s):  
Mark J. Pallen

The status Candidatus was introduced to bacterial taxonomy in the 1990s to accommodate uncultured taxa defined by analyses of DNA sequences. Here I review the strengths, weaknesses, opportunities and threats (SWOT) associated with the status Candidatus in the light of a quarter century of use, twinned with recent developments in bacterial taxonomy and sequence-based taxonomic discovery. Despite ambiguities as to its scope, philosophical objections to its use and practical problems in implementation, the status Candidatus has now been applied to over 1000 taxa and has been widely adopted by journals and databases. Although lacking priority under the International Code for Nomenclature of Prokaryotes, many Candidatus names have already achieved de facto standing in the academic literature and in databases via description of a taxon in a peer-reviewed publication, alongside deposition of a genome sequence and there is a clear path to valid publication of such names on culture. Continued and increased use of Candidatus names provides an alternative to the potential upheaval that might accompany creation of a new additional code of nomenclature and provides a ready solution to the urgent challenge of naming many thousands of newly discovered but uncultured species.


Author(s):  
Ziyan Qin ◽  
Qun Gao ◽  
Qiang Dong ◽  
Joy D. Van Nostrand ◽  
Qi Qi ◽  
...  

2021 ◽  
Vol 9 (5) ◽  
pp. 1108
Author(s):  
Oliver Phipps ◽  
Mohammed N. Quraishi ◽  
Edward A. Dickson ◽  
Helen Steed ◽  
Aditi Kumar ◽  
...  

This study aims to determine differences in the on- and off-tumor microbiota between patients with right- and left-sided colorectal cancer. Microbiome profiling of tumor and tumor-adjacent biopsies from patients with right-sided (n = 17) and left-sided (n = 7) colorectal adenocarcinoma was performed using 16S ribosomal RNA sequencing. Off-tumor alpha and beta diversity were significantly different between right- and left-sided colorectal cancer patients. However, no differences in on-tumor diversity were observed between tumor locations. Comparing the off-tumor microbiota showed the right colon to be enriched with species of the Lachnoclostridium, Selenomonas, and Ruminococcus genera. Whereas the left colon is enriched with Epsilonbacteraeota phylum, Campylobacteria class, and Pasteurellales and Campylobacterales orders, in contrast, the on-tumor microbiota showed relatively fewer differences in bacterial taxonomy between tumor sites, with left tumors being enriched with Methylophilaceae and Vadin BE97 families and Alloprevotella, Intestinibacter, Romboutsia, and Ruminococcus 2 genera. Patients with left-sided colorectal cancer had large taxonomic differences between their paired on- and off-tumor microbiota, while patients with right-sided colorectal cancer showed relatively fewer taxonomic differences. Collectively, this suggests that the right and left colon show distinctive bacterial populations; however, the presence of a colonic tumor leads to a more consistent microbiota between locations.


2021 ◽  
Vol 30 (2) ◽  
pp. 128-132
Author(s):  
Mary Lou Sole ◽  
Shibu Yooseph ◽  
Steven Talbert ◽  
Bassam Abomoelak ◽  
Chirajyoti Deb ◽  
...  

Background Interest in the pulmonary microbiome is growing, particularly in patients undergoing mechanical ventilation. Objectives To explore the pulmonary microbiome over time in patients undergoing prolonged mechanical ventilation and to evaluate the effect of an oral suctioning intervention on the microbiome. Methods This descriptive subanalysis from a clinical trial involved a random sample of 16 participants (7 intervention, 9 control) who received mechanical ventilation for at least 5 days. Five paired oral and tracheal specimens were evaluated for each participant over time. Bacterial DNA from the paired specimens was evaluated using 16S rRNA gene sequencing. Bacterial taxonomy composition, α-diversity (Shannon index), and β-diversity (Morisita-Horn index) were calculated and compared within and between participants. Results Participants were predominantly male (69%) and White (63%), with a mean age of 58 years, and underwent mechanical ventilation for a mean of 9.36 days. Abundant bacterial taxa included Prevotella, Staphylococcus, Streptococcus, Stenotrophomonas, and Veillonella. Mean tracheal α-diversity decreased over time for the total group (P = .002) and the control group (P = .02). β-Diversity was lower (P = .04) in the control group (1.905) than in the intervention group (2.607). Conclusions Prolonged mechanical ventilation was associated with changes in the pulmonary microbiome, with the control group having less diversity. The oral suctioning intervention may have reduced oral-tracheal bacterial transmission.


Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 506
Author(s):  
Christina Wimmer-Scherr ◽  
Bernard Taminiau ◽  
Benoît Renaud ◽  
Gunther van Loon ◽  
Katrien Palmers ◽  
...  

Equine atypical myopathy (AM) is caused by hypoglycin A (HGA) and methylenecyclopropylglycine (MCPG) intoxication resulting from the ingestion of seeds or seedlings of some Acer tree species. Interestingly, not all horses pasturing in the same toxic environment develop signs of the disease. In other species, it has been shown that the intestinal microbiota has an impact on digestion, metabolism, immune stimulation and protection from disease. The objective of this study was to characterize and compare fecal microbiota of horses suffering from AM and healthy co-grazers. Furthermore, potential differences in fecal microbiota regarding the outcome of diseased animals were assessed. This prospective observational study included 59 horses with AM (29 survivors and 30 non-survivors) referred to three Belgian equine hospitals and 26 clinically healthy co-grazers simultaneously sharing contaminated pastures during spring and autumn outbreak periods. Fresh fecal samples (rectal or within 30 min of defecation) were obtained from all horses and bacterial taxonomy profiling obtained by 16S amplicon sequencing was used to identify differentially distributed bacterial taxa between AM-affected horses and healthy co-grazers. Fecal microbial diversity and evenness were significantly (p < 0.001) higher in AM-affected horses as compared with their non-affected co-grazers. The relative abundance of families Ruminococcaceae, Christensenellaceae and Akkermansiaceae were higher (p ≤ 0.001) whereas those of the Lachnospiraceae (p = 0.0053), Bacteroidales (p < 0.0001) and Clostridiales (p = 0.0402) were lower in horses with AM, especially in those with a poor prognosis. While significant shifts were observed, it is still unclear whether they result from the disease or might be involved in the onset of disease pathogenesis.


2021 ◽  
Author(s):  
Oliver Phipps ◽  
Mohammed N Quraishi ◽  
Edward A Dickson ◽  
Jonathan Segal ◽  
Helen Steed ◽  
...  

Abstract Objective This study aims to determine the differences in the microbial profiles of the on- and off-tumour microbiota between patients with right- and left-sided colorectal cancer.Design Microbial profiling of on- and off-tumour biopsies from patients with right-sided (n=17) and left-sided (n=7) colorectal adenocarcinoma was performed using 16S ribosomal RNA sequencing. Results Off-tumour alpha diversity is significantly greater in right-sided compared to left-sided colorectal cancer patients. However, no differences in on-tumour alpha diversity were observed between tumour locations. Off-tumour beta diversity showed distinctive bacterial community clusters between the right and left colon, while no significant differences in beta diversity were observed in the on-tumour microbiota. The off-tumour microbiota showed the right colon to be enriched with species of the Lachnoclostridium, Selenomonas and Ruminococcus genera, whereas the left colon is enriched with Epsilonbacteraeota phylum, Campylobacteria class, and Pasteurellales and Campylobacterales orders. In contrast the on-tumour microbiota showed relatively fewer differences in bacterial taxonomy between tumour sites, with left tumours being enriched with Methylophilaceae and Vadin BE97 families and Alloprevotella, Intestinibacter, Romboutsia and Ruminococcus 2 genera. Comparison of paired on- and off-tumour microbiotas showed that patients with left-sided colorectal cancer had large taxonomic differences between their on- and off-tumour microbiota, while patients with right-sided colorectal cancer showed relatively fewer taxonomic differences.Conclusion The off-tumour microbiota is more diverse in the right compared to the left colon, showing distinct community clusters and large differences in bacterial taxonomy. In contrast the on-tumour microbiota shows no difference in bacterial diversity and relatively fewer differences in bacterial taxonomy. Collectively this suggests that the right and left colon show distinctive bacterial communities, however, the presence of a colonic tumour leads to a more consistent microbiota between locations. Trial registration number clinicaltrials.gov (NCT01701310).


Forests ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 157
Author(s):  
Vicky Waymouth ◽  
Rebecca E. Miller ◽  
Sabine Kasel ◽  
Fiona Ede ◽  
Andrew Bissett ◽  
...  

Riparian forests were frequently cleared and converted to agricultural pastures, but in recent times these pastures are often revegetated in an effort to return riparian forest structure and function. We tested if there is a change in the soil bacterial taxonomy and function in areas of riparian forest cleared for agricultural pasture then revegetated, and if soil bacterial taxonomy and function is related to vegetation and soil physicochemical properties. The study was conducted in six riparian areas in south-eastern Australia, each comprising of three land-use types: remnant riparian forest, cleared forest converted to pasture, and revegetated pastures. We surveyed three strata of vegetation and sampled surface soil and subsoil to characterize physicochemical properties. Taxonomic and functional composition of soil bacterial communities were assessed using 16S rRNA gene sequences and community level physiological profiles, respectively. Few soil physiochemical properties differed with land use despite distinct vegetation in pasture relative to remnant and revegetated areas. Overall bacterial taxonomic and functional composition of remnant forest and revegetated soils were distinct from pasture soil. Land-use differences were not consistent for all bacterial phyla, as Acidobacteria were more abundant in remnant soils; conversely, Actinobacteria were more abundant in pasture soils. Overall, bacterial metabolic activity and soil carbon and nitrogen content decreased with soil depth, while bacterial metabolic diversity and evenness increased with soil depth. Soil bacterial taxonomic composition was related to soil texture and soil fertility, but functional composition was only related to soil texture. Our results suggest that the conversion of riparian forests to pasture is associated with significant changes in the soil bacterial community, and that revegetation contributes to reversing such changes. Nevertheless, the observed changes in bacterial community composition (taxonomic and functional) were not directly related to changes in vegetation but were more closely related to soil attributes.


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