Genotyping ofBartonellabacteria and their animal hosts: current status and perspectives

SUMMARYGrowing evidence demonstrates that bacterial species diversity is substantial, and many of these species are pathogenic in some contexts or hosts. At the same time, laboratories and museums have collected valuable animal tissue and ectoparasite samples that may contain substantial novel information on bacterial prevalence and diversity. However, the identification of bacterial species is challenging, partly due to the difficulty in culturing many microbes and the reliance on molecular data. Although the genomics revolution will surely add to our knowledge of bacterial systematics, these approaches are not accessible to all researchers and rely predominantly on cultured isolates. Thus, there is a need for comprehensive molecular analyses capable of accurately genotyping bacteria from animal tissues or ectoparasites using common methods that will facilitate large-scale comparisons of species diversity and prevalence. To illustrate the challenges of genotyping bacteria, we focus on the genusBartonella, vector-borne bacteria common in mammals. We highlight the value and limitations of commonly used techniques for genotyping bartonellae and make recommendations for researchers interested in studying the diversity of these bacteria in various samples. Our recommendations could be applicable to many bacterial taxa (with some modifications) and could lead to a more complete understanding of bacterial species diversity.

Download Full-text

Large-scale cultivation of the bumblebee gut microbiota reveals an underestimated bacterial species diversity capable of pathogen inhibition

Environmental Microbiology ◽

10.1111/1462-2920.13973 ◽

2017 ◽

Vol 20 (1) ◽

pp. 214-227 ◽

Cited By ~ 16

Author(s):

Jessy Praet ◽

Anneleen Parmentier ◽

Regula Schmid-Hempel ◽

Ivan Meeus ◽

Guy Smagghe ◽

...

Keyword(s):

Species Diversity ◽

Gut Microbiota ◽

Large Scale ◽

Bacterial Species ◽

Pathogen Inhibition ◽

Large Scale Cultivation

Download Full-text

Recent Developments in the Downstream Processing of Phycobiliproteins from Algae: A Review

Current Biochemical Engineering ◽

10.2174/2212711906999210101230613 ◽

2021 ◽

Vol 06 ◽

Author(s):

Ayekpam Chandralekha Devi ◽

G. K. Hamsavi ◽

Simran Sahota ◽

Rochak Mittal ◽

Hrishikesh A. Tavanandi ◽

...

Keyword(s):

Cell Wall ◽

Large Scale ◽

Downstream Processing ◽

Review Article ◽

Current Status ◽

Wall Structure ◽

Scale Production ◽

Cell Wall Disruption ◽

Recent Developments ◽

Macro Algae

Abstract: Algae (both micro and macro) have gained huge attention in the recent past for their high commercial value products. They are the source of various biomolecules of commercial applications ranging from nutraceuticals to fuels. Phycobiliproteins are one such high value low volume compounds which are mainly obtained from micro and macro algae. In order to tap the bioresource, a significant amount of work has been carried out for large scale production of algal biomass. However, work on downstream processing aspects of phycobiliproteins (PBPs) from algae is scarce, especially in case of macroalgae. There are several difficulties in cell wall disruption of both micro and macro algae because of their cell wall structure and compositions. At the same time, there are several challenges in the purification of phycobiliproteins. The current review article focuses on the recent developments in downstream processing of phycobiliproteins (mainly phycocyanins and phycoerythrins) from micro and macroalgae. The current status, the recent advancements and potential technologies (that are under development) are summarised in this review article besides providing future directions for the present research area.

Download Full-text

Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

Genome Biology and Evolution ◽

10.1093/gbe/evab020 ◽

2021 ◽

Author(s):

Anna Lavecchia ◽

Matteo Chiara ◽

Caterina De Virgilio ◽

Caterina Manzari ◽

Carlo Pazzani ◽

...

Keyword(s):

Comparative Genomics ◽

Species Complex ◽

Large Scale ◽

Genomic Sequence ◽

Bacterial Species ◽

Taxonomic Revision ◽

Distinct Species ◽

The Novel ◽

Staphylococcus Cohnii ◽

Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

Download Full-text

Wolbachia: endosymbiont of onchocercid nematodes and their vectors

Parasites & Vectors ◽

10.1186/s13071-021-04742-1 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Ranju Ravindran Santhakumari Manoj ◽

Maria Stefania Latrofa ◽

Sara Epis ◽

Domenico Otranto

Keyword(s):

Control Strategies ◽

Molecular Data ◽

Scientific Data ◽

Growth And Survival ◽

Vector Borne Diseases ◽

Wide Range ◽

Veterinary Importance ◽

Wolbachia Endosymbiont ◽

Vector Borne ◽

And Control

Abstract Background Wolbachia is an obligate intracellular maternally transmitted, gram-negative bacterium which forms a spectrum of endosymbiotic relationships from parasitism to obligatory mutualism in a wide range of arthropods and onchocercid nematodes, respectively. In arthropods Wolbachia produces reproductive manipulations such as male killing, feminization, parthenogenesis and cytoplasmic incompatibility for its propagation and provides an additional fitness benefit for the host to protect against pathogens, whilst in onchocercid nematodes, apart from the mutual metabolic dependence, this bacterium is involved in moulting, embryogenesis, growth and survival of the host. Methods This review details the molecular data of Wolbachia and its effect on host biology, immunity, ecology and evolution, reproduction, endosymbiont-based treatment and control strategies exploited for filariasis. Relevant peer-reviewed scientic papers available in various authenticated scientific data bases were considered while writing the review. Conclusions The information presented provides an overview on Wolbachia biology and its use in the control and/or treatment of vectors, onchocercid nematodes and viral diseases of medical and veterinary importance. This offers the development of new approaches for the control of a variety of vector-borne diseases. Graphic Abstract

Download Full-text

Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

mSystems ◽

10.1128/msystems.00731-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 14

Author(s):

Matthew R. Olm ◽

Alexander Crits-Christoph ◽

Spencer Diamond ◽

Adi Lavy ◽

Paula B. Matheus Carnevali ◽

...

Keyword(s):

Bacterial Diversity ◽

Ribosomal Proteins ◽

Large Scale ◽

Bacterial Species ◽

Bacterial Genome ◽

16S Rrna Genes ◽

Rrna Genes ◽

Species Discrimination ◽

Bacterial Genomes ◽

Discrimination Power

ABSTRACT Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. To avoid these biases, we compared 5,203 bacterial genomes from 1,457 environmental metagenomic samples to test for distinct clouds of diversity and evaluated metrics that could be used to define the species boundary. Bacterial genomes from the human gut, soil, and the ocean all exhibited gaps in whole-genome average nucleotide identities (ANI) near the previously suggested species threshold of 95% ANI. While genome-wide ratios of nonsynonymous and synonymous nucleotide differences (dN/dS) decrease until ANI values approach ∼98%, two methods for estimating homologous recombination approached zero at ∼95% ANI, supporting breakdown of recombination due to sequence divergence as a species-forming force. We evaluated 107 genome-based metrics for their ability to distinguish species when full genomes are not recovered. Full-length 16S rRNA genes were least useful, in part because they were underrecovered from metagenomes. However, many ribosomal proteins displayed both high metagenomic recoverability and species discrimination power. Taken together, our results verify the existence of sequence-discrete microbial species in metagenome-derived genomes and highlight the usefulness of ribosomal genes for gene-level species discrimination. IMPORTANCE There is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is likely a key evolutionary force that maintains bacterial species integrity. We next benchmarked over 100 metrics to distinguish these bacterial species from each other and identified several genes encoding ribosomal proteins with high species discrimination power. Overall, the results from this study provide best practices for bacterial species delineation based on genome content and insight into the nature of bacterial species population genetics.

Download Full-text

Species diversity of Onchidiidae (Eupulmonata: Heterobranchia) on the mainland of China based on molecular data

Molluscan Research ◽

10.1080/13235818.2013.868860 ◽

2013 ◽

Vol 34 (1) ◽

pp. 62-70 ◽

Cited By ~ 13

Author(s):

Bianna Sun ◽

Cheng Chen ◽

Heding Shen ◽

Kunxia Zhang ◽

Na Zhou ◽

...

Keyword(s):

Species Diversity ◽

Molecular Data ◽

The Mainland Of China

Download Full-text

Antimicrobial resistance in zoonotic bacteria: lessons learned from host-specific pathogens

Animal Health Research Reviews ◽

10.1017/s1466252308001539 ◽

2008 ◽

Vol 9 (2) ◽

pp. 177-186 ◽

Cited By ~ 13

Author(s):

Trudy M. Wassenaar ◽

Peter Silley

Keyword(s):

Antimicrobial Resistance ◽

Bacterial Species ◽

Lessons Learned ◽

Animal Host ◽

Relative Contribution ◽

Single Animal ◽

Resistance Patterns ◽

Animal Hosts ◽

Zoonotic Bacteria ◽

Selection Of

AbstractThe relative contribution of veterinary and human clinical treatments to the selection of antimicrobial resistance in zoonotic pathogens remains controversial. In this review, we consider bacterial pathogens that differ in host specificity and address their resistance profiles: pathogens that only occur in the human host, pathogens that are specific to particular food-producing animals and pathogens that occur in both host types. Compared with those pathogens restricted to a single animal host, pathogens found in both human and animal hosts appear to have higher incidences of resistance. However, the most urgent and severe resistance problems occur with pathogens exclusively infecting humans. Differences exist in the available genetic repertoire of a bacterial species and these are reflected in the observed resistance patterns; it is important to note that different bacterial species do not automatically result in similarly resistant populations when they undergo comparable selection in different host species. Thus, within a bacterial species, prevalence of resistance can differ between populations isolated from different hosts. For some species, fluctuations in dominant subpopulations, for instance particular serotypes, can be the most important factor determining resistance. The frequently expressed opinion that veterinary use of antimicrobials is at the heart of many resistance problems may be an oversimplification of the complex forces at play.

Download Full-text

Adherence and competence assessment in studies of CBT for psychosis: current status and future directions

Epidemiology and Psychiatric Sciences ◽

10.1017/s2045796011000199 ◽

2011 ◽

Vol 20 (2) ◽

pp. 121-126 ◽

Cited By ~ 15

Author(s):

D. Fowler ◽

R. Rollinson ◽

P. French

Keyword(s):

Cognitive Therapy ◽

Large Scale ◽

Rating Scale ◽

Current Status ◽

Behaviour Therapy ◽

Future Directions ◽

Making Sense ◽

Cognitive Behaviour ◽

The Uk ◽

Careful Assessment

All good quality trials of psychological interventions need to check formally that therapists have used the techniques prescribed in the published therapy manuals, and that the therapy has been carried out competently. This paper reviews methods of assessing adherence and competence used in recent large-scale trials of Cognitive Behaviour Therapy (CBT) for psychosis in the UK carried out by our research groups. A combination of the Cognitive Therapy Rating Scale and specific versions of the Cognitive Therapy for Psychosis Adherence Scales provides an optimal assessment of adherence and competence. Careful assessment of the competence and adherence can help identify the procedures actually carried out with individuals within trials. The basic use of such assessments is to provide an external check on treatment fidelity on a sample of sessions. Such assessment can also provide the first step towards moving research towards making sense of CBT for psychosis as a complex intervention and identifying which techniques work for which problems of people with psychosis, at which stages of disorder?

Download Full-text