scholarly journals Dynamic interspecies interactions and robustness in a four-species model biofilm

2021 ◽  
Author(s):  
Aurélie Baliarda ◽  
Michèle Winkler ◽  
Laurent Tournier ◽  
Colin Tinsley ◽  
Stéphane Aymerich
Keyword(s):  
Mutational Analysis ◽  
Interspecific Interactions ◽  
Bacterial Species ◽  
Species Abundance ◽  
Growth Dynamics ◽  
Equilibrium Composition ◽  
Interspecies Interactions ◽  
Molecular Determinant ◽  
And Function ◽  
Final Composition

Interspecific interactions within biofilms determine relative species abundance, growth dynamics, community resilience, and success or failure of invasion by an extraneous organism. However, deciphering interspecific interactions and assessing their contribution to biofilm properties and function remain a challenge. Here, we describe the constitution of a model biofilm composed of four bacterial species belonging to four different genera (Rhodocyclus sp., Pseudomonas fluorescens, Kocuria varians, and Bacillus cereus), derived from a biofilm isolated from an industrial milk pasteurization unit. We demonstrate that the growth dynamics and equilibrium composition of this biofilm are highly reproducible. Based on its equilibrium composition, we show that the establishment of this 4-species biofilm is highly robust against initial, transient perturbations but less so towards continuous perturbations. By comparing biofilms formed from different numbers and combinations of the constituent species and by fitting a growth model to the experimental data, we reveal a network of dynamic, positive, and negative interactions that determine the final composition of the biofilm. Furthermore, we reveal that the molecular determinant of one negative interaction is the thiocillin I synthesized by the B. cereus strain, and demonstrate its importance for species distribution and its impact on robustness by mutational analysis of the biofilm ecosystem.

scholarly journals Interspecies bacterial competition determines community assembly in the C. elegans intestine

2019 ◽  
Author(s):  
Anthony Ortiz Lopez ◽  
Nicole M. Vega ◽  
Jeff Gore
Keyword(s):  
Community Assembly ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Valuable Insight ◽  
Interspecies Interactions ◽  
Bottom Up ◽  
C Elegans ◽  
Bacterial Competition ◽  
Average Fraction ◽  
And Function

AbstractFrom insects to mammals, a large variety of animals hold in their intestines complex bacterial communities that play an important role in health and disease. However, the complexity of these gut microbiomes and their hosts often constrains our ability to understand how these bacterial communities assemble and function. In order to elucidate basic principles of community assembly in a host intestine, we study the assembly of the microbiome of Caenorhabditis elegans with a bottom-up approach. We colonize the gut of the worm C. elegans with 11 bacterial species individually, in all possible pairs, and in selected trios, and we find an organized mixture of coexistence and competitive exclusion that indicates a hierarchical structure in the bacterial interactions. The capacity of a bacterial species fed in monoculture to colonize the C. elegans intestine correlates with its average fraction in co-culture experiments, yet fails to predict its abundance in many two- and three-species microbiomes. Hence, the bacterial fractional abundances in co-culture experiments—pairwise outcomes—are influenced by interspecies interactions. These pairwise outcomes accurately predict the trio outcomes in the worm intestine, further highlighting the importance of pairwise interactions in determining community composition. We also find that the C. elegans gut environment influences the outcome of co-culture experiments, and demonstrate that the low intestinal pH is one of the causes. These results highlight that a bottom-up approach to microbiome community assembly may provide valuable insight into the structure and composition of complex microbial communities.

scholarly journals Interspecies bacterial competition regulates community assembly in the C. elegans intestine

2021 ◽  
Author(s):  
Anthony Ortiz ◽  
Nicole M. Vega ◽  
Christoph Ratzke ◽  
Jeff Gore
Keyword(s):  
Community Assembly ◽  
Bacterial Communities ◽  
Mapk Pathway ◽  
Dominant Role ◽  
Bacterial Species ◽  
Environmental Filtering ◽  
Community Diversity ◽  
Interspecies Interactions ◽  
C Elegans ◽  
And Function

AbstractFrom insects to mammals, a large variety of animals hold in their intestines complex bacterial communities that play an important role in health and disease. To further our understanding of how intestinal bacterial communities assemble and function, we study the C. elegans microbiota with a bottom-up approach by feeding this nematode with bacterial monocultures as well as mixtures of two to eight bacterial species. We find that bacteria colonizing well in monoculture do not always do well in co-cultures due to interspecies bacterial interactions. Moreover, as community diversity increases, the ability to colonize the worm gut in monoculture becomes less important than interspecies interactions for determining community assembly. To explore the role of host–microbe adaptation, we compare bacteria isolated from C. elegans intestines and non-native isolates, and we find that the success of colonization is determined more by a species’ taxonomy than by the isolation source. Lastly, by comparing the assembled microbiotas in two C. elegans mutants, we find that innate immunity via the p38 MAPK pathway decreases bacterial abundances yet has little influence on microbiota composition. These results highlight that bacterial interspecies interactions, more so than host–microbe adaptation or gut environmental filtering, play a dominant role in the assembly of the C. elegans microbiota.

scholarly journals Mutational Analysis of the Flagellar Rotor Protein FliN: Identification of Surfaces Important for Flagellar Assembly and Switching

2006 ◽  
Vol 188 (14) ◽  
pp. 5240-5248 ◽  
Author(s):  
Koushik Paul ◽  
Jacob G. Harmon ◽  
David F. Blair
Keyword(s):  
Binding Sites ◽  
Mutational Analysis ◽  
Bacterial Species ◽  
Cross Linking ◽  
Binding Interaction ◽  
Dimer Interface ◽  
Hydrophobic Patch ◽  
Flagellar Assembly ◽  
And Function ◽  
Assembly Defect

ABSTRACT FliN is a component of the flagellar switch complex in many bacterial species. The crystal structure is known for most of FliN, and a targeted cross-linking study (K. Paul and D. F. Blair, J. Bacteriol. 188:2502-2511, 2006) showed that it is organized in ring-shaped tetramers at the bottom of the basal body C ring. FliN is essential for flagellar assembly and direction switching, but its precise functions have not been defined. Here, we identify functionally important regions on FliN by systematic mutagenesis. Nonconservative mutations were made at positions sampling the surface of the protein, and the effects on flagellar assembly and function were measured. Flagellar assembly was disrupted by mutations in a conserved hydrophobic patch centered on the dimer twofold axis or by mutations on the surface that forms the dimer-dimer interface in the tetramer. The assembly defect in hydrophobic-patch mutants was partially rescued by overexpression of the flagellar export proteins FliH and FliI, and coprecipitation assays demonstrated a binding interaction between FliN and FliH that was weakened by mutations in the hydrophobic patch. Thus, FliN might contribute to export by providing binding sites for FliH or FliH-containing complexes. The region around the hydrophobic patch is also important for switching; certain mutations in or near the patch caused a smooth-swimming chemotaxis defect that in most cases could be partially rescued by overexpression of the clockwise-signaling protein CheY. The results indicate that FliN is more closely involved in switching than has been supposed, possibly contributing to the binding site for CheY on the switch.

scholarly journals T6SS Mediated Stress Responses for Bacterial Environmental Survival and Host Adaptation

2021 ◽  
Vol 22 (2) ◽  
pp. 478
Author(s):  
Kai-Wei Yu ◽  
Peng Xue ◽  
Yang Fu ◽  
Liang Yang
Keyword(s):  
Protein Secretion ◽  
Stress Responses ◽  
Current Knowledge ◽  
Bacterial Species ◽  
Host Cells ◽  
Interspecies Interactions ◽  
Type Vi Secretion System ◽  
Membrane Complex ◽  
Type Vi Secretion ◽  
Bacterial Type

The bacterial type VI secretion system (T6SS) is a protein secretion apparatus widely distributed in Gram-negative bacterial species. Many bacterial pathogens employ T6SS to compete with the host and to coordinate the invasion process. The T6SS apparatus consists of a membrane complex and an inner tail tube-like structure that is surrounded by a contractile sheath and capped with a spike complex. A series of antibacterial or antieukaryotic effectors is delivered by the puncturing device consisting of a Hcp tube decorated by the VgrG/PAAR complex into the target following the contraction of the TssB/C sheath, which often leads to damage and death of the competitor and/or host cells. As a tool for protein secretion and interspecies interactions, T6SS can be triggered by many different mechanisms to respond to various physiological conditions. This review summarizes our current knowledge of T6SS in coordinating bacterial stress responses against the unfavorable environmental and host conditions.

Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

2020 ◽  
Vol 96 (3) ◽  
Author(s):  
Gavin J Fenske ◽  
Sudeep Ghimire ◽  
Linto Antony ◽  
Jane Christopher-Hennings ◽  
Joy Scaria
Keyword(s):  
Bacterial Communities ◽  
Bacterial Species ◽  
Shotgun Metagenomics ◽  
Culture Techniques ◽  
Microbiome Composition ◽  
Culture Independent ◽  
Health And Disease ◽  
The Media ◽  
And Function ◽  
Culture Dependent

ABSTRACT Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

scholarly journals Signal Integration in Quorum Sensing Enables Cross-Species Induction of Virulence in Pectobacterium wasabiae

mBio ◽  
2017 ◽  
Vol 8 (3) ◽  
Author(s):  
Rita S. Valente ◽  
Pol Nadal-Jimenez ◽  
André F. P. Carvalho ◽  
Filipe J. D. Vieira ◽  
Karina B. Xavier
Keyword(s):  
Signal Transduction ◽  
Quorum Sensing ◽  
Plant Pathogen ◽  
Bacterial Species ◽  
Homoserine Lactone ◽  
Signal Molecules ◽  
Acyl Homoserine Lactone ◽  
Interspecies Interactions ◽  
Major Factors

ABSTRACT Bacterial communities can sense their neighbors, regulating group behaviors in response to cell density and environmental changes. The diversity of signaling networks in a single species has been postulated to allow custom responses to different stimuli; however, little is known about how multiple signals are integrated and the implications of this integration in different ecological contexts. In the plant pathogen Pectobacterium wasabiae (formerly Erwinia carotovora), two signaling networks—the N-acyl homoserine lactone (AHL) quorum-sensing system and the Gac/Rsm signal transduction pathway—control the expression of secreted plant cell wall-degrading enzymes, its major virulence determinants. We show that the AHL system controls the Gac/Rsm system by affecting the expression of the regulatory RNA RsmB. This regulation is mediated by ExpR2, the quorum-sensing receptor that responds to the P. wasabiae cognate AHL but also to AHLs produced by other bacterial species. As a consequence, this level of regulation allows P. wasabiae to bypass the Gac-dependent regulation of RsmB in the presence of exogenous AHLs or AHL-producing bacteria. We provide in vivo evidence that this pivotal role of RsmB in signal transduction is important for the ability of P. wasabiae to induce virulence in response to other AHL-producing bacteria in multispecies plant lesions. Our results suggest that the signaling architecture in P. wasabiae was coopted to prime the bacteria to eavesdrop on other bacteria and quickly join the efforts of other species, which are already exploiting host resources. IMPORTANCE Quorum-sensing mechanisms enable bacteria to communicate through small signal molecules and coordinate group behaviors. Often, bacteria have various quorum-sensing receptors and integrate information with other signal transduction pathways, presumably allowing them to respond to different ecological contexts. The plant pathogen Pectobacterium wasabiae has two N-acyl homoserine lactone receptors with apparently the same regulatory functions. Our work revealed that the receptor with the broadest signal specificity is also responsible for establishing the link between the main signaling pathways regulating virulence in P. wasabiae. This link is essential to provide P. wasabiae with the ability to induce virulence earlier in response to higher densities of other bacterial species. We further present in vivo evidence that this novel regulatory link enables P. wasabiae to join related bacteria in the effort to degrade host tissue in multispecies plant lesions. Our work provides support for the hypothesis that interspecies interactions are among the major factors influencing the network architectures observed in bacterial quorum-sensing pathways. IMPORTANCE Quorum-sensing mechanisms enable bacteria to communicate through small signal molecules and coordinate group behaviors. Often, bacteria have various quorum-sensing receptors and integrate information with other signal transduction pathways, presumably allowing them to respond to different ecological contexts. The plant pathogen Pectobacterium wasabiae has two N-acyl homoserine lactone receptors with apparently the same regulatory functions. Our work revealed that the receptor with the broadest signal specificity is also responsible for establishing the link between the main signaling pathways regulating virulence in P. wasabiae. This link is essential to provide P. wasabiae with the ability to induce virulence earlier in response to higher densities of other bacterial species. We further present in vivo evidence that this novel regulatory link enables P. wasabiae to join related bacteria in the effort to degrade host tissue in multispecies plant lesions. Our work provides support for the hypothesis that interspecies interactions are among the major factors influencing the network architectures observed in bacterial quorum-sensing pathways.

Linear plasmids in Klebsiella and other Enterobacteriaceae

2021 ◽  
Author(s):  
Jane Hawkey ◽  
Hugh Cottingham ◽  
Alex Tokolyi ◽  
Ryan R Wick ◽  
Louise M Judd ◽  
...  
Keyword(s):  
Plasmid Stability ◽  
Bacterial Species ◽  
Salmonella Typhi ◽  
Multidrug Resistant ◽  
Linear Plasmid ◽  
Extrachromosomal Dna ◽  
Linear Plasmids ◽  
Future Studies ◽  
And Function

Linear plasmids are extrachromosomal DNA that have been found in a small number of bacterial species. To date, the only linear plasmids described in the Enterobacteriaceae family belong to Salmonella, first found in Salmonella Typhi. Here, we describe a collection of 12 isolates of the Klebsiella pneumoniae species complex in which we identified linear plasmids. We used this collection to search public sequence databases and discovered an additional 74 linear plasmid sequences in a variety of Enterobacteriaceae species. Gene content analysis divided these plasmids into five distinct phylogroups, with very few genes shared across more than two phylogroups. The majority of linear plasmid-encoded genes are of unknown function, however each phylogroup carried its own unique toxin-antitoxin system and genes with homology to those encoding the ParAB plasmid stability system. Passage in vitro of the 12 linear plasmid-carrying Klebsiella isolates in our collection (which include representatives of all five phylogroups) indicated that these linear plasmids can be stably maintained, and our data suggest they can transmit between K. pneumoniae strains (including members of globally disseminated multidrug resistant clones) and also between diverse Enterobacteriaceae species. The linear plasmid sequences, and representative isolates harbouring them, are made available as a resource to facilitate future studies on the evolution and function of these novel plasmids.

scholarly journals Impact of Different Carbon Sources on the in vitro Growth and Viability of Escherichia coli (SUBE01) and Salmonella spp. (SUBS01) Cells

2016 ◽  
pp. 39-44
Author(s):  
Ifra Tun Nur ◽  
Jannatun Tahera ◽  
Md Sakil Munna ◽  
M Majibur Rahman ◽  
Rashed Noor
Keyword(s):  
Escherichia Coli ◽  
Bacterial Growth ◽  
Culture Media ◽  
Bacterial Species ◽  
Carbon Sources ◽  
Growth Dynamics ◽  
Luria Bertani ◽  
Tween 20 ◽  
Salmonella Spp

With a previous observation of Escherichia coli growth cessation along with temperature variation within three different bacteriological culture media (nutrient agar, Luria-Bertani agar and minimal agar), current investigation further depicted on the possible growth dynamics of Escherichia coli (SUBE01) and Salmonella (SUBS01) growth and viability upon supplementation of different carbon sources (dextrose, sucrose, lactose, glycerol and tween 20) at 37°C under the aeration of 100 rpm. Viability of the tested bacterial species was assessed through the enumeration of the colony forming unit (cfu) appeared upon prescribed incubation for 12-24 hours on different agar plates consisting of the above mentioned carbon sources. Besides, to inspect the cellular phenotypic changes, morphological observations were conducted under the light microscope. Variations in bacterial growth (either growth acceleration or cessation) were further noticed through the spot tests on the agar plates. Considerable shortfalls in the culturable cells of E. coli and Salmonella spp. were noted in the minimal media separately consisting of sucrose, lactose, glycerol or tween 20 while an opposite impact of accelerated growth was noticed in the media supplied with dextrose. The data revealed a hierarchy of consequence of carbon sources as nutrient generators whereby the favourable bacterial growth and survival order of the carbon sources was estimated as dextrose > glycerol > lactose > tween 20 > sucrose.Bangladesh J Microbiol, Volume 32, Number 1-2,June-Dec 2015, pp 39-44

scholarly journals Context-dependent dynamics lead to the assembly of functionally distinct pitcher-plant microbiomes

2019 ◽  
Author(s):  
Leonora S. Bittleston ◽  
Matti Gralka ◽  
Gabriel E. Leventhal ◽  
Itzhak Mizrahi ◽  
Otto X. Cordero
Keyword(s):  
Resource Use ◽  
Bacterial Communities ◽  
Niche Construction ◽  
Interspecific Interactions ◽  
Sarracenia Purpurea ◽  
Strongly Correlated ◽  
Pitcher Plant ◽  
Respiration Rates ◽  
Active Debate ◽  
And Function

AbstractNiche construction through interspecific interactions can condition future community states on past ones. However, the extent to which such history dependency can steer communities towards functionally different states remains a subject of active debate. Using bacterial communities collected from wild pitchers of the carnivorous pitcher plant, Sarracenia purpurea, we tested the effects of history on composition and function across communities assembled in synthetic pitcher plant microcosms. We found that the diversity of assembled communities was determined by the diversity of the system at early, pre-assembly stages. Species composition was also contingent on early community states, not only because of differences in the species pool, but also because the same species had different dynamics in different community contexts. Importantly, compositional differences were proportional to differences in function, as profiles of resource use were strongly correlated with composition, despite convergence in respiration rates. Early differences in community structure can thus propagate to mature communities, conditioning their functional repertoire.

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