scholarly journals Phylogenetic Profiles of In-House Microflora in Drains at a Food Production Facility: Comparison and Biocontrol Implications of Listeria-Positive and -Negative Bacterial Populations

2014 ◽  
Vol 80 (11) ◽  
pp. 3369-3374 ◽  
Author(s):  
Edward M. Fox ◽  
Katie Solomon ◽  
John E. Moore ◽  
Patrick G. Wall ◽  
Séamus Fanning
Keyword(s):  
Microbial Community ◽  
Food Production ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Production Facility ◽  
Production Environment ◽  
16S Rrna Gene Analysis ◽  
Bacterial Populations ◽  
Content Type ◽  
Phylogenetic Profiles

ABSTRACTListeriaspecies experience complex interactions with other microorganisms, which may promote growth and colonization of the organism in local environments or negatively affect them. This study investigated the microbial community at a food production facility, examining interactions betweenListeriaand the associated microbiome.Listeriaspecies can be transferred between zones in the production environment by individuals or equipment, and drains may act as a reservoir for the organism, reflecting the microbial flora potentially in the production environment. Drains that were colonized byListeriaspecies and those determined to be free ofListeriawere examined. In each case, 16S rRNA gene analysis was performed using the PhyloChip platform. Some general similarities in bacterial population structure were observed whenListeria-negative and -positive drain communities were compared, with some distinct differences also noted. These included increased populations of the generaPrevotellaandJanthinobacteriumassociated with the absence ofListeriaspecies, whereasEnterococcusandRhodococcuswere in higher abundance in drains colonized byListeriaspecies. Based on these results, a selection of bacterial species were grown in coculture biofilm with aListeria monocytogenesstrain identified as having colonized a drain at the facility. Mixed-species biofilm experiments showed thatJanthinobacteriuminhibited attachment and subsequent biofilm formation ofL. monocytogenes; however,Enterococcus gallinarumsignificantly increased it. The results of this study suggest the microbial community in food processing facilities can impact the colonization ofListeriaspecies and that influencing the microbiome in favor of antilisterial species may reduce the colonization ofListeriaspecies and limit the likelihood of product/process contamination.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

scholarly journals A Vegetable Fermentation Facility Hosts Distinct Microbiomes Reflecting the Production Environment

2018 ◽  
Vol 84 (22) ◽  
Author(s):  
Jonah E. Einson ◽  
Asha Rani ◽  
Xiaomeng You ◽  
Allison A. Rodriguez ◽  
Clifton L. Randell ◽  
...  
Keyword(s):  
Cultural History ◽  
Bacterial Communities ◽  
Starter Cultures ◽  
Rrna Gene ◽  
Fermented Foods ◽  
Production Facility ◽  
Production Environment ◽  
Content Type ◽  
Bacterial Phyla ◽  
Fermented Vegetables

ABSTRACTFermented vegetables are highly popular internationally in part due to their enhanced nutritional properties, cultural history, and desirable sensorial properties. In some instances, fermented foods provide a rich source of the beneficial microbial communities that could promote gastrointestinal health. The indigenous microbiota that colonize fermentation facilities may impact food quality, food safety, and spoilage risks and maintain the nutritive value of the product. Here, microbiomes within sauerkraut production facilities were profiled to characterize variance across surfaces and to determine the sources of these bacteria. Accordingly, we used high-throughput sequencing of the 16S rRNA gene in combination with whole-genome shotgun analyses to explore biogeographical patterns of microbial diversity and assembly within the production facility. Our results indicate that raw cabbage and vegetable handling surfaces exhibit more similar microbiomes relative to the fermentation room, processing area, and dry storage surfaces. We identified biomarker bacterial phyla and families that are likely to originate from the raw cabbage and vegetable handling surfaces. Raw cabbage was identified as the main source of bacteria to seed the facility, with human handling contributing a minor source of inoculation.LeuconostocandLactobacillaceaedominated all surfaces where spontaneous fermentation occurs, as these taxa are associated with the process. Wall, floor, ceiling, and barrel surfaces host unique microbial signatures. This study demonstrates that diverse bacterial communities are widely distributed within the production facility and that these communities assemble nonrandomly, depending on the surface type.IMPORTANCEFermented vegetables play a major role in global food systems and are widely consumed by various global cultures. In this study, we investigated an industrial facility that produces spontaneous fermented sauerkraut without the aid of starter cultures. This provides a unique system to explore and track the origins of an “in-house” microbiome in an industrial environment. Raw vegetables and the surfaces on which they are handled were identified as the likely source of bacterial communities rather than human contamination. As fermented vegetables increase in popularity on a global scale, understanding their production environment may help maintain quality and safety goals.

scholarly journals Spatial and Temporal Variation in Enterococcal Abundance and Its Relationship to the Microbial Community in Hawaii Beach Sand and Water

2013 ◽  
Vol 79 (12) ◽  
pp. 3601-3609 ◽  
Author(s):  
Henglin Cui ◽  
Kun Yang ◽  
Eulyn Pagaling ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Temporal Variation ◽  
Beach Sand ◽  
Spatial And Temporal Variation ◽  
Rrna Gene ◽  
Fecal Indicator ◽  
Bacterial Populations ◽  
Mass Unit ◽  
Content Type ◽  
Beach Water

ABSTRACTRecent studies have reported high levels of fecal indicator enterococci in marine beach sand. This study aimed to determine the spatial and temporal variation of enterococcal abundance and to evaluate its relationships with microbial community parameters in Hawaii beach sand and water. Sampling at 23 beaches on the Island of Oahu detected higher levels of enterococci in beach foreshore sand than in beach water on a mass unit basis. Subsequent 8-week consecutive samplings at two selected beaches (Waialae and Kualoa) consistently detected significantly higher levels of enterococci in backshore sand than in foreshore/nearshore sand and beach water. Comparison between the abundance of enterococci and the microbial communities showed that enterococci correlated significantly with totalVibrioin all beach zones but less significantly with total bacterial density andEscherichia coli. Samples from the different zones of Waialae beach were sequenced by 16S rRNA gene pyrosequencing to determine the microbial community structure and diversity. The backshore sand had a significantly more diverse community and contained different major bacterial populations than the other beach zones, which corresponded to the spatial distribution pattern of enterococcal abundance. Taken together, multiple lines of evidence support the possibility of enterococci as autochthonous members of the microbial community in Hawaii beach sand.

scholarly journals Analysis of Bacterial Communities during Clostridium difficile Infection in the Mouse

2015 ◽  
Vol 83 (11) ◽  
pp. 4383-4391 ◽  
Author(s):  
Ekaterina G. Semenyuk ◽  
Valeriy A. Poroyko ◽  
Pehga F. Johnston ◽  
Sara E. Jones ◽  
Katherine L. Knight ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
16S Rrna ◽  
Bacterial Species ◽  
Intestinal Content ◽  
Rrna Gene ◽  
Gi Tract ◽  
Bacterial Populations ◽  
Content Type ◽  
Minority Member ◽  
Gene Sequence Analysis

ABSTRACTClostridium difficileinfection (CDI) is a major cause of health care-associated disease. CDI initiates with ingestion ofC. difficilespores, germination in the gastrointestinal (GI) tract, and then colonization of the large intestine. The interactions betweenC. difficilecells and other bacteria and with host mucosa during CDI remain poorly understood. Here, we addressed the hypothesis that, in a mouse model of CDI,C. difficileresides in multicellular communities (biofilms) in association with host mucosa. To do this, we paraffin embedded and then sectioned the GI tracts of infected mice at various days postinfection (p.i.). We then used fluorescentin situhybridization (FISH) with 16S rRNA probes targeting most bacteria as well asC. difficilespecifically. The results revealed thatC. difficileis present as a minority member of communities in the outer (loose) mucus layer, in the cecum and colon, starting at day 1 p.i. To generate FISH probes that identify bacteria within mucus-associated communities harboringC. difficile, we characterized bacterial populations in the infected mouse GI tract using 16S rRNA gene sequence analysis of bacterial DNA prepared from intestinal content. This analysis revealed the presence of genera of several families belonging toBacteroidetesandFirmicutes. These data suggest that formation of multispecies communities associated with the mucus of the cecum and colon is an important early step in GI tract colonization. They raise the possibility that other bacterial species in these communities modulate the ability ofC. difficileto successfully colonize and, thereby, cause disease.

scholarly journals Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts

2021 ◽  
Vol 71 (2) ◽  
Author(s):  
Fuyong Li ◽  
Christopher C. Cheng ◽  
Jinshui Zheng ◽  
Junhong Liu ◽  
Rodrigo Margain Quevedo ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Type Strain ◽  
Type Species ◽  
Bacterial Species ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Content Type ◽  
Link Type ◽  
Faecal Samples ◽  
Genome Phylogeny

Ten strains, BG-AF3-AT, pH52_RY, WF-MT5-AT, BG-MG3-A, Lr3000T, RRLNB_1_1, STM3_1T, STM2_1, WF-MO7-1T and WF-MA3-C, were isolated from intestinal or faecal samples of rodents, pheasant and primate. 16S rRNA gene analysis identified them as Limosilactobacillus reuteri . However, average nucleotide identity and digital DNA–DNA hybridization values based on whole genomes were below 95 and 70 %, respectively, and thus below the threshold levels for bacterial species delineation. Based on genomic, chemotaxonomic and morphological analyses, we propose five novel species with the names Limosilactobacillus balticus sp. nov. (type strain BG-AF3-AT=DSM 110574T=LMG 31633T), Limosilactobacillus agrestis sp. nov. (type strain WF-MT5-AT=DSM 110569T=LMG 31629T), Limosilactobacillus albertensis sp. nov. (type strain Lr3000T=DSM 110573T=LMG 31632T), Limosilactobacillus rudii sp. nov. (type strain STM3_1T=DSM 110572T=LMG 31631T) and Limosilactobacillus fastidiosus sp. nov. (type strain WF-MO7-1T=DSM 110576T=LMG 31630T). Core genome phylogeny and experimental evidence of host adaptation of strains of L. reuteri further provide a strong rationale to consider a number of distinct lineages within this species as subspecies. Here we propose six subspecies of L. reuteri : L. reuteri subsp. kinnaridis subsp. nov. (type strain AP3T=DSM 110703T=LMG 31724T), L. reuteri subsp. porcinus subsp. nov. (type strain 3c6T=DSM 110571T=LMG 31635T), L. reuteri subsp. murium subsp. nov. (type strain lpuph1T=DSM 110570T=LMG 31634T), L. reuteri subsp. reuteri subsp. nov. (type strain F 275T=DSM 20016T=ATCC 23272T), L. reuteri subsp. suis subsp. nov. (type strain 1063T=ATCC 53608T=LMG 31752T) and L. reuteri subsp. rodentium subsp. nov. (type strain 100-23T=DSM 17509T=CIP 109821T).

scholarly journals The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone

2016 ◽  
Vol 82 (12) ◽  
pp. 3572-3581 ◽  
Author(s):  
Kevin C. Lee ◽  
Matthew B. Stott ◽  
Peter F. Dunfield ◽  
Curtis Huttenhower ◽  
Ian R. McDonald ◽  
...  
Keyword(s):  
Microbial Community ◽  
Genomic Sequence ◽  
Geographic Distance ◽  
Taupo Volcanic Zone ◽  
Rrna Gene ◽  
Volcanic Zone ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Local Selection ◽  
Stochastic Dispersal

ABSTRACTChthonomonas calidiroseaT49Tis a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that theC. calidiroseagenome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. We tested this hypothesis by sequencing the genomes of fourC. calidiroseaisolates obtained from four separate geothermal fields in the Taupō Volcanic Zone, New Zealand. For each isolation site, we measured physicochemical attributes and defined the associated microbial community by 16S rRNA gene sequencing. Despite their ecological and geographical isolation, the genome sequences showed low divergence (maximum, 1.17%). Isolate-specific variations included single-nucleotide polymorphisms (SNPs), restriction-modification systems, and mobile elements but few major deletions and no major rearrangements. The 50-fold variation inC. calidirosearelative abundance among the four sites correlated with site environmental characteristics but not with differences in genomic content. Conversely, the carbohydrate utilization profiles of theC. calidiroseaisolates corresponded to the inferred isolate phylogenies, which only partially paralleled the geographical relationships among the sample sites. Genomic sequence conservation does not entirely parallel geographic distance, suggesting that stochastic dispersal and localized extinction, which allow for rapid population homogenization with little restriction by geographical barriers, are possible mechanisms ofC. calidiroseadistribution. This dispersal and extinction mechanism is likely not limited toC. calidiroseabut may shape the populations and genomes of many other low-abundance free-living taxa.IMPORTANCEThis study compares the genomic sequence variations and metabolisms of four strains ofChthonomonas calidirosea, a rare thermophilic bacterium from the phylumArmatimonadetes. It additionally compares the microbial communities and chemistry of each of the geographically distinct sites from which the fourC. calidiroseastrains were isolated.C. calidiroseawas previously reported to possess a highly disorganized genome, but it was unclear whether this reflected rapid evolution. Here, we show that each isolation site has a distinct chemistry and microbial community, but despite this, theC. calidiroseagenome is highly conserved across all isolation sites. Furthermore, genomic sequence differences only partially paralleled geographic distance, suggesting thatC. calidiroseagenotypes are not primarily determined by adaptive evolution. Instead, the presence ofC. calidiroseamay be driven by stochastic dispersal and localized extinction. This ecological mechanism may apply to many other low-abundance taxa.

Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Priya Lakra ◽  
Helianthous Verma ◽  
Chandni Talwar ◽  
Durgesh Narain Singh ◽  
Nirjara Singhvi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Species Delineation ◽  
16S Rrna Gene Analysis ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59T and D. radiopugnans ATCC 19172T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensi s DY59T and D. radiopugnans ATCC 19172T. Interestingly, D. swuensis DY59T and D. radiopugnans ATCC 19172T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA–DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59T and D. radiopugnans ATCC 19172T constitute a single species. Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans .

Nocardioides donggukensis sp. nov. and Hyunsoonleella aquatilis sp. nov., isolated from Jeongbang Waterfall on Jeju Island

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Inhyup Kim ◽  
Geeta Chhetri ◽  
Jiyoun Kim ◽  
Minchung Kang ◽  
Yoonseop So ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Bacterial Species ◽  
Jeju Island ◽  
Nucleotide Identity ◽  
Rrna Gene ◽  
Average Nucleotide Identity ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

Two bacterial strains, designated MJB4T and SJ7T, were isolated from water samples collected from Jeongbang Falls on Jeju Island, Republic of Korea. Phylogenetic analysis of 16S rRNA gene sequences indicated that the two strains belonged to the genera Nocardioides and Hyunsoonleella , owing to their high similarities to Nocardioides jensenii DSM 29641T (97.5 %) and Hyunsoonleella rubra FA042 T (96.3 %), respectively. These values are much lower than the gold standard for bacterial species (98.7 %). The average nucleotide identity values between strains MJB4T, SJ7T and the reference strains, Nocardioides jensenii DSM 29641T, Nocardioides daejeonensis MJ31T and Hyunsoonleella flava T58T were 77.2, 75.9 and 75.4 %, respectively. Strains MJB4T and SJ7T and the type strains of the species involved in system incidence have average nucleotide identity and average amino acid threshold values of 60.1–82.6 % for the species boundary (95–96 %), which confirms that strains MJB4T and SJ7T represent two new species of genus Nocardioides and Hyunsoonleella , respectively. Based on phylogenetic and phenotypic data, strains MJB4T and SJ7T are considered to represent novel species of the genus Nocardioides and Hyunsoonleella , respectively, for which the names Nocardioides donggukensis sp. nov. (type strain MJB4T=KACC 21724T=NBRC 114402T) and Hyunsoonleella aquatilis sp. nov., (type strain SJ7T=KACC 21715T=NBRC 114486T) have been proposed.

Pseudoalteromonas ostreae sp. nov., a new bacterial species harboured by the flat oyster Ostrea edulis

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Héléna Cuny ◽  
Clément Offret ◽  
Amine M. Boukerb ◽  
Leila Parizadeh ◽  
Olivier Lesouhaitier ◽  
...  
Keyword(s):  
Type Species ◽  
Bacterial Species ◽  
Acid Methyl Ester ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
Ostrea Edulis ◽  
Content Type ◽  
Link Type ◽  
A Genome ◽  
Flat Oyster

Three bacterial strains, named hOe-66T, hOe-124 and hOe-125, were isolated from the haemolymph of different specimens of the flat oyster Ostrea edulis collected in Concarneau bay (Finistère, France). These strains were characterized by a polyphasic approach, including (i) whole genome analyses with 16S rRNA gene sequence alignment and pangenome analysis, determination of the G+C content, average nucleotide identity (ANI), and in silico DNA–DNA hybridization (isDDH), and (ii) fatty acid methyl ester and other phenotypic analyses. Strains hOe-66T, hOe-124 and hOe-125 were closely related to both type strains Pseudoalteromonas rhizosphaerae RA15T and Pseudoalteromonas neustonica PAMC 28425T with less than 93.3% ANI and 52.3% isDDH values. Regarding their phenotypic traits, the three strains were Gram-negative, 1–2 µm rod-shaped, aerobic, motile and non-spore-forming bacteria. Cells grew optimally at 25 °C in 2.5% NaCl and at 7–8 pH. The most abundant fatty acids were summed feature 3 (C16:1 ω7c/C16:1 ω6c), C16:0 and C17:1 ω8c. The strains carried a genome average size of 4.64 Mb and a G+C content of 40.28 mol%. The genetic and phenotypic results suggested that strains hOe-66T, hOe-124 and hOe-125 belong to a new species of the genus Pseudoalteromonas . In this context, we propose the name Pseudoalteromonas ostreae sp. nov. The type strain is hOe-66T (=CECT 30303T=CIP 111911T).

scholarly journals Riddles in the cold: Antarctic endemism and microbial succession impact methane cycling in the Southern Ocean

2020 ◽  
Vol 287 (1931) ◽  
pp. 20201134 ◽  
Author(s):  
Andrew R. Thurber ◽  
Sarah Seabrook ◽  
Rory M. Welsh
Keyword(s):  
Microbial Community ◽  
Greenhouse Gas Emission ◽  
Ross Sea ◽  
Methane Flux ◽  
Rrna Gene ◽  
Methane Seep ◽  
Microbial Succession ◽  
Methane Cycle ◽  
16S Rrna Gene Analysis ◽  
Successional Stage

Antarctica is estimated to contain as much as a quarter of earth's marine methane, however we have not discovered an active Antarctic methane seep limiting our understanding of the methane cycle. In 2011, an expansive (70 m × 1 m) microbial mat formed at 10 m water depth in the Ross Sea, Antarctica which we identify here to be a high latitude hydrogen sulfide and methane seep. Through 16S rRNA gene analysis on samples collected 1 year and 5 years after the methane seep formed, we identify the taxa involved in the Antarctic methane cycle and quantify the response rate of the microbial community to a novel input of methane. One year after the seep formed, ANaerobic MEthane oxidizing archaea (ANME), the dominant sink of methane globally, were absent. Five years later, ANME were found to make up to 4% of the microbial community, however the dominant member of this group observed (ANME-1) were unexpected considering the cold temperature (−1.8°C) and high sulfate concentrations (greater than 24 mM) present at this site. Additionally, the microbial community had not yet formed a sufficient filter to mitigate the release of methane from the sediment; methane flux from the sediment was still significant at 3.1 mmol CH 4 m −2 d −1 . We hypothesize that this 5 year time point represents an early successional stage of the microbiota in response to methane input. This study provides the first report of the evolution of a seep system from a non-seep environment, and reveals that the rate of microbial succession may have an unrealized impact on greenhouse gas emission from marine methane reservoirs.

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