Longitudinal assessment of the bovine ocular bacterial community dynamics in calves

Abstract Background Infectious Bovine Keratoconjunctivitis (IBK), commonly known as pinkeye, is one of the most significant diseases of beef cattle. As such, IBK costs the US beef industry at least 150 million annually. However, strategies to prevent IBK are limited, with most cases resulting in treatment with antibiotics once the disease has developed. Longitudinal studies evaluating establishment of the ocular microbiota may identify critical risk periods for IBK outbreaks or changes in the microbiota that may predispose animals to IBK. Results In an attempt to characterize the establishment and colonization patterns of the bovine ocular microbiota, we conducted a longitudinal study consisting of 227 calves and evaluated the microbiota composition over time using amplicon sequence variants (ASVs) based on 16S rRNA sequencing data and culture-based approaches. Beef calves on trial consisted of both male (intact) and females. Breeds were composed of purebred Angus and composites with varying percentages of Simmental, Angus, and Red Angus breeds. Average age at the start of the trial was 65 days ±15.02 and all calves remained nursing on their dam until weaning (day 139 of the study). The trial consisted of 139 days with four sampling time points on day 0, 21, 41, and 139. The experimental population received three different vaccination treatments (autogenous, commercial (both inactivated bacteria), and adjuvant placebo), to assess the effectiveness of different vaccines for IBK prevention. A significant change in bacterial community composition was observed across time periods sampled compared to the baseline (p < 0.001). However, no treatment effect of vaccine was detected within the ocular bacterial community. The bacterial community composition with the greatest time span between sampling time periods (98d span) was most similar to the baseline sample collected, suggesting re-establishment of the ocular microbiota to baseline levels over time after perturbation. The effect of IgA levels on the microbial community was investigated in a subset of cattle within the study. However, no significant effect of IgA was observed. Significant changes in the ocular microbiota were identified when comparing communities pre- and post-clinical signs of IBK. Additionally, dynamic changes in opportunistic pathogens Moraxella spp. were observed and confirmed using culture based methods. Conclusions Our results indicate that the bovine ocular microbiota is well represented by opportunistic pathogens such as Moraxella and Mycoplasma. Furthermore, this study characterizes the diversity of the ocular microbiota in calves and demonstrates the plasticity of the ocular microbiota to change. Additionally, we demonstrate the ocular microbiome in calves is similar between the eyes and the perturbation of one eye results in similar changes in the other eye. We also demonstrate the bovine ocular microbiota is slow to recover post perturbation and as a result provide opportunistic pathogens a chance to establish within the eye leading to IBK and other diseases. Characterizing the dynamic nature of the ocular microbiota provides novel opportunities to develop potential probiotic intervention to reduce IBK outbreaks in cattle.

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Temporal Dynamics of South End Tidal Creek (Sapelo Island, Georgia) Bacterial Communities

Applied and Environmental Microbiology ◽

10.1128/aem.01725-08 ◽

2008 ◽

Vol 75 (4) ◽

pp. 1058-1064 ◽

Cited By ~ 9

Author(s):

Emily Kara ◽

Ashley Shade

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Community Dynamics ◽

Tidal Creek ◽

Temporal Dynamics ◽

Bacterial Community Composition ◽

High Tide ◽

Cycle Period ◽

Sapelo Island ◽

End Tidal

ABSTRACT Bacterial community dynamics in South End tidal creek, Sapelo Island, GA, were studied over a 74-h, five-tidal-cycle period. Observations were made hourly for the first consecutive 24 hours, every 3 hours on the second day, and every 6 hours on the third day. Tide most strongly influenced bacterial community composition (high-tide versus low-tide community analysis of similarities, R = 0.41, P < 0.03). Dissolved oxygen concentration and conductivity were important proximate drivers. However, after accounting for tide and environmental variables colinear with tide, cumulative time became more important in describing community variation. In-stream physical processes, including particulate suspension and sedimentation, may explain tide-associated trends in the bacterial community composition observed.

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Dynamics of Bacterial Community Composition and Activity during a Mesocosm Diatom Bloom

Applied and Environmental Microbiology ◽

10.1128/aem.66.2.578-587.2000 ◽

2000 ◽

Vol 66 (2) ◽

pp. 578-587 ◽

Cited By ~ 403

Author(s):

Lasse Riemann ◽

Grieg F. Steward ◽

Farooq Azam

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Growth Rates ◽

Community Dynamics ◽

Bacterial Community Composition ◽

Size Fraction ◽

Microbial Colonization ◽

Rrna Gene ◽

Bacterial Community Dynamics ◽

Diatom Blooms

ABSTRACT Bacterial community composition, enzymatic activities, and carbon dynamics were examined during diatom blooms in four 200-liter laboratory seawater mesocosms. The objective was to determine whether the dramatic shifts in growth rates and ectoenzyme activities, which are commonly observed during the course of phytoplankton blooms and their subsequent demise, could result from shifts in bacterial community composition. Nutrient enrichment of metazoan-free seawater resulted in diatom blooms dominated by a Thalassiosira sp., which peaked 9 days after enrichment (≈24 μg of chlorophylla liter−1). At this time bacterial abundance abruptly decreased from 2.8 × 106 to 0.75 × 106 ml−1, and an analysis of bacterial community composition, by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments, revealed the disappearance of three dominant phylotypes. Increased viral and flagellate abundances suggested that both lysis and grazing could have played a role in the observed phylotype-specific mortality. Subsequently, new phylotypes appeared and bacterial production, abundance, and enzyme activities shifted from being predominantly associated with the <1.0-μm size fraction towards the >1.0-μm size fraction, indicating a pronounced microbial colonization of particles. Sequencing of DGGE bands suggested that the observed rapid and extensive colonization of particulate matter was mainly by specialized α-Proteobacteria- andCytophagales-related phylotypes. These particle-associated bacteria had high growth rates as well as high cell-specific aminopeptidase, β-glucosidase, and lipase activities. Rate measurements as well as bacterial population dynamics were almost identical among the mesocosms indicating that the observed bacterial community dynamics were systematic and repeatable responses to the manipulated conditions.

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Dynamic succession of substrate-associated bacterial composition and function duringGanoderma lucidumgrowth

PeerJ ◽

10.7717/peerj.4975 ◽

2018 ◽

Vol 6 ◽

pp. e4975 ◽

Cited By ~ 7

Author(s):

Bo Zhang ◽

Lijuan Yan ◽

Qiang Li ◽

Jie Zou ◽

Hao Tan ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Community Dynamics ◽

Bacterial Community Composition ◽

Growth Stages ◽

Bacterial Phyla ◽

Medicinal Fungus ◽

Bacterial Community Dynamics ◽

Functional Pathway ◽

And Function

BackgroundGanoderma lucidum, a valuable medicinal fungus, is widely distributed in China. It grows alongside with a complex microbial ecosystem in the substrate. As sequencing technology advances, it is possible to reveal the composition and functions of substrate-associated bacterial communities.MethodsWe analyzed the bacterial community dynamics in the substrate during the four typical growth stages ofG. lucidumusing next-generation sequencing.ResultsThe physicochemical properties of the substrate (e.g. acidity, moisture, total nitrogen, total phosphorus and total potassium) changed between different growth stages. A total of 598,771 sequences from 12 samples were obtained and assigned to 22 bacterial phyla.ProteobacteriaandFirmicuteswere the dominant phyla. Bacterial community composition and diversity significantly differed between the elongation stage and the other three growth stages. LEfSe analysis revealed a large number of bacterial taxa (e.g.Bacteroidetes,AcidobacteriaandNitrospirae) with significantly higher abundance at the elongation stage. Functional pathway prediction uncovered significant abundance changes of a number of bacterial functional pathways between the elongation stage and other growth stages. At the elongation stage, the abundance of the environmental information processing pathway (mainly membrane transport) decreased, whereas that of the metabolism-related pathways increased.DiscussionThe changes in bacterial community composition, diversity and predicted functions were most likely related to the changes in the moisture and nutrient conditions in the substrate with the growth ofG. lucidum, particularly at the elongation stage. Our findings shed light on theG. lucidum-bacteria-substrate relationships, which should facilitate the industrial cultivation ofG. lucidum.

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Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes

mSphere ◽

10.1128/msphere.00169-17 ◽

2017 ◽

Vol 2 (3) ◽

Cited By ~ 20

Author(s):

Alexandra M. Linz ◽

Benjamin C. Crary ◽

Ashley Shade ◽

Sarah Owens ◽

Jack A. Gilbert ◽

...

Keyword(s):

Time Series ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Community Dynamics ◽

Environmental Gradients ◽

Bacterial Community Composition ◽

Bacterial Community Dynamics ◽

Long Time ◽

Bog Lakes

ABSTRACT Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series. Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likely reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and “Candidatus Omnitrophica” in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. IMPORTANCE Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series.

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The shift of bacterial community composition magnifies over time in response to different sources of soybean residues

Applied Soil Ecology ◽

10.1016/j.apsoil.2019.01.001 ◽

2019 ◽

Vol 136 ◽

pp. 163-167 ◽

Cited By ~ 2

Author(s):

Tengxiang Lian ◽

Zhenhua Yu ◽

Yansheng Li ◽

Jian Jin ◽

Guanghua Wang ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Community Composition ◽

Different Sources ◽

Over Time

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Evaluation of a therapy for Idiopathic Chronic Enterocolitis in rhesus macaques (Macaca mulatta) and linked microbial community correlates

PeerJ ◽

10.7717/peerj.4612 ◽

2018 ◽

Vol 6 ◽

pp. e4612 ◽

Cited By ~ 3

Author(s):

Joshua M. Taylor ◽

Erik L. Clarke ◽

Kate Baker ◽

Abigail Lauder ◽

Dorothy Kim ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Macaca Mulatta ◽

Rhesus Macaques ◽

Bacterial Community Composition ◽

Food Additives ◽

Clinical Signs ◽

Healthy Controls ◽

Microbiome Analysis ◽

Over Time

Idiopathic chronic enterocolitis (ICE) is one of the most commonly encountered and difficult to manage diseases of captive rhesus macaques (Macaca mulatta). The etiology is not well understood, but perturbations in gut microbial communities have been implicated. Here we evaluated the effects of a 14-day course of vancomycin, neomycin, and fluconazole on animals affected with ICE, comparing treated, untreated, and healthy animals. We performed microbiome analysis on duodenal and colonic mucosal samples and feces in order to probe bacterial and/or fungal taxa potentially associated with ICE. All treated animals showed a significant and long-lasting improvement in stool consistency over time when compared to untreated and healthy controls. Microbiome analysis revealed trends associating bacterial community composition with ICE, particularly lineages of the Lactobacillaceae family. Sequencing of DNA from macaque food biscuits revealed that fungal sequences recovered from stool were dominated by yeast-derived food additives; in contrast, bacteria in stool appeared to be authentic gut residents. In conclusion, while validation in larger cohorts is needed, the treatment described here was associated with significantly improved clinical signs; results suggested possible correlates of microbiome structure with disease, though no strong associations were detected between single microbes and ICE.

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Copper in Wood Preservatives Delayed Wood Decomposition and Shifted Soil Fungal but Not Bacterial Community Composition

Applied and Environmental Microbiology ◽

10.1128/aem.02391-18 ◽

2018 ◽

Vol 85 (4) ◽

Cited By ~ 1

Author(s):

Sandra Lasota ◽

Ina Stephan ◽

Marcus A. Horn ◽

Wolfgang Otto ◽

Matthias Noll

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Community Composition ◽

Wood Preservative ◽

Wood Preservatives ◽

Preservative Treatment ◽

Soil Microbial ◽

Copy Numbers ◽

Ammonium Compounds ◽

Over Time

ABSTRACTCopper-based fungicides are routinely used for wood and plant protection, which can lead to an enrichment of copper-tolerant microbial communities in soil. To investigate the effect of such wood preservatives on the soil fungal and bacterial community compositions, five different vineyard and fruit-growing soil environments were evaluated using incubation studies over time. Pine sapwood specimens were impregnated with either water or different biocide treatment solutions containing a mixture of copper, triazoles, and quaternary ammonium compounds (CuTriQAC), a mixture of triazoles and quaternary ammonium compounds (TriQAC), or copper alone (Cu). Specimens were incubated in soil from each sample site for 8, 16, 24, and 32 weeks. The effects of preservative treatment on the modulus of elasticity (MOE) of the wood specimens and on the soil fungal as well as bacterial community composition at the soil-wood interface were assessed by quantitative PCR and amplicon sequencing of the fungal internal transcribed spacer (ITS) region and bacterial 16S rRNA gene. Specimens impregnated with CuTriQAC and Cu showed decreased MOE and reduced fungal and bacterial copy numbers over time compared to those impregnated with water and TriQAC. Fungal but not bacterial community composition was significantly affected by wood preservative treatment. The relative abundance of members of the family Trichocomaceae compared to other genera increased in the presence of the Cu and CuTriQAC treatments at three sites, suggesting these to be Cu-tolerant fungi. In conclusion, the copper-containing treatments resulted in marginally increased MOE, lowered microbial gene copy numbers compared to those in the TriQAC and water treatments, and thus enhanced wood protection against soil microbial wood degradation.IMPORTANCECopper-containing rather than TRIQAC formulations are efficient wood preservatives irrespective of the origin and composition of the soil microbial communities. However, some fungi appear to be naturally insensitive to copper and should be the focus of future wood preservative formulations to facilitate the life span of wooden construction in contact with soil while also minimizing the overall environmental impact.

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Bacterial community composition and dynamics spanning five years in freshwater bog lakes

10.1101/127035 ◽

2017 ◽

Cited By ~ 1

Author(s):

Alexandra M. Linz ◽

Benjamin C. Crary ◽

Ashley Shade ◽

Sarah Owens ◽

Jack A. Gilbert ◽

...

Keyword(s):

Time Series ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Community Dynamics ◽

Bacterial Community Composition ◽

Rrna Gene ◽

Bacterial Community Dynamics ◽

Bog Lakes

AbstractBacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multi-year time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. Multiple sites and sampling events were necessary to begin to fully describe the bacterial communities. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likely reflected the environmental conditions of each site. The community present in each year and site was also unique. Despite high interannual variability in community composition, we detected a core community of ubiquitous freshwater taxa. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term observations, as analyzing only a single year of data would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here.ImportanceLakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community dynamics operate on multi-year timescales, a finding which likely applies to other ecosystems, with implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities, and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource to anyone seeking to answer their own microbial ecology questions using a multi-year time series.

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Collection of Environmental Variables and Bacterial Community Compositions in Marian Cove, Antarctica, during Summer 2018

Data ◽

10.3390/data6030027 ◽

2021 ◽

Vol 6 (3) ◽

pp. 27

Author(s):

Hyo-Ryeon Kim ◽

Jae-Hyun Lim ◽

Ju-Hyoung Kim ◽

Il-Nam Kim

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Marine Bacteria ◽

Environmental Variables ◽

Environmental Changes ◽

Bacterial Community Composition ◽

Composition Data ◽

Decomposition Of Organic Matter ◽

Class Level ◽

Earth’S Climate

Marine bacteria, which are known as key drivers for marine biogeochemical cycles and Earth’s climate system, are mainly responsible for the decomposition of organic matter and production of climate-relevant gases (i.e., CO₂, N₂O, and CH₄). However, research is still required to fully understand the correlation between environmental variables and bacteria community composition. Marine bacteria living in the Marian Cove, where the inflow of freshwater has been rapidly increasing due to substantial glacial retreat, must be undergoing significant environmental changes. During the summer of 2018, we conducted a hydrographic survey to collect environmental variables and bacterial community composition data at three different layers (i.e., the seawater surface, middle, and bottom layers) from 15 stations. Of all the bacterial data, 17 different phylum level bacteria and 21 different class level bacteria were found and Proteobacteria occupy 50.3% at phylum level following Bacteroidetes. Gammaproteobacteria and Alphaproteobacteria, which belong to Proteobacteria, are the highest proportion at the class level. Gammaproteobacteria showed the highest relative abundance in all three seawater layers. The collection of environmental variables and bacterial composition data contributes to improving our understanding of the significant relationships between marine Antarctic regions and marine bacteria that lives in the Antarctic.

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Artificial neural network analysis of microbial diversity in the central and southern Adriatic Sea

Scientific Reports ◽

10.1038/s41598-021-90863-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Danijela Šantić ◽

Kasia Piwosz ◽

Frano Matić ◽

Ana Vrdoljak Tomaš ◽

Jasna Arapov ◽

...

Keyword(s):

Neural Network ◽

Network Analysis ◽

Bacterial Community ◽

Microbial Diversity ◽

Community Composition ◽

Adriatic Sea ◽

Bacterial Community Composition ◽

Environmental Data ◽

Large Contribution ◽

Neural Network Analysis

AbstractBacteria are an active and diverse component of pelagic communities. The identification of main factors governing microbial diversity and spatial distribution requires advanced mathematical analyses. Here, the bacterial community composition was analysed, along with a depth profile, in the open Adriatic Sea using amplicon sequencing of bacterial 16S rRNA and the Neural gas algorithm. The performed analysis classified the sample into four best matching units representing heterogenic patterns of the bacterial community composition. The observed parameters were more differentiated by depth than by area, with temperature and identified salinity as important environmental variables. The highest diversity was observed at the deep chlorophyll maximum, while bacterial abundance and production peaked in the upper layers. The most of the identified genera belonged to Proteobacteria, with uncultured AEGEAN-169 and SAR116 lineages being dominant Alphaproteobacteria, and OM60 (NOR5) and SAR86 being dominant Gammaproteobacteria. Marine Synechococcus and Cyanobium-related species were predominant in the shallow layer, while Prochlorococcus MIT 9313 formed a higher portion below 50 m depth. Bacteroidota were represented mostly by uncultured lineages (NS4, NS5 and NS9 marine lineages). In contrast, Actinobacteriota were dominated by a candidatus genus Ca. Actinomarina. A large contribution of Nitrospinae was evident at the deepest investigated layer. Our results document that neural network analysis of environmental data may provide a novel insight into factors affecting picoplankton in the open sea environment.

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