Deterministic Assembly of Complex Bacterial Communities in Guts of Germ-Free Cockroaches

ABSTRACTThe gut microbiota of termites plays important roles in the symbiotic digestion of lignocellulose. However, the factors shaping the microbial community structure remain poorly understood. Because termites cannot be raised under axenic conditions, we established the closely related cockroachShelfordella lateralisas a germ-free model to study microbial community assembly and host-microbe interactions. In this study, we determined the composition of the bacterial assemblages in cockroaches inoculated with the gut microbiota of termites and mice using pyrosequencing analysis of their 16S rRNA genes. Although the composition of the xenobiotic communities was influenced by the lineages present in the foreign inocula, their structure resembled that of conventional cockroaches. Bacterial taxa abundant in conventional cockroaches but rare in the foreign inocula, such asDysgonomonasandParabacteroidesspp., were selectively enriched in the xenobiotic communities. Donor-specific taxa, such as endomicrobia or spirochete lineages restricted to the gut microbiota of termites, however, either were unable to colonize germ-free cockroaches or formed only small populations. The exposure of xenobiotic cockroaches to conventional adults restored their normal microbiota, which indicated that autochthonous lineages outcompete foreign ones. Our results provide experimental proof that the assembly of a complex gut microbiota in insects is deterministic.

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Defining the Core Citrus Leaf- and Root-Associated Microbiota: Factors Associated with Community Structure and Implications for Managing Huanglongbing (Citrus Greening) Disease

Applied and Environmental Microbiology ◽

10.1128/aem.00210-17 ◽

2017 ◽

Vol 83 (11) ◽

Cited By ~ 22

Author(s):

Ryan A. Blaustein ◽

Graciela L. Lorca ◽

Julie L. Meyer ◽

Claudio F. Gonzalez ◽

Max Teplitski

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Illumina Sequencing ◽

Symptom Severity ◽

16S Rrna Genes ◽

Rrna Genes ◽

Content Type ◽

The Core ◽

Symptom Progression

ABSTRACTStable associations between plants and microbes are critical to promoting host health and productivity. The objective of this work was to test the hypothesis that restructuring of the core microbiota may be associated with the progression of huanglongbing (HLB), the devastating citrus disease caused byLiberibacter asiaticus,Liberibacter americanus, andLiberibacter africanus. The microbial communities of leaves (n= 94) and roots (n= 79) from citrus trees that varied by HLB symptom severity, cultivar, location, and season/time were characterized with Illumina sequencing of 16S rRNA genes. The taxonomically rich communities contained abundant core members (i.e., detected in at least 95% of the respective leaf or root samples), some overrepresented site-specific members, and a diverse community of low-abundance variable taxa. The composition and diversity of the leaf and root microbiota were strongly associated with HLB symptom severity and location; there was also an association with host cultivar. The relative abundance ofLiberibacterspp. among leaf microbiota positively correlated with HLB symptom severity and negatively correlated with alpha diversity, suggesting that community diversity decreases as symptoms progress. Network analysis of the microbial community time series identified a mutually exclusive relationship betweenLiberibacterspp. and members of theBurkholderiaceae,Micromonosporaceae, andXanthomonadaceae. This work confirmed several previously described plant disease-associated bacteria, as well as identified new potential implications for biological control. Our findings advance the understanding of (i) plant microbiota selection across multiple variables and (ii) changes in (core) community structure that may be a precondition to disease establishment and/or may be associated with symptom progression.IMPORTANCEThis study provides a comprehensive overview of the core microbial community within the microbiomes of plant hosts that vary in extent of disease symptom progression. With 16S Illumina sequencing analyses, we not only confirmed previously described bacterial associations with plant health (e.g., potentially beneficial bacteria) but also identified new associations and potential interactions between certain bacteria and an economically important phytopathogen. The importance of core taxa within broader plant-associated microbial communities is discussed.

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Revealing microbial species diversity using sequence capture by hybridization

Microbial Genomics ◽

10.1099/mgen.0.000714 ◽

2021 ◽

Vol 7 (12) ◽

Author(s):

Sophie Marre ◽

Cyrielle Gasc ◽

Camille Forest ◽

Yacine Lebbaoui ◽

Pascale Mosoni ◽

...

Keyword(s):

Gut Microbiota ◽

16S Rdna ◽

16S Rrna Genes ◽

Rrna Genes ◽

Taxonomic Resolution ◽

Human Gut ◽

Content Type ◽

Innovative Strategy ◽

Human Gut Microbiota ◽

Rare Biosphere

Targeting small parts of the 16S rDNA phylogenetic marker by metabarcoding reveals microorganisms of interest but cannot achieve a taxonomic resolution at the species level, precluding further precise characterizations. To identify species behind operational taxonomic units (OTUs) of interest, even in the rare biosphere, we developed an innovative strategy using gene capture by hybridization. From three OTU sequences detected upon polyphenol supplementation and belonging to the rare biosphere of the human gut microbiota, we revealed 59 nearly full-length 16S rRNA genes, highlighting high bacterial diversity hidden behind OTUs while evidencing novel taxa. Inside each OTU, revealed 16S rDNA sequences could be highly distant from each other with similarities down to 85 %. We identified one new family belonging to the order Clostridiales , 39 new genera and 52 novel species. Related bacteria potentially involved in polyphenol degradation have also been identified through genome mining and our results suggest that the human gut microbiota could be much more diverse than previously thought.

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Simple Absolute Quantification Method Correcting for Quantitative PCR Efficiency Variations for Microbial Community Samples

Applied and Environmental Microbiology ◽

10.1128/aem.07878-11 ◽

2012 ◽

Vol 78 (12) ◽

pp. 4481-4489 ◽

Cited By ~ 95

Author(s):

Robert Brankatschk ◽

Natacha Bodenhausen ◽

Josef Zeyer ◽

Helmut Bürgmann

Keyword(s):

Microbial Community ◽

Quantitative Pcr ◽

Environmental Samples ◽

Absolute Quantification ◽

Geobacter Sulfurreducens ◽

16S Rrna Genes ◽

Rrna Genes ◽

Gene Copy ◽

Nostoc Commune ◽

Content Type

ABSTRACTReal-time quantitative PCR (qPCR) is a widely used technique in microbial community analysis, allowing the quantification of the number of target genes in a community sample. Currently, the standard-curve (SC) method of absolute quantification is widely employed for these kinds of analysis. However, the SC method assumes that the amplification efficiency (E) is the same for both the standard and the sample target template. We analyzed 19 bacterial strains and nine environmental samples in qPCR assays, targeting thenifHand 16S rRNA genes. TheEvalues of the qPCRs differed significantly, depending on the template. This has major implications for the quantification. If the sample and standard differ in theirEvalues, quantification errors of up to orders of magnitude are possible. To address this problem, we propose and test the one-point calibration (OPC) method for absolute quantification. The OPC method corrects for differences inEand was derived from the ΔΔCTmethod with correction forE, which is commonly used for relative quantification in gene expression studies. The SC and OPC methods were compared by quantifying artificial template mixtures fromGeobacter sulfurreducens(DSM 12127) andNostoc commune(Culture Collection of Algae and Protozoa [CCAP] 1453/33), which differ in theirEvalues. While the SC method deviated from the expectednifHgene copy number by 3- to 5-fold, the OPC method quantified the template mixtures with high accuracy. Moreover, analyzing environmental samples, we show that even small differences inEbetween the standard and the sample can cause significant differences between the copy numbers calculated by the SC and the OPC methods.

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Microbial Community Response during the Iron Fertilization Experiment LOHAFEX

Applied and Environmental Microbiology ◽

10.1128/aem.01814-12 ◽

2012 ◽

Vol 78 (24) ◽

pp. 8803-8812 ◽

Cited By ~ 40

Author(s):

Stefan Thiele ◽

Bernhard M. Fuchs ◽

Nagappa Ramaiah ◽

Rudolf Amann

Keyword(s):

Microbial Community ◽

Total Cell ◽

16S Rrna Genes ◽

Rrna Genes ◽

Thymidine Uptake ◽

Phytoplankton Blooms ◽

Minor Response ◽

Content Type ◽

Cell Numbers ◽

Iron Fertilization

ABSTRACTIron fertilization experiments in high-nutrient, low-chlorophyll areas are known to induce phytoplankton blooms. However, little is known about the response of the microbial community upon iron fertilization. As part of the LOHAFEX experiment in the southern Atlantic Ocean,BacteriaandArchaeawere monitored within and outside an induced bloom, dominated byPhaeocystis-like nanoplankton, during the 38 days of the experiment. The microbial production increased 1.6-fold (thymidine uptake) and 2.1-fold (leucine uptake), while total cell numbers increased only slightly over the course of the experiment. 454 tag pyrosequencing of partial 16S rRNA genes and catalyzed reporter deposition fluorescencein situhybridization (CARD FISH) showed that the composition and abundance of the bacterial and archaeal community in the iron-fertilized water body were remarkably constant without development of typical bloom-related succession patterns. Members of groups usually found in phytoplankton blooms, such asRoseobacterandGammaproteobacteria, showed no response or only a minor response to the bloom. However, sequence numbers and total cell numbers of the SAR11 and SAR86 clades increased slightly but significantly toward the end of the experiment. It seems that although microbial productivity was enhanced within the fertilized area, a succession-like response of the microbial community upon the algal bloom was averted by highly effective grazing. Only small-celled members like the SAR11 and SAR86 clades could possibly escape the grazing pressure, explaining a net increase of those clades in numbers.

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Mediation Analysis as a Means of Identifying Dietary Components That Differentially Affect the Fecal Microbiota of Infants Weaned by Modified Baby-Led and Traditional Approaches

Applied and Environmental Microbiology ◽

10.1128/aem.00914-18 ◽

2018 ◽

Vol 84 (18) ◽

Cited By ~ 10

Author(s):

Claudia Leong ◽

Jillian J. Haszard ◽

Blair Lawley ◽

Anna Otal ◽

Rachael W. Taylor ◽

...

Keyword(s):

Gut Microbiota ◽

Dietary Fiber ◽

Complementary Feeding ◽

Alpha Diversity ◽

The United States ◽

16S Rrna Genes ◽

Rrna Genes ◽

Content Type ◽

Diet Records ◽

Dietary Components

ABSTRACT The introduction of “solids” (i.e., complementary foods) to the milk-only diet in early infancy affects the development of the gut microbiota. The aim of this study was to determine whether a “baby-led” approach to complementary feeding that encourages the early introduction of an adult-type diet results in alterations of the gut microbiota composition compared to traditional spoon-feeding. The Baby-Led Introduction to SolidS (BLISS) study randomized 206 infants to BLISS (a modified version of baby-led weaning [BLW], the introduction of solids at 6 months of age, followed by self-feeding of family foods) or control (traditional spoon-feeding of purées) groups. Fecal microbiotas and 3-day weighed-diet records were analyzed for a subset of 74 infants at 7 and 12 months of age. The composition of the microbiota was determined by sequencing of 16S rRNA genes amplified by PCR from bulk DNA extracted from feces. Diet records were used to estimate food and dietary fiber intake. Alpha diversity (number of operational taxonomic units [OTUs]) was significantly lower in BLISS infants at 12 months of age (difference [95% confidence interval {CI}] of 31 OTUs [3.4 to 58.5]; P = 0.028), and while there were no significant differences between control and BLISS infants in relative abundances of Bifidobacteriaceae, Enterobacteriaceae, Veillonellaceae, Bacteroidaceae, Erysipelotrichaceae, Lachnospiraceae, or Ruminococcaceae at 7 or 12 months of age, OTUs representing the genus Roseburia were less prevalent in BLISS microbiotas at 12 months. Mediation models demonstrated that the intake of “fruit and vegetables” and “dietary fiber” explained 29% and 25%, respectively, of the relationship between group (BLISS versus control) and alpha diversity. IMPORTANCE The introduction of solid foods (complementary feeding or weaning) to infants leads to more-complex compositions of microbial communities (microbiota or microbiome) in the gut. In baby-led weaning (BLW), infants are given only finger foods that they can pick up and feed themselves—there is no parental spoon-feeding of puréed baby foods—and infants are encouraged to eat family meals. BLW is a new approach to infant feeding that is increasing in popularity in the United States, New Zealand, the United Kingdom, and Canada. We used mediation modeling, commonly used in health research but not in microbiota studies until now, to identify particular dietary components that affected the development of the infant gut microbiota.

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Revisiting the Dilution Procedure Used To Manipulate Microbial Biodiversity in Terrestrial Systems

Applied and Environmental Microbiology ◽

10.1128/aem.00958-15 ◽

2015 ◽

Vol 81 (13) ◽

pp. 4246-4252 ◽

Cited By ~ 28

Author(s):

Yan Yan ◽

Eiko E. Kuramae ◽

Peter G. L. Klinkhamer ◽

Johannes A. van Veen

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Terrestrial Ecosystems ◽

Diversity Indices ◽

Soil Samples ◽

16S Rrna Genes ◽

Rrna Genes ◽

Dilution Method ◽

Soil Suspension ◽

Content Type

ABSTRACTIt is hard to assess experimentally the importance of microbial diversity in soil for the functioning of terrestrial ecosystems. An approach that is often used to make such assessment is the so-called dilution method. This method is based on the assumption that the biodiversity of the microbial community is reduced after dilution of a soil suspension and that the reduced diversity persists after incubation of more or less diluted inocula in soil. However, little is known about how the communities develop in soil after inoculation. In this study, serial dilutions of a soil suspension were made and reinoculated into the original soil previously sterilized by gamma irradiation. We determined the structure of the microbial communities in the suspensions and in the inoculated soils using 454-pyrosequencing of 16S rRNA genes. Upon dilution, several diversity indices showed that, indeed, the diversity of the bacterial communities in the suspensions decreased dramatically, withProteobacteriaas the dominant phylum of bacteria detected in all dilutions. The structure of the microbial community was changed considerably in soil, withProteobacteria,Bacteroidetes, andVerrucomicrobiaas the dominant groups in most diluted samples, indicating the importance of soil-related mechanisms operating in the assembly of the communities. We found unique operational taxonomic units (OTUs) even in the highest dilution in both the suspensions and the incubated soil samples. We conclude that the dilution approach reduces the diversity of microbial communities in soil samples but that it does not allow accurate predictions of the community assemblage during incubation of (diluted) suspensions in soil.

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Effect of Sodium Bisulfite Injection on the Microbial Community Composition in a Brackish-Water-Transporting Pipeline

Applied and Environmental Microbiology ◽

10.1128/aem.05891-11 ◽

2011 ◽

Vol 77 (19) ◽

pp. 6908-6917 ◽

Cited By ~ 53

Author(s):

Hyung Soo Park ◽

Indranil Chatterjee ◽

Xiaoli Dong ◽

Sheng-Hung Wang ◽

Christoph W. Sensen ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Microbial Community Composition ◽

Sodium Bisulfite ◽

16S Rrna Genes ◽

Rrna Genes ◽

Iron Corrosion ◽

Injection Point ◽

Content Type ◽

Sulfate Reducing

ABSTRACTPipelines transporting brackish subsurface water, used in the production of bitumen by steam-assisted gravity drainage, are subject to frequent corrosion failures despite the addition of the oxygen scavenger sodium bisulfite (SBS). Pyrosequencing of 16S rRNA genes was used to determine the microbial community composition for planktonic samples of transported water and for sessile samples of pipe-associated solids (PAS) scraped from pipeline cutouts representing corrosion failures. These were obtained from upstream (PAS-616P) and downstream (PAS-821TP and PAS-821LP, collected under rapid-flow and stagnant conditions, respectively) of the SBS injection point. Most transported water samples had a large fraction (1.8% to 97% of pyrosequencing reads) ofPseudomonasnot found in sessile pipe samples. The sessile population of PAS-616P had methanogens (Methanobacteriaceae) as the main (56%) community component, whereasDeltaproteobacteriaof the generaDesulfomicrobiumandDesulfocapsawere not detected. In contrast, PAS-821TP and PAS-821LP had lower fractions (41% and 0.6%) ofMethanobacteriaceaearchaea but increased fractions of sulfate-reducingDesulfomicrobium(18% and 48%) and of bisulfite-disproportionatingDesulfocapsa(35% and 22%) bacteria. Hence, SBS injection strongly changed the sessile microbial community populations. X-ray diffraction analysis of pipeline scale indicated that iron carbonate was present both upstream and downstream, whereas iron sulfide and sulfur were found only downstream of the SBS injection point, suggesting a contribution of the bisulfite-disproportionating and sulfate-reducing bacteria in the scale to iron corrosion. Incubation of iron coupons with pipeline waters indicated iron corrosion coupled to the formation of methane. Hence, both methanogenic and sulfidogenic microbial communities contributed to corrosion of pipelines transporting these brackish waters.

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Berberine Blocks the Relapse of Clostridium difficile Infection in C57BL/6 Mice after Standard Vancomycin Treatment

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.04794-14 ◽

2015 ◽

Vol 59 (7) ◽

pp. 3726-3735 ◽

Cited By ~ 22

Author(s):

Zhi Lv ◽

Guoli Peng ◽

Weihua Liu ◽

Hufeng Xu ◽

JianRong Su

Keyword(s):

Clostridium Difficile ◽

Mouse Model ◽

Gut Microbiota ◽

Inflammatory Responses ◽

Relative Weight ◽

16S Rrna Genes ◽

Rrna Genes ◽

Therapeutic Effects ◽

Content Type ◽

Vancomycin Treatment

ABSTRACTVancomycin is a preferred antibiotic for treatingClostridium difficileinfection (CDI) and has been associated with a rate of recurrence of CDI of as high as 20% in treated patients. Recent studies have suggested that berberine, an alternative medical therapy for gastroenteritis and diarrhea, exhibits several beneficial effects, including induction of anti-inflammatory responses and restoration of the intestinal barrier function. This study investigated the therapeutic effects of berberine on preventing CDI relapse and restoring the gut microbiota in a mouse model. Berberine was administered through gavage to C57BL/6 mice with established CDI-induced intestinal injury and colitis. The disease activity index (DAI), mean relative weight, histopathology scores, and levels of toxins A and B in fecal samples were measured. An Illumina sequencing-based analysis of 16S rRNA genes was used to determine the overall structural change in the microbiota in the mouse ileocecum. Berberine administration significantly promoted the restoration of the intestinal microbiota by inhibiting the expansion of members of the familyEnterobacteriaceaeand counteracting the side effects of vancomycin treatment. Therapy consisting of vancomycin and berberine combined prevented weight loss, improved the DAI and the histopathology scores, and effectively decreased the mortality rate. Berberine prevented CDIs from relapsing and significantly improved survival in the mouse model of CDI. Our data indicate that a combination of berberine and vancomycin is more effective than vancomycin alone for treating CDI. One of the possible mechanisms by which berberine prevents a CDI relapse is through modulation of the gut microbiota. Although this conclusion was generated in the case of the mouse model, use of the combination of vancomycin and berberine and represent a novel therapeutic approach targeting CDI.

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The Lumen of Human Intestinal Organoids Poses Greater Stress to Bacteria Compared to the Germ-Free Mouse Intestine: Escherichia coli Deficient in RpoS as a Colonization Probe

mSphere ◽

10.1128/msphere.00777-20 ◽

2020 ◽

Vol 5 (6) ◽

Author(s):

Madeline R. Barron ◽

Roberto J. Cieza ◽

David R. Hill ◽

Sha Huang ◽

Veda K. Yadagiri ◽

...

Keyword(s):

Escherichia Coli ◽

Stress Response ◽

Content Type ◽

General Stress Response ◽

E Coli ◽

Germ Free ◽

General Stress ◽

Microbe Interactions ◽

Mouse Intestine ◽

Host Microbe Interactions

ABSTRACT Pluripotent stem-cell-derived human intestinal organoids (HIOs) are three-dimensional, multicellular structures that model a naive intestinal epithelium in an in vitro system. Several published reports have investigated the use of HIOs to study host-microbe interactions. We recently demonstrated that microinjection of the nonpathogenic Escherichia coli strain ECOR2 into HIOs induced morphological and functional maturation of the HIO epithelium, including increased secretion of mucins and cationic antimicrobial peptides. In the current work, we use ECOR2 as a biological probe to further characterize the environment present in the HIO lumen. We generated an isogenic mutant in the general stress response sigma factor RpoS and employed this mutant to compare challenges faced by a bacterium during colonization of the HIO lumen relative to the germ-free mouse intestine. We demonstrate that the loss of RpoS significantly decreases the ability of ECOR2 to colonize HIOs, although it does not prevent colonization of germ-free mice. These results indicate that the HIO lumen is a more restrictive environment to E. coli than the germ-free mouse intestine, thus increasing our understanding of the HIO model system as it pertains to studying the establishment of intestinal host-microbe symbioses. IMPORTANCE Technological advancements have driven and will continue to drive the adoption of organotypic systems for investigating host-microbe interactions within the human intestinal ecosystem. Using E. coli deficient in the RpoS-mediated general stress response, we demonstrate that the type or severity of microbial stressors within the HIO lumen is more restrictive than those of the in vivo environment of the germ-free mouse gut. This study provides important insight into the nature of the HIO microenvironment from a microbiological standpoint.

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Pyrosequencing Analysis of Bacterial Diversity in 14 Wastewater Treatment Systems in China

Applied and Environmental Microbiology ◽

10.1128/aem.01617-12 ◽

2012 ◽

Vol 78 (19) ◽

pp. 7042-7047 ◽

Cited By ~ 272

Author(s):

Xiaohui Wang ◽

Man Hu ◽

Yu Xia ◽

Xianghua Wen ◽

Kun Ding

Keyword(s):

Wastewater Treatment ◽

Microbial Community ◽

Bacterial Community ◽

16S Rrna Genes ◽

Rrna Genes ◽

Microbial Populations ◽

Operational Parameters ◽

Geographic Locations ◽

Content Type ◽

Wastewater Treatment Systems

ABSTRACTTo determine if there is a core microbial community in the microbial populations of different wastewater treatment plants (WWTPs) and to investigate the effects of wastewater characteristics, operational parameters, and geographic locations on microbial communities, activated sludge samples were collected from 14 wastewater treatment systems located in 4 cities in China. High-throughput pyrosequencing was used to examine the 16S rRNA genes of bacteria in the wastewater treatment systems. Our results showed that there were 60 genera of bacterial populations commonly shared by all 14 samples, includingFerruginibacter,Prosthecobacter,Zoogloea, Subdivision 3 generaincertae sedis, Gp4, Gp6, etc., indicating that there is a core microbial community in the microbial populations of WWTPs at different geographic locations. The canonical correspondence analysis (CCA) results showed that the bacterial community variance correlated most strongly with water temperature, conductivity, pH, and dissolved oxygen (DO) content. Variance partitioning analyses suggested that wastewater characteristics had the greatest contribution to the bacterial community variance, explaining 25.7% of the variance of bacterial communities independently, followed by operational parameters (23.9%) and geographic location (14.7%). Results of this study provided insights into the bacterial community structure and diversity in geographically distributed WWTPs and discerned the relationships between bacterial community and environmental variables in WWTPs.

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