Microbiome Diversity and Community-Level Change Points within Manure-Based Small Biogas Plants

Efforts to integrate biogas plants into bioeconomy concepts will lead to an expansion of manure-based (small) biogas plants, while their operation is challenging due to critical characteristics of some types of livestock manure. For a better process understanding, in this study, three manure-based small biogas plants were investigated with emphasis on microbiome diversity. Due to varying digester types, feedstocks, and process conditions, 16S rRNA gene amplicon sequencing showed differences in the taxonomic composition. Dynamic variations of each investigated biogas plant microbiome over time were analyzed by terminal restriction fragment length polymorphism (TRFLP), whereby nonmetric multidimensional scaling (NMDS) revealed two well-running systems, one of them with a high share of chicken manure, and one unstable system. By using Threshold Indicator Taxa Analysis (TITAN), community-level change points at ammonium and ammonia concentrations of 2.25 g L-1 and 193 mg L-1 or volatile fatty acid concentrations of 0.75 g L-1were reliably identified which are lower than the commonly reported thresholds for critical process stages based on chemical parameters. Although a change in the microbiome structure does not necessarily indicate an upcoming critical process stage, the recorded community-level change points might be a first indication to carefully observe the process.

Download Full-text

Indicative Marker Microbiome Structures Deduced from the Taxonomic Inventory of 67 Full-Scale Anaerobic Digesters of 49 Agricultural Biogas Plants

Microorganisms ◽

10.3390/microorganisms9071457 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1457

Author(s):

Julia Hassa ◽

Johanna Klang ◽

Dirk Benndorf ◽

Marcel Pohl ◽

Benedikt Hülsemann ◽

...

Keyword(s):

Stable Process ◽

Process Condition ◽

Full Scale ◽

Process Models ◽

Process Efficiency ◽

Process Conditions ◽

Rrna Gene ◽

General Process ◽

Specific Distribution ◽

Biogas Plants

There are almost 9500 biogas plants in Germany, which are predominantly operated with energy crops and residues from livestock husbandry over the last two decades. In the future, biogas plants must be enabled to use a much broader range of input materials in a flexible and demand-oriented manner. Hence, the microbial communities will be exposed to frequently varying process conditions, while an overall stable process must be ensured. To accompany this transition, there is the need to better understand how biogas microbiomes respond to management measures and how these responses affect the process efficiency. Therefore, 67 microbiomes originating from 49 agricultural, full-scale biogas plants were taxonomically investigated by 16S rRNA gene amplicon sequencing. These microbiomes were separated into three distinct clusters and one group of outliers, which are characterized by a specific distribution of 253 indicative taxa and their relative abundances. These indicative taxa seem to be adapted to specific process conditions which result from a different biogas plant operation. Based on these results, it seems to be possible to deduce/assess the general process condition of a biogas digester based solely on the microbiome structure, in particular on the distribution of specific indicative taxa, and without knowing the corresponding operational and chemical process parameters. Perspectively, this could allow the development of detection systems and advanced process models considering the microbial diversity.

Download Full-text

Biphasic Study to Characterize Agricultural Biogas Plants by High-Throughput 16S rRNA Gene Amplicon Sequencing and Microscopic Analysis

Journal of Microbiology and Biotechnology ◽

10.4014/jmb.1605.05083 ◽

2017 ◽

Vol 27 (2) ◽

pp. 321-334 ◽

Cited By ~ 18

Author(s):

Irena Maus ◽

Yong Sung Kim ◽

Daniel Wibberg ◽

Yvonne Stolze ◽

Sandra Off ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

High Throughput ◽

Microscopic Analysis ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Biogas Plants

Download Full-text

Is Fluorescence Technology a Promising Tool for Detecting Infected Dentin in Deep Carious Lesions?

Caries Research ◽

10.1159/000505643 ◽

2020 ◽

Vol 54 (3) ◽

pp. 205-217

Author(s):

Leslie H. Trippe ◽

Apoena Aguiar Ribeiro ◽

M. Andrea Azcarate-Peril ◽

John S. Preisser ◽

Rujin Wang ◽

...

Keyword(s):

Rank Correlation ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Human Teeth ◽

Operational Taxonomic Units ◽

Promising Tool ◽

Carious Lesions ◽

Microbiome Diversity ◽

Bacterial Microbiome ◽

Deep Carious Lesions

The purpose of this study was to determine if the degree of fluorescence detected by fluorescence-aided caries excavation (FACE) correlates with dentin bacterial microbiome diversity, as assessed by 16S rRNA gene amplicon sequencing, and with traditional tactile dentin caries assessment. Unidentified human teeth were obtained from a dental facility. The included teeth had a carious lesion two-thirds into the dentin, verified by radiography, and were red-fluorescing (RF) using FACE technology (SIROInspect; Sirona, Bensheim, Germany). Two independent examiners performed visual/tactile assessment of the lesions. RF sites were sampled with a sterile spoon excavator and dentin characteristics were evaluated. Once RF dentin was removed, a second sample of pink-fluorescing (PF) dentin was obtained. After excavation with a sterile round bur to nonfluorescing (NF) dentin, a third sample was collected with a slow-speed round bur. The samples were processed at the UNC (University of North Carolina at Chapel Hill) Microbiome Core Facility. Out of 134 extracted teeth collected, 21 fit the inclusion criteria, yielding 61 dentin samples. RF samples had the highest number of observed operational taxonomic units (n = 154), followed by PF (n = 109) and NF (n = 100). RF carious dentin was primarily “soft,” and NF dentin was assessed as “hard” 100% of the time by both examiners (rank correlation χ2: p < 0.001). However, approximately one-third of the tactile assessments of hard dentin still displayed some fluorescence, either pink or red. We concluded that the sampled fluorescing (RF and PF) and NF carious dentin layers displayed diverse bacterial taxa, and tactile assessments of soft, leathery, and hard corresponded with RF, PF, and NF.

Download Full-text

Effect of Chicken Manure-Based Fertiliser on Bacterial Communities and Diversity of Tomato Endosphere Microbiota

Agriculture (Pol nohospodárstvo) ◽

10.2478/agri-2021-0013 ◽

2021 ◽

Vol 67 (3) ◽

pp. 144-154

Author(s):

Hafeez Ul Haq ◽

Ye Li ◽

Lingyue Jin ◽

Ting Zhang ◽

Linjie Cheng ◽

...

Keyword(s):

Bacterial Communities ◽

Amplicon Sequencing ◽

Shannon Index ◽

Chicken Manure ◽

Rrna Gene ◽

Beneficial Bacteria ◽

Bacterial Phyla ◽

Frequent Use ◽

Significant Difference ◽

Harmful Effects

Abstract The frequent use of chemical fertiliser produces harmful effects on the soil ecosystem. Therefore, biocompatible methods are used to improve plant health and production through natural fertiliser or plant beneficial microorganisms. This study aims to investigate the effect of amended chicken manure-based natural fertiliser on bacterial communities and plant beneficial bacteria of tomato endosphere microbiome using the high throughput 16S rRNA gene amplicon sequencing. The results showed Proteobacteria (89.4 ± 4.7% to 86.7 ± 3.9%), Actinobacteria (6.03 ± 2.9% to 3.56 ± 2.1%), and Firmicutes (3.34 ± 1.3% to 0.59 ± 0.3%) as the dominant bacterial phyla of tomato endophytic microbiome. Pseudomonas and Bacillus were the most abundant identifiable genera in the chicken manure root (CMR) (amended manure treatments) sample. There was no significant difference in alpha bacterial diversity (Shannon index: p = 0.48) and species richness (Chao 1: p = 0.43) between control original root (OR) and CMR. However, the distribution of the dominant phyla was mainly affected by manure fertilisation. The non-metric multidimensional scaling (NMDS) and PCoA of beta diversity analysis suggested a significant separation in bacterial communities of tomato endophytes between CMR and OR. The most differently abundant bacterial taxa belong to Bacteroidetes in the OR group, whereas the beneficial bacterial communities of Actinobacteria and Firmicutes were more abundant in the CMR group. Therefore, the chicken manure application can significantly affect bacterial communities of tomatoes´ root endophytic microbiome and effectively improve the abundance of the beneficial microbes as biofertilisers.

Download Full-text

Monitoring of seven industrial anaerobic digesters supplied with biochar

Biotechnology for Biofuels ◽

10.1186/s13068-021-02034-5 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Kerstin Heitkamp ◽

Adriel Latorre-Pérez ◽

Sven Nefigmann ◽

Helena Gimeno-Valero ◽

Cristina Vilanova ◽

...

Keyword(s):

Microbial Diversity ◽

Methanogenic Archaea ◽

Amplicon Sequencing ◽

Joint Analysis ◽

Rrna Gene ◽

Anaerobic Digesters ◽

Metabolic Route ◽

Biogas Plants ◽

One Year ◽

The Impact

Abstract Background Recent research articles indicate that direct interspecies electron transfer (DIET) is an alternative metabolic route for methanogenic archaea that improves microbial methane productivity. It has been shown that multiple conductive materials such as biochar can be supplemented to anaerobic digesters to increase the rate of DIET. However, the industrial applicability, as well as the impact of such supplements on taxonomic profiles, has not been sufficiently assessed to date. Results Seven industrial biogas plants were upgraded with a shock charge of 1.8 kg biochar per ton of reactor content and then 1.8 kg per ton were added to the substrate for one year. A joint analysis for all seven systems showed a decreasing trend for the concentration of acetic acid (p < 0.0001), propionic acid (p < 0.0001) and butyric acid (p = 0.0022), which was significant in all cases. Quantification of the cofactor F420 using fluorescence microscopy showed a reduction in methanogenic archaea by up to a power of ten. Methanogenic archaea could grow within the biochar, even if the number of cells was 4 times less than in the surrounding sludge. 16S-rRNA gene amplicon sequencing showed a higher microbial diversity in the biochar particles than in the sludge, as well as an accumulation of secondary fermenters and halotolerant bacteria. Taxonomic profiles indicate microbial electroactivity, and show the frequent occurrence of Methanoculleus, which has not been described in this context before. Conclusions Our results shed light on the interplay between biochar particles and microbial communities in anaerobic digesters. Both the microbial diversity and the absolute frequency of the microorganisms involved were significantly changed between sludge samples and biochar particles. This is particularly important against the background of microbial process monitoring. In addition, it could be shown that biochar is suitable for reducing the content of inhibitory, volatile acids on an industrial scale.

Download Full-text

Relative contributions of egg-associated and substrate-associated microorganisms to black soldier fly larval performance and microbiota

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab054 ◽

2021 ◽

Vol 97 (5) ◽

Author(s):

Stijn J. J. Schreven ◽

Hugo de Vries ◽

Gerben D. A. Hermes ◽

Hauke Smidt ◽

Marcel Dicke ◽

...

Keyword(s):

Animal Feed ◽

Bacterial Community Composition ◽

Amplicon Sequencing ◽

Larval Survival ◽

Chicken Manure ◽

Minor Role ◽

Larval Performance ◽

Rrna Gene ◽

Microbiota Composition ◽

Black Soldier Fly

ABSTRACT Larvae of the black soldier fly (BSF) can be used to convert organic waste into insect biomass for animal feed. In this process, they interact with microorganisms originating from the substrate, the insect and the environment. The substrate is the main determinant of the larval gut microbiota composition, but inoculation of the substrate with egg-associated bacteria can improve larval performance. We aimed to quantify the relative importance of substrate-associated and egg-associated microorganisms in BSF larval performance, bacterial abundance and bacterial community composition, when larvae were fed with chicken feed or chicken manure. For this, we inactivated substrate-associated microorganisms by autoclaving, or disinfected BSF eggs. Larval survival, weight and proportion of prepupae were determined on day 15. We collected substrate and larval samples on days 0 and 15 and performed 16S rRNA gene-targeted qPCR and amplicon sequencing. In both chicken feed and chicken manure, egg disinfection did not cause any difference in larval performance or overall microbiota composition. In contrast, in chicken manure, substrate-associated microorganisms increased larval biomass and sterilizing the substrate caused major shifts in microbiota. Thus, substrate-associated microorganisms impact not only larval microbiota but also larval performance, whereas egg-associated microorganisms have a minor role in the densities present.

Download Full-text

Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

Genome Biology ◽

10.1186/s13059-019-1831-z ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 14

Author(s):

Robert C. Kaplan ◽

Zheng Wang ◽

Mykhaylo Usyk ◽

Daniela Sotres-Alvarez ◽

Martha L. Daviglus ◽

...

Keyword(s):

Community Health ◽

Gut Microbiome ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Shannon Index ◽

Health Study ◽

Rrna Gene ◽

Cross Sectional ◽

Hispanic Community ◽

The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

Download Full-text

Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals

Microbiome ◽

10.1186/s40168-021-01012-1 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Janis R. Bedarf ◽

Naiara Beraza ◽

Hassan Khazneh ◽

Ezgi Özkurt ◽

David Baker ◽

...

Keyword(s):

Parkinson’S Disease ◽

16S Rrna ◽

16S Rrna Gene ◽

False Positive ◽

Gene Sequencing ◽

Bacterial Biomass ◽

16S Rrna Gene Sequencing ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Rrna Gene Sequencing

Abstract Background Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson’s disease (PD) and Alzheimer’s disease (AD) or as a “brain microbiome” in the context of healthy patients’ brain samples. Methods Using 16S rRNA gene sequencing, we tested the hypothesis that there is a bacterial brain microbiome. We evaluated brain samples from healthy human subjects and individuals suffering from PD (olfactory bulb and pre-frontal cortex), as well as murine brains. In line with state-of-the-art recommendations, we included several negative and positive controls in our analysis and estimated total bacterial biomass by 16S rRNA gene qPCR. Results Amplicon sequencing did detect bacterial signals in both human and murine samples, but estimated bacterial biomass was extremely low in all samples. Stringent reanalyses implied bacterial signals being explained by a combination of exogenous DNA contamination (54.8%) and false positive amplification of host DNA (34.2%, off-target amplicons). Several seemingly brain-enriched microbes in our dataset turned out to be false-positive signals upon closer examination. We identified off-target amplification as a major confounding factor in low-bacterial/high-host-DNA scenarios. These amplified human or mouse DNA sequences were clustered and falsely assigned to bacterial taxa in the majority of tested amplicon sequencing pipelines. Off-target amplicons seemed to be related to the tissue’s sterility and could also be found in independent brain 16S rRNA gene sequences. Conclusions Taxonomic signals obtained from (extremely) low biomass samples by 16S rRNA gene sequencing must be scrutinized closely to exclude the possibility of off-target amplifications, amplicons that can only appear enriched in biological samples, but are sometimes assigned to bacterial taxa. Sequences must be explicitly matched against any possible background genomes present in large quantities (i.e., the host genome). Using close scrutiny in our approach, we find no evidence supporting the hypothetical presence of either a brain microbiome or a bacterial infection in PD brains.

Download Full-text

Retinitis pigmentosa is associated with shifts in the gut microbiome

Scientific Reports ◽

10.1038/s41598-021-86052-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Oksana Kutsyr ◽

Lucía Maestre-Carballa ◽

Mónica Lluesma-Gomez ◽

Manuel Martinez-Garcia ◽

Nicolás Cuenca ◽

...

Keyword(s):

Retinitis Pigmentosa ◽

Gut Microbiome ◽

Functional Decline ◽

Retinal Disease ◽

Photoreceptor Cells ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sequencing Data ◽

Alpha And Beta Diversity ◽

Potential Biomarker

AbstractThe gut microbiome is known to influence the pathogenesis and progression of neurodegenerative diseases. However, there has been relatively little focus upon the implications of the gut microbiome in retinal diseases such as retinitis pigmentosa (RP). Here, we investigated changes in gut microbiome composition linked to RP, by assessing both retinal degeneration and gut microbiome in the rd10 mouse model of RP as compared to control C57BL/6J mice. In rd10 mice, retinal responsiveness to flashlight stimuli and visual acuity were deteriorated with respect to observed in age-matched control mice. This functional decline in dystrophic animals was accompanied by photoreceptor loss, morphologic anomalies in photoreceptor cells and retinal reactive gliosis. Furthermore, 16S rRNA gene amplicon sequencing data showed a microbial gut dysbiosis with differences in alpha and beta diversity at the genera, species and amplicon sequence variants (ASV) levels between dystrophic and control mice. Remarkably, four fairly common ASV in healthy gut microbiome belonging to Rikenella spp., Muribaculaceace spp., Prevotellaceae UCG-001 spp., and Bacilli spp. were absent in the gut microbiome of retinal disease mice, while Bacteroides caecimuris was significantly enriched in mice with RP. The results indicate that retinal degenerative changes in RP are linked to relevant gut microbiome changes. The findings suggest that microbiome shifting could be considered as potential biomarker and therapeutic target for retinal degenerative diseases.

Download Full-text

Oral Microbiota Identifies Patients in Early Onset Rheumatoid Arthritis

Microorganisms ◽

10.3390/microorganisms9081657 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1657

Author(s):

Anders Esberg ◽

Linda Johansson ◽

Ingegerd Johansson ◽

Solbritt Rantapää Dahlqvist

Keyword(s):

Rheumatoid Arthritis ◽

Early Onset ◽

Amplicon Sequencing ◽

Oral Bacteria ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

Disease Manifestation ◽

Periodontal Status ◽

Quality Register

Rheumatoid arthritis (RA) is the most common autoimmune inflammatory disease, and single periodontitis-associated bacteria have been suggested in disease manifestation. Here, the oral microbiota was characterized in relation to the early onset of RA (eRA) taking periodontal status into consideration. 16S rRNA gene amplicon sequencing of saliva bacterial DNA from 61 eRA patients without disease-modifying anti-rheumatic drugs and 59 matched controls was performed. Taxonomic classification at 98.5% was conducted against the Human Oral Microbiome Database, microbiota functions were predicted using PICRUSt, and periodontal status linked from the Swedish quality register for clinically assessed caries and periodontitis. The participants were classified into three distinct microbiota-based cluster groups with cluster allocation differences by eRA status. Independently of periodontal status, eRA patients had enriched levels of Prevotella pleuritidis, Treponema denticola, Porphyromonas endodontalis and Filifactor alocis species and in the Porphyromonas and Fusobacterium genera and functions linked to ornithine metabolism, glucosylceramidase, beta-lactamase resistance, biphenyl degradation, fatty acid metabolism and 17-beta-estradiol-17-dehydrogenase metabolism. The results support a deviating oral microbiota composition already in eRA patients compared with healthy controls and highlight a panel of oral bacteria that may be useful in eRA risk assessment in both periodontally healthy and diseased persons.

Download Full-text