The division "Synergistes"

Effects of diets for three growing stages by rumen inocula donors on in vitro rumen fermentation and microbiome

Hanwoo and Jeju Black cattle (Jeju Black) are native breeds of Korean cattle. Jeju Black cattle are recognized as natural monuments and are known to exhibit slower growth rates compared to Hanwoo. While several studies have analyzed the genetic characteristics of these cattle, there has been limited research on the differences in their microbiome. In this study, rumen fluid was obtained from three Hanwoo steers and three Jeju Black steers, and three different diets (total mixed rations [TMRs] for growing, early fattening, and late fattening periods) were used as substrates for in vitro fermentation. The in vitro incubation was conducted for 3 h and 24 h following a 2 × 3 factorial arrangement. After both incubation periods, fermentation characteristics were analyzed, and ruminal microbiome analysis was performed using 16S rRNA gene sequencing, employing both QIIME2 and PICRUSt2. The results revealed significant differences in the ruminal microbiota due to the inoculum effect. At the phylum level, Patescibacteria and Synergistota were found to be enriched in the Jeju Black inoculum-treated group. Additionally, using different inocula also affected the relative abundance of major taxa, including Ruminococcus, Pseudoramibacter, Ruminococcaceae CAG-352, and the [Eubacterium] ruminantium group. These microbial differences induced by the inoculum may have originated from varying levels of domestication between the two subspecies of donor animals, which mainly influenced the fermentation and microbiome features in the early incubation stages, although this was only partially offset afterward. Furthermore, predicted commission numbers of microbial enzymes, some of which are involved in the biosynthesis of secondary metabolites, fatty acids, and alpha amylase, differed based on the inoculum effect. However, these differences may account for only a small proportion of the overall metabolic pathway. Conversely, diets were found to affect protein biosynthesis and its related metabolism, which showed differential abundance in the growing diet and were potentially linked to the growth-promoting effects in beef cattle during the growing period. In conclusion, this study demonstrated that using different inocula significantly affected in vitro fermentation characteristics and microbiome features, mainly in the early stages of incubation, with some effects persisting up to 24 h of incubation.

Comparative Analysis of Rumen Microbiota Composition in Dairy Cows with Simple Indigestion and Healthy Cows

Simple indigestion in cows leads to substantial economic losses in the dairy industry. Despite ongoing efforts, an effective treatment for this issue remains elusive. Previous studies have emphasized the vital role of rumen microbes in maintaining ruminant health. To deepen our comprehension of the intricate interplay between rumen microbiota and simple indigestion, we undertook a study involving the analysis of rumen fluid from eight cows with simple indigestion and ten healthy cows. Additionally, we collected data pertaining to milk production, rumination behavior, and rumen characteristics. The results showed that cows with simple indigestion displayed significantly lower milk yield, reduced rumination duration, and weakened rumen contraction when contrasted with the healthy cows (p < 0.05). However, no significant difference in microbiota α-diversity emerged (p > 0.05). Principal coordinate analysis (PCoA) illuminated substantial variations in rumen microbial structure among the two groups (p < 0.05). Further analysis spotlighted distinctive bacteria in the rumen of the cows with indigestion, including Allisonella, Synergistes, Megasphaera, Clostridium_XIVb, Campylobacter, and Acidaminococcus. In contrast, Coraliomargarita, Syntrophococcus, and Coprococcus are the dominant bacterial genera in the rumen of healthy dairy cows. Importantly, these key bacterial genera also dominated the overarching microbial interaction network. The observation suggests that changes in the abundance of these dominant bacterial genera potentially underlie the principal etiology of cows with simple indigestion. The present findings can provide insights into simple indigestion prevention and treatment in dairy cows.

Combined disposal of methyl orange and corn straw via stepwise adsorption-biomethanation-composting

Agriculture wastes have been proved to be the potential adsorbents to remove azo dye from textile wastewater, but the post-treatment of azo dye loaded agriculture waste is generally ignored. A three-step strategy including sequential adsorption-biomethanation-composting was developed to realize the co-processing of azo dye and corn straw (CS). Results showed that CS represented a potential adsorbent to remove methyl orange (MO) from textile wastewater, with the maximum MO adsorption capacity of 10.00 ± 0.46 mg/g, deriving from the Langmuir model. During the biomethanation, CS could serve as electron donor for MO decolorization and substrate for biogas production simultaneously. Though the cumulative methane yield of CS loaded with MO was 11.7 ± 2.28% lower than that of blank CS, almost complete de-colorization of MO could be achieved within 72 h. Composting could achieve the further degradation of aromatic amines (intermediates during the degradation of MO) and decomposition of digestate. After 5 days' composting, 4-aminobenzenesulfonic acid (4-ABA) was not detectable. The germination index (GI) also indicated that the toxicity of aromatic amine was eliminated. The overall utilization strategy gives novel light on the management of agriculture waste and textile wastewater.

Request for an Opinion on the standing and retention of Firmicutes as a phylum name

Oren and Garrity recently published 42 new prokaryotic phylum names, including Bacillota, which they describe as a synonym of the effectively published name Firmacutes and its orthographic correction Firmicutes. However, the name Firmacutes was listed as a division in the Approved Lists of Bacterial Names, which suggests that it should be treated as having been validly published. Recent emendations to rules require that a named phylum now requires a named type genus and a phylum name is formed by the addition of the suffix -ota to the stem of the name of the designated type genus. However, there are strong practical arguments for retaining the name Firmicutes, notwithstanding the uncertainty over whether the name already has standing. This matter is referred to the Judicial Commission, asking for an opinion on the standing and retention of the name Firmicutes.

Tea Consumption and Gut Microbiome in Older Chinese Adults

BACKGROUND

Animal and small-cohort human studies have shown that tea consumption affects the gut microbiome, but evidence from large cohort studies is lacking.

OBJECTIVES

We examined associations between tea consumption and gut microbiome composition among older Chinese adults.

METHODS

The study included 1179 men and 1078 women from the Shanghai Men's and Women's Health Studies, who reported tea drinking status, type, amount, and duration at baseline and follow-up surveys (1996-2017) and were free of cancer, cardiovascular disease, and diabetes at stool collection (2015-2018). Fecal microbiome was profiled using 16S rRNA sequencing. Associations of tea variables with microbiome diversity and taxa abundance were evaluated using linear or negative binomial hurdle models after adjusting for sociodemographics, lifestyle, and hypertension status.

RESULTS

Mean age at stool collection was 67.2 ± 9.0 y in men and 69.6 ± 8.5 y in women. Tea drinking was not associated with microbiome ɑ-diversity in men or women; however, all tea variables were associated with β-diversity in men (P < 0.001). Significant associations with taxa abundance were also observed mostly in men. Current tea drinking, mainly green tea drinking, was associated with increase in orders Synergistales and RF39 in men (β = 0.30 to 0.42, all PFDR ≤ 0.10) but not in women (PInteraction-sex = 0.01). Also, increase in families Coriobacteriaceae, Odoribacteraceae, genera Collinsella, Odoribacter, and species Collinsella aerofaciens, Coprococcus catus, and Dorea formicigenerans were observed among men who drank >3.3 cups (781 mL)/d compared to that of nondrinkers (all PFDR <0.10). The increased Coprococcus catus related to tea drinking was more evident among men without hypertension and inversely associated with the prevalence of hypertension (OR: 0.90; 95% CI: 0.84, 0.97; PFDR = 0.03).

CONCLUSIONS

Tea consumption may affect gut microbiome β-diversity and abundance of some bacteria, which may contribute to reduced hypertension risk in Chinese men. Future studies should examine the sex-specific tea-gut microbiome associations and how certain bacteria may mediate the health benefits of tea.

Gut Microbiota and Cognitive Function Among Women Living with HIV

BACKGROUND

Altered gut microbiota has been associated with cognitive dysfunction and Alzheimer's disease, but little is known among people living with HIV.

OBJECTIVE

To examine associations between gut microbiota and cognitive impairment among women with or without HIV.

METHODS

This is a cross-sectional study of 446 women (302 HIV+) who had completed a neuropsychological test battery and stool sample collected within 1 year. Gut microbiota composition was quantified using 16SV4 rRNA gene sequencing and microbial functional pathways were predicted using PICRUSt. Cognitive domains included attention, executive function, learning, memory, fluency, processing speed, and motor function. Cognitive impairment was defined as two or more domains with T scores < 1 SD below mean. ANCOM-II was used to identify taxa and functional pathways associated with cognitive impairment, and the associations were further examined by multivariable logistic regression.

RESULTS

In overall sample, adjusting for multiple covariates including HIV status, we found that higher abundance of Methanobrevibacter, Odoribacter, Pyramidobacter, Eubacterium, Ruminococcus, and Gemmiger, and lower abundance of Veillonella were associated with cognitive impairment. The associations between these taxa and cognitive impairment were more profound in HIV+ women compared to HIV- women. Most associations with bacterial taxa were observed for learning and memory. We found accompanying microbial functional differences associated with cognitive impairment, including twelve enriched pathways and three depleted pathways.

CONCLUSIONS

In women with or without HIV infection, this study identified multiple altered gut bacterial taxa and functional pathways associated with cognitive impairment, supporting the potential role of gut microbiota in cognitive dysfunction and Alzheimer's disease.

Changes in antibiotic residues and the gut microbiota during ciprofloxacin administration throughout Silkie chicken development

The use of antibiotics leads to antibiotic residues in livestock and poultry products, adversely affecting human health. Ciprofloxacin (CFX) is a broad-spectrum antibiotic shared between animals and humans that is useful in treatments besides infections. However, changes in the gut microbiota caused by CFX and the possible link with the elimination of CFX residues have not been investigated. Herein, we used the Silkie chicken model to study the changes in the gut microbiota during the entire CFX-metabolic repertoire. We detected CFX residues in different tissues and showed that the elimination time of CFX from different tissues was dissimilar (liver > kidney > chest muscle > skin). Analysis of liver and kidney injury biomarkers and plasma antioxidant indices indicated slight hepatotoxicity and nephrotoxicity in the Silkie chickens. Importantly, the changes in the gut microbial community predominantly occurred early in the metabolic process. Correlation analysis revealed that the particular bacterial microbiota were associated with the pharmacokinetics of CFX in different Silkie chicken tissues (e.g., aerobic bacteria, including Escherichia and Coprococcus, and anaerobic bacteria, including Fusobacterium, Ruminococcus, Bifidobacterium, and Eubacterium). Collectively, certain microbiota may boost antibiotic metabolism and participate in restoring the microbial consortia after CFX is metabolized. Therefore, regulating the core intestinal microbiota may reduce foodborne antibiotics and accelerate the development of drug resistance.

Current Trends in Biological Valorization of Waste-Derived Biomass: The Critical Role of VFAs to Fuel A Biorefinery

The looming climate and energy crises, exacerbated by increased waste generation, are driving research and development of sustainable resource management systems. Research suggests that organic materials, such as food waste, grass, and manure, have potential for biotransformation into a range of products, including: high-value volatile fatty acids (VFAs); various carboxylic acids; bioenergy; and bioplastics. Valorizing these organic residues would additionally reduce the increasing burden on waste management systems. Here, we review the valorization potential of various sustainably sourced feedstocks, particularly food wastes and agricultural and animal residues. Such feedstocks are often micro-organism-rich and well-suited to mixed culture fermentations. Additionally, we touch on the technologies, mainly biological systems including anaerobic digestion, that are being developed for this purpose. In particular, we provide a synthesis of VFA recovery techniques, which remain a significant technological barrier. Furthermore, we highlight a range of challenges and opportunities which will continue to drive research and discovery within the field. Analysis of the literature reveals growing interest in the development of a circular bioeconomy, built upon a biorefinery framework, which utilizes biogenic VFAs for chemical, material, and energy applications.

Removal of denatured protein particles enhanced UASB treatment of oxytetracycline production wastewater

Enhanced hydrolysis, which can selectively destroy antibiotic potency, has been previously demonstrated to be an effective pretreatment technology for the biological treatment of antibiotic production wastewater. However, full-scale application of enhanced hydrolysis to the treatment of real oxytetracycline production wastewater showed that the up-flow anaerobic sludge blanket (UASB) reactors treating the pretreated wastewater could only be stable under a low organic loading rate (OLR) of 1.8 ± 0.4 g·COD/L/d. Deterioration of UASB was also confirmed in treating the same wastewater using a bench-scale reactor (R1) at an OLR of 4.4 ± 0.3 g·COD/L/d. Assuming that the particles formed due to the denaturation of soluble proteins under the hydrolysis temperature (110 °C), resulting in the significant increase of suspended solids (SS) in oxytetracycline production wastewater from less than 200 mg/L to 1200 ± 500 mg/L, were responsible for the deterioration of UASB, the pretreated wastewater was filtered using polypropylene cotton fiber and ultrafiltration membrane, and then fed into two parallel bench-scale UASB reactors (R2 and R3). Both reactors maintained a stable COD removal (53.2% ~ 61.1%) even at an OLR as high as 8.0 g·COD/L/d. When the feed of R3 was switched to unfiltered wastewater, however, deterioration of the reactor occurred again. Microscopic observation showed that the granules in R3 were fully covered by protein particles after the switch of the feed. It was possible that the tight layer of the denatured protein particles blocked the inner pores of the granules, resulting in the obstruction of substrate transfer and biogas emission, while removing the protein particles could abate such blockage problem. This study provides a scientific basis for the efficient treatment of antibiotic production wastewater.

DNA- and RNA-based bacterial communities and geochemical zonation under changing sediment porewater dynamics on the Aldabra Atoll

The remote Aldabra Atoll, Seychelles, provides the rare opportunity to study bacterial communities in pristine carbonate sediments across an entire biome. The four sampled sites cover sand with high porewater exchange, bioturbated silt and mud with intermediate exchange, as well as a seasonally and episodically desiccated landlocked pool. As sediments harbour dead cells and environmental DNA alongside live cells, we used bacterial 16S rRNA gene and transcript analysis to distinguish between past and present inhabitants. Previously described laminated sediments mirroring past conditions in the Cerin, France could not be retrieved. Thus, the aim was adjusted to determine whether bacterial community composition and diversity follow typical geochemical zonation patterns at different locations of the atoll. Our data confirm previous observations that diversity decreases with depth. In the lagoon, the bacterial community composition changed from Pseudomonas dominating in the sand to diverse mixed surface and sulphate reduction zones in the anaerobic mud with strongly negative Eh. The latter correlated with high total alkalinity, ammonia, and total sulphide, alongside a decrease in SO₄²⁻/Cl⁻ and high relative abundances of sulphate reducing (Halo-) Desulfovibrio, sulphur oxidizing Arcobacteraceae, photo(hetero)troph Cyanobacteria, Alphaproteobacteria, and fermenting Propionigenium. In contrast to expectations, deeper mud and pool sediments harboured high abundances of Halomonas or Alphaproteobacteria alongside high C/N and increased salinity. We believe that this atypical community shift may be driven by a change in the complexity of available organic matter.

Night-Restricted Feeding Improves Gut Health by Synchronizing Microbe-Driven Serotonin Rhythm and Eating Activity-Driven Body Temperature Oscillations in Growing Rabbits

The circadian misalignment of the gut microbiota caused by unusual eating times in adult animals is related to disease development. However, whether the composition and diurnal rhythm of gut microbiota can be optimized by synchronizing the window period of eating with natural eating habits to reduce the risk of diarrhea remains unclear, especially in growing animals. In this study, 108 5-week-old weaned rabbits (nocturnal animals) were randomly subjected to daytime feeding (DF) and night-restricted feeding (NRF). At age 12 weeks, six rabbits were selected from each group, and caecum and cecal contents, as well as serum samples were collected at 4-h intervals during 24 h. Overall, NRF was found to reduce the risk of diarrhea in growing rabbits, improved the diurnal rhythm and abundance of beneficial microorganisms, along with the production of beneficial metabolites, whereas reduced the abundance of potential pathogens (Synergistes, Desulfovibrio, and Alistipes). Moreover, NRF improved diurnal rhythm of tryptophan hydroxylase isoform 1 and serotonin. Furthermore, NRF strengthened the diurnal amplitude of body core temperature, and promoted the diurnal expression of intestinal clock genes (BMAL1, CLOCK, REV-ERBα, and PER1), and genes related to the regulation of the intestinal barrier (CLAUDIN-1), and intestinal epithelial cell self-proliferation and renewal (BMI1). In vitro simulation experiments further revealed that synchronization of microbial-driven serotonin rhythm and eating activity-driven body temperature oscillations, which are important zeitgebers, could promote the diurnal expression of clock genes and CLAUDIN-1 in rabbit intestinal epithelial cells (RIEC), and enhance RIEC proliferation. This is the first study to reveal that NRF reprograms the diurnal rhythm of the gut microbiome, promotes the diurnal expression of clock genes and tight junction genes via synchronization of microbial-driven serotonin rhythm and eating activity-driven body temperature oscillations, thereby improving intestinal health and reducing the risk of diarrhea in growing rabbits. Collectively, these results provide a new perspective for the healthy feeding and management of growing animals.

Comparative evaluation of subgingival microbiome in healthy periodontium and gingivitis using next-generation sequencing technology: A case–control study

Background:

Human dental plaque is a complex microbial community containing millions of species. Gingivitis is a dysregulated immune-inflammatory response induced by dysbiotic plaque biofilm that interrupts symbiosis. The emergence of next-generation sequencing with 16S rRNA gene has greatly contributed in understanding the complexity of microbiota. However, studies focusing on microbiome in gingivitis are limited. The whole bacterial community is important in causing periodontal disease than a small number of periodontal pathogens. In this study, we attempted to profile the subgingival microbiome from individuals with healthy gingiva and in patients with gingivitis using next-generation sequencing technology.

Materials and Methods:

Subgingival plaque samples from 15 healthy periodontium (Group I) and 15 gingivitis (Group II) were collected and 16s rRNA sequencing was done in Illumina Solexa Sequencer. Data analysis using 16s metagenomics tool from BaseSpace onsite operational taxonomic units was assigned to each sequence using HOMD database. Individual variation in the microbiome of the subgingival samples between the two groups was also evaluated.

Results:

The comparison of top 20 species between Group I and Group II revealed no significant species group between them. Synergistetes was absent in Group I samples but found in Group II. At the genus level, HACEK group species were found in both the groups, while Dialister and Aneroglobus were found abundantly in the Group II.

Conclusion:

The presence of unique genera and species seen in Group II samples could point toward a dysbiotic shift that could be taking place in the subgingival environment leading to gingivitis.

Changes in the Gut Microbiome and Predicted Functional Metabolic Effects in an Australian Parkinson's Disease Cohort

Background: There has been increasing recognition of the importance of the gut microbiome in Parkinson's disease (PD), but the influence of geographic location has received little attention. The present study characterized the gut microbiota and associated changes in host metabolic pathways in an Australian cohort of people with PD (PwP). Methods: The study involved recruitment and assessment of 87 PwP from multiple Movement Disorders Clinics in Australia and 47 healthy controls. Illumina sequencing of the V3 and V4 regions of the 16S rRNA gene was used to distinguish inter-cohort differences in gut microbiota; KEGG analysis was subsequently performed to predict functional changes in host metabolic pathways. Results: The current findings identified significant differences in relative abundance and diversity of microbial operational taxonomic units (OTUs), and specific bacterial taxa between PwP and control groups. Alpha diversity was significantly reduced in PwP when compared to controls. Differences were found in two phyla (Synergistetes and Proteobacteria; both increased in PwP), and five genera (Colidextribacter, Intestinibacter, Kineothrix, Agathobaculum, and Roseburia; all decreased in PwP). Within the PD cohort, there was no association identified between microbial composition and gender, constipation or use of gastrointestinal medication. Furthermore, KEGG analysis identified 15 upregulated and 11 downregulated metabolic pathways which were predicted to be significantly altered in PwP. Conclusion: This study provides the first comprehensive characterization of the gut microbiome and predicted functional metabolic effects in a southern hemisphere PD population, further exploring the possible mechanisms whereby the gut microbiota may exert their influence on this disease, and providing evidence for the incorporation of such data in future individualized therapeutic strategies.

Effect of temperature on the persistence of fecal bacteria in ambient anaerobic digestion systems treating swine manure

This study aimed to explore the effect of temperature on the persistence of fecal bacteria by multiple approaches in ambient anaerobic digestion systems treating swine manure. Both lab-scale (15 °C, 20 °C, and 25 °C) and field (26 °C on average) studies were conducted by high-throughput sequencing and culture-based methods. A community-wide Bayesian SourceTracker method was used to identify and estimate the fecal bacterial proportion in anaerobic effluent. High proportional contributions of fecal bacteria were observed in effluent at 15 °C (73%) and 20 °C (75%), while less was found at 25 °C (19%). This was further verified by a field study (23%) and an anaerobic reactor study at 37 °C (0.01%). To explore the potential reasons for differences in fecal bacterial proportions, bacterial taxa were divided into "lost" and "survivor" taxa in manure waste by LEfSe. The "survivor" taxa abundance was positively correlated with SourceTracker proportion (r = 0.913, P = 0.001), but negatively correlated with temperature (r = -0.826, P = 0.006). In addition, biomarkers in effluent were divided into "enriched" and "de novo" taxa. "Enriched" taxa, including acidogenic and acetogenic bacteria, were found at all temperatures, whereas taxa related to organic degradation were multiplied "de novo" at 25 °C. Variation partition analysis showed that temperature could explain 30% of variations in effluent bacterial community. Moreover, coliforms isolated from the manure and effluents at 15 °C and 20 °C were also phylogenetically related. This study provided comprehensive insight into the impact of temperature on the persistence of fecal bacteria in anaerobic effluent, with temperatures over 25 °C recommended to reduce fecal pollution.

Prevalence of unculturable bacteria in the periapical abscess: A systematic review and meta-analysis

OBJECTIVE

To assess the prevalence of unculturable bacteria in periapical abscess, radicular cyst, and periapical granuloma.

METHODS

PubMed, Scopus, Science Direct, and Ovid databases were systematically searched from January 1990 to May 2020. All the included studies were cross-sectional design. The risk of bias was assessed using Joanna Briggs Institute check-list. Heterogeneity was described using meta-regression and mixed-effects model for lesion, country, and sequence technique moderators. Funnel plot and unweighted Egger's regression test were used to estimate the publication bias. Microbiome data on diversity, abundance, and frequency of unculturable bacteria in the periapical lesions were reviewed, analysed, and the principal component analysis (PCA) was performed.

RESULTS

A total of 13 studies out of 14,780, were selected for the final analysis. These studies focused on the prevalence of unculturable bacteria in periapical abscesses and related lesions. Approximately 13% (95% CI: 7-23%) of the cumulative number of bacteria derived from periapical abscesses was unculturable. Country moderator significantly (P = 0.05) affects the diversity summary proportion. While the pooled frequency of unculturable bacteria was 8%; 95% CI: 5, 14%, the estimate of the pooled abundance of unculturable bacteria was 5%; 95% CI: 2, 12% with a significant (P = 0.05) country moderator that affects the abundance summary proportion. Of the 62 unculturable bacteria, 35 were subjected to PCA and Peptostreptococcus sp. oral clone CK035 was the most abundant species in periapical abscesses. Hybridization techniques were found to be the most reliable molecular methods in detecting the abundance and frequency of unculturable bacteria.

CONCLUSION

The significant prevalence of unculturable bacteria in the periapical abscess, suggests that they are likely to play, a yet unknown, critical role in the pathogenesis and progression of the disease. Further research remains to be done to confirm their specific contributions in the virulence and disease progression.

Statistical optimization of methane production from brewery spent grain: Interaction effects of temperature and substrate concentration

This study evaluated the effects of thermal pretreatment of brewery spent grain (BSG) (by autoclave 121 °C, 1.45 atm for 30 min) on methane production (CH₄). Operation temperature (31-59 °C) and substrate concentration (8.3-19.7 g BSG.L^-1) factors were investigated by Response Surface Methodology (RSM) and Central Composite Design (CCD). Values ranging from 81.1 ± 2.0 to 290.1 ± 3.5 mL CH₄.g^-1 TVS were obtained according to operation temperature and substrate concentration variation. The most adverse condition for methanogenesis (81.1 ± 2.0 mL CH₄.g^-1 TVS) was at 59 °C and 14 g BSG.L^-1, in which there was increase in the organic matter concentration from 173.6 ± 4.94 to 3036 ± 7.78 mg.L^-1) result of a higher final concentration of volatile fatty acids (VFA, 2662.7 mg.L^-1). On the other hand, the optimum condition predicted by the statistical model was at 35 °C and 18 g BSG.L^-1 (289.1 mL CH₄.g^-1 TVS), which showed decrease in the organic matter concentration of 78.6% and a lower final concentration of VFA (533.2 mg.L^-1). Hydrogenospora and Methanosaeta were identified in this optimum CH₄ production condition, where acetoclastic methanogenic pathway prevailed. The CH₄ production enhancement was concomitant to acetic acid concentration decrease (from 578.9 to 135.7 mg.L^-1).

Endogenous bacteria inhabiting the Ophiocordyceps highlandensis during fruiting body development

Background

The genus Ophiocordyceps, which includes Ophiocordyceps sinensis, has been demonstrated to be one of the most valuable medicinal taxa. The low rate of larval infection and slow development that characterize the cultivation of this genus should be urgently addressed. To identify potential bioinoculants that stimulate the growth of Ophiocordyceps, O. highlandensis was selected as a model system, and a total of 72 samples were collected to systematically compare the microbial communities present during fruiting body development. By applying high-throughput 16S and ITS2 amplicon sequencing technology, the bacterial and fungal communities were identified in O. highlandensis and its surrounding soil, and the functional dynamics of the bacteria were explored.

Results

The results indicate that the most abundant bacteria across all the samples from O. highlandensis were Proteobacteria, Firmicutes and Bacteroidetes, while members of Ascomycota were detected among the fungi. The pathways enriched in the developmental stages were associated with carbohydrate degradation, nucleotides and pyridoxal biosynthesis, and the TCA cycle. Compared with that in the fungal community, an unexpectedly high taxonomic and functional fluctuation was discovered in the bacterial community during the maturation of O. highlandensis. Furthermore, bipartite network analysis identified four potential supercore OTUs associated with O. highlandensis growth.

Conclusions

All the findings of this study suggest unexpectedly high taxonomic and functional fluctuations in the bacterial community of O. highlandensis during its maturation. O. highlandensis may recruit different endogenous bacteria across its life cycle to enhance growth and support rapid infection. These results may facilitate Ophiocordyceps cultivation and improve the development of strategies for the identification of potential bioinoculant resources.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02227-w.

The impact of propagule pressure on whole community invasions in biomethane-producing communities

Microbes can invade as whole communities, but the ecology of whole community invasions is poorly understood. Here, we investigate how invader propagule pressure (the number of invading organisms) affects the composition and function of invaded laboratory methanogenic communities. An invading community was equally successful at establishing itself in a resident community regardless of propagule pressure, which varied between 0.01 and 10% of the size resident community. Invasion resulted in enhanced biogas production (to the level of the pure invading community) but only when propagule pressure was 1% or greater. This inconsistency between invasion success and changes in function can be explained by a lower richness of invading taxa at lower propagule pressures, and an important functional role of the taxa that were absent. Our results highlight that whole community invasion ecology cannot simply be extrapolated from our understanding of single species invasions. Moreover, we show that methane production can be enhanced by invading poorly performing reactors with a better performing community at levels that may be practical in industrial settings.

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Complex communities can successfully invade other communities

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Invasions change the community composition independently of propagule pressure

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Number of taxa invading increases with increased propagule pressure

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Larger propagule pressure impacts both the community structure and function

Archaeal and bacterial community structures of rural household biogas digesters with different raw materials in Qinghai Plateau

The present study aims to investigate microbial community structures household biogas digesters with different raw materials in Qinghai Plateau rural. High-throughput 16S rRNA gene sequencing analysis revealed that Firmicutes, Bacteroidetes, and Proteobacteria are the most abundant bacterial phyla (64.08%). Prevotella group 7 was the most abundant genus in digester YL9 and YL10 (69.72% and 26.96%, respectively) using vegetable waste raw materials. Trichococcus exhibited the highest abundance (14.55%) in YL1 digester using sheep and pig manure. Clostridium sensu stricto 1 (13.89%) and Synergistaceae_uncultured (15.52%) comprised the highest abundances in digester YL5 with mixed raw materials (i.e., dairy manure, sheep manure, and human feces). In addition, Proteiniphilum and Pseudomonas exhibited the highest abundances among bacterial genera in YL4 digester using pig manure. Methanomicrobiales was the most dominant archaeal communities, ranging from 13.35% to 81.34% in abundance. Methanocorpusculum exhibited dominant abundances in all digesters using various raw materials. Methanogenium was the most abundant archaeal genera in YL4 and YL6 digesters, which consume pig manure as primary raw material. In addition, Methanosarcina and Methanosaeta exhibited the highest abundances in digester YL1 (55.03%) and YL9 (51.40%), respectively. Moreover, fermentation temperatures and pH both contributed to the archaeal and bacterial community structures in all the investigated digesters. Specially, fermentation temperature showed positive correlation with the abundances of Synergistaceae_uncultured, Methanogenium, and Methanosaeta, and pH was positively correlated with the abundances of Prevotella group 7 and Methanosarcina abundances.

Targeted Delivery of Persulfides to the Gut: Effects on the Microbiome

Persulfides (R-SSH) have been hypothesized as potent redox modulators and signaling compounds. Reported herein is the synthesis, characterization, and in vivo evaluation of a persulfide donor that releases N-acetyl cysteine persulfide (NAC-SSH) in response to the prokaryote-specific enzyme nitroreductase. The donor, termed NDP-NAC, decomposed in response to E. coli nitroreductase, resulting in release of NAC-SSH. NDP-NAC elicited gastroprotective effects in mice that were not observed in animals treated with control compounds incapable of persulfide release or in animals treated with Na2 S. NDP-NAC induced these effects by the upregulation of beneficial small- and medium-chain fatty acids and through increasing growth of Turicibacter sanguinis, a beneficial gut bacterium. It also decreased the populations of Synergistales bacteria, opportunistic pathogens implicated in gastrointestinal infections. This study reveals the possibility of maintaining gut health or treating microbiome-related diseases by the targeted delivery of reactive sulfur species.

Rumen epithelial transcriptome and microbiome profiles of rumen epithelium and contents of beef cattle with and without liver abscesses

Abscess is the highest cause of liver condemnation and is estimated to cost the beef industry US$64 million annually. Fusobacterium necrophorum, commonly found in the bovine rumen, is the primary bacteria associated with liver abscess in cattle. Theoretically, damage to the rumen wall allows F. necrophorum to invade the bloodstream and colonize the liver. The objective of this study was to determine the changes in gene expression in the rumen epithelium and microbial populations adherent to the rumen epithelium and in the rumen contents of beef cattle with liver abscesses compared with those with no liver abscesses. Rumen epithelial tissue and rumen content were collected from 31 steers and heifers with liver abscesses and 30 animals with no liver abscesses. Ribonucleic acid (RNA) sequencing was performed on the rumen epithelium, and a total of 221 genes were identified as differentially expressed in the animals with liver abscesses compared with animals with no abscesses, after removal of genes that were identified as a result of interaction with sex. The nuclear factor kappa-light-chain enhancer of activated B cells signaling and interferon signaling pathways were significantly enriched in the differentially expressed gene (DEG) set. The majority of the genes in these pathways were downregulated in animals with liver abscesses. In addition, RNA translation and protein processing genes were also downregulated, suggesting that protein synthesis may be compromised in animals with liver abscesses. The rumen content bacterial communities were significantly different from the rumen wall epimural bacterial communities. Permutational multivariate analysis of variance (PERMANOVA) analysis did not identify global differences in the microbiome of the rumen contents but did identify differences in the epimural bacterial communities on the rumen wall of animals without and with liver abscesses. In addition, associations between DEG and specific bacterial amplicon sequence variants of epimural bacteria were observed. The DEG and bacterial profile on the rumen papillae identified in this study may serve as a method to monitor animals with existing liver abscesses or to predict those that are more likely to develop liver abscesses.

New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments

Members of the archaeal order Methanomassiliicoccales are methanogens mainly associated with animal digestive tracts. However, environmental members remain poorly characterized as no representatives not associated with a host have been cultivated so far. In this study, metabarcoding screening combined with quantitative PCR analyses on a collection of diverse non-host-associated environmental samples revealed that Methanomassiliicoccales were very scarce in most terrestrial and aquatic ecosystems. Relative abundance of Methanomassiliicoccales and substrates/products of methanogenesis were monitored during incubation of environmental slurries. A sediment slurry enriched in Methanomassiliicoccales was obtained from a freshwater sample. It allowed the reconstruction of a high-quality metagenome-assembled genome (MAG) corresponding to a new candidate species, for which we propose the name of Candidatus 'Methanomassiliicoccus armoricus MXMAG1'. Comparison of the annotated genome of MXMAG1 with the published genomes and MAGs from Methanomassiliicoccales belonging to the 2 known clades ('free-living'/non-host-associated environmental clade and 'host-associated'/digestive clade) allowed us to explore the putative physiological traits of Candidatus 'M. armoricus MXMAG1'. As expected, Ca. 'Methanomassiliicoccus armoricus MXMAG1' had the genetic potential to produce methane by reduction of methyl compounds and dihydrogen oxidation. This MAG encodes for several putative physiological and stress response adaptations, including biosynthesis of trehalose (osmotic and temperature regulations), agmatine production (pH regulation), and arsenic detoxication, by reduction and excretion of arsenite, a mechanism that was only present in the 'free-living' clade. An analysis of co-occurrence networks carried out on environmental samples and slurries also showed that Methanomassiliicoccales detected in terrestrial and aquatic ecosystems were strongly associated with acetate and dihydrogen producing bacteria commonly found in digestive habitats and which have been reported to form syntrophic relationships with methanogens.

Anaerobic degradation of protein-rich biomass in an UASB reactor: Organic loading rate effect on product output and microbial communities dynamics

Anaerobic degradation of enzymatically pretreated Chlorella vulgaris was aimed in an upflow anaerobic sludge blanket reactor (UASB) to evaluate the organic loading rate (OLR) effect on biomass valorization. Low OLRs resulted in high methane yields (171 mL CH₄/g CODin) at low hydraulic retention time (HRT of 6 days). Firmicutes (35-43%), Bacteroidetes (17-18%) and Euryarchaeota (11%) dominated at low OLRs, promoting methanogenic activity. On the contrary, the highest OLRs resulted in low methane yield (86 mL CH₄/gCODin) with a concomitant short-chain fatty acids (SCFAs) accumulation of 37% SCFAs-COD/CODin. The highest OLR decreased UASB reactor biodiversity, hampering Euryarchaeota population development (2.5%) and boosting Firmicutes (55%) and Proteobacteria (14%). These results demonstrated the suitability of UASB reactor configuration to reach high bioprocess efficiency for both, biogas and SCFAs production, with lower energetic and area requirements than those normally needed in continuous stirred tank reactors.

Phylum Synergistetes in the oral cavity: A possible contributor to periodontal disease

Microbial contributions to periodontal disease have been under renewed scrutiny with the advent of newer technologies to identify their presence and gene expression at the molecular level. Members of the phylum Synergistetes are some of the more recent bacteria to be associated with periodontal disease. Bacteria classified in this phylum can be found in a wide variety of habitats including both inside and outside of a mammalian host. Members of this phylum have been identified as part of the human microbiome. Indeed, many of the identified phylotypes have yet to be cultivated. Here we consider contributions of three named and formally described species to the oral microbial community and to pathogenesis of periodontal disease.

Establishing practical strategies to run high loading corn stover anaerobic digestion: Methane production performance and microbial responses

It is significant to understand corn stover (CS) in anaerobic digestion (AD) under high organic loadings. A semi-continuous mesophilic (37 ± 1 °C) CS AD was conducted in this study with increasing loadings. The initial total solids (TS) gradually increased with 1% gradient at every 10 days from 8% to 15% until the system was acidified. Adding different ratios of cattle manure (CM) (20%, 30% and 40% (v/v)) to rescue this system back to a stable operation was adopted. The diversity of bacteria and archaea was analyzed by 16S rRNA gene sequencing technology. The results showed that when loading TS content was increased to 15%, AD system was acidized with pH value of 5.13. 30% of CM was the optimal ratio to recover biogas production. High abundance (31.07%) of Bathyarchaeota was first found in AD system. Acidification of high loading CS AD can be highly correlating with bacterial community, specially Clostridium and Caproiciproducens.

Behçet's Disease Under Microbiotic Surveillance? A Combined Analysis of Two Cohorts of Behçet's Disease Patients

Background: In Behçet's disease (BD), an auto-inflammatory vasculitis, an unbalanced gut microbiota can contribute to pro-inflammatory reactions. In separate studies, distinct pro- and anti-inflammatory bacteria associated with BD have been identified.

Methods: To establish disease-associated determinants, we performed gut microbiome profiling in BD patients from the Netherlands (n = 19) and Italy (n = 13), matched healthy controls (HC) from the Netherlands (n = 17) and Italy (n = 15) and oral microbiome profiling in Dutch BD patients (n = 18) and HC (n = 15) by 16S rRNA gene sequencing. In addition, we used fecal IgA-SEQ analysis to identify specific IgA coated bacterial taxa in Dutch BD patients (n = 13) and HC (n = 8).

Results: In BD stool samples alpha-diversity was conserved, whereas beta-diversity analysis showed no clustering based on disease, but a significant segregation by country of origin. Yet, a significant decrease of unclassified Barnesiellaceae and Lachnospira genera was associated with BD patients compared to HC. Subdivided by country, the Italian cohort displays a significant decrease of unclassified Barnesiellaceae and Lachnospira genera, in the Dutch cohort this decrease is only a trend. Increased IgA-coating of Bifidobacterium spp., Dorea spp. and Ruminococcus bromii species was found in stool from BD patients. Moreover, oral Dutch BD microbiome displayed increased abundance of Spirochaetaceae and Dethiosulfovibrionaceae families.

Conclusions: BD patients show decreased fecal abundance of Barnesiellaceae and Lachnospira and increased oral abundance of Spirochaetaceae and Dethiosulfovibrionaceae. In addition, increased fecal IgA coating of Bifidobacterium, Ruminococcus bromii and Dorea may reflect retention of anti-inflammatory species and neutralization of pathosymbionts in BD, respectively. Additional studies are warranted to relate intestinal microbes with the significance of ethnicity, diet, medication and response with distinct pro- and inflammatory pathways in BD patients.

Inhibition during Anaerobic Co-Digestion of Aqueous Pyrolysis Liquid from Wastewater Solids and Synthetic Primary Sludge

Pyrolysis can convert wastewater solids into useful byproducts such as pyrolysis gas (py-gas), bio-oil and biochar. However, pyrolysis also yields organic-rich aqueous pyrolysis liquid (APL), which presently has no beneficial use. Autocatalytic pyrolysis can beneficially increase py-gas production and eliminate bio-oil; however, APL is still generated. This study aimed to utilize APLs derived from conventional and autocatalytic wastewater solids pyrolysis as co-digestates to produce biomethane. Results showed that digester performance was not reduced when conventional APL was co-digested. Despite having a lower phenolics concentration, catalyzed APL inhibited methane production more than conventional APL and microbial community analysis revealed a concomitant reduction in acetoclastic Methanosaeta. Long-term (over 500-day) co-digestion of conventional APL with synthetic primary sludge was performed at different APL organic loading rates (OLRs). Acclimation resulted in a doubling of biomass tolerance to APL toxicity. However, at OLRs higher than 0.10 gCOD/Lr-d (COD = chemical oxygen demand, Lr = liter of reactor), methane production was inhibited. In conclusion, conventional APL COD was stoichiometrically converted to methane in quasi steady state, semi-continuous fed co-digesters at OLR ≤ 0.10 gCOD/Lr-d. Undetected organic compounds in the catalyzed APL ostensibly inhibited anaerobic digestion. Strategies such as use of specific acclimated inoculum, addition of biochar to the digester and pretreatment to remove toxicants may improve future APL digestion efforts.

Effects of Alternative Administration Programs of a Synbiotic Supplement on Broiler Performance, Foot Pad Dermatitis, Caecal Microbiota, and Blood Metabolites

This research investigated the effects of different synbiotic administration programs on broiler productive performance and foot pad dermatitis (FPD). Molecular insights on caecal microbiota and plasma metabolomics were also performed. - A total of 1000 one-day-old male chicks were grouped by the synbiotic treatment. The synbiotic was either sprayed as gel droplets onto newly hatched chicks at the hatchery (100 g/10,000 birds) or supplemented in-feed during the entire rearing period (1000, 500, and 250 g/ton according to feeding phase), or both. Only the treatments' combination produced significant results in comparison with the control group (untreated), improving feed conversion ratio from 14 to 29 d and in the overall period of the trial (1.570 vs. 1.509 and 1.643 vs. 1.596, respectively; p < 0.05) while lowering FPD occurrence at slaughter (17% vs. 5%; p < 0.05). These findings can be related to significant variations of caecal microbiota, like higher Firmicutes to Bacteroidetes ratio (with favorable implications for host's energy-harvesting potential from the diet) and more beneficial microbial consortium presumably sustaining eubiosis. Overall, these results indicate that administering synbiotics through gel droplets at the hatchery combined to in-feed supplementation for the whole growing cycle positively affects broiler feed efficiency and welfare.

Increased loading stress leads to convergence of microbial communities and high methane yields in adapted anaerobic co-digesters

Enhancing biogas production, while avoiding inhibition of methanogenesis during co-digestion of grease interceptor waste (GIW), can help water resource recovery facilities reduce their carbon footprint. Here we used pre-adapted and non-adapted digesters to link microbial community structure to digester function. Before disturbance, the pre-adapted and non-adapted digesters showed similar methane production and microbial community diversity but dissimilar community composition. When exposed to an identical disturbance, the pre-adapted digester achieved better performance, while the non-adapted digester was inhibited. When re-exposed to disturbance after recovery, communities and performance of both digesters converged, regardless of the temporal variations. Co-digestion of up to 75% GIW added on a volatile solids (VS) basis was achieved, increasing methane yield by 336% from 0.180 to 0.785 l-methane/g-VS-added, the highest methane yield reported to date for lipid-rich waste. Progressive perturbation substantially enriched fatty acid-degrading Syntrophomonas from less than 1% to 24.6% of total 16S rRNA gene sequences, acetoclastic Methanosaeta from 2.3% to 11.9%, and hydrogenotrophic Methanospirillum from less than 1% to 6.6% in the pre-adapted digester. Specific hydrolytic and fermentative populations also increased. These ecological insights demonstrated how progressive perturbation can be strategically used to influence methanogenic microbiomes and improve co-digestion of GIW.

Long-Term Mesophilic Anaerobic Co-Digestion of Swine Manure with Corn Stover and Microbial Community Analysis

Long-term anaerobic co-digestion of swine manure (SM) and corn stover (CS) was conducted using semi-continuously loaded digesters under mesophilic conditions. A preliminary test was first conducted to test the effects of loading rates, and results indicated the 3 g-VS L⁻¹ d⁻¹ was the optimal loading rate. Based on the preliminary results, a verification replicated test was conducted with 3 g-VS L⁻¹ d⁻¹ loading rate and different SM/CS ratios (1:1, 2:1 and 1:2). Results showed that a SM/CS ratio of 2/1 was optimal, based on maximum observed methane-VS_des generation and carbon conversion efficiency (72.56 ± 3.40 mL g⁻¹ and 40.59%, respectively). Amplicon sequencing analysis suggested that microbial diversity was increased with CS loading. Amino-acid-degrading bacteria were abundant in the treatment groups. Archaea Methanoculleus could enhance biogas and methane productions.

The effect of temperature fluctuation on the microbial diversity and community structure of rural household biogas digesters at Qinghai Plateau

Seasonal temperature-fluctuation has been regarded as a key environmental factor affecting rural biogas fermentation yields. The present study investigated the impact of seasonal temperature-fluctuation on operating-temperatures and biogas production in rural household digesters at Qinghai Plateau and revealed the related changes in microbial diversity and community structure by 16S rRNA gene high-throughput sequencing (HTS) analysis. Our results showed closely positive correlation between operating-temperatures and biogas production. HTS analysis indicated the highest diversity for bacteria community in autumn (at highest operating-temperatures) and late winter (at lowest operating-temperatures) and for archaea community only in autumn. HTS analysis classified bacteria into 21 phyla and 346 genera with the most predominant phyla Firmicutes, Bacteroidetes and Proteobacteria (> 72.4% in total) and the most predominant genera Proteiniphilum, Clostridium sensustricto 1, Petrimonas, Pseudomonas and Fastidiosipila (37.09-38.61% in total). HTS analysis also revealed two main archaea orders (Methanomicrobiales and Methanobacteriales) and one predominant genus Methanogenium to support plateau biogas fermentation. Especially, a remarkable impact of temperature on the community abundances of bacteria phyla Synergistetes and archaea genera Methanogenium and Thermogymnomonas was observed, and such microbial community structure changes were positively consistent with the biogas production. The present work provided the first set of evidences to link temperature-controlled modulation of microbial community structure with rural household biogas production at Qinghai Plateau.

Acclimatization contributes to stable anaerobic digestion of organic fraction of municipal solid waste under extreme ammonia levels: Focusing on microbial community dynamics

The organic fraction of municipal solid waste (OFMSW) is an abundant and sustainable substrate for the anaerobic digestion (AD) process, yet ammonia released during OFMSW hydrolysis could result in suboptimal biogas production. Acclimatized ammonia tolerant microorganisms offer an efficient way to alleviate ammonia inhibition during AD. This study aimed to achieve an efficient AD of OFMSW under extreme ammonia levels and elucidate the dynamics of the acclimatized microbial community. Thus, two mesophilic continuous stirred tank reactors (CSTR), fed only with OFMSW, were successfully acclimatized up to 8.5 g NH₄⁺-N/L, and their methane yields fluctuated <10%, compared to the methane yields without ammonia addition. Microbiological analyses showed that Methanosaeta concilii and Methanosarcina soligelidi were the dominant methanogens at low and high ammonia levels, respectively. Whilst, a unique metabolic pathway shift, from aceticlastic to hydrogenotrophic methanogenesis, of M. soligelidi was identified during the acclimatization process.

Evaluation of Predation Capability of Periodontopathogens Bacteria by Bdellovibrio Bacteriovorus HD100. An in Vitro Study

Treatment options against periodontitis attempt to completely remove oral microbiota even if several species in dental plaque demonstrate protective features. Predatory bacteria that selectively predate solely on Gram-negative bacteria might be a viable therapeutic alternative. Therefore, the aim of this study is to in vitro evaluate the susceptibility of some oral pathogens to predation by B. bacteriovorus HD100 in liquid suspension. Cultures of prey cell were prepared in brain heart infusion broth (BHI) broth incubating overnight at the appropriate conditions for each organism to reach log phase of growth. Predatory activity was assessed by measuring optical density at 600 nm after 12, 24, 48 and 72 hours. Statistical analysis was performed using the Mann-Whitney U test and p values less than 0.05 were considered statistically significant. The study demonstrated that B. bacteriovorus is able to predate on aerobic species and on microaerophilic ones (p < 0.05) but also that its predatory capacity is strongly compromised by the conditions of anaerobiosis. B. bacteriovorus, in fact, was unable to predate the anaerobic species involved in the present study (F. nucleatum and P. gingivalis). The findings of the study suggest that B. bacteriovorus is able to tolerate microaerophilic conditions and that in anaerobiosis it cannot exert its predatory capacity. Such evidence could lead to its use as an agent to prevent recolonization of the periodontal pocket following therapy. Further studies are needed to investigate the activity of B. bacteriovorus against recently recognized periodontopathogens, alone or organized in biofilms of multi-species communities.

Effect of thermal hydrolysis pretreatment on volatile fatty acids production in sludge acidification and subsequent polyhydroxyalkanoates production

The study compared the differences in VFAs production between raw sludge and thermal hydrolyzed sludge (TH-sludge) at different temperature (35 °C and 55 °C) in four semi-continuous acidification reactors. Optimal VFAs yield was obtained from TH-sludge at 35 °C (0.22 gVFA_COD/gVS), 44.6% higher than raw sludge at 35 °C, since the advantage of TH-sludge in SCOD solubilization overcame its disadvantage of lower carbon biodegradability. Moreover, high temperature (55 °C) was proved to aid the acidification of raw sludge by 15.7% (in Y_VFAs), but inhibit that of TH-sludge by 12.2%, mainly due to the suppressed microbial activities under heat. Microbial community analysis showed that TH-sludge had a larger proportion of acidogenic microbes than raw sludge, mainly attributing to the increase of Selenomonadales (37.3% vs. 3.7%); high temperature enriched thermophilic proteolytic microbes, Anaerobaculum and Coprothermobacter. Finally, optimal acidified liquid from TH-sludge at 35 °C was applied for PHAs production and achieved a competitive yield of 34.6% PHAs/DCW.

Feed supplementation with biochar may reduce poultry pathogens, including Campylobacter hepaticus, the causative agent of Spotty Liver Disease

Increased global regulation and restrictions on the non-therapeutic use of antibiotics in the poultry industry means that there is a need to identify alternatives that prevent infection while still conveying the growth and performance benefits afforded by their use. Biochars are produced by the incomplete pyrolysis of organic materials, with reports of use as a feed supplement and activity against pathogenic bacteria. In the current study the dose-dependent effects of biochar dietary inclusion in layer diets at 1%, 2% and 4% w/w were investigated to determine a) the efficacy of biochar as an anti-pathogenic additive on the intestinal microbiota and b) the optimal inclusion level. Biochar inclusion for anti-pathogenic effects was found to be most beneficial at 2% w/w. Poultry pathogens such as Gallibacterium anatis and campylobacters, including Campylobacter hepaticus, were found to be significantly lower in biochar fed birds. A shift in microbiota was also associated with the incorporation of 2% w/w biochar in the feed in two large scale trials on two commercial layer farms. Biochar inclusion for anti-pathogenic effects was found to be most beneficial at 2% w/w. Differential effects of the timing of biochar administration (supplementation beginning at hatch or at point of lay) were also evident, with greater impact on community microbial structure at 48 weeks of age when birds were fed from hatch rather than supplemented at point of lay.

Evaluation of anionic surfactant removal by anaerobic degradation of commercial laundry wastewater and domestic sewage

An expanded granular sludge bed reactor was evaluated for the anaerobic digestion of commercial laundry wastewater and domestic sewage focused on the removal of linear alkylbenzene sulfonate (LAS). The reactor was operated in three stages, all under mesophilic conditions and with a hydraulic retention time of 36 h. At stage I, the laundry wastewater was diluted with tap water (influent: 15.3 ± 4.9 mg LAS/L); at stage II, 50% of the feed volume was domestic sewage and 50% was a mixture of tap water and laundry wastewater (influent: 15.8 ± 4.9 mg LAS/L); and at stage III, only domestic sewage was used as a diluent of the laundry wastewater (influent: 24.1 ± 4.1 mg LAS/L). Due to the addition of domestic sewage the organic compounds content and LAS in the influent increased. Under such conditions, it was observed that LAS removal rate decreased from 77.2 ± 14.9% (stage I) to 55.3 ± 18.4% (stage III). Statistical tests indicated that the decrease of the LAS removal rate was significant and indicated a correlation between the removal of LAS and specific organic loading rate. The analysis of 16S rRNA gene sequencing revealed genera similar to Geobacter, Desulfovibrio, Syntrophomonas, Syntrophus, Desulfobulbus, Desulfomonile, and Desulfomicrobium, which were related to the degradation of LAS.

Antibiotic resistance genes allied to the pelagic sediment microbiome in the Gulf of Khambhat and Arabian Sea

Antibiotics have been widely spread in the environments, imposing profound stress on the resistome of the residing microbes. Marine microbiomes are well established large reservoirs of novel antibiotics and corresponding resistance genes. The Gulf of Khambhat is known for its extreme tides and complex sedimentation process. We performed high throughput sequencing and applied bioinformatics techniques on pelagic sediment microbiome across four coordinates of the Gulf of Khambhat to assess the marine resistome, its corresponding bacterial community and compared with the open Arabian Sea sample. We identified a total of 2354 unique types of resistance genes, with most abundant and diverse gene profile in the area that had anthropogenic activities being carried out on-shore. The genes with >1% abundance in all samples included carA, macB, sav1866, tlrC, srmB, taeA, tetA, oleC and bcrA which belonged to the macrolides, glycopeptides and peptide drug classes. ARG enriched phyla distribution was quite varying between all the sites, with Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes among the dominant phyla. Based on the outcomes, we also propose potential biomarker candidates Desulfovibrio, Thermotaga and Pelobacter for antibiotic monitoring in the two of the Gulf samples probable contamination prone environments, and genera Nitrosocccus, Marinobacter and Streptomyces in the rest of the three studied samples. Outcomes support the concept that ARGs naturally originate in environments and human activities contribute to the dissemination of antibiotic resistance.

Response of the reactor performance and microbial community to a shift of ISDD process from micro-aerobic to anoxic condition

Micro-aerobic condition has proven to be effective in enhancing sulfide oxidation to elemental sulfur (S⁰) during integrated simultaneous desulfurization and denitrification process (ISDD). In this study we investigated and compared the performance and microbial community of ISDD process operating under initially anoxic, then micro-aerobic and finally switch back to anoxic condition. For all the three tested scenarios, comparable bioreactor performance in terms of sulfate (95.0 ± 4.4%, 90.6 ± 3.8%, 89.8 ± 3.5%) and nitrate (∼100%) removal was achieved. However, a shift of ISDD bioreactor from micro-aerobic to anoxic environment clearly increased the S⁰ production (30.6%), relative to that at initial anoxic condition (14.2%). Further anoxic bioreactor operation with different influent nitrate concentrations also obtained satisfactory performance particularly in terms of S⁰ production. Microbial community analysis results showed that functional microorganisms selectively enriched at micro-aerobic condition, particularly sulfide-oxidizing bacteria (SOB), could also function well and enhance S⁰ production when bioreactor switching from micro-aerobic to anoxic environment. We proposed that micro-aerobic strategy could function as a bio-selector and provide a new idea in functional microorganisms selectively enrichment for wastewater treatment.

Performance of two differently designed permeable reactive barriers with sulfate and zinc solutions

For the first time, this laboratory-scale study evaluates the feasibility of incorporating diffusive exchange in permeable reactive barriers. In order to do this, the performance of two permeable reactive barriers (PRB) with different internal substrate arrangements were compared during the administration of a sulfate solution without metals (for 163 days) and with metals (for 60 days), simulating groundwater contaminated with acid mine drainage (AMD). In order to simulate a traditional PRB, a homogeneous distribution was implemented in the first reactor and the other PRB reactor utilized diffusion-active technology (DAPRB). In the DAPRB, the distribution of the reactive material was interspersed with the conductive material. The measurements in the internal ports showed that transverse gradients of sulfide formed in the DAPRB, causing the diffusion of sulfide from the substrate toward the layer interface, which is where the sulfide reacts by forming complexes with the metal. The DAPRB prevents the microorganisms from direct contact with AMD. This protection caused greater activity (sulfide production).

Effect of long residence time and high temperature over anaerobic biodegradation of Scenedesmus microalgae grown in wastewater

Anaerobic digestion of indigenous Scenedesmus spp. microalgae was studied in continuous lab-scale anaerobic reactors at different temperatures (35 °C and 55 °C), and sludge retention time - SRT (50 and 70 days). Mesophilic digestion was performed in a continuous stirred-tank reactor (CSTR) and in an anaerobic membrane bioreactor (AnMBR). Mesophilic CSTR operated at 50 days SRT only achieved 11.9% of anaerobic biodegradability whereas in the AnMBR at 70 days SRT and 50 days HRT reached 39.5%, which is even higher than the biodegradability achieved in the thermophilic CSTR at 50 days SRT (30.4%). Microbial analysis revealed a high abundance of cellulose-degraders in both reactors, AnMBR (mainly composed of 9.4% Bacteroidetes, 10.1% Chloroflexi, 8.0% Firmicutes and 13.2% Thermotogae) and thermophilic CSTR (dominated by 23.8% Chloroflexi and 12.9% Firmicutes). However, higher microbial diversity was found in the AnMBR compared to the thermophilic CSTR which is related to the SRT. since high SRT promoted low growth-rate microorganisms, increasing the hydrolytic potential of the system. These results present the membrane technology as a promising approach to revalue microalgal biomass, suggesting that microalgae biodegradability and consequently the methane production could be improved operating at higher SRT.

Cold adaptation and replicable microbial community development during long-term low-temperature anaerobic digestion treatment of synthetic sewage

The development and activity of a cold-adapting microbial community was monitored during low-temperature anaerobic digestion (LtAD) treatment of wastewater. Two replicate hybrid anaerobic sludge bed-fixed-film reactors treated a synthetic sewage wastewater at 12°C, at organic loading rates of 0.25-1.0 kg chemical oxygen demand (COD) m-3 d-1, over 889 days. The inoculum was obtained from a full-scale anaerobic digestion reactor, which was operated at 37°C. Both LtAD reactors readily degraded the influent with COD removal efficiencies regularly exceeding 78% for both the total and soluble COD fractions. The biomass from both reactors was sampled temporally and tested for activity against hydrolytic and methanogenic substrates at 12°C and 37°C. Data indicated that significantly enhanced low-temperature hydrolytic and methanogenic activity developed in both systems. For example, the hydrolysis rate constant (k) at 12°C had increased 20-30-fold by comparison to the inoculum by day 500. Substrate affinity also increased for hydrolytic substrates at low temperature. Next generation sequencing demonstrated that a shift in a community structure occurred over the trial, involving a 1-log-fold change in 25 SEQS (OTU-free approach) from the inoculum. Microbial community structure changes and process performance were replicable in the LtAD reactors.

Insights into biomethane production and microbial community succession during semi-continuous anaerobic digestion of waste cooking oil under different organic loading rates

High content of lipids in food waste could restrict digestion rate and give rise to the accumulation of long chain fatty acids in anaerobic digester. In the present study, using waste cooking oil skimmed from food waste as the sole carbon source, the effect of organic loading rate (OLR) on the methane production and microbial community dynamics were well investigated. Results showed that stable biomethane production was obtained at an organic loading rate of 0.5-1.5 g VS L-1 days-1. The specific biogas/methane yield values at OLR of 1.0 were 1.44 ± 0.15 and 0.98 ± 0.11 L g VS-1, respectively. The amplicon pyrosequencing revealed the distinct microbial succession in waste cooking oil AD reactors. Acetoclastic methanogens belonging to the genus Methanosaeta were the most dominant archaea, while the genera Syntrophomona, Anaerovibrio and Synergistaceae were the most common bacteria during AD process. Furthermore, redundancy analysis indicated that OLR showed more significant effect on the bacterial communities than that of archaeal communities. Additionally, whether the OLR of lipids increased had slight influence on the acetate fermentation pathway.

Methane production and characteristics of the microbial community in the co-digestion of spent mushroom substrate with dairy manure

Spent mushroom substrate (SMS) is a potential biomass material generated during mushroom cultivation. In this study, the methane yield and microbial community resulting from co-digestion of SMS and dairy manure (DM) at different mixing ratios (0:4, 1:1, 3:1, and 1:3), were evaluated. Co-digestion analysis showed that the methane yield from the mixtures was 6%-61% higher than the yield from SMS or DM alone, indicating a synergistic effect of co-digestion of SMS with DM. For the SMS of F.velutipes (SFv) and P.erygii var. tuoliensis (SPt), co-digestion of DM/SMS at a ratio of 1:1 was optimal, but for the SMS of P. eryngi (SPe), co-digestion of DM/SMS at a ratio of 3:1 was ideal. The pH at all co-digestion ratios was in the range of 6.8-8.0, indicating that adding DM could increase the systemic buffering capacity. Methanosaetaceae was shown to be the predominant methanogens present during the co-digestion of DM/SMS.

Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring

A bacterium belonging to the phylum Synergistetes, genus Dethiosulfovibrio was isolated in 2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis USBA 82^T (DSM 21565^T= KCTC 5659^T) is a mesophilic, strictly anaerobic, slightly halophilic, Gram negative bacterium with a diderm cell envelope. The strain ferments peptides, amino acids and a few organic acids. Here we present the description of the complete genome sequencing and annotation of the type species Dethiosulfovibrio salsuginis USBA 82^T. The genome consisted of 2.68 Mbp with a 53.7% G + C. A total of 2609 genes were predicted and of those, 2543 were protein coding genes and 66 were RNA genes. We detected in USBA 82^T genome six Synergistetes conserved signature indels (CSIs), specific for Jonquetella, Pyramidobacter and Dethiosulfovibrio. The genome of D. salsuginis contained, as expected, genes related to amino acid transport, amino acid metabolism and thiosulfate reduction. These genes represent the major gene groups of Synergistetes, related with their phenotypic traits, and interestingly, 11.8% of the genes in the genome belonged to the amino acid fermentation COG category. In addition, we identified in the genome some ammonification genes such as nitrate reductase genes. The presence of proline operon genes could be related to de novo synthesis of proline to protect the cell in response to high osmolarity. Our bioinformatics workflow included antiSMASH and BAGEL3 which allowed us to identify bacteriocins genes in the genome.

Effects of coffee processing residues on anaerobic microorganisms and corresponding digestion performance

The objective of this study was to delineate the effects of different coffee processing residues on the anaerobic microbes and corresponding digestion performance. The results elucidated that mucilage-rich feed enhanced the accumulation of methanogens, which consequently led to better digestion performance of biogas production. Fifty percent more methane and up to 3 times more net energy (heat and electricity) output were achieved by the digestion of the mucilage-rich feed (M3). The microbial community and statistical analyses further elucidated that different residues in the feed had significant impact on microbial distribution and correspondingly influenced the digestion performance.