A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets

High immigration rates critical for establishing emigration-driven diversity in microbial communities

Unraveling the mechanisms governing the diversity of ecological communities is a central goal in ecology. Although microbial dispersal constitutes an important ecological process, the effect of dispersal on microbial diversity is poorly understood. Here, we sought to fill this gap by combining a generalized Lotka-Volterra model with experimental investigations. Our model showed that emigration increases the diversity of the community when the immigration rate crosses a defined threshold, which we identified as Ineutral. We also found that at high immigration rates, emigration weakens the relative abundance of fast-growing species and thus enhances the mass effect and increases the diversity. We experimentally confirmed this finding using co-cultures of 20 bacterial strains isolated from the soil. Our model further showed that Ineutral decreases with the increase of species pool size, growth rate, and interspecies interaction. Our work deepens the understanding of the effects of dispersal on the diversity of natural communities.

Functional Redundancy Secures Resilience of Chain Elongation Communities upon pH Shifts in Closed Bioreactor Ecosystems

For anaerobic mixed cultures performing microbial chain elongation, it is unclear how pH alterations affect the abundance of key players, microbial interactions, and community functioning in terms of medium-chain carboxylate yields. We explored pH effects on mixed cultures enriched in continuous anaerobic bioreactors representing closed model ecosystems. Gradual pH increase from 5.5 to 6.5 induced dramatic shifts in community composition, whereas product range and yields returned to previous states after transient fluctuations. To understand community responses to pH perturbations over long-term reactor operation, we applied Aitchison PCA clustering, linear mixed-effects models, and random forest classification on 16S rRNA gene amplicon sequencing and process data. Different pH preferences of two key chain elongation species─one Clostridium IV species related to Ruminococcaceae bacterium CPB6 and one Clostridium sensu stricto species related to Clostridium luticellarii─were determined. Network analysis revealed positive correlations of Clostridium IV with lactic acid bacteria, which switched from Olsenella to Lactobacillus along the pH increase, illustrating the plasticity of the food web in chain elongation communities. Despite long-term cultivation in closed systems over the pH shift experiment, the communities retained functional redundancy in fermentation pathways, reflected by the emergence of rare species and concomitant recovery of chain elongation functions.

Phage therapy minimally affects the water microbiota in an Atlantic salmon (Salmo salar) rearing system while still preventing infection

Excessive usage of antibiotics threatens the bacterial diversity in the microbiota of animals. An alternative to antibiotics that has been suggested to not disturb the microbiota is (bacterio)phage therapy. In this study, we challenged germ-free and microbially colonized yolk sac fry of Atlantic salmon with Flavobacterium columnare and observed that the mere presence of a microbiota protected the fish against lethal infection. We then investigated the effect of phage- or oxytetracycline treatment on fish survival and rearing water bacterial community characteristics using 16S rRNA gene amplicon sequencing. Phage treatment led to an increased survival of F. columnare-challenged fish and reduced the relative amounts of the pathogen in the water microbiota. In the absence of F. columnare, phage treatment did not affect the composition or the α-diversity of the rearing water microbiota. In the presence of the phage's host, phage treatment induced minor changes to the bacterial community composition, without affecting the α-diversity. Surprisingly, oxytetracycline treatment had no observable effect on the water microbiota and did not reduce the relative abundance of F. columnare in the water. In conclusion, we showed that phage treatment prevents mortality while not negatively affecting the rearing water microbiota, thus suggesting that phage treatment may be a suitable alternative to antibiotics. We also demonstrated a protective effect of the microbiota in Atlantic salmon yolk sac fry.

The stability and composition of the gut and skin microbiota of Atlantic salmon throughout the yolk sac stage

The bacterial colonization of newly hatched fish is important for the larval development and health. Still, little is known about the ontogeny of the early microbiota of fish. Here, we conducted two independent experiments with yolk sac fry of Atlantic salmon that were (1) either reared conventionally, with the eggs as the only source for bacteria (egg-derived microbiota; EDM) or (2) hatched germ-free and re-colonized using lake water (lake-derived microbiota; LDM). First, we characterized the gut and skin microbiota at 6, 9, and 13 weeks post hatching based on extracted RNA. In the second experiment, we exposed fry to high doses of either a fish pathogen or a commensal bacterial isolate and sampled the microbiota based on extracted DNA. The fish microbiota differed strongly between EDM and LDM treatments. The phyla Proteobacteria, Bacteroidetes, and Actinobacteria dominated the fry microbiota, which was found temporarily dynamic. Interestingly, the microbiota of EDM fry was more stable, both between replicate rearing flasks, and over time. Although similar, the skin and gut microbiota started to differentiate during the yolk sac stage, several weeks before the yolk was consumed. Addition of high doses of bacterial isolates to fish flasks had only minor effects on the microbiota.

An Update on the Ocular Surface Bacterial Microbiota in Small Animals

High-throughput sequencing (HTS) techniques have revolutionized the way we understand microbial communities in both research and clinical settings and are bringing new insights into what constitutes a healthy ocular surface (and a diseased one). As more diagnostic laboratories incorporate HTS into their technique repertoire, practitioners can expect this technology to become increasingly accessible for clinical practice, potentially becoming the new standard. However, particularly regarding ophthalmic microbiota, considerable research remains to render HTS accessible and applicable.

Effect of Alkaline and Mechanical Pretreatment of Wheat Straw on Enrichment Cultures from Pachnoda marginata Larva Gut

In order to partially mimic the efficient lignocellulose pretreatment process performed naturally in the gut system of Pachnoda marginata larvae, two wheat straw pretreatments were evaluated: a mechanical pretreatment via cutting the straw into two different sizes and an alkaline pretreatment with calcium hydroxide. After pretreatment, gut enrichment cultures on wheat straw at alkaline pH were inoculated and kept at mesophilic conditions over 45 days. The methanogenic community was composed mainly of the Methanomicrobiaceae and Methanosarcinaceae families. The combined pretreatment, size reduction and alkaline pretreatment, was the best condition for methane production. The positive effect of the straw pretreatment was higher in the midgut cultures, increasing the methane production by 192%, while for hindgut cultures the methane production increased only by 149% when compared to non-pretreated straw. Scanning electron microscopy (SEM) showed that the alkaline pretreatment modified the surface of the wheat straw fibers, which promoted biofilm formation and microbial growth. The enrichment cultures derived from larva gut microbiome were able to degrade larger 1 mm alkaline treated and smaller 250 µm but non-pretreated straw at the same efficiency. The combination of mechanical and alkaline pretreatments resulted in increased, yet not superimposed, methane yield.

Aquaculture rearing systems induce no legacy effects in Atlantic cod larvae or their rearing water bacterial communities

The microbial rearing quality influences the survival of marine larvae. Microbially matured water treatment systems (MMS) provide a more favourable rearing water microbiome than flow-through systems (FTS). It has previously been hypothesised, but not investigated, that initial rearing in MMS leaves a protective legacy effect in Atlantic cod larvae (Gadus morhua). We tested this hypothesis through a crossover 2 × 2 factorial experiment varying the rearing water treatment system (MMS vs FTS) and the microbial carrying capacity (+ /- added organic matter). At 9 days post-hatching, we switched the rearing water treatment system. By comparing switched and unswitched rearing tanks, we evaluated if legacy effects had been established in the larvae or their surrounding rearing water bacterial community. We analysed the bacterial communities with flow cytometry and 16S rRNA gene sequencing. We found no evidence that the initial rearing condition left a legacy effect in the communities by evaluating the bacterial community diversity and structure. Instead, the present rearing condition was the most important driver for differences in the rearing water microbiota. Furthermore, we found that MMS with high microbial carrying capacity appeared to seed a stable bacterial community to the rearing tanks. This finding highlights the importance of keeping a similar carrying capacity between the inlet and rearing water. Moreover, we reject the hypothesis that the initial rearing condition leaves a protective legacy effect in larvae, as the larval survival and robustness were linked to the present rearing condition. In conclusion, our results highlight the importance of maintaining a beneficial microbial rearing environment from hatching and throughout the larval rearing period.

Absence of oxygen effect on microbial structure and methane production during drying and rewetting events

Natural environments with frequent drainage experience drying and rewetting events that impose fluctuations in water availability and oxygen exposure. These relatively dramatic cycles profoundly impact microbial activity in the environment and subsequent emissions of methane and carbon dioxide. In this study, we mimicked drying and rewetting events by submitting methanogenic communities from strictly anaerobic environments (anaerobic digestors) with different phylogenetic structures to consecutive desiccation events under aerobic (air) and anaerobic (nitrogen) conditions followed by rewetting. We showed that methane production quickly recovered after each rewetting, and surprisingly, no significant difference was observed between the effects of the aerobic or anaerobic desiccation events. There was a slight change in the microbial community structure and a decrease in methane production rates after consecutive drying and rewetting, which can be attributed to a depletion of the pool of available organic matter or the inhibition of the methanogenic communities. These observations indicate that in comparison to the drying and rewetting events or oxygen exposure, the initial phylogenetic structure and the organic matter quantity and quality exhibited a stronger influence on the methanogenic communities and overall microbial community responses. These results change the current paradigm of the sensitivity of strict anaerobic microorganisms to oxygen exposure.

Randomized controlled trial for time-restricted eating in healthy volunteers without obesity

Time-restricted feeding (TRF) improves metabolic health. Both early TRF (eTRF, food intake restricted to the early part of the day) and mid-day TRF (mTRF, food intake restricted to the middle of the day) have been shown to have metabolic benefits. However, the two regimens have yet to be thoroughly compared. We conducted a five-week randomized trial to compare the effects of the two TRF regimens in healthy individuals without obesity (ChiCTR2000029797). The trial has completed. Ninety participants were randomized to eTRF (n=30), mTRF (n=30), or control groups (n=30) using a computer-based random-number generator. Eighty-two participants completed the entire five-week trial and were analyzed (28 in eTRF, 26 in mTRF, 28 in control groups). The primary outcome was the change in insulin resistance. Researchers who assessed the outcomes were blinded to group assignment, but participants and care givers were not. Here we show that eTRF was more effective than mTRF at improving insulin sensitivity. Furthermore, eTRF, but not mTRF, improved fasting glucose, reduced total body mass and adiposity, ameliorated inflammation, and increased gut microbial diversity. No serious adverse events were reported during the trial. In conclusion, eTRF showed greater benefits for insulin resistance and related metabolic parameters compared with mTRF. Clinical Trial Registration URL: http://www.chictr.org.cn/showproj.aspx?proj=49406.

Time-restricted eating, both early (eTRF) and mid-day (mTRF), have been shown to have metabolic benefits. Here the authors report a randomized controlled trial to compare the effects of eTRF and mTRF in healthy volunteers without obesity, and find that eTRF is more effective in improving the primary outcome insulin sensitivity.

Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar

Pe poke is a naturally fermented sticky soybean food of Myanmar. The present study was aimed to profile the whole microbial community structure and their predictive gene functionality of pe poke samples prepared in different fermentation periods viz. 3 day (3ds), 4 days (4ds), 5 days (5ds) and sun-dried sample (Sds). The pH of samples was 7.6 to 8.7, microbial load was 2.1-3.9 x 108 cfu/g with dynamic viscosity of 4.0±1.0 to 8.0±1.0cP. Metataxonomic profile of pe poke samples showed different domains viz. bacteria (99.08%), viruses (0.65%), eukaryota (0.08%), archaea (0.03%) and unclassified sequences (0.16%). Firmicutes (63.78%) was the most abundant phylum followed by Proteobacteria (29.54%) and Bacteroidetes (5.44%). Bacillus thermoamylovorans was significantly abundant in 3ds and 4ds (p<0.05); Ignatzschineria larvae was significantly abundant in 5ds (p<0.05), whereas, Bacillus subtilis was significantly abundant in Sds (p <0.05). A total of 172 species of Bacillus was detected. In minor abundance, the existence of bacteriophages, archaea, and eukaryotes were also detected. Alpha diversity analysis showed the highest Simpson's diversity index in Sds comparable to other samples. Similarly, a non-parametric Shannon's diversity index was also highest in Sds. Good's coverage of 0.99 was observed in all samples. Beta diversity analysis using PCoA showed no significant clustering. Several species were shared between samples and many species were unique to each sample. In KEGG database, a total number of 33 super-pathways and 173 metabolic sub-pathways were annotated from the metagenomic Open Reading Frames. Predictive functional features of pe poke metagenome revealed the genes for the synthesis and metabolism of wide range of bioactive compounds including various essential amino acids, different vitamins, and enzymes. Spearman's correlation was inferred between the abundant species and functional features.

The effect of periodic disturbances and carrying capacity on the significance of selection and drift in complex bacterial communities

Understanding how periodical disturbances affect the community assembly processes is vital for predicting temporal dynamics in microbial communities. However, the effect of dilutions as disturbances are poorly understood. We used a marine bacterial community to investigate the effect of disturbance (+/-) and carrying capacity (high/low) over 50 days in a dispersal-limited 2 × 2 factorial study in triplicates, with a crossover in the disturbance regime between microcosms halfway in the experiment. We modelled the rate of change in community composition between replicates and used this rate to quantify selection and ecological drift. The disturbed communities increased in Bray-Curtis similarity with 0.011 ± 0.0045 (Period 1) and 0.0092 ± 0.0080 day-1 (Period 2), indicating that selection dominated community assembly. The undisturbed communities decreased in similarity at a rate of -0.015 ± 0.0038 day-1 in Period 1 and were stable in Period 2 at 0.00050 ± 0.0040 day-1, suggesting drift structured community assembly. Interestingly, carrying capacity had minor effects on community dynamics. This study is the first to show that stochastic effects are suppressed by periodical disturbances resulting in exponential growth periods due to density-independent biomass loss and resource input. The increased contribution of selection as a response to disturbances implies that ecosystem prediction is achievable.

Selecting fermentation products for food waste valorisation with HRT and OLR as the key operational parameters

Acidogenic fermentation is attractive for food waste valorisation. A better understanding is required on how operation affects product selectivity. This study demonstrated that the hydraulic retention time (HRT) and organic loading rate (OLR) selected fermentation pathways in a single-stage, semi-continuous stirred tank reactor. Three combinations of HRT and OLR were tested to distinguish the effect of each parameter. Three fermentation profiles with distinct microbial communities were obtained. Predominantly n-butyric acid (13 ± 2 gCOD L^-1, 55 ± 14% of carboxylates) was produced at an HRT of 8.5 days and OLR around 12 gCOD L^-1d^-1. Operating at an HRT two days longer, yet with similar OLR, stimulated chain elongation (up to 13.6 gCOD L^-1 of n-caproic acid). This was reflected by a microbial community twice as diverse at longer HRT as indicated by first and second order Hill number (¹D = 24 ± 4, ²D = 12 ± 3) and by a higher relative abundance of genera related to secondary fermentation, such as the VFA-elongating Caproiciproducens spp., and secondary lactic acid fermenter Secundilactobacillus spp.. Operating at a higher OLR (20 gCOD L^-1d^-1) but HRT of 8.5 days, resulted in typical lactic acid fermentation (34 ± 5 gCOD L^-1) harbouring a less diverse community (¹D = 8.0 ± 0.7, ²D = 5.7 ± 0.9) rich in acid-resistant homofermentative Lactobacillus spp. These findings demonstrate that a flexible product portfolio can be achieved by small adjustments in two key operating conditions. This improves the economic potential of acidogenic fermentation for food waste valorisation.

Microbial Communities in Flexible Biomethanation of Hydrogen Are Functionally Resilient Upon Starvation

Ex situ biomethanation allows the conversion of hydrogen produced from surplus electricity to methane. The flexibility of the process was recently demonstrated, yet it is unknown how intermittent hydrogen feeding impacts the functionality of the microbial communities. We investigated the effect of starvation events on the hydrogen consumption and methane production rates (MPRs) of two different methanogenic communities that were fed with hydrogen and carbon dioxide. Both communities showed functional resilience in terms of hydrogen consumption and MPRs upon starvation periods of up to 14 days. The origin of the inoculum, community structure and dominant methanogens were decisive for high gas conversion rates. Thus, pre-screening a well performing inoculum is essential to ensure the efficiency of biomethanation systems operating under flexible gas feeding regimes. Our results suggest that the type of the predominant hydrogenotrophic methanogen (here: Methanobacterium) is important for an efficient process. We also show that flexible biomethanation of hydrogen and carbon dioxide with complex microbiota is possible while avoiding the accumulation of acetate, which is relevant for practical implementation. In our study, the inoculum from an upflow anaerobic sludge blanket reactor treating wastewater from paper industry performed better compared to the inoculum from a plug flow reactor treating cow manure and corn silage. Therefore, the implementation of the power-to-gas concept in wastewater treatment plants of the paper industry, where biocatalytic biomass is readily available, may be a viable option to reduce the carbon footprint of the paper industry.

Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne

The use of straw for biofuel production is encouraged by the European Union. A previous study showed the feasibility of producing biomethane in upflow anaerobic sludge blanket (UASB) reactors using hydrolyzed, steam-pretreated wheat straw, before and after dark fermentation with Caldicellulosiruptor saccharolyticus, and lucerne. This study provides information on overall microbial community development in those UASB processes and changes related to acidification. The bacterial and archaeal community in granular samples was analyzed using high-throughput amplicon sequencing. Anaerobic digestion model no. 1 (ADM1) was used to predict the abundance of microbial functional groups. The sequencing results showed decreased richness and diversity in the microbial community, and decreased relative abundance of bacteria in relation to archaea, after process acidification. Canonical correspondence analysis showed significant negative correlations between the concentration of organic acids and three phyla, and positive correlations with seven phyla. Organic loading rate and total COD fed also showed significant correlations with microbial community structure, which changed over time. ADM1 predicted a decrease in acetate degraders after a decrease to pH ≤ 6.5. Acidification had a sustained effect on the microbial community and process performance.

Diversity of Filamentous Fungi Isolated From Some Amylase and Alcohol-Producing Starters of India

Filamentous fungi are important organisms in traditionally prepared amylase and alcohol-producing dry starters in India. We collected 40 diverse types of amylase and alcohol-producing starters from eight states in North East India viz. marcha, thiat, humao, hamei, chowan, phut, dawdim, and khekhrii. The average fungal population was 4.9 × 10⁵ cfu/g with an average of pH 5.3 and 10.7%, respectively. In the present study, 131 fungal isolates were isolated and characterized based on macroscopic and microscopic characteristics and were grouped into 44 representative fungal strains. Based on results of morphological characteristics and ITS gene sequencing, 44 fungal strains were grouped into three phyla represented by Ascomycota (48%), Mucoromycota (38%), and Basidiomycota (14%). Taxonomical keys to species level was illustrated on the basis of morphological characteristics and ITS gene sequencing, aligned to the fungal database of NCBI GenBank, which showed seven genera with 16 species represented by Mucor circinelloides (20%), Aspergillus sydowii (11%), Penicillium chrysogenum (11%), Bjerkandera adusta (11%), Penicillium citrinum (7%), Rhizopus oryzae (7%), Aspergillus niger (5%), Aspergillus flavus (5%), Mucor indicus (5%) Rhizopus microsporus (5%), Rhizopus delemar (2%), Aspergillus versicolor (2%), Penicillium oxalicum (2%), Penicillium polonicum (2%), Trametes hirsuta (2%), and Cladosporium parahalotolerans (2%). The highest Shannon diversity index H was recorded in marcha of Sikkim (H: 1.74) and the lowest in hamei of Manipur (H: 0.69). Fungal species present in these amylolytic starters are morphologically, ecologically and phylogenetically diverse and showed high diversity within the community.

Effect of Cobalt, Nickel, and Selenium/Tungsten Deficiency on Mesophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds

Trace elements (TEs) are vital for anaerobic digestion (AD), due to their role as cofactors in many key enzymes. The aim of this study was to evaluate the effects of specific TE deficiencies on mixed microbial communities during AD of soluble polymer-free substrates, thus focusing on AD after hydrolysis. Three mesophilic (37 °C) continuous stirred-tank biogas reactors were depleted either of Co, Ni, or a combination of Se and W, respectively, by discontinuing their supplementation. Ni and Se/W depletion led to changes in methane kinetics, linked to progressive volatile fatty acid (VFA) accumulation, eventually resulting in process failure. No significant changes occurred in the Co-depleted reactor, indicating that the amount of Co present in the substrate in absence of supplementation was sufficient to maintain process stability. Archaeal communities remained fairly stable independent of TE concentrations, while bacterial communities gradually changed with VFA accumulation in Ni- and Se-/W-depleted reactors. Despite this, the communities remained relatively similar between these two reactors, suggesting that the major shifts in composition likely occurred due to the accumulating VFAs. Overall, the results indicate that Ni and Se/W depletion primarily lead to slower metabolic activities of methanogenic archaea and their syntrophic partners, which then has a ripple effect throughout the microbial community due to a gradual accumulation of intermediate fermentation products.

Competition Between Butyrate Fermenters and Chain-Elongating Bacteria Limits the Efficiency of Medium-Chain Carboxylate Production

Medium-chain carboxylates such as n-caproate and n-caprylate are valuable chemicals, which can be produced from renewable feedstock by anaerobic fermentation and lactate-based microbial chain elongation. Acidogenic microbiota involved in lactate-based chain elongation and their interplay with lactic acid bacteria have not been characterized in detail yet. Here, the metabolic and community dynamics were studied in a continuous bioreactor with xylan and lactate as sole carbon sources. Four succession stages were observed during 148 days of operation. After an adaptation period of 36 days, a relatively stable period of 28 days (stage I) was reached with n-butyrate, n-caproate and n-caprylate productivities of 7.2, 8.2 and 1.8 gCOD L-1 d-1, respectively. After a transition period, the process changed to another period (stage II), during which 46% more n-butyrate, 51% less n-caproate and 67% less n-caprylate were produced. Co-occurrence networks of species based on 16S rRNA amplicon sequences and correlations with process parameters were analyzed to infer ecological interactions and potential metabolic functions. Diverse functions including hydrolysis of xylan, primary fermentation of xylose to acids (e.g., to acetate by Syntrophococcus, to n-butyrate by Lachnospiraceae, and to lactate by Lactobacillus) and chain-elongation with lactate (by Ruminiclostridium 5 and Pseudoramibacter) were inferred from the metabolic network. In stage I, the sub-network characterized by strongest positive correlations was mainly related to the production of n-caproate and n-caprylate. Lactic acid bacteria of the genus Olsenella co-occurred with potentially chain-elongating bacteria of the genus Pseudoramibacter, and their abundance was positively correlated with n-caproate and n-caprylate concentrations. A new sub-network appeared in stage II, which was mainly related to n-butyrate production and revealed a network of different lactic acid bacteria (Bifidobacterium) and potential n-butyrate producers (Clostridium sensu stricto 12). The synergy effects between lactate-producing and lactate-consuming bacteria constitute a division of labor cooperation of mutual benefit. Besides cooperation, competition between different taxa determined the bacterial community assembly over the four succession stages in this resource-limited system. During long-term reactor operation under constant conditions, chain-elongating bacteria were outcompeted by butyrate-producing bacteria, leading to the increase of n-butyrate yield at the cost of medium-chain carboxylate yields in this closed model system.

Effects of wastewater disinfectants on the soil: Implications for soil microbial and chemical attributes

In most cases, chlorination is used for effluent disinfection. However, this process can lead to the formation of byproducts hazardous to the environment and public health. Therefore, new disinfectants, such as calcium hypochlorite (CH) and peracetic acid (PAA), were investigated as alternatives. This study aimed at determining doses of the disinfectants PAA and CH to be applied to the soil and analyzing the possible changes in the major chemical and microbiological attributes of the soil, thus encouraging the practice of reusing wastewater in agriculture. Initially, toxicity bioassays were conducted with lettuce (Lactuca sativa L.) seeds in order to determine which concentrations affected germination and also which would be analyzed. From these trials, three concentrations of each disinfectant were chosen to be subjected to basal respiration, microbial biomass carbon and metabolic quotient analyses. Doses of 3, 5 and 10 mg L^-1 were used for PAA, and concentrations of 25, 32 and 64 mg L^-1 for CH. Thus, it was observed that the greater concentration of each disinfectant provided a significant increase in the metabolic potential of microorganisms. However, it was observed that PAA increased ecotoxicity besides promoting changes in the chemical attributes of the soil, compared to CH. On the other hand, concentrations of 3 mg L^-1 and 25 mg L^-1 of PAA and CH, respectively, did not cause large impacts and could be an alternative in effluent disinfection with the aim of recycling it in agriculture.

Stability of the vaginal, oral, and gut microbiota across pregnancy among African American women: the effect of socioeconomic status and antibiotic exposure

OBJECTIVE

A growing body of research has investigated the human microbiota and pregnancy outcomes, especially preterm birth. Most studies of the prenatal microbiota have focused on the vagina, with fewer investigating other body sites during pregnancy. Although pregnancy involves profound hormonal, immunological and metabolic changes, few studies have investigated either shifts in microbiota composition across pregnancy at different body sites or variation in composition at any site that may be explained by maternal characteristics. The purpose of this study was to investigate: (1) the stability of the vaginal, oral, and gut microbiota from early (8-14 weeks) through later (24-30 weeks) pregnancy among African American women according to measures of socioeconomic status, accounting for prenatal antibiotic use; (2) whether measures of socioeconomic status are associated with changes in microbiota composition over pregnancy; and (3) whether exposure to prenatal antibiotics mediate any observed associations between measures of socioeconomic status and stability of the vaginal, oral, and gut microbiota across pregnancy.

METHODS

We used paired vaginal, oral, or gut samples available for 16S rRNA gene sequencing from two time points in pregnancy (8-14 and 24-30 weeks) to compare within-woman changes in measures of alpha diversity (Shannon and Chao1) and beta-diversity (Bray-Curtis dissimilarity) among pregnant African American women (n = 110). Multivariable linear regression was used to examine the effect of level of education and prenatal health insurance as explanatory variables for changes in diversity, considering antibiotic exposure as a mediator, adjusting for age, obstetrical history, and weeks between sampling.

RESULTS

For the oral and gut microbiota, there were no significant associations between measures of socioeconomic status or prenatal antibiotic use and change in Shannon or Chao1 diversity. For the vaginal microbiota, low level of education (high school or less) was associated with an increase in Shannon and Chao1 diversity over pregnancy, with minimal attenuation when controlling for prenatal antibiotic use. Conversely, for within-woman Bray-Curtis dissimilarity for early compared to later pregnancy, low level of education and prenatal antibiotics were associated with greater dissimilarity for the oral and gut sites, with minimal attenuation when controlling for prenatal antibiotics, and no difference in dissimilarity for the vaginal site.

CONCLUSIONS

Measures of maternal socioeconomic status are variably associated with changes in diversity across pregnancy for the vaginal, oral, and gut microbiota, with minimal attenuation by prenatal antibiotic exposure. Studies that evaluate stability of the microbiota across pregnancy in association with health outcomes themselves associated with socioeconomic status (such as preterm birth) should incorporate measures of socioeconomic status to avoid finding spurious relationships.

Microbial community shifts in the oxic-settling-anoxic process in response to changes to sludge interchange ratio

This particular study set out to demonstrate alterations on the microbial community of the oxic-settling-anaerobic/anoxic (OSA) process treating real domestic wastewater by changing interchange ratios (IRs). The sludge yield of systems operated at different IRs (1/13, 1/17 and 1/20) to assess sludge reduction was used to analyze microbial community composition variations. The highest IR (1/13) resulted in the highest sludge reduction (52.1%), while the OSA systems with IR of 1/17 and 1/20 reduced sludge production by 37.4% and 35.5%, respectively, in comparison to conventional systems. 16S rRNA gene amplicon sequencing analysis showed that the bacterial communities were composed of similar phylogenetic groups, Proteobacteria, Acidobacteria, and Bacteroidetes being dominant. The relative abundances differed due to the applied IRs. The highest abundance of Actinobacteria was determined at the highest IR (1/13) and increasing of the HRT to 1/20 caused a significant reduction in Actinobacteria species and the lowest abundance (6%) was determined in the OSA systems. The abundant of Thiothrix species that are boosted in the OSA trials may have a vital role in OSA systems, where its abundance was below the detection limits in the seed sludge sample. Therefore, they could be used as bioindicators in the OSA system.

Effects of various feedstocks on isotope fractionation of biogas and microbial community structure during anaerobic digestion

Feedstock type influences bacterial and methanogenic communities in anaerobic digestion. These two communities work tightly to maintain the stability of anaerobic digestion. How to quick report the changes of microbial community structure especially methanogenesis is the key issue for optimizing anaerobic digestion process. In this study, ¹³C isotope fractionations of CH₄ and CO₂ in biogas and microbial community composition were analyzed in 5 different feedstocks. Our results showed that grass silage, maize silage and swine manure fed reactors had similar δ ¹³C values and methanogenic community composition, dominated by Methanosarcinaceae. The lowest δ ¹³CH₄ values were detected in straw and chicken manure fed reactors, reflecting reduced microbial degradation of material or the presence of toxic components in these feedstocks. The straw fed bioreactor lead to low δ ¹³CH₄ values, probably reflecting relatively high levels of the syntrophic acetate oxidizing bacteria, Synergistaceae and Syntrophaceae, which might work collectively with hydrogenotrophic methanogens, resulting in the low δ ¹³CH₄ values in this bioreactor. Significantly, all core microbes in the 5 different feedstock fed bioreactors were either Clostridia species or related to the Synergistaceae (syntrophic acetate oxidizing bacteria).

Sulfide level in municipal sludge digesters affects microbial community response to long-chain fatty acid loads

BACKGROUND

Waste lipids are attractive substrates for co-digestion with primary and activated sewage sludge (PASS) to improve biogas production at wastewater treatment plants. However, slow conversion rates of long-chain fatty acids (LCFA), produced during anaerobic digestion (AD), limit the applicability of waste lipids as co-substrates for PASS. Previous observations indicate that the sulfide level in PASS digesters affects the capacity of microbial communities to convert LCFA to biogas. This study assessed the microbial community response to LCFA loads in relation to sulfide level during AD of PASS by investigating process performance and microbial community dynamics upon addition of oleate (C_18:1) and stearate (C_18:0) to PASS digesters at ambient and elevated sulfide levels.

RESULTS

Conversion of LCFA to biogas was limited (30% of theoretical biogas potential) during continuous co-digestion with PASS, which resulted in further LCFA accumulation. However, the accumulated LCFA were converted to biogas (up to 66% of theoretical biogas potential) during subsequent batch-mode digestion, performed without additional substrate load. Elevated sulfide level stimulated oleate (but not stearate) conversion to acetate, but oleate and sulfide imposed a synergistic limiting effect on acetoclastic methanogenesis and biogas formation. Next-generation sequencing of 16S rRNA gene amplicons of bacteria and archaea showed that differences in sulfide level and LCFA type resulted in microbial community alterations with distinctly different patterns. Taxonomic profiling of the sequencing data revealed that the phylum Cloacimonetes is likely a key group during LCFA degradation in PASS digesters, where different members take part in degradation of saturated and unsaturated LCFA; genus W5 (family Cloacimonadaceae) and family W27 (order Cloacimonadales), respectively. In addition, LCFA-degrading Syntrophomonas, which is commonly present in lipid-fed digesters, increased in relative abundance after addition of oleate at elevated sulfide level, but not without sulfide or after stearate addition. Stearate conversion to biogas was instead associated with increasing abundance of hydrogen-producing Smithella and hydrogenotrophic Methanobacterium.

CONCLUSIONS

Long-chain fatty acid chain saturation and sulfide level are selective drivers for establishment of LCFA-degrading microbial communities in municipal sludge digesters.

Dynamics of a Perturbed Microbial Community during Thermophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds

Knowledge of microbial community dynamics in relation to process perturbations is fundamental to understand and deal with the instability of anaerobic digestion (AD) processes. This study aims to investigate the microbial community structure and function of a thermophilic AD process, fed with a chemically defined substrate, and its association with process performance stability. Next generation amplicon sequencing of 16S ribosomal RNA (rRNA) genes revealed that variations in relative abundances of the predominant bacterial species, Defluviitoga tunisiensis and Anaerobaculum hydrogeniformans, were not linked to the process performance stability, while dynamics of bacterial genera of low abundance, Coprothermobacter and Defluviitoga (other than D. tunisiensis), were associated with microbial community function and process stability. A decrease in the diversity of the archaeal community was observed in conjunction with process recovery and stable performance, implying that the high abundance of specific archaeal group(s) contributed to the stable AD. Dominance of hydrogenotrophic Methanoculleus particularly corresponded to an enhanced microbial acetate and propionate turnover capacity, whereas the prevalence of hydrogenotrophic Methanothermobacter and acetoclastic Methanosaeta was associated with instable AD. Acetate oxidation via syntrophic interactions between Coprothermobacter and Methanoculleus was potentially the main methane-formation pathway during the stable process. We observed that supplementation of Se and W to the medium improved the propionate turnover by the thermophilic consortium. The outcomes of our study provided insights into the community dynamics and trace element requirements in relation to the process performance stability of thermophilic AD.

Intermittent fasting for microbes: how discontinuous feeding increases functional stability in anaerobic digestion

BACKGROUND

Demand-driven biogas production could play an important role for future sustainable energy supply. However, feeding a biogas reactor according to energy demand may lead to organic overloading and, thus, to process failures. To minimize this risk, digesters need to be actively steered towards containing more robust microbial communities. This study focuses on acetogenesis and methanogenesis as crucial process steps for avoiding acidification. We fed lab-scale anaerobic digesters with volatile fatty acids under various feeding regimes and disturbances. The resulting microbial communities were analyzed on DNA and RNA level by terminal restriction fragment length polymorphism of the mcrA gene, 16S rRNA gene amplicon sequencing, and a [2-13C]-acetate assay. A modified Anaerobic Digestion Model 1 (ADM1) that distinguishes between the acetoclastic methanogens Methanosaeta and Methanosarcina was developed and fitted using experimental abiotic and biotic process parameters.

RESULTS

Discontinuous feeding led to more functional resilience than continuous feeding, without loss in process efficiency. This was attributed to a different microbial community composition. Methanosaeta dominated the continuously fed reactors, while its competitor Methanosarcina was washed out. With discontinuous feeding, however, the fluctuating acetic acid concentrations provided niches to grow and co-exist for both organisms as shown by transcription analysis of the mcrA gene. Our model confirmed the higher functional resilience due to the higher abundance of Methanosarcina based on its higher substrate uptake rate and higher resistance to low pH values. Finally, we applied our model to maize silage as a more complex and practically relevant substrate and showed that our model is likely transferable to the complete AD process.

CONCLUSIONS

The composition of the microbial community determined the AD functional resilience against organic overloading in our experiments. In particular, communities with higher share of Methanosarcina showed higher process stability. The share of these microorganisms can be purposefully increased by discontinuous feeding. A model was developed that enables derivation of the necessary feeding regime for a more robust community with higher share of Methanosarcina.

Anaerobic Benzene Mineralization by Nitrate-Reducing and Sulfate-Reducing Microbial Consortia Enriched From the Same Site: Comparison of Community Composition and Degradation Characteristics

Benzene mineralization under nitrate-reducing conditions was successfully established in an on-site reactor continuously fed with nitrate and sulfidic, benzene-containing groundwater extracted from a contaminated aquifer. Filling material from the reactor columns was used to set up anoxic enrichment cultures in mineral medium with benzene as electron donor and sole organic carbon source and nitrate as electron acceptor. Benzene degradation characteristics and community composition under nitrate-reducing conditions were monitored and compared to those of a well-investigated benzene-mineralizing consortium enriched from the same column system under sulfate-reducing conditions. The nitrate-reducing cultures degraded benzene at a rate of 10.1 ± 1.7 μM d^-1, accompanied by simultaneous reduction of nitrate to nitrite. The previously studied sulfate-reducing culture degraded benzene at similar rates. Carbon and hydrogen stable isotope enrichment factors determined for nitrate-dependent benzene degradation differed significantly from those of the sulfate-reducing culture (Λ^{H/C nitrate} = 12 ± 3 compared to Λ^{H/C sulfate} = 28 ± 3), indicating different benzene activation mechanisms under the two conditions. The nitrate-reducing community was mainly composed of Betaproteobacteria, Ignavibacteria, and Anaerolineae. Azoarcus and a phylotype related to clone Dok59 (Rhodocyclaceae) were the dominant genera, indicating an involvement in nitrate-dependent benzene degradation. The primary benzene degrader of the sulfate-reducing consortium, a phylotype belonging to the Peptococcaceae, was absent in the nitrate-reducing consortium.

Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters

Cattle manure is frequently used as an inoculum for the start-up of agricultural biogas plants or as a co-substrate in the anaerobic digestion of lignocellulosic feedstock. Ruminal microbiota are considered to be effective plant fiber degraders, but the microbes contained in manure do not necessarily reflect the rumen microbiome. The aim of this study was to compare the microbial community composition of cow rumen and manure with respect to plant fiber-digesting microbes. Bacterial and methanogenic communities of rumen and manure samples were examined by 454 amplicon sequencing of bacterial 16S rRNA genes and mcrA genes, respectively. Rumen fluid samples were dominated by Prevotellaceae (29%), whereas Ruminococcaceae was the most abundant family in the manure samples (31%). Fibrobacteraceae (12%) and Bacteroidaceae (13%) were the second most abundant families in rumen fluid and manure, respectively. The high abundances of fiber-degrading bacteria belonging to Prevotellaceae and Fibrobacteraceae might explain the better performance of anaerobic digesters inoculated with rumen fluid. Members of the genus Methanobrevibacter were the predominant methanogens in the rumen fluid, whereas methanogenic communities of the manure samples were dominated by the candidate genus Methanoplasma. Our results suggest that inoculation or bioaugmentation with fiber-digesting rumen microbiota can enhance the anaerobic digestion of lignocellulosic biomass.