Microbial Population Dynamics Research Articles

Fecal microbiota transplantation alters gut phage communities in a clinical trial for obesity

BackgroundFecal microbiota transplantation (FMT) is a therapeutic intervention used to treat diseases associated with the gut microbiome. In the human gut microbiome, phages have been implicated in influencing human health, with successful engraftment of donor phages correlated with FMT treatment efficacy. The impact that gastrointestinal phages exert on human health has primarily been connected to their ability to modulate the bacterial communities in the gut. Nonetheless, how FMT affects recipients’ phage populations, and in turn, how this influences the gut environment, is not yet fully understood. In this study, we investigated the effects of FMT on the phageome composition of participants within the Gut Bugs Trial (GBT), a double-blind, randomized, placebo-controlled trial that investigated the efficacy of FMT in treating obesity and comorbidities in adolescents. Stool samples collected from donors at the time of treatment and recipients at four time points (i.e., baseline and 6 weeks, 12 weeks, and 26 weeks post-intervention), underwent shotgun metagenomic sequencing. Phage sequences were identified and characterized in silico to examine evidence of phage engraftment and to assess the extent of FMT-induced alterations in the recipients’ phageome composition.ResultsDonor phages engrafted stably in recipients following FMT, composing a significant proportion of their phageome for the entire course of the study (33.8 ± 1.2% in females and 33.9 ± 3.7% in males). Phage engraftment varied between donors and donor engraftment efficacy was positively correlated with their phageome alpha diversity. FMT caused a shift in recipients’ phageome toward the donors’ composition and increased phageome alpha diversity and variability over time.ConclusionsFMT significantly altered recipients' phage and, overall, microbial populations. The increase in microbial diversity and variability is consistent with a shift in microbial population dynamics. This proposes that phages play a critical role in modulating the gut environment and suggests novel approaches to understanding the efficacy of FMT in altering the recipient’s microbiome.Trial registrationThe Gut Bugs Trial was registered with the Australian New Zealand Clinical Trials Registry (ACTR N12615001351505). Trial protocol: the trial protocol is available at https://bmjopen.bmj.com/content/9/4/e026174.A4HmAXiKAUhp3nsywzn7_QVideo

Soil and Mineral Nutrients in Plant Health: A Prospective Study of Iron and Phosphorus in the Growth and Development of Plants.

Plants being sessile are exposed to different environmental challenges and consequent stresses associated with them. With the prerequisite of minerals for growth and development, they coordinate their mobilization from the soil through their roots. Phosphorus (P) and iron (Fe) are macro- and micronutrient; P serves as an important component of biological macromolecules, besides driving major cellular processes, including photosynthesis and respiration, and Fe performs the function as a cofactor for enzymes of vital metabolic pathways. These minerals help in maintaining plant vigor via alterations in the pH, nutrient content, release of exudates at the root surface, changing dynamics of root microbial population, and modulation of the activity of redox enzymes. Despite this, their low solubility and relative immobilization in soil make them inaccessible for utilization by plants. Moreover, plants have evolved distinct mechanisms to cope with these stresses and coregulate the levels of minerals (Fe, P, etc.) toward the maintenance of homeostasis. The present study aims at examining the uptake mechanisms of Fe and P, and their translocation, storage, and role in executing different cellular processes in plants. It also summarizes the toxicological aspects of these minerals in terms of their effects on germination, nutrient uptake, plant-water relationship, and overall yield. Considered as an important and indispensable component of sustainable agriculture, a separate section covers the current knowledge on the cross-talk between Fe and P and integrates complete and balanced information of their effect on plant hormone levels.

Deciphering linkages between DON and the microbial community for nitrogen removal using two green sorption media in a surface water filtration system

The presence of dissolved organic nitrogen (DON) in stormwater treatment processes is a continuous challenge because of the intertwined nature of its decomposition, bioavailability, and biodegradability and its unclear molecular characteristics. In this paper, 21 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in combination with quantitative polymerase chain reaction was applied to elucidate the molecular change of DON and microbial population dynamics in a field-scale water filtration system filled with two specialty adsorbents for comparison in South Florida where the dry and wet seasons are distinctive annually. The adsorbents included CPS (clay-perlite and sand sorption media) and ZIPGEM (zero-valent iron and perlite-based green environmental media). Our study revealed that seasonal effects can significantly influence the dynamic characteristics and biodegradability of DON. The microbial population density in the filter beds indicated that three microbial species in the nitrogen cycle were particularly thrived for denitrification, dissimilatory nitrate reduction to ammonium, and anaerobic ammonium oxidation via competition and commensalism relationships during the wet season. Also, there was a decrease in the compositional complexity and molecular weight of the DON groups (CnHmOpN1, CnHmOpN2, CnHmOpN3, and CnHmOpN4), revealed by the 21 T FT-ICR MS bioassay, driven by a microbial population quantified by polymerase chain reaction from the dry to the wet season. These findings indirectly corroborate the assumption that the metabolism of microorganisms is much more vigorous in the wet season. The results affirm that the sustainable materials (CPS and ZIPGEM) can sustain nitrogen removal intermittently by providing a suitable living environment in which the metabolism of microbial species can be cultivated and enhanced to facilitate physico-chemical nitrogen removal across the two types of green sorption media.

Modelling the dynamics of microbial populations and Salmonella spp. in milk kefir

Kefir is a fermented dairy product based on the fermentation of milk by bacteria and yeasts. It is produced by adding kefir grains, consisting of a consortium of microorganisms, to milk in order to start a natural fermentation (Garofalo et al., 2020). Kefir is well recognized for its potential health value as a source of probiotics, however, there have been concerns about the potential growth of pathogenic microorganisms in kefir and the potential health hazards associated (Leite et al., 2013) A mathematical model was developed to describe the evolution of microbes present during kefir fermentation and the potential growth of Salmonella spp. as one example of a potential food safety hazard. For this, equations previously described in the scientific literature were combined and adapted to the milk kefir matrix. To assess the safety of the product, the growth of Salmonella was predicted considering its interaction with the medium and the other species. The drop in pH; generation of yeasts metabolites such as ethanol; and buffer capacity was described and considered when modelling Salmonellas’ kinetics. Interaction between the pathogenic species and the background microflora was included in the model. Parameters of some well-described systems were taken from literature. Alongside, some other parameters describing specific assets from the system were estimated using experimental data of microbial population kinetics during kefir fermentation. The growth of yeasts, lactic acid bacteria, Salmonella together with the pH were experimentally collected at critical processing times and fitted to the mathematical model by minimizing the residual sum of squares (RSS). Confidence intervals of 95 % were calculated. For further validation, the output of the model was contrasted with an independent data set. It was concluded that Salmonella is able to increase its population during the first hours of the kefir fermentation process. Inactivation can be apportioned to the drop of pH as a consequence of the LAB metabolism, once the pH reaches values below 4. After this no growth of Salmonella seems to be found in milk kefir as confirmed by the model. No residual population of the pathogen is observed. This suggests that by controlling the growth and metabolism of the background microflora, safety can be assured in milk kefir. This process was successfully described by a novel mathematical model and the estimation of its´parameters.

Impact of diverse weed management strategies on soil microbial population dynamics in maize

Impact of diverse weed management strategies on soil microbial population dynamics in maize

Optimization of Fermentation and Sensory Quality of Mango Yogurt Using Various Sucrose Concentration Fermented by Lacticaseibaciluus paracasei Strain Shirota

This research explores the optimization of mango yogurt production, leveraging mango as the primary fermentation ingredient and Lacticaseibacillus paracasei strain Shirota (LcS) as the probiotic inoculum. Traditional yogurt, typically derived from animal milk, faces competition from plant-based alternatives. The research objective is to investigate the impact of inoculum ratios and sucrose concentrations on LcS density and sensory attributes, with a focus on the Substrate to Inoculum Ratio (S/I) as a critical parameter influencing microbial metabolism and population dynamics. Various inoculum ratios (1:1, 1:2, 1:4, 1:8 v/v) and sucrose concentrations (0%, 2.5%, 5%, 7.5%) were applied in mango yogurt production. Results from ANOVA analysis indicated significant differences in LcS density among inoculum ratios (F3,16 = 37.01, P = 0.000) and sucrose concentrations (F3,16 = 19.07, P = 0.000). The 1:2 inoculum ratio and 7.5% sucrose concentration emerged as optimal, as evidenced by stable pH conditions and lactic acid profiles within recommended standards. Sensory analysis, employing a 5-point hedonic scale for color, odor, taste, and texture evaluation, revealed moderate acceptance. In conclusion, this study introduces an innovative approach to mango yogurt production, highlighting the potential of specific inoculum ratios and sucrose concentrations for optimal results. The findings contribute to the broader landscape of plant-based yogurt alternatives, underscoring the need for ongoing refinement to meet commercial standards and ensure consumer satisfaction.

Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia.

Increasing levels of industrialization have been associated with changes in gut microbiome structure and loss of features thought to be crucial for maintaining gut ecological balance. The stability of gut microbial communities over time within individuals seems to be largely affected by these changes but has been overlooked among transitioning populations from low- to middle-income countries. Here, we used metagenomic sequencing to characterize the temporal dynamics in gut microbiomes of 24 individuals living an urban non-industrialized lifestyle in the Brazilian Amazon. We further contextualized our data with 165 matching longitudinal samples from an urban industrialized and a rural non-industrialized population. We show that gut microbiome composition and diversity have greater variability over time among non-industrialized individuals when compared to industrialized counterparts and that taxa may present diverse temporal dynamics across human populations. Enterotype classifications show that community types are generally stable over time despite shifts in microbiome structure. Furthermore, by tracking genomes over time, we show that levels of bacterial population replacements are more frequent among Amazonian individuals and that non-synonymous variants accumulate in genes associated with degradation of host dietary polysaccharides. Taken together, our results suggest that the stability of gut microbiomes is influenced by levels of industrialization and that tracking microbial population dynamics is important to understand how the microbiome will adapt to these transitions.IMPORTANCEThe transition from a rural or non-industrialized lifestyle to urbanization and industrialization has been linked to changes in the structure and function of the human gut microbiome. Understanding how the gut microbiomes changes over time is crucial to define healthy states and to grasp how the gut microbiome interacts with the host environment. Here, we investigate the temporal dynamics of gut microbiomes from an urban and non-industrialized population in the Amazon, as well as metagenomic data sets from urban United States and rural Tanzania. We showed that healthy non-industrialized microbiomes experience greater compositional shifts over time compared to industrialized individuals. Furthermore, bacterial strain populations are more frequently replaced in non-industrialized microbiomes, and most non-synonymous mutations accumulate in genes associated with the degradation of host dietary components. This indicates that microbiome stability is affected by transitions to industrialization, and that strain tracking can elucidate the ecological dynamics behind such transitions.

Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils.

Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H218O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.IMPORTANCEMicrobial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.

Comparative microbiome analysis of beef cattle, the feedyard environment, and airborne particulate matter as a function of probiotic and antibiotic use, and change in pen environment.

Intensive beef cattle production systems are frequently implicated as a source of bacteria that can be transferred to nearby humans and animals via effluent water, manure used as fertilizer, or airborne particulate matter. It is crucial to understand microbial population dynamics due to manure pack desiccation, antibiotic usage, and antibiotic alternatives within beef cattle and their associated feedyard environment. Understanding how bacterial communities change in the presence of antibiotics can also improve management practices for reducing the spread of foodborne bacteria. In this study, we aimed to compare the microbiomes within cattle feces, the feedyard environment and artificially produced airborne particulate matter as a function of pen change and treatment with tylosin or probiotics. We utilized 16S rRNA sequencing to compare bacterial communities among sample types, study days, and treatment groups. Bacterial community diversity varied as a function of sampling day and pen change (old or new) within fecal and manure pack samples. Manure pack samples from old pens and new pens contained diverse communities of bacteria on days 0 and 84; however, by day 119 of the study these taxonomic differences were less evident. Particulate matter samples exhibited significant differences in community diversity and predominant bacterial taxa compared to the manure pack they originated from. Treatment with tylosin did not meaningfully impact bacterial communities among fecal, environmental, or particulate matter samples; however, minor differences in bacterial community structure were observed in feces from cattle treated with probiotics. This study was the first to characterize and compare microbial communities within feces, manure pack, and airborne particulate matter from the same location and as a function of tylosin and probiotic treatment, and pen change. Although fecal and environmental samples are commonly used in research studies and other monitoring programs to infer public health risk of bacteria and antimicrobial resistance determinants from feedyard environments, our study suggests that these samples may not be appropriate to infer public health risk associated with airborne particulate matter.

A Monte‐Carlo approach for the simulation of microbial population dynamics in an heterogeneous scale‐down bioreactor

AbstractPopulation heterogeneity is due to intrinsic and extrinsic noises; cell to cell variability is related to cell partitioning at division and external forcing by the environment. In this article, a Monte‐Carlo calculation of integral source terms is coupled to a compartment approach. The biological phase is represented by an ensemble of discrete particles which are equipped with a coarse‐grained model that describes the intracellular response to extracellular conditions. The redistribution of cell properties at division generates unbalanced cells and introduces additional time scales into the population dynamics. Using this fully two‐way coupled approach, the consequences of repeated exposure to feast and famine events on both the reactor and the population heterogenities are investigated in a CSTR+PFR scale‐down bioreactor. It is shown that the integration of intrinsic noise due to cell division continuously produces cells that are not at equilibrium with their environment and this contributes to population heterogeneity, even in homogeneous environments.

Dynamics of microbial populations in the composting process of marine organic waste

It is estimated that marine waste consist of 60% organic material. Therefore, waste must be handled using a composting process. The main determining factor in the composting process is the microorganisms associated with the C/N ratio. Therefore, this research was conducted to observe the dynamics of microbial populations during the decomposition of marine organic waste. The research method for calculating microbial populations (bacteria and fungi) is the dilution method using a colony counter with the Pour Platedilution technique (CFU/g). The results showed that the microbial population, both fungi and bacteria, fluctuated from week 1 to 10 of the composting process. This is related to the temperature during the composting process and the C/N ratio. The highest population of bacteria and fungi was found in the sixth week of composting at 300 x 107 CFU/g where the process entered the thermophilic phase with a C/N of 55.

Influence of season on the microbial population dynamics of activated sludge.

This review discusses critically how seasonal changes might affect the community composition and dynamics of activated sludge wastewater treatment plants (WWTP), and examines the factors thought more generally to control microbial community assembly, including the role of taxa-time relationships and stochastic and deterministic influences. The review also questions the differences in protocols used in these studies, which make any subsequent attempts at data comparisons problematic. These include bacterial DNA extraction and PCR methodologies, 16S rRNA sequencing and especially its depth, and subsequent statistical analyses of the data, which together often fail to reveal seasonal dynamic community shifts. Suggestions are given as to how experimental protocols need to be improved and standardized, and especially the requirement to examine bacterial populations at the species level. This review looks critically at what is known currently about seasonal influences on key members of this community, including viruses, the bacteria responsible for nitrogen and phosphorus removal and those causing bulking and foaming. The data show many of these species exhibit replicative seasonal abundances over several years, but not under all conditions, illustrating how complex these community dynamics are. Fungal and protozoal/metazoal seasonal community dynamics, less studied, are also discussed. The current data suggest that seasonal temperature fluctuations are responsible for most of seasonal community dynamics by selectively favouring or otherwise individual populations. However, more longer term studies carried out under much stricter controlled conditions are required.

Effect of low oxygen modified- and controlled-atmospheres on quality attributes and microbial population dynamics in fresh-cut iceberg lettuce

Effect of low oxygen modified- and controlled-atmospheres on quality attributes and microbial population dynamics in fresh-cut iceberg lettuce

Biomass attachment and microbiota shifts during porcine faecal in vitro fermentation of almond and macadamia nuts differing in particle sizes.

Nuts are highly nutritious and good sources of dietary fibre, when consumed as part of a healthy human diet. Upon consumption, nut particles of various sizes containing lipids entrapped by the plant cell walls enter the large intestine where they are fermented by the resident microbiota. This study investigated the microbial community shifts during in vitro fermentation of almond and macadamia substrates, of two particle sizes including fine particles (F = 250-500 μm) and cell clusters (CC = 710-1000 μm). The aim was to determine how particle size and biomass attachment altered the microbiota. Over the 48 h fermentation duration, short chain fatty acid concentrations increased due to particle size rather than nut type (almond or macadamia). However, nut type did change microbial population dynamics by stimulating specific genera. Tyzzerella, p253418B5 gut group, Lachnospiraceae UCG001, Geotrichum, Enterococcus, Amnipila and Acetitomaculum genera were unique for almonds. For macadamia, three unique genera including Prevotellaceae UCG004, Candidatus Methanomethylophilus and Alistipes were noted. Distinct shifts in the attached microbial biomass were noted due to nut particle size. Bacterial attachment to nut particles was visualised in situ during fermentation, revealing a decrease in lipids and an increase in attached bacteria over time. This interaction may be a pre-requisite for lipid breakdown during nut particle disappearance. Overall, this study provides insights into how nut fermentation alters the gut microbiota and the possible role that gut microbes have in lipid degradation.

Enhanced biological phosphorus removal from wastewater and dynamics of microbial population in dual PAOs symbiosis system

Low level of volatile fatty acids (VFAs) is a key factor limiting the performance of enhanced biological phosphorus removal (EBPR) by traditional polyphosphate accumulating organisms (PAOs). A newly discovered PAOs capable of fermenting macromolecular organic matter into short-chain VFAs could solve the problem. However, the roles of traditional and fermented PAOs in wastewater treatment processes and the collaboration between functional microorganisms remain unknown. In this study, a sequencing batch reactor (SBR) was operated with alternating anaerobic oxic (An/O) mode to investigate the effect of mixed carbon source ratios, namely, acetate (NaAc):casein hydrolysate (Cas aa) = 4:0, 3:1, 1:1, 1:3 and 0:4, on EBPR performance and microbial community structure. The results showed that the phosphorus removal efficiency remained stable as NaAc was the sole carbon source. When NaAc:Cas aa varied from 3:1 to 1:3, the recovery of system performance took less time compared to the last Run, implying an adaptation of PAOs to Cas aa. Moreover, the anaerobic phosphorus release time was found to increase with the increasing amount of VFAs from Cas aa degradation, indicating the enrichment of fermented bacteria and the utilization of VFAs by traditional PAOs. Increasing the dose of Cas aa also generated more NH4+-N, owing to the reaction of the groups in the amino acids with water, causing a drastic decrease of ammonium removal efficiency from 88.9 % to 15.2 %. The ideal process performance implied that EBPR by dual PAOs synergistic symbiosis occurred in the system with NaAc:Cas aa = 1:1. Meanwhile, the results of 16S ribosomal RNA (16S rRNA) genes-Illumina MiSeq high-throughput sequencing showed that the abundance of traditional PAOs decreased from 22.4 % (4:0) to 11.6 % (1:1) and to 4.9 % (0:4), but fermented PAOs increased from 9.9 % to 19.5 %, then decreased to 17.3 %. Dual PAOs synergistic symbiosis could be of great potential for EBPR in treating low VFAs wastewater.

A full-scale bioremediation study of diesel fuel-contaminated soil: the effect of plant species and soil amendments

This article presents a comprehensive on-site bioremediation of an excavated diesel fuel-contaminated soil aided by various soil amendments and plant species. In the first 125 days, the excavated soil was placed in a land treatment unit, mixed with compost, and seeded with white clover (Trifolium repens). In the next 155 days, the land treatment unit was re-established and divided into four experimental plots. Experimental plots 2 and 3 were seeded with a mixture of plant seeds (Trifolium alexandrinum, Fagopyrum esculentum Moench, Trifolium incarnatum, Phacelia tanacetifolia, Sinapis alba, Trifolium repens), while experimental plots 1 and 4 were left without seeded vegetation. Moreover, a zeolite and an Ascophyllum nodosum-based biostimulant were added to experimental plots 3 and 4. The objectives were to select the most beneficial plant species for the plant-based bioremediation process, to evaluate applicability of different soil amendments for an enhanced hydrocarbon biodegradation, and to study their effects on the microbial community in soil. Our results showed an overall reduction in hydrocarbon pollution by more than 95% within 280 days. The rates of hydrocarbon degradation and changes in the microbial population were not affected by the presence of the zeolite and the biostimulant. In addition, the use of different plant species did not have a statistically significant effect on hydrocarbon degradation but affected microbial population dynamics, confirming stabile and diverse indigenous hydrocarbon-degrading microbial community in the native soil.

Depth-driven patterns in lytic viral diversity, auxiliary metabolic gene content, and productivity in offshore oligotrophic waters.

Marine viruses regulate microbial population dynamics and biogeochemical cycling in the oceans. The ability of viruses to manipulate hosts' metabolism through the expression of viral auxiliary metabolic genes (AMGs) was recently highlighted, having important implications in energy production and flow in various aquatic environments. Up to now, the presence and diversity of viral AMGs is studied using -omics data, and rarely using quantitative measures of viral activity alongside. In the present study, four depth layers (5, 50, 75, and 1,000 m) with discrete hydrographic features were sampled in the Eastern Mediterranean Sea; we studied lytic viral community composition and AMG content through metagenomics, and lytic production rates through the viral reduction approach in the ultra-oligotrophic Levantine basin where knowledge regarding viral actions is rather limited. Our results demonstrate depth-dependent patterns in viral diversity and AMG content, related to differences in temperature, nutrients availability, and host bacterial productivity and abundance. Although lytic viral production rates were similar along the water column, the virus-to-bacteria ratio was higher and the particular set of AMGs was more diverse in the bathypelagic (1,000 m) than the shallow epipelagic (5, 50, and 75 m) layers, revealing that the quantitative effect of viruses on their hosts may be the same along the water column through the intervention of different AMGs. In the resource- and energy-limited bathypelagic waters of the Eastern Mediterranean, the detected AMGs could divert hosts' metabolism toward energy production, through a boost in gluconeogenesis, fatty-acid and glycan biosynthesis and metabolism, and sulfur relay. Near the deep-chlorophyll maximum depth, an exceptionally high percentage of AMGs related to photosynthesis was noticed. Taken together our findings suggest that the roles of viruses in the deep sea might be even more important than previously thought as they seem to orchestrate energy acquisition and microbial community dynamics, and thus, biogeochemical turnover in the oceans.

Deciphering the evolvement of microbial communities from hydrothermal vent sediments in a global change perspective

Microbial communities first respond to changes of external environmental conditions. Observing the microbial responses to environmental changes in terms of taxonomic and functional biodiversity is therefore of great interest, particularly in extreme environments, where the already extreme conditions can become even harsher. In this study, sediment samples from three different shallow hydrothermal vents in Levante Bay (Vulcano Island, Aeolian Islands, Italy) were used to set up microcosm experiments with the aim to explore the microbial dynamics under changing conditions of pH and redox potential over a 90-days period. The leading hypothesis was to establish under microcosm conditions whether the starting microbial communities of the sediments evolved differently depending on their origin. To profile the dynamics of microbial populations over time, biodiversity, enzymatic profile, total cell abundance estimations, total/respiring cell ratio were estimated by using different approaches. An evident change in the microbial community structure was observed, mainly in the microcosm containing the sediment from the most acidified site, which was characterized by a highly diversified microbial community (in prevalence composed of Thermotoga, Desulfobacterota, Planctomycetota, Synergistota and Deferribacterota). An increase in microbial resistant forms (e.g., spore-forming species) with anaerobic metabolism was detected in all experimental conditions. Differential physiological responses characterized the sedimentary microbial communities. Proteolytic activity appeared to be stimulated under microcosm conditions, whereas the alkaline phosphatase activity was significantly depressed at low pH values, like those that were measured at the station showing intermediate pH-conditions. The results confirmed a differential response of microbial communities depending on the starting environmental conditions.

Alfalfa intervention alters the colonization of rumen epithelial bacteria to promote rumen development and lamb health during early life

Understanding the rumen epithelial (RE) microbial community structure and population dynamics of young ruminant during development is fundamental in promoting the establishment of a well-developed rumen for animal health and production. In this study, 10-day-old Hu lambs were fed with milk replacer (B-10), milk replacer and starter (STA) or milk replacer and starter supplemented with alfalfa (S-ALF). The RE bacteria of lambs at d10, 17, 24, 38, 45 and 66 were assessed to characterize RE bacterial colonization during early life and its response to fiber intervention. In B-10 lambs, 434 operational taxonomic units (OTUs) belonging to 57 core genera were observed in the RE. A number of the fibrolytic bacteria (Butyrivibrio and unclassified Ruminococcaceae), the pectinolytic bacterium (Treponema), the protein and fat digester (p-75-a5), the short-chain fatty acids producers ([Eubacterium], Succiniclasticum, unclassified Succinivibrionaceae, and Clostridiales), and the non-fermentive bacterium (Mogibacterium) were induced by alfalfa intervention in the S-ALF group during preweaning period, which attributed to a more mature RE bacterial community. OTUs belonging to Butyrivibrio, Succiniclasticum, Bacteroidales, Desulfovibrio, Clostridiales, and Succiniclasticum induced by alfalfa intervention were positively correlated with rumen tissue genes involved in fatty acid metabolism, barrier function, and PI3K-Akt, FoxO, and calcium signaling pathways. During the postweaning period, the RE bacterial composition of STA group changed significantly, while the S-ALF group did not. Our results suggested that alfalfa induced changes in RE bacteria during preweaning period which was associated with rumen health. The findings provide guidance for improving rumen health by manipulating RE bacteria during early life.

Main Challenges Expected from the Impact of Climate Change on Microbial Biodiversity of Table Olives: Current Status and Trends.

Climate change is a global emergency that is affecting agriculture in Mediterranean countries, notably the production and the characteristics of the final products. This is the case of olive cultivars, a source of olive oil and table olives. Table olives are the most important fermented vegetables in the Mediterranean area, whose world production exceeds 3 million tons/year. Lactic acid bacteria and yeast are the main microorganisms responsible for the fermentation of this product. The microbial diversity and population dynamics during the fermentation process are influenced by several factors, such as the content of sugars and phenols, all of which together influence the quality and safety of the table olives. The composition of fruits is in turn influenced by environmental conditions, such as rainfall, temperature, radiation, and the concentration of minerals in the soil, among others. In this review, we discuss the effect of climate change on the microbial diversity of table olives, with special emphasis on Spanish and Portuguese cultivars. The alterations expected to occur in climate change scenario(s) include changes in the microbial populations, their succession, diversity, and growth kinetics, which may impact the safety and quality of the table olives. Mitigation and adaptation measures are proposed to safeguard the authenticity and sensorial features of this valuable fermented food while ensuring food safety requirements.