I need help answering this queshtion based on the answer in the article you are whitin a bacterium travelling from the outside of a Gouda wheel through the rind and into the core. What can you say about the chemical environment of the areas you pass through?https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-018-1323-4 goal of this study was to determine the baseline micro-biota associated with Gouda cheese via 16S rDNAmetagenomic sequencing. Gouda cheese in particularwas selected as the model product because it is an agedcheese that is required to be held at ≥35 °F for at least60 days if manufactured from unpasteurized milk inorder to ensure product safety. Variables examined inthis study included milk type (i.e. unpasteurized, pas-teurized), milk origin (i.e. bovine, caprine), aging dur-ation (from 2 to 4 to 12-18 months), and samplinglocation (i.e. inner or outer cheese). Elucidation of thenative microbiota of Gouda cheese will allow estimationof product quality potential and overall safety.ResultsComposition analysis of commercial gouda cheeseIn this study, Gouda cheese samples were analyzed formoisture, salt, fat, pH, and aw to assess variations inthese physical property characteristics (see Tables 1 and 2).All cheese samples met the CFR requirement for moisturecontent (maximum of 45% ) [25], however a wide rangeof values were determined: 18.06 (brand C, under therind) to 42.41% (brand A, under the rind). The Goudacheeses made with goat milk (F-H) had the highest fatin solid content: 51.62-55.91%. Fat content rangedfrom 43.09 (brand D) to 55.91% (brand G) . Brands D, I,K, and N had slightly lower fat in solid content thanthe 45% minimum specified in the CFR, ranging from43.09-44.25%.The pH of the Gouda cheese samples ranged from5.26-6.37. pH was highest in samples removed fromunder the rind compared with the respective core andinside samples for 11 brands (73%). The sample takenunder the rind of brand A had the highest pH overall(6.37). This brand also had the lowest overall pH inthe core sample (5.26), leading to a pH difference be-tween the two regions of 1.11; a similar difference of1.02 was also observed in brand I. All other brandshad pH differences between regions of less than 0.53.Overall, no substantial differences in pH values wereobserved between pasteurized and unpasteurizedGouda cheeses.The aw of the cheese samples ranged from 0.877(brand C, under the rind) to 0.957 (brand A, both coreand inside). In general, the water activity under the rindwas lower than the inside or core samples from the samebrand. Similarly to pH, differences in a values betweenpasteurized and unpasteurized Gouda cheeses were in-significant. The largest water activity difference betweenregions of the same brand was 0.030 observed in brandO (0.879 in the sample taken under the rind and 0.909in the inside sample). A correlation between moisturecontent and water activity was observed; cheeses whichhad low moisture contents also had low water activities,which was expected. Salt content for the cheeses rangedfrom 1.21-2.39%.Native microbiota assessment in commercial goudacheeseRarefaction curves of all Gouda cheese samples had simi-lar diversity (Fig. 1). All samples displayed similar rarefac-tion curves in this study. Figure 2 displays the bacterialcomposition of the pasteurized and unpasteurized Goudacheeses based on percentage of sequence reads identifiedat the family or genus levels. Identifications greater than1% and common to all cheeses included the genera ofLactococcus and Staphylococcus, and unidentifiedmembers of the family Bacillaceae. The family Bacillaceaeincluded organisms which could not be further identifiedto genus. Lactococcus populations were comparableand ranged from 40.1-49.1%. Bacteria from the familyBacillaceae comprised 40.5, 38.5, and 46.3% of thepopulation of pasteurized cow and goat cheese andunpasteurized cow Gouda cheese, respectively. Staphylococcusreads were found in low numbers in the three cheesecategories: 2.0, 13.4, and 1.3% of the population ofpasteurized cow, goat, and unpasteurized cow Goudacheeses, respectively.A total of 92, 138, and 120 genus- or family-level iden-tifications were made for pasteurized cow, pasteurizedgoat, and unpasteurized cow Gouda cheeses, respect-ively. Eight bacterial genera were identified only in pas-teurized cow Gouda cheese and included Anoxybacillus,Curtobacterium, and Yersinia. A total of 28 genera wereidentified only in the pasteurized goat Gouda cheese inthis study and included Mannheimia, Leptotrichia, Bal-neimonas, Klebsiella, and Pseudoalteromonas.Spatial variability of bacterial genera in commercialgouda cheeseKronograhs of the bacterial composition of the core,under the rind, and the inside of the commercialGouda cheeses assessed in this study are presented inFig. 3. A total of 41 bacterial genera were common toall three locations (core, under the rind, and inside)including Lactococcus (55.1, 41.5, and 46.6%), uniden-tified members of Bacillaceae (40.9, 43.1, and 40.6%),Lactobacillus (2.8, 0.2, and 5.1%), Staphylococcus(0.02, 9.6, and 6.0%), and Tetragenococcus (0.004, 4.8,and 0.03%). Overall, the composition of the cores andinsides of the Gouda cheeses were more similar toeach other based on sequence reads than to the sam-ples taken under the rind. Lactococcus and Lactobacil-lus populations were less in the samples taken underthe rind. Generally, all the bacterial genera identifiedin this study were present in all three cheese regions.However, Megasphaera, Caloramator, and Hymonella,were only detected in the cheese cores, and Starter cultures, generally comprised of lactic acidbacteria, aid in acidification and fermentation duringcheese production and, in some instances, are re-placed by more competitive organisms during brining,rind development, and aging [14]. Other microorgan-isms, such as fungi, are integral to the manufactureof smear-ripened cheeses such as Reblochon andTaleggio. Metagenomics can aid in understanding themicrobiota of cheese, how these organisms interact,and how the presence of certain organisms aid orhinder aspects of food quality and safety. For ex-ample, it is known that certain microbial consortia incheese contain antilisterial properties [15-17]. Studieshave assessed the microbiomes of various cheeses in-oculated with Listeria monocytogenes and determinedthat the pathogen was inhibited by a combination oflactic acid bacteria and Gram-positive, catalase-positive bacteria [17]. Ultimately, the identification ofthe microbial communities in cheese is important andmust include how factors such as raw materials,aging, storage conditions, and specific product charac-teristics impact diversity.Manufacturing of cheeses is divided into several steps.The first step is the addition of starter cultures whichacidify the milk during the ripening process. The milkand starter culture mixture is subsequently warmedprior to the addition of rennet, leading to curd forma-tion and whey separation. The resulting curd is cut,cooked, and placed in molds that are pressed into thedesired shape. The finished cheese wheels are brinedand aged depending on the cheese type being processed.Cheeses can be manufactured using either pasteurizedor unpasteurized milk. The pasteurization of milk in-volves heat treatment to eliminate harmful pathogensand lower the overall microbial burden. Therefore,cheeses prepared using unpasteurized milk are generallycomprised of more diverse and heterogeneous microor-ganisms. Previous research has determined that the na-tive microbiota in unpasteurized milk contributes to thesensory properties of the resulting cheese, and researchsuggests that these organisms aid in producing a morerobust flavor [18, 19]. The microbiota in unpasteurizedmilk is influenced by the animal's teat canal and sur-rounding skin, the environmental conditions, seasonal-ity, pasture and grazing changes, personnel hygiene,starter culture selection, process and post-process con-tamination [14, 20-22]. For pasteurized milk, the micro-bial community is influenced by the thermoduricbacteria that survive pasteurization, and post-processcontamination.The composition and distribution of microbiota incheeses differ not only by milk type and environmentalfactors, but also by sampling location (i.e., core, rind) [8,16, 21, 23]. The rind of the cheese is a more openecosystem exposed to the environment and abiotic con-ditions and is comprised of a high diversity of organisms[21]. Aerobic bacteria, as well as yeasts and molds, dom-inate the rind of cheese. Halophiles are also present dueto their ability to survive high salt concentrations thatwould be encountered during brining. Hygienic condi-tions during aging also play a role in shaping the micro-biota of the rind. Conversely, the core of the cheese ismore anaerobic and generally exhibits a lower pH, lead-ing to less biodiversity [21]. For this reason, lactic acidbacteria, including those in the added starter cultures,are predominant in the core, often reaching populationlevels near 9 log CFU/g shortly after cheese manufacture[21]. These bacteria acidify the milk and hinder thegrowth of other less-competitive species and some spoil-age bacteria. Less dominant organisms in the core in-clude yeasts, Gram-positive catalase-positive bacteria,and enterococci. These different microenvironments en-countered throughout cheese affect the types of micro-biota present and how these organisms interact.Cheeses can be categorized on their degree of firmnessof texture and are grouped as hard, semi-hard and soft.Hard and semi-hard cheeses are often aged. For agedcheeses, such as Gouda, Cheddar, and Parmesan, thelength of the aging process plays a significant role in thecomposition and diversity of microbiota. When cheesesare aged, moisture content and water activity decrease.Due to increasingly limited nutrients during aging, somebacteria undergo autolysis, contributing cellular compo-nents, including enzymes and sugars, to the overall char-acteristics of the cheese [24]. It is known thatpopulations of starter lactic acid bacteria are reducedbut survive during aging. In the U. S., cheeses craftedusing unpasteurized milk must be aged for at least60 days at a minimum temperature of 35 °F (1.67 °C)prior to introduction into interstate commerce [25]. Thisaging period is intended to eliminate pathogens thatmay have been present in the unpasteurized milk. How-ever, it has been determined that pathogens can survivepast the 60 day aging process [26-28]. Understandingthe microbiome of Gouda, an aged cheese, will aid in de-signing studies to reduce the risk of illness due to patho-gens from consumption of this type of cheese madeusing unpasteurized milk.During 1998-2015 a total of 113 outbreaks associatedwith cheese consumption were reported to the CDC,resulting in 2418 illnesses, 291 hospitalizations, and 18deaths [CDC FOOD Tool, wwwn.cdc.gov/foodborneout-breaks]. Of the total number of outbreaks, 20% (n = 23)were specifically stated to be associated with cheesesmade using unpasteurized milk. Gouda cheese has fre-quently been implicated in product recalls and outbreaks[29-31] attributed to various foodborne pathogens in-cluding Listeria monocytogenes and E. coli O157:H7. The

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I need help answering this queshtion based on the answer in the article

you are whitin a bacterium travelling from the outside of a Gouda wheel through the rind and into the core. What can you say about the chemical environment of the areas you pass through?

https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-018-1323-4

Transcribed Image Text:goal of this study was to determine the baseline micro- biota associated with Gouda cheese via 16S rDNA metagenomic sequencing. Gouda cheese in particular was selected as the model product because it is an aged cheese that is required to be held at ≥35 °F for at least 60 days if manufactured from unpasteurized milk in order to ensure product safety. Variables examined in this study included milk type (i.e. unpasteurized, pas- teurized), milk origin (i.e. bovine, caprine), aging dur- ation (from 2 to 4 to 12-18 months), and sampling location (i.e. inner or outer cheese). Elucidation of the native microbiota of Gouda cheese will allow estimation of product quality potential and overall safety. Results Composition analysis of commercial gouda cheese In this study, Gouda cheese samples were analyzed for moisture, salt, fat, pH, and aw to assess variations in these physical property characteristics (see Tables 1 and 2). All cheese samples met the CFR requirement for moisture content (maximum of 45% ) [25], however a wide range of values were determined: 18.06 (brand C, under the rind) to 42.41% (brand A, under the rind). The Gouda cheeses made with goat milk (F-H) had the highest fat in solid content: 51.62-55.91%. Fat content ranged from 43.09 (brand D) to 55.91% (brand G) . Brands D, I, K, and N had slightly lower fat in solid content than the 45% minimum specified in the CFR, ranging from 43.09-44.25%. The pH of the Gouda cheese samples ranged from 5.26-6.37. pH was highest in samples removed from under the rind compared with the respective core and inside samples for 11 brands (73%). The sample taken under the rind of brand A had the highest pH overall (6.37). This brand also had the lowest overall pH in the core sample (5.26), leading to a pH difference be- tween the two regions of 1.11; a similar difference of 1.02 was also observed in brand I. All other brands had pH differences between regions of less than 0.53. Overall, no substantial differences in pH values were observed between pasteurized and unpasteurized Gouda cheeses. The aw of the cheese samples ranged from 0.877 (brand C, under the rind) to 0.957 (brand A, both core and inside). In general, the water activity under the rind was lower than the inside or core samples from the same brand. Similarly to pH, differences in a values between pasteurized and unpasteurized Gouda cheeses were in- significant. The largest water activity difference between regions of the same brand was 0.030 observed in brand O (0.879 in the sample taken under the rind and 0.909 in the inside sample). A correlation between moisture content and water activity was observed; cheeses which had low moisture contents also had low water activities, which was expected. Salt content for the cheeses ranged from 1.21-2.39%. Native microbiota assessment in commercial gouda cheese Rarefaction curves of all Gouda cheese samples had simi- lar diversity (Fig. 1). All samples displayed similar rarefac- tion curves in this study. Figure 2 displays the bacterial composition of the pasteurized and unpasteurized Gouda cheeses based on percentage of sequence reads identified at the family or genus levels. Identifications greater than 1% and common to all cheeses included the genera of Lactococcus and Staphylococcus, and unidentified members of the family Bacillaceae. The family Bacillaceae included organisms which could not be further identified to genus. Lactococcus populations were comparable and ranged from 40.1-49.1%. Bacteria from the family Bacillaceae comprised 40.5, 38.5, and 46.3% of the population of pasteurized cow and goat cheese and unpasteurized cow Gouda cheese, respectively. Staphylococcus reads were found in low numbers in the three cheese categories: 2.0, 13.4, and 1.3% of the population of pasteurized cow, goat, and unpasteurized cow Gouda cheeses, respectively. A total of 92, 138, and 120 genus- or family-level iden- tifications were made for pasteurized cow, pasteurized goat, and unpasteurized cow Gouda cheeses, respect- ively. Eight bacterial genera were identified only in pas- teurized cow Gouda cheese and included Anoxybacillus, Curtobacterium, and Yersinia. A total of 28 genera were identified only in the pasteurized goat Gouda cheese in this study and included Mannheimia, Leptotrichia, Bal- neimonas, Klebsiella, and Pseudoalteromonas. Spatial variability of bacterial genera in commercial gouda cheese Kronograhs of the bacterial composition of the core, under the rind, and the inside of the commercial Gouda cheeses assessed in this study are presented in Fig. 3. A total of 41 bacterial genera were common to all three locations (core, under the rind, and inside) including Lactococcus (55.1, 41.5, and 46.6%), uniden- tified members of Bacillaceae (40.9, 43.1, and 40.6%), Lactobacillus (2.8, 0.2, and 5.1%), Staphylococcus (0.02, 9.6, and 6.0%), and Tetragenococcus (0.004, 4.8, and 0.03%). Overall, the composition of the cores and insides of the Gouda cheeses were more similar to each other based on sequence reads than to the sam- ples taken under the rind. Lactococcus and Lactobacil- lus populations were less in the samples taken under the rind. Generally, all the bacterial genera identified in this study were present in all three cheese regions. However, Megasphaera, Caloramator, and Hymonella, were only detected in the cheese cores, and

Starter cultures, generally comprised of lactic acid
bacteria, aid in acidification and fermentation during
cheese production and, in some instances, are re-
placed by more competitive organisms during brining,
rind development, and aging [14]. Other microorgan-
isms, such as fungi, are integral to the manufacture
of smear-ripened cheeses such as Reblochon and
Taleggio. Metagenomics can aid in understanding the
microbiota of cheese, how these organisms interact,
and how the presence of certain organisms aid or
hinder aspects of food quality and safety. For ex-
ample, it is known that certain microbial consortia in
cheese contain antilisterial properties [15-17]. Studies
have assessed the microbiomes of various cheeses in-
oculated with Listeria monocytogenes and determined
that the pathogen was inhibited by a combination of
lactic acid bacteria and Gram-positive, catalase-
positive bacteria [17]. Ultimately, the identification of
the microbial communities in cheese is important and
must include how factors such as raw materials,
aging, storage conditions, and specific product charac-
teristics impact diversity.
Manufacturing of cheeses is divided into several steps.
The first step is the addition of starter cultures which
acidify the milk during the ripening process. The milk
and starter culture mixture is subsequently warmed
prior to the addition of rennet, leading to curd forma-
tion and whey separation. The resulting curd is cut,
cooked, and placed in molds that are pressed into the
desired shape. The finished cheese wheels are brined
and aged depending on the cheese type being processed.
Cheeses can be manufactured using either pasteurized
or unpasteurized milk. The pasteurization of milk in-
volves heat treatment to eliminate harmful pathogens
and lower the overall microbial burden. Therefore,
cheeses prepared using unpasteurized milk are generally
comprised of more diverse and heterogeneous microor-
ganisms. Previous research has determined that the na-
tive microbiota in unpasteurized milk contributes to the
sensory properties of the resulting cheese, and research
suggests that these organisms aid in producing a more
robust flavor [18, 19]. The microbiota in unpasteurized
milk is influenced by the animal's teat canal and sur-
rounding skin, the environmental conditions, seasonal-
ity, pasture and grazing changes, personnel hygiene,
starter culture selection, process and post-process con-
tamination [14, 20-22]. For pasteurized milk, the micro-
bial community is influenced by the thermoduric
bacteria that survive pasteurization, and post-process
contamination.
The composition and distribution of microbiota in
cheeses differ not only by milk type and environmental
factors, but also by sampling location (i.e., core, rind) [8,
16, 21, 23]. The rind of the cheese is a more open
ecosystem exposed to the environment and abiotic con-
ditions and is comprised of a high diversity of organisms
[21]. Aerobic bacteria, as well as yeasts and molds, dom-
inate the rind of cheese. Halophiles are also present due
to their ability to survive high salt concentrations that
would be encountered during brining. Hygienic condi-
tions during aging also play a role in shaping the micro-
biota of the rind. Conversely, the core of the cheese is
more anaerobic and generally exhibits a lower pH, lead-
ing to less biodiversity [21]. For this reason, lactic acid
bacteria, including those in the added starter cultures,
are predominant in the core, often reaching population
levels near 9 log CFU/g shortly after cheese manufacture
[21]. These bacteria acidify the milk and hinder the
growth of other less-competitive species and some spoil-
age bacteria. Less dominant organisms in the core in-
clude yeasts, Gram-positive catalase-positive bacteria,
and enterococci. These different microenvironments en-
countered throughout cheese affect the types of micro-
biota present and how these organisms interact.
Cheeses can be categorized on their degree of firmness
of texture and are grouped as hard, semi-hard and soft.
Hard and semi-hard cheeses are often aged. For aged
cheeses, such as Gouda, Cheddar, and Parmesan, the
length of the aging process plays a significant role in the
composition and diversity of microbiota. When cheeses
are aged, moisture content and water activity decrease.
Due to increasingly limited nutrients during aging, some
bacteria undergo autolysis, contributing cellular compo-
nents, including enzymes and sugars, to the overall char-
acteristics of the cheese [24]. It is known that
populations of starter lactic acid bacteria are reduced
but survive during aging. In the U. S., cheeses crafted
using unpasteurized milk must be aged for at least
60 days at a minimum temperature of 35 °F (1.67 °C)
prior to introduction into interstate commerce [25]. This
aging period is intended to eliminate pathogens that
may have been present in the unpasteurized milk. How-
ever, it has been determined that pathogens can survive
past the 60 day aging process [26-28]. Understanding
the microbiome of Gouda, an aged cheese, will aid in de-
signing studies to reduce the risk of illness due to patho-
gens from consumption of this type of cheese made
using unpasteurized milk.
During 1998-2015 a total of 113 outbreaks associated
with cheese consumption were reported to the CDC,
resulting in 2418 illnesses, 291 hospitalizations, and 18
deaths [CDC FOOD Tool, wwwn.cdc.gov/foodborneout-
breaks]. Of the total number of outbreaks, 20% (n = 23)
were specifically stated to be associated with cheeses
made using unpasteurized milk. Gouda cheese has fre-
quently been implicated in product recalls and outbreaks
[29-31] attributed to various foodborne pathogens in-
cluding Listeria monocytogenes and E. coli O157:H7. The

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