DISCUSSION
Humans continuously and intimately interact with microorganisms. This study
demonstrates that spontaneous, or traditional, fermentation promotes a diversity of
microorganisms, including some Lactobacillus strains that may potentially interact with
human and environmental microbes during production and consumption. Spontaneous
fermentation and consumption of its product can be a microbial exchange between the
environment and the human microbiome that is mediated by human behavior, abiotic
factors, and random chance (Fig. 5). The microbial community of chicha could be initiated
from a variety of sources including saliva added to each new batch, tools and vessels that
may contain remnants or bacterial residue from a previous ferment, the water added to
thin the cassava mash, the substrate of the raw material, or the household and airborne
environment. In turn, ferments by lactic acid bacteria are consumed and become a
potential source of microbes for the human body. While not all LAB confer benefits, many
Colehour et al. (2014), PeerJ, DOI 10.7717/peerj.479 10/18
Lactobacilli have been positively associated with human health. (Dethlefsen, McFall-Ngai
& Relman, 2007; Costello et al., 2009; Spor, Koren & Ley, 2011; Human Microbiome Project
Consortium, 2012; Linnenbrink et al., 2013). All of the numerically dominant OTUs we
detected in chicha were related to Lactobacillus species that have also been reported in
the human oral and fecal microbiome (Dewhirst et al., 2010). Our conclusions are based
on short reads so a much more detailed study is necessary to determine if any of the
Lactobacillus taxa we detected might confer health benefits or even successfully assimilate
into the human microbiome.
Lactic-acid bacteria are found in association with nutrient rich environments on
animals and plants. While some strains produce biogenic amines that can be detrimental to
human health (Halasz ´ et al., 1994), other research highlights positive effects of consuming
LAB in moderate amounts. In the human intestinal tract, high rates of adhesion to the
mucus membrane allow for direct interface with the human intestine, and have been
shown to protect against pathogens, modulate immune response, and promote mucus
secretions to soothe the intestinal lining. In addition, lactic-acid bacteria provide digestion
assistance, improving vitamin and mineral bioavailability while degrading antinutrients
and other phytotoxins such as cyanide (Campbell-Platt, 1994; Westby, Reilly & Bainbridge,
1997; Aro, 2008; Chelule, Mokoena & Gqaleni, 2010; Turpin et al., 2010).
To better understand the spatial and household variability in microbial community
composition in spontaneous ferments, we were interested in knowing if bacterial
composition showed phylogenetic divergence over geographic space. We observed that the
bacterial communities in chicha were more similar within a village than between villages
(p = 0.038). This variation could result from a combination of mechanisms, including
distance-limited dispersal, stochastic succession (including horizontal gene-transfer),
and human-mediated selection. Since our sample size is modest, we recognize that the
significant difference we found could be driven by one particular sample (Fig. 1) but our
Adonis results are supported by our ANOVA analysis showing significant within-village
OTU overlaps, strengthening evidence for higher rates of bacterial similarity within a
village.
We observed that chicha is generously shared with neighbors within a village so it is
not surprising that we did not see significant phylogenetic dissimilarity at the household
level. Dispersal between chicha ferments could occur if starter cultures are mixed or if a
brewer contributes saliva to her neighbor’s chicha. Based on ethnographic evidence, oral
microbiome swapping is actually more likely to happen during consumption, when the
drinking cup, pilchis, are passed around a social gathering and dipped repeatedly into the
fermentation vessel after each individual takes a drink. Distance and geographic barriers
(e.g., a bridgeless river in our case) limit social interaction and subsequently the opportunity
for dispersal between the two villages, which may partially explain the observed
variation in the bacterial community (Bokulich & Mills, 2013; Linnenbrink et al., 2013).
Each new chicha batch represents a unique opportunity for succession, which could
be contingent on the order and frequency of species arrival. In addition, competition
between microbes, abiotic conditions, rate of horizontal gene transfer, and random chance
Colehour et al. (2014), PeerJ, DOI 10.7717/peerj.479 11/18
could all shape the communities within each chicha vessel. The water source used in the
fermentation vessel (V1: hauled in vessels from a spring; V2: piped to outdoor spigots
near houses from a reservoir) may represent a source of either facilitative or competing
microbes that could influence the final composition of the ferment. Since households
within a village rely primarily on the same water source, this could help explain why
chicha is more similar within a village but not within an individual household. It is
possible that soil differences between gardens or village areas could yield variation in
the plant-associated bacteria present on the raw material, but this seems unlikely since the
raw material is peeled and boiled in preparation for fermentation, although contamination
of pre-boiled product via tools and skin is possible.
Differences in ferment cultivation practice between the two villages may also contribute
to variation (human-mediated selection). Expressions among the Shuar such as “the
prettiest girls makes the best chicha” suggest individuality, personal preferences, or oral
hygiene could also play a role in the cultivation of this ferment. The addition of saliva could
be another source of variance, particularly if genetic or lifestyle differences contribute to
distinct oral microbiome communities. Finally, any bacteria leftover in the fermentation
vessel or on the tools used to make the mash may act as a starter culture for each new batch.
Although beyond the scope of this article, it is tempting to speculate that distinct bacterial
communities may be maintained over time, and that the combination of these factors
suggest an example of microbial domestication.
These three processes, human-mediated selection, distance-limited dispersal, and
stochastic variance help explain the cross-sectional bacterial community variation we
observed in chicha. If site-specific bacteria communities are consistent over time this would
indicate that the ferment may be a player in a co-evolutionary relationship with human
and environmental microbes (Fig. 5), but future work with higher sample size is necessary
to explore these ideas in greater depth
สนทนามนุษย์อย่างต่อเนื่อง และจึงโต้ตอบกับจุลินทรีย์ การศึกษานี้แสดงให้เห็นถึงที่อยู่ หรือ ดั้งเดิม หมักส่งเสริมความหลากหลายของจุลินทรีย์ รวมถึงบางสายพันธุ์แลคโตบาซิลลัสที่อาจอาจโต้ตอบกับมนุษย์ และสิ่งแวดล้อมจุลินทรีย์ในระหว่างการผลิตและ ขาดหมักและปริมาณของผลิตภัณฑ์สามารถแลกเปลี่ยนจุลินทรีย์ระหว่างการสภาพแวดล้อมและ microbiome มนุษย์ที่ mediated โดยพฤติกรรมมนุษย์ abioticปัจจัย และมีโอกาสสุ่ม (Fig. 5) สามารถเริ่มต้นชุมชนจุลินทรีย์ของ chichaจากหลากหลายแหล่งรวมน้ำลายที่เพิ่มในแต่ละชุดใหม่ เครื่องมือ และเรือที่อาจประกอบด้วยเศษหรือแบคทีเรียสารตกค้างจากก่อนหน้านี้ความสับสนอลหม่านต่อ น้ำเพิ่มบางคลุกเคล้ามันสำปะหลัง พื้นผิวของ วัตถุดิบ หรือในครัวเรือน และอากาศสภาพแวดล้อม กลับ ferments โดยแบคทีเรียกรดแลกติกจะถูกใช้ และเป็นการแหล่งที่มีศักยภาพของจุลินทรีย์ในร่างกายมนุษย์ ในขณะที่แล็บไม่ประสาทประโยชน์ มากColehour et al. (2014), PeerJ, 10.7717/peerj.479 ดอย 10/18Lactobacilli มีสัมพันธ์เชิงบวกกับสุขภาพของมนุษย์ (Dethlefsen, McFall-ไหง& Relman, 2007 Costello et al., 2009 Spor, Koren และ ระเบียง 2011 โครงการ Microbiome มนุษย์กิจการร่วมค้า 2012 Linnenbrink et al., 2013) OTUs หลักเรียงตามตัวเลขทั้งหมดเราตรวจพบใน chicha เกี่ยวข้องกับสายพันธุ์แลคโตบาซิลลัสที่ยังมีการรายงานในมนุษย์พูด และ fecal microbiome (Dewhirst et al., 2010) บทสรุปของเราอยู่บนสั้นอ่านเพื่อศึกษารายละเอียดมากจำเป็นต้องกำหนดว่าถ้ามีของแลคโตบาซิลลัส taxa ที่เราพบอาจประสาทสุขภาพ หรือแม้กระทั่งประสบความสำเร็จอย่างเป็น microbiome มนุษย์แบคทีเรียกรดแลกติกอยู่ในความสัมพันธ์กับสภาพแวดล้อมที่อุดมไปด้วยธาตุอาหารบนสัตว์และพืช ในขณะที่บางสายพันธุ์ผลิต biogenic amines ที่ได้ผลดีกับสุขภาพของมนุษย์ (Halasz ´ et al., 1994), วิจัยอื่น ๆ เน้นผลในเชิงบวกของการบริโภคปฏิบัติปานกลางจำนวน ในตัวมนุษย์ลำไส้ทางเดิน สูงอัตราการยึดเกาะเยื่อเมือกให้ติดต่อโดยตรงกับลำไส้มนุษย์ และได้รับแสดง การป้องกันโรค modulate ตอบสนองภูมิคุ้มกัน ส่งเสริมมูกหลั่งปลอบเยื่อบุลำไส้ นอกจากนี้ แบคทีเรียกรดแล็กติกให้ย่อยอาหารความช่วยเหลือ การปรับปรุงการดูดซึมแร่ธาตุและวิตามินในขณะที่ลด antinutrientsและ phytotoxins อื่น ๆ เช่นไซยาไนด์ (Campbell-Platt, 1994 Westby, Reilly และ Bainbridge1997 พักส 2008 Chelule, Mokoena และ Gqaleni, 2010 Turpin et al., 2010)เพื่อให้เข้าใจความแปรผันปริภูมิ และครัวเรือนในชุมชนจุลินทรีย์องค์ประกอบใน ferments อยู่ เราไม่รู้ถ้าแบคทีเรียองค์ประกอบที่แสดงให้เห็น phylogenetic divergence ผ่านพื้นที่ทางภูมิศาสตร์ เราสังเกตที่การชุมชนแบคทีเรียใน chicha ก็คล้ายมากภายในหมู่บ้านกว่าระหว่างหมู่บ้าน(p = 0.038). This variation could result from a combination of mechanisms, includingdistance-limited dispersal, stochastic succession (including horizontal gene-transfer),and human-mediated selection. Since our sample size is modest, we recognize that thesignificant difference we found could be driven by one particular sample (Fig. 1) but ourAdonis results are supported by our ANOVA analysis showing significant within-villageOTU overlaps, strengthening evidence for higher rates of bacterial similarity within avillage.We observed that chicha is generously shared with neighbors within a village so it isnot surprising that we did not see significant phylogenetic dissimilarity at the householdlevel. Dispersal between chicha ferments could occur if starter cultures are mixed or if abrewer contributes saliva to her neighbor’s chicha. Based on ethnographic evidence, oralmicrobiome swapping is actually more likely to happen during consumption, when thedrinking cup, pilchis, are passed around a social gathering and dipped repeatedly into thefermentation vessel after each individual takes a drink. Distance and geographic barriers(e.g., a bridgeless river in our case) limit social interaction and subsequently the opportunityfor dispersal between the two villages, which may partially explain the observedvariation in the bacterial community (Bokulich & Mills, 2013; Linnenbrink et al., 2013).Each new chicha batch represents a unique opportunity for succession, which couldbe contingent on the order and frequency of species arrival. In addition, competitionbetween microbes, abiotic conditions, rate of horizontal gene transfer, and random chanceColehour et al. (2014), PeerJ, DOI 10.7717/peerj.479 11/18could all shape the communities within each chicha vessel. The water source used in thefermentation vessel (V1: hauled in vessels from a spring; V2: piped to outdoor spigotsnear houses from a reservoir) may represent a source of either facilitative or competingmicrobes that could influence the final composition of the ferment. Since householdswithin a village rely primarily on the same water source, this could help explain whychicha is more similar within a village but not within an individual household. It ispossible that soil differences between gardens or village areas could yield variation inthe plant-associated bacteria present on the raw material, but this seems unlikely since theraw material is peeled and boiled in preparation for fermentation, although contaminationof pre-boiled product via tools and skin is possible.Differences in ferment cultivation practice between the two villages may also contributeto variation (human-mediated selection). Expressions among the Shuar such as “theprettiest girls makes the best chicha” suggest individuality, personal preferences, or oralhygiene could also play a role in the cultivation of this ferment. The addition of saliva couldbe another source of variance, particularly if genetic or lifestyle differences contribute todistinct oral microbiome communities. Finally, any bacteria leftover in the fermentationvessel or on the tools used to make the mash may act as a starter culture for each new batch.Although beyond the scope of this article, it is tempting to speculate that distinct bacterialcommunities may be maintained over time, and that the combination of these factorssuggest an example of microbial domestication.These three processes, human-mediated selection, distance-limited dispersal, andstochastic variance help explain the cross-sectional bacterial community variation weobserved in chicha. If site-specific bacteria communities are consistent over time this wouldindicate that the ferment may be a player in a co-evolutionary relationship with humanand environmental microbes (Fig. 5), but future work with higher sample size is necessaryto explore these ideas in greater depth
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